Exhibit 10.2

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

EXECUTION COPY

AGREEMENT

THIS AGREEMENT, together with the schedules attached hereto, (this “Agreement”)
is entered into as of the Execution Date and effective as of August 31, 2012
(the “Effective Date”), by and between Equilon Enterprises LLC dba Shell Oil
Products US, a Delaware limited liability company, having a place of business at
910 Louisiana Street, Houston, Texas 77002 (“Shell”), and Codexis, Inc., a
Delaware corporation, having a place of business at 200 Penobscot Drive, Redwood
City, California 94063 (“Codexis”). Shell and Codexis may each be referred to
herein individually as a “Party” or, collectively, as the “Parties.”

RECITALS

WHEREAS, Shell and Codexis entered into a certain Amended and Restated License
Agreement, entered into as of November 1, 2007 and effective as of November 1,
2006, as amended (the “License Agreement”), pursuant to which Codexis granted to
Shell certain license rights under Codexis Patent Rights, Codexis Licensed
Technology, Program Patent Rights and Program Technology so that Shell can
manufacture, use, sell, offer for sale and import Licensed Products (as such
terms are defined below).

WHEREAS, the Parties desire to amend the License Agreement as of the Effective
Date, pursuant to which Shell would grant to Codexis a certain royalty-bearing,
non-exclusive license under Codexis Patent Rights, Codexis Licensed Technology,
Program Patent Rights and Program Technology so that Codexis can manufacture,
use, sell, offer for sale and import Licensed Products in the Intermediate Field
of Use (as such term is defined below), in accordance with the terms and
conditions herein.

WHEREAS, Shell and Codexis entered into a certain Amended and Restated
Collaborative Research Agreement, entered into as of November 1, 2007 and
effective as of November 1, 2006, as amended (the “Research Agreement”),
pursuant to which the Parties have collaborated to develop certain new
biocatalytic processes for use in the conversion of biomass to fuels and/or fuel
additives and/or lubricants.

WHEREAS, the Parties desire to amend and to terminate the Research Agreement as
of the Effective Date, pursuant to which Shell would pay to Codexis a certain
payment in full satisfaction of Shell’s remaining FTE funding obligation under
the Research Agreement and Codexis and its Affiliates would have no further
obligations to Shell to provide any FTEs to perform work under the Program (as
such term is defined below), in accordance with the terms and conditions herein.

WHEREAS, Shell, Shell Chemicals Canada Limited (“Shell Canada”), Codexis and
Iogen Energy Corporation (“IE”) entered into a certain Collaborative Research
and License Agreement, effective as of July 10, 2009 (the “IE/Codexis/Shell
Agreement”), pursuant to which Codexis and IE collaborated to develop technology
relating to the conversion of biomass to ethanol, focusing in particular on
development of yeasts for the production of ethanol from C5 and C6 sugars and
enzymes for saccharification of pretreated biomass.

 

1

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WHEREAS, Codexis and Dyadic International (USA), Inc. and Dyadic International,
Inc. (together with Dyadic International (USA), Inc., hereinafter “Dyadic”),
entered into a certain License Agreement, effective as of November 14, 2008 (the
“Dyadic License”), pursuant to which Codexis obtained a non-exclusive license
under certain Dyadic patent rights and know-how relating to the generation and
use of Dyadic’s proprietary C1 (as such term is defined below) technology for
the expression of certain genes and secretion of certain corresponding enzymes.

WHEREAS, Shell and Codexis entered into a certain letter agreement, dated
November 3, 2008 (the “Dyadic Letter”), pursuant to which Shell agreed to make
certain payments under the Dyadic License with respect to certain Shell
activities using the C1 technology, directly to Dyadic.

WHEREAS, the Parties desire to amend and restate each Party’s responsibility for
payments under the Dyadic License for such Party’s manufacture, use, sale, offer
for sale or importation of Licensed Products (as defined in the Dyadic License).

NOW, THEREFORE, in consideration of the promises and undertakings set forth
herein, the Parties agree as follows:

ARTICLE 1

DEFINITIONS

Capitalized terms not otherwise defined herein will have the meaning set forth
below.

1.1 Unless specified elsewhere in this Agreement, “Affiliate” means,

(a) with respect to Codexis, any business entity controlling, controlled by, or
under common control with Codexis. For the purpose of this Section 1.1(a) only,
“control” means (i) the possession, directly or indirectly, of the power to
direct the management or policies of a business entity, whether through the
ownership of voting securities, by contract or otherwise, or (ii) the ownership,
directly or indirectly, of at least fifty percent (50%) of the voting securities
or other ownership interest of a business entity; provided that, if local law
requires a minimum percentage of local ownership, control will be established by
direct or indirect beneficial ownership of one hundred percent (100%) of the
maximum ownership percentage that may, under such local law, be owned by foreign
interests; and

(b) with respect to Shell, Royal Dutch Shell plc and any company (other than
Shell) which is from time to time directly or indirectly affiliated with Royal
Dutch Shell plc. For the purpose of this Section 1.1(b) only, a particular
company is (i) directly affiliated with another company or companies if that
latter company beneficially owns or those latter companies together beneficially
own fifty percent (50%) or more of the voting rights attached to the ownership
interest of the particular company; and (ii) is indirectly affiliated with
company or companies if a series of companies can be specified, beginning with
that latter company or companies and ending with the first mentioned company, so
related that each company of the series (except the latter company or companies)
is directly affiliated with one or more of the companies earlier in the series.

 

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1.2 “Assignee” has the meaning set forth in Section 7.1.

1.3 “Assignment” has the meaning set forth in Section 7.1.

1.4 “Associated Company” means any business entity controlling, controlled by,
or under common control with any other business entity. For the purpose of the
definition of “Associated Company” only, “control” means (a) the possession,
directly or indirectly, of the power to direct the management or policies of a
business entity, whether through the ownership of voting securities, by contract
or otherwise, or (b) the ownership, directly or indirectly, of at least fifty
percent (50%) of the voting securities or other ownership interest of a business
entity; provided that, if local law requires a minimum percentage of local
ownership, control will be established by direct or indirect beneficial
ownership of one hundred percent (100%) of the maximum ownership percentage that
may, under such local law, be owned by foreign interests. Notwithstanding
anything to the contrary, for purposes of this Agreement, neither Shell nor any
of its Affiliates (other than IE or Raízen Energia Participações S.A., a
Brazilian company, having offices at Avenida Presidente Juscelino Kubitcheck,
1327 6 O Andar, São Paulo, D5 04543-011, Brazil (“Raízen”)) shall be deemed to
be an Associated Company of IE or Raízen.

1.5 “Biocatalyst” has the meaning set forth in the License Agreement.

1.6 “Biomass” has the meaning set forth in the License Agreement.

1.7 “C1” means any fungal strain, enzyme, gene or other material that was
licensed by Dyadic to Codexis pursuant to the Dyadic License, and any progeny,
derivative or modification of the foregoing.

1.8 “Calendar Year” means (a) for the first Calendar Year of the term of this
Agreement, the period beginning on the Effective Date and ending on December 31,
2012, (b) for each Calendar Year during the term of this Agreement thereafter,
each successive period beginning on January 1 and ending twelve (12) consecutive
calendar months later on December 31, and (c) for the last Calendar Year of the
term of this Agreement, the period beginning on January 1 of the Calendar Year
in which this Agreement expires or terminates and ending on the effective date
of expiration or termination of this Agreement.

1.9 “Cellulase Technology” means any Microbe or Biocatalyst developed by Codexis
and/or its Affiliates that is a derivative of C1 and/or C1-derived enzymes for
which Shell receives rights to such Microbe or Biocatalyst pursuant to and/or in
accordance with, (a) Section 2.1 of the License Agreement, (b) Section 4.5 of
the IE/Codexis/Shell Agreement and/or (c) Section 4.2 of this Agreement, in each
case for use in the Intermediate Field of Use.

1.10 “Codexis Licensed Technology” has the meaning set forth in the License
Agreement.

1.11 “Codexis Patent Rights” has the meaning set forth in the License Agreement.

 

3

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1.12 “Codexis Qualified Transaction” means any transfer or assignment by Codexis
of its rights and obligations to a successor of all or substantially all of the
business or assets relating to this Agreement, whether by sale, acquisition,
merger, operation of law or otherwise.

1.13 “Confidential Information” means any and all non-public and proprietary
Information that is specifically designated as such and that is disclosed by
either Party to the other in written or other similar form in connection with
this Agreement and that, if orally or visually disclosed, shall be summarized in
writing in detail and specifically designated as proprietary and such summary
delivered to the receiving Party within thirty (30) days after such disclosure.

1.14 “Cost” shall have the meaning set forth on Schedule A attached hereto.

1.15 “Covered Information” means Confidential Information under the Research
Agreement that is related to, or useful in, the use or practice of Technology
(as defined in the Research Agreement) that falls within the Intermediate Field
of Use.

1.16 “Covered Technology” means the intellectual property licensed by Codexis to
Shell pursuant to Section 4.2(a) only. For purposes of clarification, “Covered
Technology” shall not include any intellectual property or other technology
covered under the license grants in Section 2.1 of the License Agreement or
Section 4.5 of the IE Agreement/Codexis/Shell Agreement.

1.17 “Covered Use” means the use (or proposed use) of a Sample in the Sample
Territory that is fully compliant with all instructions and guidance provided by
Codexis to Shell with respect to the applicable Sample pursuant to
Section 4.2(d).

1.18 “Dyadic Letter” has the meaning set forth in the Recitals.

1.19 “Dyadic License” has the meaning set forth in the Recitals.

1.20 “First Commercial Sale” means the first transfer by Codexis and/or a
Codexis Affiliate of a Biocatalyst to a Third Party in exchange for cash, or
cash equivalent to which value can be assigned after achievement of the
Triggering Event.

1.21 “FTE” means the efforts of one or more employees of Codexis, its
Affiliates, the Assignee and/or its Associated Companies equivalent to the
efforts of one full time employee (i.e., an employee that works at least one
thousand seven hundred sixty (1760) hours per year).

1.22 “Fuel Field of Use” has the meaning set forth in the License Agreement.

1.23 “Gross Margin” means Net Sales minus Cost, the difference of which is then
divided by Net Sales.

1.24 “IE/Codexis/Shell Agreement” has the meaning set forth in the Recitals.

1.25 “Information” means data, results, evaluations, inventories, Microbes,
show-how, know-how, computer chip and programs, processes, machines, biological
chemicals, enzymes, proteins, intermediates, trade secrets, techniques, methods,
developments, materials, methods of analysis, compositions of matter, copyrights
or other information.

 

4

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1.26 “Intermediate Field of Use” has the meaning set forth in the License
Agreement.

1.27 “License Agreement” has the meaning set forth in the Recitals.

1.28 “Licensed Field Information” shall mean Confidential Information under the
License Agreement that is related to, or useful in, the use or practice of
Technology and Materials (as such term is defined in the License Agreement) that
fall within the Intermediate Field of Use.

1.29 “Licensed Product” has the meaning set forth in the License Agreement.

1.30 “Losses” means any and all liability, damage, loss, cost or expense
(including without limitation reasonable attorneys’ fees).

1.31 “Lubricant” has the meaning set forth in the License Agreement.

1.32 “Lubricant Field of Use” has the meaning set forth in the License
Agreement.

1.33 “Microbes” has the meaning set forth in the License Agreement.

1.34 “Most Favored Nation Pricing” has the meaning set forth in Section 8.2.

1.35 “Net Sales” means the proceeds, expressed in United States Dollars, from
the sale of a Biocatalyst by Codexis and/or its Affiliates to Third Parties
(other than Shell Facilities) less: (i) bad debts related to such Biocatalyst;
(ii) compulsory payments and rebates, actually paid or deducted; (iii) customs
duties and other governmental charges, as well as sales, use, excise, inventory,
value added, and other taxes, related directly and only to the sale of such
Biocatalyst; (iv) commissions allowed or paid to Third Parties, including
without limitation distributors, brokers, or agents; and (v) Transportation
Costs of such Biocatalyst.

1.36 “Patents” means all patent applications and patents, corresponding foreign
patent applications and patents, and all continuations and divisions of any such
patent applications and of patent applications from which such patents issued,
all patents issuing from any of such patent applications, and all renewals,
reissues, re-examinations and extensions of any of such patents.

1.37 “Program” has the meaning set forth in the Research Agreement.

1.38 “Program Licensed Technology” has the meaning set forth in the License
Agreement.

1.39 “Program Patent Rights” has the meaning set forth in the License Agreement.

1.40 “Research Agreement” has the meaning set forth in the Recitals.

1.41 “Sample” has the meaning set forth in Section 4.2(d).

 

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1.42 “Sample Territory” has the meaning set forth in Section 4.2(d).

1.43 “Shell Facility” means any cellulosic fuel production facility in which
Shell and/or a Shell Affiliate (other than [***] or any Associated Company of
[***]) collectively own, and thereafter continues to own, at least [***] percent
([***]%) but less than [***] percent ([***]%) of the outstanding equity of the
entity or, if the entity is not an equity issuing entity, has made at least
[***] percent ([***]%) but less than [***] percent ([***]%) of the aggregate
capital contribution to the entity and continues to maintain these minimum
capital contribution requirements.

1.44 “Shell-Modified Sample” means a Sample that has been modified by Shell, a
Shell Affiliate, a Shell Facility or any Third Party.

1.45 “Technology Licensed to Shell” has the meaning set forth in Section 7.1(b).

1.46 “Territory” means worldwide, except Brazil.

1.47 “Third Party” means any party other than Codexis, Shell or Affiliates of
either Party.

1.48 “Third Party Patents” means, on a Sample-by-Sample basis, all issued
Patents owned by Third Parties in the Sample Territory that cover (a) the
composition of matter of such Sample or (b) any Covered Use, and that, in each
of (a) and (b), were known to Codexis, or should have been known to Codexis
after due inquiry, at the time Codexis transferred such Sample to Shell pursuant
to Section 4.2(d).

1.49 “Transportation Costs” means, with respect to transport of any Biocatalyst,
all costs associated with any packages and packing, transportation, storage
and/or insurance for such Biocatalyst.

1.50 “Triggering Event” means the production of sugars in the Intermediate Field
of Use in the Territory derived from the use of Biocatalysts by Codexis, its
Affiliates and/or its customers sufficient to produce the first thirty million
(30,000,000) gallons of liquid fuel.

ARTICLE 2

AMENDMENT AND TERMINATION OF THE RESEARCH AGREEMENT

2.1 Amendments to the Research Agreement.

(a) Amendment to First Sale Payment. Section 3.4(h) of the Research Agreement
shall be deleted and replaced with the following:

Shell shall pay to Codexis a one-time, non-refundable, non-creditable milestone
payment equal to Three Million United States Dollars ($3,000,000) upon the
earlier of the First Sale (a) in the Intermediate Field of Use in Brazil, (b) in
the Fuel Field of Use or (c) in the Lubricant Field of Use. Such payment shall
be due within thirty (30) days after the receipt by Shell of an invoice from
Codexis, such invoice to be issued by Codexis to Shell after receipt by Codexis
of notification, in writing, from Shell of such First Sale.

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

6

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(b) Amendment to the Survival Provision of the Research Agreement.
Section 11.4(b) of the Research Agreement shall be deleted and replaced with the
following:

The following Articles and Sections of this Amended and Restated Research
Agreement shall survive its termination or expiration: Articles 4, 5, 10 and 12,
and Sections 2.4(a)(iii), 2.9, 3.4(h), 3.7, 6.1, 8.3, 9.4, 9.5, 11.4(b) and
11.4(c).

(c) Amendment to Assignment Provision of the Research Agreement. The Parties
agree that Section 12.2 of the Research Agreement will be deleted and replaced
in its entirety with the following:

Neither Party may transfer or assign its rights and obligations under this
Amended and Restated Research Agreement without the prior written consent of the
other Party; provided that either Party may transfer or assign its rights and
obligations under this Amended and Restated Research Agreement to an Affiliate
of such Party or to a successor to all or substantially all of its business or
assets relating to the Amended and Restated Collaborative Research Agreement or,
separately, to the Intermediate Field of Use (as defined in the Amended and
Restated License Agreement) whether by sale, acquisition, merger, operation of
law or otherwise. Notwithstanding anything to the contrary, any transferee,
assignee or successor of a Party shall agree in writing to be bound by the terms
of this Amended and Restated Research Agreement prior to the effective date of
transfer or assignment of this Amended and Restated Research Agreement and,
thereafter, this Amended and Restated Research Agreement shall be binding upon
such transferee, assignee or successor. Any attempted transfer or assignment of
this Amended and Restated Research Agreement not in accordance with this
Section 12.2 will be null and void.

(d) Amendment to the Confidentiality Provision of the Research Agreement.
Notwithstanding anything to the contrary in the Research Agreement, the Parties
agree that Codexis and its Affiliates can disclose Covered Information (other
than Shell business plans and economic models) to Third Parties, Shell
Affiliates or Shell Facilities so long as each Third Party, Shell Affiliate or
Shell Facility agrees, prior to such disclosure, to be bound by obligations of
confidentiality and non-use no less restrictive than those set forth in Article
6 of the Research Agreement.

2.2 Buy-Out and Termination of Research Agreement. The Parties agree that the
Research Agreement shall terminate on August 31, 2012. Notwithstanding anything
to the contrary in the Research Agreement, within sixty (60) days after the
Effective Date, Shell shall pay to Codexis a payment equal to Seven Million Five
Hundred Forty-Three Thousand Three Hundred Thirty-Three United States Dollars
($7,543,333) in full, complete and final satisfaction of any and all payments
that Shell may owe Codexis under Sections 3.3(c), 3.4(b) and 3.4(f) of the
Research Agreement. For the avoidance of doubt, beginning September 1, 2012,
(a) Codexis and its Affiliates shall have no further obligations to Shell under
the Research Agreement to

 

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provide any FTEs to perform work under or after the Program and (b) Shell and
its Affiliates shall have no further obligations to Codexis under the Research
Agreement to provide funding for any FTEs to perform work under or after the
Program.

2.3 Removal of Research Restrictions. The Parties hereby agree that Section 9.4
of the Research Agreement shall be null and void solely with respect to
development of enzymes and Microbes for use in the Intermediate Field of Use in
the Territory upon the occurrence of any of the following: (a) the appointment
of a trustee, receiver or custodian for all or substantially all of the property
of Codexis, which appointment is not dismissed within sixty (60) days
thereafter; (b) the filing of a petition for relief in bankruptcy by Codexis on
its own behalf, or the filing of any such petition against Codexis if the
proceeding is not dismissed or withdrawn within sixty (60) days thereafter;
(c) the termination, pursuant to Section 7.1(b) of this Agreement, of the rights
granted to Codexis and its Affiliates by Shell under Section 4.1 of this
Agreement; or (d) the termination of this Agreement by Shell pursuant to
Section 13.2; provided that, in the event of any of (a), (b), (c) or (d), Shell
shall have a right to conduct research to make improvements to enzymes and
Microbes only for use in the Intermediate Field of Use in the Territory.
Notwithstanding the foregoing, nothing in this Agreement shall exempt Shell or
any Shell Affiliate from complying with any of the restrictions related to the
development or use of (i) Dyadic Materials and/or Production Strains (in each
case, as defined in the Dyadic License) contained in the Dyadic License and/or
the Dyadic Letter or (ii) C1 Materials and/or C1 Strains (in each case, as
defined in the IE/Codexis/Shell Agreement) contained in the IE/Codexis/Shell
Agreement, including without limitation Section 4.4 of the IE/Codexis/Shell
Agreement.

ARTICLE 3

IP COMMITTEE

3.1 IP Committee.

(a) Function. Shell and Codexis shall establish an IP Committee (the “IP
Committee”) to keep the Parties informed as to the filing, maintenance,
enforcement and defense of Patents licensed by a Party or to a Party pursuant to
Section 4.1 or Section 4.2. Codexis will consult with Shell, and will consider
Shell’s comments and recommendations, with respect to such Patents to be filed
and the maintenance, enforcement and defense of such Patents, and will provide a
status update to Shell regarding such Patents at least once per year.

(b) Membership. Shell and Codexis each, in its sole discretion, shall appoint
one (1) member to the IP Committee and shall provide written notice to the other
Party of the name and contact information of such member within five (5) days
after the Effective Date. Each Party may appoint substitutes for its member at
any time, such substitution to be effective immediately upon providing the name
and contact information of such substitute to the other Party’s representative
on the IP Committee.

(c) Chair. The IP Committee shall be chaired by the Codexis representative.

(d) Meetings. The IP Committee shall meet (in person or via teleconference) at
Codexis’ discretion but not less frequently than once per year, unless otherwise
agreed, at places and on dates agreed upon by Shell and Codexis. Representatives
of Shell or Codexis or both, in addition to members of the IP Committee, may
attend such meetings at the invitation of either Party.

 

8

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(e) Minutes. Codexis will provide accurate written minutes of meetings of the IP
Committee in a timely manner after each meeting.

(f) Decisions. All decisions of the IP Committee shall be made by consensus of
the Parties. The Codexis representative shall have one (1) vote and the Shell
representative shall have one (1) vote; provided, however, that in the case
where consensus of the Parties has not been reached, the final decision shall be
made by Codexis; provided, further, that in the event Codexis exercises such
final decision right with respect to the maintenance, enforcement or defense of
any applicable Patent then, notwithstanding anything to the contrary in this
Agreement, the Research Agreement or the License Agreement, Shell shall have no
obligation to co-fund any such maintenance, enforcement or defense decision with
respect to such Patent.

(g) Expenses. Shell and Codexis shall each bear all expenses of their respective
members related to their participation on the IP Committee.

(h) Disbanding of the IP Committee. The Parties shall have the right to disband
the IP Committee upon mutual agreement. Failure to agree to disband the IP
Committee shall not constitute a breach of this Agreement, nor trigger the
Dispute Resolution process as described in Section 14.6.

ARTICLE 4

LICENSE GRANTS

4.1 License by Shell to Codexis Under Program Patent Rights and Program Licensed
Technology. Subject to the restrictions of the Dyadic License, as may be amended
in the future, Shell hereby grants to Codexis and its Affiliates an irrevocable
(subject to Section 7.1(b) and Section 13.3(b)), non-exclusive, royalty-bearing
right and license under the Program Patent Rights and Program Licensed
Technology to develop, manufacture, have manufactured, use, have used, sell,
have sold, offer for sale, have offered for sale, import and have imported,
(a) Biocatalysts (including improvements to any Biocatalysts) and (b) Microbes,
and in each case of (a) and (b), in the Intermediate Field of Use in the
Territory, such license to include the right to grant sublicenses solely for
purposes of manufacturing enzymes and Microbes. For the avoidance of doubt,
Program Patent Rights and Program Licensed Technology in the preceding sentence
comprise the Program Patent Rights and Program Licensed Technology under the
License Agreement.

4.2 License Grant by Codexis to Shell.

(a) License Grant.

(i) Codexis hereby grants to Shell, subject to the terms set out in Schedule B,
an irrevocable (subject to Section 13.3(c)), non-exclusive, royalty-free license
in the Territory under intellectual property rights and Patents developed by
Codexis during the period

 

9

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beginning on the Effective Date and ending on the ten (10) year anniversary of
the Effective Date to manufacture, have manufactured, use and import, in each
case solely for use by Shell or Shell Affiliates, (i) enzymes developed by
Codexis outside of the Research Agreement for use in the Intermediate Field of
Use in the Territory, and (ii) improvements to any Microbe developed by Codexis
outside of the Research Agreement that is a derivative of C1 for use in the
Intermediate Field of Use in the Territory, and in each case of (i) and (ii),
such license to include the right, subject to the restrictions contained in the
Dyadic License, to grant sublicenses only to Shell Affiliates (other than [***]
and its Associated Companies) and Shell Facilities (other than a Shell Facility
in which [***] and/or its Associated Companies is an equity participant).
Notwithstanding anything to the contrary, a Shell Facility that is a sublicensee
of Shell or a Shell Affiliate under this Section 4.2(a) shall have no right to
grant any further sublicense to any party (including, for example, any equity
participant in such Shell Facility), except that such Shell Facility shall
retain the right to “have manufactured” such enzymes and/or Microbes solely for
use by such Shell Facility.

(ii) In the event that the collective ownership interest of Shell and/or a Shell
Affiliate (other than [***] or any Associated Company of [***]) in a Shell
Facility drops below [***] percent ([***]%), then if such Shell Facility, prior
to the date of such ownership interest drop, used enzymes and Microbes, and the
right to use intellectual property rights and Patents covering such enzymes and
Microbes, that are the subject of the license grant in Section 4.2(a)(i) in the
Intermediate Field of Use to produce liquid fuels in the amount:

(1) less than [***] of liquid fuel, then any and all sublicense rights granted
by Shell to such Shell Facility with respect to such enzymes, such Microbes, and
the right to use such intellectual property rights and Patents, shall
automatically terminate in the entirety; or

(2) equal to or greater than [***] of liquid fuel, then the sublicense rights
granted by Shell to such Shell Facility with respect to such enzymes and
Microbes, and right to use such intellectual property rights and Patents, shall
continue in effect but solely with respect to such enzymes, Microbes and
intellectual property rights and Patents developed by Codexis prior to the date
of such ownership drop. For the avoidance of doubt, sublicense rights to such
Shell Facility shall not include any enzymes or Microbes, or the right to use
any intellectual property rights or Patents, developed by Codexis after the date
of the ownership interest drop;

provided that, in either (1) or (2), upon request of a Shell Facility, Codexis
will use commercially reasonable efforts to negotiate with such Shell Facility
commercial terms for access to Codexis technology.

(iii) For the avoidance of doubt, in the event of any Assignment, the license
grant in this Section 4.2(a): (1) shall not apply to any enzymes, Microbes or
other technology developed, in-licensed and/or acquired by an Assignee prior to
the effective date of such Assignment, and (2) shall only apply to enzymes
developed after the effective date of such Assignment that are derivatives of
(A) any Biocatalyst and/or (B) any enzymes developed by Codexis and/or its
Affiliates from C1, and in each case of (A) and (B), solely to the extent
developed prior to the effective date of such Assignment.

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

10

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(b) For the avoidance of doubt, nothing in this Agreement shall impact the scope
of the license grant set forth in Section 4.5 of the IE/Codexis/Shell Agreement.

(c) Technical and Business Updates.

(i) Beginning six (6) months following the Effective Date and ending upon the
ten (10) year anniversary of the Effective Date, (i) Codexis shall provide Shell
with semi-annual written updates of Codexis commercially relevant technical
developments that are subject to the license grant in Section 4.2(a) during the
previous six (6) months, and (ii) at Shell’s prior request, Codexis shall, at
its own expense, participate semi-annually in a teleconference with Shell, at
its own expense, to provide an overview of Codexis’ progress towards
commercialization in the Intermediate Field of Use during the previous six
(6) months, such overview to be limited by confidentiality obligations of
Codexis and/or its Affiliates.

(ii) Beginning six (6) months following the Effective Date and ending upon
either Codexis’ expenditure (including, without limitation, any expenditure by a
Codexis Affiliate or a Third Party) of [***] United States Dollars ($[***]) on
improvement of the Cellulase Technology, or an Assignment as described in
Section 7.1, (A) Codexis shall provide Shell with semi-annual financial reports
on the number of FTEs assigned to improve the Cellulase Technology, and (B) at
Shell’s prior request and sole expense, but no more than once in any two
(2) consecutive calendar years, Codexis shall permit an independent Third Party,
mutually acceptable to Shell and Codexis, to conduct an audit of work directed
to improvement of the Cellulase Technology, such audit to be limited by
reasonable confidentiality obligations to Codexis and/or its Affiliates and to
be conducted at times that are reasonably acceptable to Codexis, to determine
the amount of expenditure directed to improvement of the Cellulase Technology as
of the date of such audit, and for no other purpose. The Third Party audit firm
will be required to treat all materials made available for inspection by Codexis
as Confidential Information of Codexis in accordance with Article 12.

(d) Technology Transfer. Beginning six (6) months following the Effective Date
and ending upon the ten (10) year anniversary of the Effective Date, upon the
reasonable written request of Shell but no more often than once every twelve
(12) months, Codexis, subject to the restrictions in the Dyadic License, will
provide Shell, or a Shell Affiliate (other than IE and its Associated Companies)
or a Shell Facility (other than a Shell Facility in which IE and/or its
Associated Companies is an equity participant), in each case identified by Shell
in writing to Codexis, with samples of commercially relevant Microbes and
enzymes that are the subject of the license grant in Section 4.2(a) (each, a
“Sample”). Such written request of Shell shall include a listing of
jurisdictions in which Shell intends to use such Samples (the “Sample
Territory”). Upon delivery of a Sample to Shell, or a Shell Affiliate (other
than [***] and its Associated Companies) or a Shell Facility (other than a Shell
Facility in which [***] and/or its Associated Companies is an equity
participant), so long as each such Affiliate or such Shell Facility has been
identified by Shell in writing, Codexis shall deliver written instructions
and/or guidance with respect to Covered Uses for such Sample in the applicable
jurisdictions in the Sample Territory. Such instructions and/or guidance may
include reference to, and limitations imposed as a result of, Third Party
Patents. In the event that Codexis provides Shell a Sample, and Shell then
desires to provide such Sample to a Shell Affiliate (other than [***] and its
Associated Companies) or a Shell Facility (other than a Shell Facility in which
[***] and/or its Associated Companies is an

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

11

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equity participant), Shell shall notify Codexis in writing, prior to providing
such a Sample, of the identity and location of such Shell Affiliate or such
Shell Facility. Shell covenants and agrees that Shell will not, and Shell will
not authorize or permit any Shell Affiliate or Shell Facility to, provide,
transfer or sell any Sample to any Third Party (including, without limitation
[***]), [***], or any Associated Company of [***] (including, without limitation
[***]). If Shell desires reasonable additional technology transfer assistance,
Codexis will use commercially reasonable efforts to provide such reasonable
assistance to the extent Codexis has personnel qualified to provide such
assistance and that Codexis can provide such assistance without undue disruption
to its other projects and business activities. Shell shall pay for any such
Codexis assistance at Codexis’ then prevailing market rates for such activities.
Codexis shall, from time-to-time, submit to Shell written invoices for any such
assistance provided to Shell, and Shell shall pay to Codexis such invoiced
amounts within thirty (30) days after receipt thereof.

(e) Intellectual Property Claims. Each Party shall promptly inform the other
Party in writing of any claim or suit brought by a Third Party alleging that the
practice of any Covered Technology (including without limitation, any Covered
Use) may infringe any Patent controlled by such Third Party. In the event of
such claim or suit, and upon [***] written request, [***] shall use commercially
reasonable efforts to (1) [***] and/or (2) recommend and/or make [***], and in
each case of (1) and (2), to the extent [***] has personnel qualified to provide
such assistance and that [***] can provide such assistance without undue
disruption to its other projects and business activities. In the event such
Patent controlled by such Third Party is:

(i) a Third Party Patent, [***] shall provide such assistance at [***] cost and
expense; or

(ii) not a Third Party Patent, [***] shall pay for such assistance at [***] then
prevailing market rates and, in connection with such assistance, [***] shall,
from time-to-time, submit to [***] written invoices for such assistance, and
[***] shall pay to [***] such invoiced amounts within thirty (30) days after
receipt thereof.

ARTICLE 5

AMENDMENT TO THE IE/CODEXIS/SHELL AGREEMENT

5.1 Consent to Assignment Provision of the IE/Codexis/Shell Agreement. Shell
covenants and agrees that it shall, upon the written request of Codexis,
promptly and without qualification or request for any consideration, provide
Codexis with Shell’s prior written consent under Section 11.2 of the
IE/Codexis/Shell Agreement to a Codexis Qualified Transaction.

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

12

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ARTICLE 6

AMENDMENTS TO THE LICENSE AGREEMENT

6.1 Amendment to Shell’s Covenant in the License Agreement. Section 7.3 of the
License Agreement shall be revised to include the following at the end of
Section 7.3 of the License Agreement:

In addition, Shell covenants that, notwithstanding anything to the contrary in
this Amended and Restated License Agreement, Shell shall not (d) sell, offer for
sale, transfer or import any Biocatalyst to [***] or any Third Party in the
Intermediate Field of Use, so long as such Biocatalyst qualifies as a Commercial
Improvement to any and all Biocatalysts that are derived from Research
Technology (as defined in the IE/Codexis/Shell Agreement), except that such
limitation, subject to the Dyadic License, shall not apply to (i) organizations
for contract manufacture with respect to the manufacture of Biocatalysts solely
for use by Shell or (ii) Shell’s or its Affiliates’ or sublicensees’ activities
in Brazil.

In addition, Shell covenants that, notwithstanding anything to the contrary in
this Amended and Restated License Agreement, Shell shall not authorize or grant
a sublicense to (e) any Shell Affiliate (other than [***]), [***], or any Third
Party to sell, offer for sale, transfer or import any Biocatalyst to [***] or
any Third Party in the Intermediate Field of Use, so long as such Biocatalyst
qualifies as a Commercial Improvement to any and all Biocatalysts that are
derived from Research Technology (as defined in the IE/Codexis/Shell Agreement),
except that such limitation, subject to the Dyadic License, shall not apply to
(i) organizations for contract manufacture with respect to the manufacture of
Biocatalysts solely for use by Shell or (ii) Shell’s or its Affiliates’ or
sublicensees’ activities in Brazil.

6.2 Amendment to Assignment Provision of the License Agreement. The Parties
agree that Section 10.2 (Assignments) of the License Agreement will be deleted
and replaced in its entirety with the following:

Neither Party may transfer or assign its rights and obligations under this
Amended and Restated License Agreement without the prior written consent of the
other Party; provided that either Party may transfer or assign its rights and
obligations under this Amended and Restated License Agreement to an Affiliate of
such Party or to a successor to all or substantially all of its business or
assets relating to the Amended and Restated License Agreement or, separately, to
the Intermediate Field of Use whether by sale, acquisition, merger, operation of
law or otherwise. Notwithstanding anything to the contrary, any transferee,
assignee or successor of a Party shall agree in writing to be bound by the terms
of this Amended and Restated License Agreement prior to the effective date of
transfer or assignment of this Amended and Restated License Agreement and,
thereafter, this Amended and Restated License Agreement shall be binding upon
such transferee, assignee or successor. Any attempted transfer or assignment of
this Amended and Restated License Agreement not in accordance with this
Section 10.2 will be null and void.

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

13

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6.3 Amendment to Confidentiality Provisions of the License Agreement.
Notwithstanding anything to the contrary in the License Agreement, the Parties
agree that Codexis and its Affiliates can disclose Licensed Field Information
(other than Shell business plans and economic models) to Third Parties, Shell
Affiliates or Shell Facilities, so long as each such Third Party, Shell
Affiliate or Shell Facility agrees prior to such disclosure to be bound by
obligations of confidentiality and non-use no less restrictive than those set
forth in Article 5 of the License Agreement.

6.4 Removal of Research Restrictions. The Parties hereby agree that Section 7.3
of the License Agreement shall be null and void solely with respect to
development of enzymes and Microbes for use in the Intermediate Field of Use in
the Territory upon the occurrence of any of the following (a) the appointment of
a trustee, receiver or custodian for all or substantially all of the property of
Codexis, which appointment is not dismissed within sixty (60) days thereafter;
(b) the filing of a petition for relief in bankruptcy by Codexis on its own
behalf, or the filing of any such petition against Codexis if the proceeding is
not dismissed or withdrawn within sixty (60) days thereafter; or (c) the
termination of this Agreement by Shell pursuant to Section 13.2. Notwithstanding
the foregoing, nothing in this Agreement shall exempt Shell or any Shell
Affiliate from complying with any of the restrictions related to the development
or use of (i) Dyadic Materials and/or Production Strains (in each case, as
defined in the Dyadic License) contained in the Dyadic License and/or the Dyadic
Letter or (ii) C1 Materials and/or C1 Strains (in each case, as defined in the
IE/Codexis/Shell Agreement) contained in the IE/Codexis/Shell Agreement,
including without limitation Section 4.4 of the IE/Codexis/Shell Agreement.

6.5 Limitation. In the event that (a) the Assignee, pursuant to Section 7.1(b),
terminates the rights granted to Codexis and its Affiliates by Shell under
Section 4.1 of this Agreement or (b) Shell terminates this Agreement pursuant to
Section 13.2 for a material failure by Codexis to comply with any of Codexis’
obligations contained in this Agreement, the terms of this Article 6 shall not
apply to Shell as of the effective date of such termination.

ARTICLE 7

TECHNOLOGY DEVELOPMENT OBLIGATION UPON THIRD PARTY ASSIGNMENT BY CODEXIS

7.1 In the event of a valid assignment of this Agreement by Codexis to a Third
Party in accordance with Section 14.2 of this Agreement (an “Assignment”), the
Third Party assignee (the “Assignee”) must, within ninety (90) days after the
effective date of the Assignment, provide Shell a written notice stating its
intention to do one of the following:

(a) Expend [***] United States Dollars ($[***]) either on (1) the development of
any Cellulase Technology, or (2) in payments directly to Shell, net of certain
expenditures of Codexis, its Affiliates and/or Third Parties, such expenditures
and such payments as set forth, together with examples for purposes of
illustration, in Schedule C; or

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

14

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(b) Terminate the rights granted to Codexis and its Affiliates by Shell under
Section 4.1 of this Agreement; provided, that in the event the Assignee elects
to terminate the rights granted to Codexis and its Affiliates by Shell under
Section 4.1 of this Agreement, (i) the license granted by Codexis to Shell
pursuant to Section 4.2(a) of this Agreement shall automatically be converted to
an exclusive license (subject to any pre-existing agreements or commitments),
with unrestricted sublicense rights (subject to the restrictions in the Dyadic
License and/or any pre-existing agreements or commitments); and (ii) Shell shall
have the right, at Shell’s sole expense, to bring an infringement action or
similar proceeding against any Third Party that Shell reasonably suspects of
infringement or unauthorized use of the Program Licensed Technology and/or the
Patents that are subject to the license grant in Section 4.2(a) (collectively,
the “Technology Licensed to Shell”), in each case in the Intermediate Field of
Use in the Territory; provided, however, that Shell shall, at least thirty
(30) days prior to commencing any such infringement action or similar
proceeding, provide to the Assignee written notice of Shell’s intention to
commence such infringement action or similar proceeding, including a reasonable
description of the alleged infringement and the identity of the alleged
infringing party, and Shell shall reasonably and in good faith consider the
Assignee’s comments thereto. If requested to do so by Shell, the Assignee shall
cooperate with Shell in any such action, including, but not limited to, by
joining the action as a party if necessary to maintain standing; provided that
Shell will reimburse the Assignee for any reasonable expenses (including
reasonable attorneys’ fees) actually incurred by the Assignee in cooperating
with Shell in any such action or proceeding, which Shell shall pay to Assignee
reasonably promptly after receiving from Assignee any written invoices thereto.
Any award recovered by Shell in any such action or proceeding shall belong
solely to Shell. Shell shall not enter into any settlement of any such action
that would restrict the scope, or adversely affect the enforceability of, the
“Technology Licensed to Shell”, without Assignee’s prior written consent. Upon
reasonable request by the Assignee, Shell shall keep the Assignee reasonably
informed of the status of its activities regarding any litigation, settlement or
other resolution thereof concerning the Technology Licensed to Shell.

7.2 Notwithstanding anything to the contrary in this Agreement, including
without limitation Section 13.2, in the event that the Assignee delivers a
notice to Shell pursuant to Section 7.1(a) and then fails to achieve the
required level of expenditure under Section 7.1(a), Shell shall have the right
to provide a written notice to Assignee requiring Assignee to make good or
otherwise cure such failure. In the event that Assignee’s annualized FTE
expenditure at the end of such sixty (60) day period is sufficient to meet its
minimum expenditure requirements pursuant to Section 7.1(a), then Assignee shall
be deemed to have “cured” such breach. If such default is not cured within sixty
(60) days after the date such notice was sent, then Assignee shall pay Shell
[***] United States Dollars ($[***]), net of any permissible reductions set
forth in the relevant subsection of Section 7.1(a). Notwithstanding anything to
the contrary in this Agreement, the obligations of Assignee under the preceding
sentence shall be Shell’s sole and exclusive remedy under this Agreement for
Assignee’s failure to achieve the required level of expenditure under
Section 7.1(a) and is in lieu of any other remedy, whether at law or at equity.

7.3 In the event that the Assignee delivers a notice to Shell pursuant to
Section 7.1(a) above, the Assignee shall provide a report to Shell within
forty-five (45) days of such notice setting forth (a) the number of FTEs
assigned by Codexis, its Affiliates and/or Third Parties to develop Cellulase
Technology during the period beginning on the Effective Date and ending on the
effective date of the Assignment and (b) the Assignee’s remaining development
obligations

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

15

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under Section 7.1(a), if any. In the event that the Assignee has remaining
development obligations under Section 7.1(a), within forty-five (45) days after
the end of each calendar quarter, the Assignee shall provide Shell with a report
setting forth the number of FTEs assigned by the Assignee and its Associated
Companies for the development of the Cellulase Technology during the just ended
calendar quarter. Such reporting obligation shall continue until the Assignee
has fulfilled the expenditure requirements set forth in Section 7.1(a). Codexis,
its Affiliates, the Assignee and its Associated Companies shall keep complete,
true and accurate books of account and records for the purpose of verifying the
reports presented by Codexis to Shell pursuant to this Section 7.3. Said books
and records will be kept for a period of at least three (3) years following the
reporting period to which they pertain and shall be available, after not less
than fifteen (15) business days prior written notice, for inspection, such
inspection not to occur more frequently than once in any Calendar Year, by Shell
using Shell personnel or by an independent public accountant, certified in the
U.S. and affiliated with a recognized accounting firm selected by Shell and
reasonably acceptable to the Assignee, solely in order to, and only to the
extent necessary to, verify the accuracy of the reports delivered by the
Assignee to Shell pursuant to this Section 7.3. Such independent public
accountant will be obliged by Shell to treat all materials made available for
inspection by Codexis as Confidential Information in accordance with Article 12.
Shell shall bear the full cost of the performance of any audit performed
pursuant to this Section 7.3.

7.4 Notwithstanding anything to the contrary in this Agreement, in the event
that Codexis and/or its Affiliates have expended [***] United States Dollars
($[***]) to develop the Cellulase Technology prior to the forty-eight (48) month
anniversary of the Effective Date, including an expenditure of at least [***]
United States Dollars ($[***]) prior to the twenty-four (24) month anniversary
of the Effective Date, Codexis shall provide written notice thereof to Shell and
the provisions of this Article 7 shall be null and void as of the date of such
notice. The expenditures of Codexis and/or its Affiliates shall be calculated by
multiplying the number of FTEs assigned by Codexis and/or its Affiliates to
develop the Cellulase Technology during the relevant period by [***] United
States Dollars ($[***]) per year.

7.5 The Parties agree that the FTE rates set forth in this Article 7 for
purposes of calculating expenditures by Codexis, its Affiliates, the Assignee
and its Associated Companies shall be used even if the amounts that Codexis, its
Affiliates, the Assignee and/or its Associated Companies (i) receive as
reimbursement, or (ii) actually expend, for the development of the Cellulase
Technology are different than such FTE rates.

ARTICLE 8

FINANCIAL TERMS

8.1 Royalty Payment from Codexis to Shell.

(a) In consideration for the rights granted to Codexis and its Affiliates under
this Agreement by Shell, Codexis shall pay to Shell royalty payments as follows:
(i) for the sale by Codexis and/or its Affiliates of any Biocatalyst to any
Third Party for use in the Intermediate Field of Use in the Territory after the
First Commercial Sale, Codexis shall pay to Shell a royalty equal to [***]
percent ([***] %) of Net Sales and (ii) for the use of any Biocatalyst by
Codexis

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

16

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and/or its Affiliates in the Intermediate Field of Use in the Territory after
the Triggering Event, Codexis shall pay to Shell a royalty equal to [***]
percent ([***] %) of the fair market price of such Biocatalysts as indicated by
Net Sales during the prior twelve (12) months for such Biocatalyst or, if no
such Net Sales have occurred, then as mutually agreed upon by the Parties acting
reasonably and in good faith. Notwithstanding the foregoing, the Parties agree
that in the event that a particular sale of any Biocatalyst to any Third Party
for use in the Intermediate Field of Use by Codexis and/or its Affiliates would
trigger a royalty obligation to Shell and/or its Affiliates under this Agreement
and any other agreement that Shell and/or its Affiliates is a party to (each
such agreement, an “Other Agreement”), Codexis and/or its Affiliates shall owe
only one (1) payment to Shell and/or its Affiliates for such sale, such payment
to be equal to the average royalty among the parties to the Other Agreement that
would owe to Shell a royalty to be paid under this Agreement and any Other
Agreement for such sale, such average royalty to be weighted to reflect each
such party’s relative economic benefit in such sale. For purposes of
illustration, not intended to be limiting, example calculations of royalty
payments to Shell are set forth in Schedule D.

(b) Within ninety (90) days after the end of each calendar quarter in which any
sales that would give rise to a payment obligation under this Article 8 have
occurred, Codexis shall provide Shell a written statement of royalties due to
Shell and, together with such written statement, all payments due to Shell based
on such written statement.

8.2 Most Favored Nation Pricing. In the event that Codexis supplies Biocatalysts
to Shell and Shell Affiliates during the term of this Agreement, Codexis agrees
that it will supply Biocatalysts to Shell and Shell Affiliates in the
Intermediate Field of Use in the Territory at a price equal to [***] (a) the
United States Dollar [***] (excluding [***] included in [***]) for which [***]
has sold such Biocatalysts to [***] in the Intermediate Field of Use in the
Territory [***], and (b) [***] United States Dollar [***] in the Intermediate
Field of use in the Territory [***] and in each case of (a) and (b), plus all
applicable [***] for such Biocatalysts; provided, however, under no
circumstances will Codexis be required to supply Biocatalysts to Shell at a
transfer price less than [***] for such Biocatalysts (collectively, “Most
Favored Nation Pricing”). Notwithstanding anything to the contrary, Codexis
shall have no obligation to supply any Biocatalyst to Shell or any Shell
Affiliate. For purposes of illustration, examples of Most Favored Nation Pricing
are set forth in Schedule E.

8.3 Audits.

(a) Codexis will keep, and will require its Affiliates to keep, complete, true
and accurate books of account and records for the purpose of showing the
derivation of (i) all royalties payable to Shell under Section 8.1 or (ii) Most
Favored Nation Pricing pursuant to Section 8.2. Said books and records will be
kept for at least three (3) years following the end of the Calendar Year to
which they pertain and shall be available, after not less than fifteen
(15) business days prior written notice, for inspection by an independent public
accountant, certified in the U.S. and affiliated with a recognized accounting
firm selected by Shell and reasonably acceptable to Codexis, for the purpose of
verifying statements provided to Shell (A) pursuant to Section 8.1(b) regarding
royalties due to Shell or (B) Most Favored Nation Pricing pursuant to
Section 8.2. Such independent public accountant will be obliged by Shell to
treat all materials made available for inspection by Codexis as Confidential
Information in accordance with Article 12.

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

17

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(b) In the event that the independent public accountant described in
Section 8.3(a) alleges that an underpayment or an overpayment has been made, and
the Parties agree on the amount of such underpayment or such overpayment,
Codexis, in the event of an underpayment, will pay to Shell the full amount of
such underpayment within ten (10) days after such agreement between the Parties
or, in the event of an overpayment, may credit the amount of such overpayment
against any future payment due to Shell under this Agreement. Shell shall bear
the full cost of the performance of any audit performed under Section 8.3(a),
unless such audit discloses a variance to the detriment of Shell of more than
ten percent (10%) (determined on an aggregate basis for all payments covered by
the audit), and the Parties agree that such variance is correct, in which case,
Codexis shall bear the full cost of the performance of such audit.

(c) Notwithstanding the provisions of Section 14.6, in the event that the
independent public accountant described in Section 8.3(a) alleges that an
underpayment or an overpayment has been made, and a Party provides written
notice to the other Party disputing such allegation within thirty (30) days
after such allegation, the Parties shall mutually select a U.S.-based recognized
public accounting firm which shall review the amount in dispute (including
supporting documentation) and resolve such dispute within thirty (30) days after
selection of such firm. Such U.S.-based recognized public accounting firm will
be obliged to Codexis to treat all materials made available for inspection as
Confidential Information of Codexis or Shell in accordance with Article 12. In
the event that such U.S.-based recognized public accounting firm determines that
an underpayment or an overpayment has been made, Codexis, in the event of an
underpayment, will pay to Shell the full amount of such underpayment within ten
(10) days after such agreement between the Parties or, in the event of an
overpayment, may credit the amount of such overpayment against any future
payment due to Shell under this Agreement. Each Party shall pay fifty percent
(50%) of the expenses for such public accounting firm; provided, however, that
if the audit performed by such accounting firm discloses a variance to the
detriment of Shell of more than ten percent (10%) (determined on an aggregate
basis for all payments covered by the audit), Codexis shall reimburse Shell for
Shell’s portion of the expenses for such audit with fifteen (15) days after
Shell’s written request for such reimbursement and, in addition, the cost of the
initial audit by Shell pursuant to Section 8.1(a). The determination of such
US-based recognized public accounting firm pursuant to this Section 8.3(c) shall
be final and binding upon the Parties, and shall not be subject to dispute
resolution pursuant to Section 14.6.

8.4 Dyadic Payments.

(a) Notwithstanding anything to the contrary in the Dyadic Letter, the Parties
hereby agree that (i) [***] will be directly responsible [***] and (ii) [***] to
make payments due under the [***]; provided that in the event that the supply of
enzymes [***] any particular payment [***] make such payment [***].

(b) [***] solely with respect to the activities of Codexis and its Affiliates in
Category A and/or Category F (as each is defined in the Dyadic License).

8.5 No Royalties to Codexis on Third Party Enzyme Sales by Codexis.
Notwithstanding anything to the contrary in the License Agreement, Shell shall
not owe Codexis any Intermediate Royalty (as such term is defined in the License
Agreement) under Section 3.1(a) of the License Agreement as a result of the sale
of any enzyme or Microbe by Codexis and/or its Affiliates to any Third Party in
the Intermediate Field of Use in the Territory.

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

18

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8.6 Mode of Payment; Late Payment Interest.

(a) All payments made by Codexis to Shell under this Agreement shall be made by
direct wire transfer of United States Dollars in immediately available funds in
the requisite amount to such bank account as Shell may from time to time
designate by written notice to Codexis. For the purpose of determining royalties
payable under this Agreement, any revenues Codexis and/or its Affiliates receive
in currencies other than United States Dollars shall be converted into United
States Dollars according to Codexis’ reasonable standard internal conversion
procedures. To the extent permitted under applicable law, the Parties shall use
diligent efforts to utilize any exemption available to minimize any taxes, fees
or other charges imposed on payments to Shell under the terms of this Agreement.

(b) Any payment due and payable to Shell under the terms and conditions of this
Agreement made by Codexis after the date such payment is due to be paid shall
bear interest as of the day after the date such payment was due to be paid and
shall continue to accrue such interest until payment of the amount due is made.
The interest rate to be applied to any payment not paid when due shall be equal
to the lesser of either (a) two percent (2%) above the prime rate as reported by
Citibank, New York, New York on the date such payment was due to be paid, or
(b) the maximum rate permitted by applicable law on such date, and shall apply
until the date that payment is issued by Codexis to Shell.

ARTICLE 9

IP Matters

9.1 Abandonment of Patents. In the event that Codexis decides to abandon any of
the Patents within the Technology Licensed to Shell, Codexis shall, at least
forty-five (45) days prior to any abandonment thereof, provide advance written
notice thereof to Shell. Shell may elect to receive assignment of such Patents
by providing to Codexis written notice of such election within fifteen
(15) business days after Shell’s receipt of such Codexis notice of abandonment.
In the event Shell elects to receive such assignment, Codexis shall, to the
extent feasible and as soon as reasonably practicable, assign such Patents to
Shell (or otherwise transfer to Shell responsibility for, including without
limitation all costs associated with, the prosecution, maintenance, enforcement
and defense of such Patents and all costs associated therewith).

ARTICLE 10

REPRESENTATIONS AND WARRANTIES

10.1 Mutual Representations and Warranties. Each Party represents and warrants
to the other that: (a) it is duly organized and validly existing under the
applicable laws of the jurisdiction of its incorporation, and has full corporate
power and authority to enter into this Agreement and to carry out the provisions
hereof; (b) it is qualified to do business and is in good standing in each
jurisdiction in which it conducts business; (c) it is duly authorized to execute

 

19

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and deliver this Agreement and to perform its obligations hereunder, and the
person executing this Agreement on its behalf has been duly authorized to do so
by all requisite corporate action; and (d) this Agreement is legally binding
upon it and enforceable in accordance with its terms and the execution, delivery
and performance of this Agreement by it does not conflict with any agreement,
instrument or understanding, oral or written, to which it is a party or by which
it may be bound, nor violate any material law. In addition, each Party
represents and warrants to the other that, as of the Effective Date, to its
knowledge, there is no action, suit or inquiry or investigation instituted by
any person which questions or threatens the validity of this Agreement.

10.2 Disclaimer of Warranties. EXCEPT AS SPECIFICALLY SET FORTH IN THIS ARTICLE
10, NEITHER PARTY MAKES ANY REPRESENTATION OR WARRANTY, EXPRESS OR IMPLIED,
INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
PURPOSE OR USE, NON-INFRINGEMENT, AND ANY OTHER STATUTORY WARRANTY.

ARTICLE 11

INDEMNIFICATION

11.1 Employees and Property. Each Party (each, the “Indemnitor”) shall
indemnify, defend and hold the other Party and its Affiliates and their
respective agents, employees, consultants, officers and directors (the
“Indemnitees”) harmless from and against any and all Losses, arising from any
claims or suits arising from (a) bodily injuries, including without limitation
fatal injury or disease, to the Indemnitor’s employees, and (b) damage to
tangible, real or personal property of Indemnitor and/or Indemnitor’s employees,
in each case arising from or in connection with the performance of this
Agreement or the practice or use of the rights conferred to an Indemnitor by
this Agreement; except, in any such case, for Losses to the extent, and only to
the extent, reasonably attributable to the gross negligence, recklessness or
willful misconduct of the applicable Indemnitee.

11.2 Indemnification by Codexis. Codexis shall fully indemnify, defend and hold
the Shell Indemnitees harmless from and against any and all Losses arising out
of Third Party claims or suits (but not any Shell Facility claims or suits)
arising from:

(a) breach by Codexis of any of its representations and warranties under this
Agreement;

(b) failure to perform its obligations under this Agreement;

(c) the negligence or willful misconduct of Codexis or its Affiliates, and its
or their directors, officers, agents, employees, sublicensees or consultants;

(d) bodily injuries, including without limitation fatal injury or disease, to
the employees of such a Third Party, and/or damage to tangible, real or personal
property of such a Third Party or employees of such a Third Party, in each case
arising from or in connection with the practice or use of rights granted by
Shell to Codexis under the terms of this Agreement and conferred by Codexis to
such a Third Party, or

 

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(e) breach of the covenant set forth in Section 2.7(b) of the Dyadic License as
a result of any claim or suit brought by Codexis;

except in any such case under clause (a), (b), (c) or (d) for Losses to the
extent, and only to the extent, reasonably attributable to a breach by Shell of
its representations and warranties set forth in this Agreement or the gross
negligence, recklessness or willful misconduct of any Shell Indemnitee.

11.3 Indemnification by Shell. Shell shall fully indemnify, defend and hold the
Codexis Indemnitees harmless from and against any and all Losses arising out of
Third Party claims or suits arising from:

(a) breach by Shell of any of its representations and warranties under this
Agreement;

(b) failure to perform its obligations under this Agreement;

(c) the negligence or willful misconduct of Shell or its Affiliates, and its or
their directors, officers, agents, employees, sublicensees, or consultants;

(d) bodily injuries, including without limitation fatal injury or disease, to
the employees of such a Third Party, and/or damage to tangible, real or personal
property of such a Third Party or employees of such a Third Party, in each case
arising from or in connection with the practice or use of rights granted by
Codexis to Shell under the terms of this Agreement and conferred by Shell to
such a Third Party, or

(e) for the avoidance of doubt, breach of Shell’s covenant set forth in Schedule
B;

except in any such case under clause (a), (b), (c) or (d) for Losses to the
extent, and only to the extent, reasonably attributable to a breach by Codexis
of its representations and warranties set forth in this Agreement or the gross
negligence, recklessness or willful misconduct of any Codexis Indemnitee.

11.4 Intellectual Property.

(a) Indemnification by Codexis. Codexis shall fully indemnify, defend and hold
the Shell Indemnitees harmless from and against any and all Losses arising out
of Third Party claims or suits (but not any Shell Facility claims or suits)
arising from (i) infringement of Third Party Patents of a Covered Use of a
Sample by a Shell Indemnitee; or (ii) use by Codexis or its Affiliates of
Program Patent Rights and Program Licensed Technology licensed by Shell to
Codexis and its Affiliates pursuant to Section 4.1 of this Agreement; provided
that Codexis’ indemnification obligations pursuant to this Section 11.4(a) for
any particular Loss shall be as follows:

(A) if an indemnified use is a use by Shell, independent of Codexis, Codexis’
liability for such use shall be limited to [***] United States Dollars ($[***]),
and the aggregate indemnification obligations of Codexis shall be capped for all
Losses at [***] United States Dollars ($[***]);

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

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(B) if an indemnified use is a use by Shell, not independent of Codexis, and is
a use by Codexis and Shell jointly in a joint venture or other similar
enterprise, Codexis’ liability for such use shall be limited to [***] United
States Dollars ($[***]), and the aggregate indemnification obligations of
Codexis shall be capped for all Losses at [***] United States Dollars ($[***]);
and

(C) if an indemnified use is a use by Codexis, independent of Shell, [***];

provided, however, in each of (A) and/or (B), Codexis obligation under this
Section 11.4(a) shall not extend to continued activities of the Shell
Indemnitees, activities that gave rise to such Third Party claims or suits,
after (1) receipt by Codexis of a Claim Notice in accordance with
Section 11.6(b), and (2) a reasonable period of time for Codexis to provide the
Shell Indemnitees an alternative, non-infringing technology for implementation
by the Shell Indemnitees.

(b) Indemnification by Shell. Shell shall fully indemnify, defend and hold the
Codexis Indemnitees harmless from and against any and all Losses arising out of
Third Party claims or suits arising from (i) infringement of any Patents owned
or otherwise controlled by such Third Party by any use by Shell or a Shell
Affiliate or a Shell Facility of the Samples that is not a Covered Use; (ii) the
use, other than a Covered Use, of any Sample by Shell or a Shell Affiliate or a
Shell Facility in the Intermediate Field of Use; (iii) the use of any Shell
Modified Sample by Shell or a Shell Affiliate or a Shell Facility, regardless of
whether such use is inside or outside the Intermediate Field of Use; (iv) the
use of any Sample by Shell or a Shell Affiliate or a Shell Facility, whether
such use is a Covered Use or not a Covered Use, in combination with other
technology not provided by Codexis and such claim or suit would not have arose
by use of such Sample without such other technology; or (v) infringement of
Patents owned or otherwise controlled by such Third Party by the practice of
intellectual property provided to Codexis or any Affiliate of Codexis by or on
behalf of Shell or any Affiliate of Shell (at the time such intellectual
property was provided), or to improvements made by Codexis or any Affiliate of
Codexis to such intellectual property; except in each case of (i)-(v), to the
extent such Losses are subject to indemnification by Codexis pursuant to
Section 11.4(a).

11.5 Environmental. Notwithstanding any other indemnification obligation in this
Agreement, and in addition to any rights the Parties may have under relevant
federal, state, or local statutory and common laws, each Party shall fully
indemnify, defend and hold the other Party and its Affiliates harmless from and
against any and all Losses incurred as a result of Environmental Matters (as
such term is defined below); provided, however, that this indemnification shall
not apply to the extent any such Losses result from the acts or omissions of
personnel of the Indemnitee or its Affiliates which occur at any site of the
Indemnitee or the site of any supplier of the Indemnitee.

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

 

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For purposes of this Section 11.5, “Environment Matters” shall mean:

(a) the operation by the Indemnitor, its Affiliates, sublicensees, or
subcontractors of any site or facility in a manner that is not in compliance
with and in violation of any applicable Environmental Law (as such term is
defined below);

(b) any release of Hazardous Materials (as such term is defined below) into the
environment by the Indemnitor, its Affiliates, sublicensees, or its
subcontractors; or any Hazardous Materials that have been Disposed (as such term
is defined in applicable Environmental Law) of at a site of the Indemnitor or
any site of any supplier (other than Codexis as supplier) of the Indemnitor or
other site or facility operated by the Indemnitor, its Affiliates or its
subcontractors;

(c) any failure to obtain or maintain all permits and provide all notices
required by any applicable Environmental Law for the lawful operation of any
site of the Indemnitor or any site of any supplier of the Indemnitor or other
facilities or sites operated by the Indemnitor, its Affiliates, sublicensees, or
its subcontractors; and

(d) any other actual or alleged act or omission relating to the handling or
disposal of Hazardous Materials at any site of the Indemnitor or any site of any
supplier of the Indemnitor or the handling or disposal of Hazardous Materials by
the Indemnitor, its Affiliates, sublicensees, or its subcontractors at any other
facility or site.

For purposes of this Section 11.5, “Environmental Law” shall mean any treaty,
law, ordinance, regulation or order of any jurisdiction, relating to
environmental matters, including, but not limited to, matters governing air
pollution; water pollution; the use, handling, reporting, release, storage,
transport, or disposal of Hazardous Materials as defined herein above; exposure
to or discharge of Hazardous Materials; occupational safety and health; and
public health.

For purposes of this Section 11.5, “Hazardous Materials” includes, but is not
limited to, air contaminant, water pollutant, hazardous material, hazardous
waste, hazardous substance, toxic and hazardous substance, medical waste,
infectious waste, “chemicals known to the State of California to cause cancer or
reproductive toxicity”, asbestos and PCB’s, as such substances are defined under
any applicable federal, state or local statute, regulation, rule or ordinance.

11.6 Notification of Claim; Conditions to Indemnification Obligations.

(a) Generally. Except with respect to Shell’s right to receive indemnification
under Section 11.4(a), as a condition to a Party’s right to receive
indemnification under this Section 10, that Party shall: (i) promptly notify
(“Claim Notice”) the other Party as soon as it becomes aware of a claim or suit
for which indemnification may be sought pursuant hereto (provided that the
failure to give a Claim Notice promptly shall not prejudice the rights of an
Indemnitee except to the extent that the failure to give such prompt notice
materially adversely affects the ability of the Indemnitor to defend the claim
or suit); (ii) cooperate with the Indemnitor in the defense of such claim or
suit, at the expense of the Indemnitor; and (iii) if the Indemnitor confirms in
writing to the Indemnitee its intention to defend such claim or suit within
fifteen (15) business days of receipt of the Claim Notice, permit the Indemnitor
to control the defense of such claim or suit, including without limitation the
right to select defense counsel; provided that if the

 

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Indemnitor fails to (A) provide such confirmation in writing within the fifteen
(15) business day period; or (B) diligently and reasonably defend such suit or
claim at any time, its right to defend the claim or suit shall terminate
immediately in the case of (A) and upon twenty (20) days’ written notice to the
Indemnitor in the case of (B), the Indemnitee may assume the defense of such
claim or suit at the sole expense of the Indemnitor and may settle or compromise
such claim or suit without the consent of the Indemnitor. In no event, however,
may the Indemnitor compromise or settle any claim or suit in a manner which
admits fault or negligence on the part of any Indemnitee or that otherwise
materially affects such Indemnitee’s rights under this Agreement or requires any
payment by an Indemnitee without the prior written consent of such Indemnitee.
Except as expressly provided above, the Indemnitor will have no liability under
this Section 9 with respect to claims or suits settled or compromised without
its prior written consent. The Indemnitee and, in the event of a valid
assignment of this Agreement by Codexis to a Third Party in accordance with
Section 14.2, the Assignee’s Indemnitees, shall have the right, but not the
duty, at its sole cost and expense, to participate in the defense of any claim
or suit hereunder with attorneys of its own selection without relieving the
Indemnitor and, in the event of a valid assignment of this Agreement by Codexis
to a Third Party in accordance with Section 14.2, the Assignee’s Indemnitor, of
any of its obligations hereunder.

(b) Claims by Shell With Respect to Third Party Patents. As a condition to
Shell’s right to receive indemnification under Section 11.4(a), Shell shall
(i) promptly provide Codexis with a Claim Notice as soon as it becomes aware of
a claim or suit for which indemnification may be sought pursuant to
Section 11.4(a) (provided that the failure to give a Claim Notice promptly shall
not prejudice the rights of Shell except to the extent that the failure to give
such prompt notice materially adversely affects the ability of Codexis to defend
the claim or suit); (ii) cooperate with Codexis in the defense of any suit,
action or proceeding alleging the infringement of any Third Party Patent by
reason of the manufacture, use, sale, offer for sale or importation of any
Sample, including by providing information and assistance necessary to defend or
settle any such suit, action or proceeding; and (iii) give to Codexis the right
to exclusive control of the defense of any such suit, action or proceeding and
the exclusive right after consultation with Shell, to compromise, litigate,
settle or otherwise dispose of any such suit, action or proceeding, at Codexis’
expense; provided, however, Codexis shall, upon the written request of Shell,
keep Shell informed of the status of any such suit, action or proceeding in a
timely manner, and must obtain Shell’s prior written consent to such part of any
settlement which contemplates payment or other action by Shell or has a material
adverse effect on Shell’s business or the use of the Samples. Codexis shall give
Shell prompt written notice of the commencement of any such suit, action or
proceeding or claim of infringement. If it becomes necessary for defense of the
suit, action or proceeding for Codexis to join Shell in any such suit, action or
proceeding, Codexis may join Shell as a co-defendant if necessary or desirable,
and thereafter Shell may participate in the prosecution of such suit, action or
proceeding, at Shell’s expense, and shall execute all documents and take all
other actions, including giving testimony, which may reasonably be required in
connection with such suit, action or proceeding.

 

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ARTICLE 12

CONFIDENTIALITY

12.1 Confidentiality Obligations. The Parties agree that, during the term of
this Agreement and for five (5) years thereafter, all Confidential Information
disclosed by one Party to the other Party hereunder shall be received and
maintained by the receiving Party in strict confidence, shall not be used for
any purpose other than the purposes expressly permitted by this Agreement, and
shall not be disclosed to any Third Party except to the extent necessary to
enable the receiving Party to practice the rights granted to it pursuant to this
Agreement; provided that such disclosure is made under obligations of
confidentiality and non-use no less restrictive than the obligations contained
herein. The Parties acknowledge and agree that the structure and composition of
each particular Biocatalyst developed under the Program shall be deemed
Confidential Information of Codexis, subject to the confidentiality and non-use
obligations set forth in this Article 12. The obligations of confidentiality and
non-use set forth in the first sentence of this Section 12.1 will not apply to
any information to the extent that it can be established by the receiving Party
that such information:

(a) was already known to the receiving Party or its Affiliates at the time of
disclosure without restriction as to confidentiality or use, as evidenced by
competent evidence;

(b) was generally available to the public or was otherwise part of the public
domain at the time of its disclosure to the receiving Party or its Affiliates;

(c) became generally available to the public or otherwise becomes part of the
public domain after its disclosure and other than through any fault of the
receiving Party or its Affiliates in breach of this Agreement;

(d) was subsequently disclosed to the receiving Party or its Affiliates by a
Third Party without (i) restriction as to confidentiality or use and
(ii) violating any confidentiality obligation of such Third Party to the
disclosing Party or its Affiliates; or

(e) is independently developed by employees or agents of the receiving Party or
its Affiliates without reliance upon or access (directly or indirectly) to
Confidential Information of the disclosing Party or its Affiliates, as evidenced
by competent evidence.

12.2 Each Party (the “first Party”) represents and warrants that it has or will
obtain written agreements from each person who has a need to know the other
Party’s (the “second Party’s”) Confidential Information, which agreements will
obligate such person to obligations of confidentiality and non-use no less
restrictive than the obligations set forth herein, and to assign to such first
Party, and such first Party shall and hereby does assign to the second Party,
all inventions made by such person during the course of performing any tasks
associated with the second Party’s Confidential Information. Further, each Party
represents and warrants that those of its employees which have a need to know
the other Party’s Confidential Information are bound by obligations of
confidentiality and non-use to the employee’s employer Party.

 

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12.3 Notwithstanding this Article 12, the receiving Party may disclose any
Confidential Information of the disclosing Party that the receiving Party is
required to disclose under applicable laws or regulations, including without
limitation applicable securities laws, or an order by a court or other
regulatory body having competent jurisdiction; provided, however, that, except
where impracticable, the receiving Party shall give the disclosing Party
reasonable advance notice of such disclosure requirement (which shall include a
copy of any applicable subpoena or order) and, except where impracticable, shall
afford the disclosing Party a reasonable opportunity to oppose, limit or secure
confidential treatment for such required disclosure. In the event of any such
required disclosure, the receiving Party shall disclose only that portion of the
Confidential Information of the disclosing Party that the receiving Party is
legally required to disclose and, in the event a protective order is obtained by
the disclosing Party, nothing in this Article 12 shall be construed to authorize
the receiving Party to use or disclose any disclosing Party Confidential
Information to parties other than such court or regulatory body or beyond the
scope of the protective order. Codexis and its Affiliates may disclose this
Agreement if required to be disclosed by applicable state or federal tax or
securities laws to the extent, and only to the extent, such laws require such
disclosure and Codexis provides Shell a reasonable opportunity to review and
comment on the general text of such disclosure.

ARTICLE 13

TERM AND TERMINATION

13.1 Term. The term of this Agreement will commence on the Effective Date and,
unless earlier terminated in accordance with Section 13.2, shall continue in
effect until the later of (a) twenty (20) years after the Effective Date or
(b) the date of the last to expire Program Patent Rights that claim a
Biocatalyst and/ or a Microbe for use in the Intermediate Field of Use in the
Territory.

13.2 Termination Upon Material Breach. Material failure by a Party to comply
with any of its obligations contained herein shall entitle the Party not in
default to give to the Party in default written notice (a “Default Notice”)
specifying the nature of the default in reasonable detail, requiring such
defaulting Party to make good or otherwise cure such default, and stating the
non-defaulting Party’s intention to terminate the defaulting Party’s rights
under this Agreement if such default is not cured. If such default is not cured
within sixty (60) days after the date the Default Notice was sent, then the
Party not in default shall be entitled, without prejudice to any other rights
conferred on it by this Agreement, and in addition to any other remedies
available to it by law or in equity, to terminate the defaulting Party’s rights
under this Agreement by written notice of termination to the defaulting Party;
provided, however, that if the defaulting Party presents evidence within five
(5) days before the expiration of such sixty (60) day cure period of its
diligent efforts to effect a cure within such sixty (60) days, but such a cure
has not been effected, the non-defaulting Party may not terminate the defaulting
Party’s rights under this Agreement until such diligent efforts have ceased;
provided further, however, that if the Party receiving such Default Notice (the
“Disputing Party”) has a reasonable basis for disputing that it is in default
and such Party provides written notice thereof to the other Party before the
expiration of such sixty (60) day cure period, then the Disputing Party shall
have the right, prior to the expiration of such sixty (60) day period, to submit
such dispute for resolution in accordance with the provisions of Section 14.6;
provided further that in the event that as a result of such resolution, the
Disputing Party is found to be in default and such default is not cured within
forty-five (45) days after the date of such resolution, then the Party not in
default

 

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shall be entitled, without prejudice to any other rights conferred on it by this
Agreement, and in addition to any other remedies available to it by law or in
equity, to terminate the defaulting Party’s rights under this Agreement by
written notice of termination to the Disputing Party. In the event that the
non-defaulting Party terminates this Agreement in accordance with this
Section 13.2, the rights of the non-defaulting Party, and the obligations of the
defaulting Party, shall continue in full force and effect until the expiration
of this Agreement.

13.3 Consequences of Expiration or Termination.

(a) The following Articles and Sections of this Agreement shall survive its
termination or expiration: 1, 2, 4.1, 4.2(a) (including Schedule B), 4.2(b)
(including Schedule B), 5, 6, 8.1 (including Schedule D) (solely to the extent
payments thereunder remain unpaid at termination or expiration), 8.3 (for the
period set forth therein), 8.4, 8.5, 8.6 (solely to the extent payments
thereunder remain unpaid at termination or expiration), 10.2, 11 (including
Schedule B), 12 (for the period set forth therein), 13.3 and 14.

(b) Notwithstanding Section 13.3(a), in the event of termination of this
Agreement by Shell pursuant to Section 13.2, the license granted by Shell to
Codexis pursuant to Sections 4.1 and 6 shall terminate.

(c) Notwithstanding Section 13.3(a), in the event of termination of this
Agreement by Codexis pursuant to Section 13.2, the license granted by Codexis to
Shell pursuant to Section 4.2(a) shall terminate.

(d) Termination of this Agreement shall be without prejudice to any other
remedies which either Party may otherwise have, including each Party’s rights to
receive payments accrued under this Agreement prior to the effective date of
such termination.

ARTICLE 14

GENERAL PROVISIONS

14.1 Relationship of the Parties. The Parties shall perform their obligations
under this Agreement as independent contractors and nothing contained in this
Agreement shall be construed to make either Codexis or Shell partners, joint
venturers, principals, representatives or employees of the other. Neither Party
shall have any right, power or authority, express or implied, to bind the other.
Shell and Codexis agree that this Agreement shall not constitute a partnership
for tax purposes. In the event, however, that this Agreement was so construed,
then Shell and Codexis agree to be excluded from the provisions of Subchapter K
of the United States Internal Revenue Code of 1986, as amended.

14.2 Assignments. Neither Party may transfer or assign its rights and
obligations under this Agreement without the prior written consent of the other
Party; provided that, subject to Article 7 with respect to transfer or
assignment by Codexis, either Party may transfer or assign its rights and
obligations under this Agreement to an Affiliate of such Party or to a successor
to all or substantially all of its business or assets relating to this Agreement
whether by sale, acquisition, merger, operation of law or otherwise.
Notwithstanding anything to the contrary, any transferee, assignee or successor
of a Party shall agree in writing to be bound by the terms of

 

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this Agreement prior to the effective date of transfer or assignment of this
Agreement and, thereafter, this Agreement shall be binding upon such transferee,
assignee or successor. Any attempted transfer or assignment of this Agreement
not in accordance with this Section 14.2 will be null and void.

14.3 Force Majeure. Except for the payment of money, neither Party shall be
liable to the other for failure or delay in the performance of any of its
obligations under this Agreement for the time and to the extent such failure or
delay is caused by earthquake, riot, civil commotion, war, terrorist acts,
strike, flood, or governmental acts or restriction that is beyond the control of
the respective Party. The Party affected by such force majeure will provide the
other Party with full particulars thereof as soon as it becomes aware of the
same (including its best estimate of the likely extent and duration of the
interference with its activities), and will use commercially reasonable efforts
to overcome the difficulties created thereby and to resume performance of its
obligations as soon as practicable.

14.4 Captions. The captions to this Agreement are for convenience only, and are
to be of no force or effect in construing or interpreting any of the provisions
of this Agreement.

14.5 Governing Law. This Agreement will be governed by and interpreted in
accordance with the laws of the State of New York, applicable to contracts
entered into and to be performed wholly within the State of New York, excluding
conflict of laws principles.

14.6 Dispute Resolution; Jurisdiction and Venue. Any controversy or claim
(“Dispute”), whether based on contract, tort, statute or other legal or
equitable theory (including but not limited to any claim of fraud,
misrepresentation or fraudulent inducement or any question of validity or effect
of this Agreement including this clause) arising out of or related to this
Agreement (including but not limited to any amendments, annexations, and
extensions to this Agreement) or the breach thereof shall be settled by
consultation between the Parties initiated by written notice of the Dispute to
the other Party. In the event such consultation does not settle the Dispute
within thirty (30) days after written notice of such Dispute, then the Dispute
shall be settled by binding arbitration in accordance with the then current
commercial arbitration rules of the American Arbitration Association and this
provision. The arbitration shall be governed by the United States Arbitration
Act, 9 U.S.C. §§ 1-16 (the “Act”) to the exclusion of any provision of state law
inconsistent therewith or which would produce a different result. Judgment upon
the award rendered by the arbitrator may be entered by any court having
jurisdiction. The arbitration shall be held in New York, New York. The Parties
shall agree on a single neutral arbitrator with relevant industry experience to
conduct the arbitration. If the Parties do not agree on a single neutral
arbitrator within ten (10) days after receipt of an arbitration notice, each
Party shall select one (1) arbitrator and the two (2) Party-selected arbitrators
shall select a third arbitrator with relevant industry experience to constitute
a panel of three (3) arbitrators to conduct the arbitration in accordance with
the Act. In the event that only one of the Parties selects an arbitrator, then
such arbitrator shall be entitled to act as the sole arbitrator to resolve the
Dispute or any and all unresolved issues subject to the arbitration. Each and
all arbitrator(s) of the arbitration panel conducting the arbitration must and
shall agree to render an opinion within twenty (20) days after the final hearing
before the panel. The arbitrator(s) shall determine the claim of the Parties and
render a final award in accordance with the substantive law of the State of New
York, excluding the conflicts provisions of such law. The arbitrator shall set
forth the

 

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reasons for the award in writing. The terms hereof shall not limit any
obligations of a Party to defend, indemnify or hold harmless another Party
against court proceedings or other claims, losses damages or expenses. All
proceedings and decisions of the arbitrator(s) shall be deemed Confidential
Information of each of the Parties. Notwithstanding anything herein to the
contrary, a Party may seek a temporary restraining order or a preliminary
injunction from any court of competent jurisdiction in order to prevent
immediate and irreparable injury, loss, or damage on a provisional basis,
pending the decision of the arbitrator(s) on the ultimate merits of any Dispute.

14.7 Notices and Deliveries. Any notice, request, delivery, approval or consent
required or permitted to be given under this Agreement will be in writing and
will be deemed to have been sufficiently given on the date of receipt if
delivered in person, transmitted by telecopier (receipt verified) or by express
courier service (signature required) or five (5) days after it was sent by
registered letter, return receipt requested (or its equivalent), provided that
no postal strike or other disruption is then in effect or comes into effect
within two (2) days after such mailing, to the Party to which it is directed at
its address or facsimile number shown below or such other address or facsimile
number as such Party will have last given by notice to the other Party.

 

If to Codexis, addressed to:

     Codexis, Inc.      200 Penobscot Drive      Redwood City, CA 94063     
Attention: Chief Executive Officer      Telephone: 650-421-2388      Fax:
650-421-8102

with a copy to:

     Codexis, Inc.      200 Penobscot Drive      Redwood City, CA 94063     
Attention: General Counsel      Telephone: 650-421-8160      Fax: 650-421-8108

If to Shell, addressed to:

     Shell Oil Products (US)      910 Louisiana Street      Houston, TX 77002   
  Attention: Fuel Development Program Manager (Americas)      Telephone:
713-241-1461      Fax: 713-241-9800

 

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with a copy to:

     Shell Oil Company      Associate General Counsel, Intellectual Property
Services      910 Louisiana      Houston, TX 77002      Fax: 713-241-6617

14.8 No Consequential Damages. EXCEPT PURSUANT TO ARTICLE 11 OR 12, IN NO EVENT
WILL A PARTY OR ANY OF ITS RESPECTIVE AFFILIATES BE LIABLE TO THE OTHER PARTY OR
ANY OF ITS AFFILIATES FOR SPECIAL, INDIRECT, CONSEQUENTIAL OR PUNITIVE DAMAGES,
WHETHER IN CONTRACT, WARRANTY, TORT, NEGLIGENCE, STRICT LIABILITY OR OTHERWISE,
INCLUDING BUT NOT LIMITED TO, LOSS OF PROFITS OR REVENUE, OR CLAIMS OF CUSTOMERS
OF ANY OF THEM OR OTHER THIRD PARTIES FOR SUCH DAMAGES.

14.9 Waiver. A waiver by a Party of any of the terms and conditions of this
Agreement in any instance will not be deemed or construed to be a waiver of such
term or condition for the future, or of any subsequent breach hereof. All
rights, remedies, undertakings, obligations and agreements contained in this
Agreement will be cumulative and none of them will be in limitation of any other
remedy, right, undertaking, obligation or agreement of either Party.

14.10 Entire Agreement. This Agreement, together with the attached schedules,
the Research Agreement (as amended herein), the License Agreement (as amended
herein), the Dyadic Letter and the IE/Codexis/Shell Agreement are the sole
agreements with respect to the subject matter hereof and supersede all other
prior and contemporaneous agreements and understandings between the Parties with
respect to the same. Except as expressly amended by this Agreement, the terms of
the Research Agreement, the License Agreement, the Dyadic Letter and the
IE/Codexis/Shell Agreement shall remain in full force and effect. In addition,
nothing in this Agreement shall be interpreted as altering or otherwise amending
any right or obligation of IE under the IE/Codexis/Shell Agreement. As between
the Parties, in the event that any terms of this Agreement conflicts with the
terms of Research Agreement, the License Agreement, the Dyadic Letter or the
IE/Codexis/Shell Agreement, the terms of this Agreement shall control.

14.11 Severability. When possible, each provision of this Agreement will be
interpreted in such manner as to be effective and valid under applicable law,
but if any provision of this Agreement is held to be prohibited by or invalid
under applicable law, such provision will be ineffective but only to the extent
of such prohibition or invalidity, without invalidating the remainder of such
provision or of this Agreement. The Parties will make an effort to replace the
invalid or unenforceable provision with a valid one which in its economic effect
is most consistent with the invalid or unenforceable provision.

14.12 Counterparts. This Agreement may be executed simultaneously in
counterparts, any one of which need not contain the signature of more than one
Party but both such counterparts taken together will constitute one and the same
agreement.

 

30

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14.13 Compliance with Laws. Each Party shall comply with all applicable
statutes, laws, regulations, enactments, directives and ordinances and all
injunctions, decisions, directives, judgments and orders of any governmental
authority in effect at any time in connection with the performance of its
obligations under this Agreement.

14.14 Amendment. No amendment of any provision of this Agreement shall be
binding on a Party to this Agreement unless consented to in writing and signed
by such Party.

[Signature page follows]

 

31

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IN WITNESS WHEREOF, the Parties have caused this Agreement to be executed by
their respective duly authorized officers.

 

AGREED TO:

 

     

AGREED TO:

 

Codexis, Inc.     Equilon Enterprises LLC       By:   /s/ John
Nicols                                        
                                         By:  

/s/ Matias Sanchez Cane

Name:   John Nicols     Name:   Matias Sanchez Cane Title:   President & CEO    
Title:   Agent Date:   August 31, 2012       Date:   August 31, 2012

[Signature Page to Agreement]

--------------------------------------------------------------------------------

SCHEDULE A

Definition of “Cost”

“Costs” shall mean, with respect to the Biocatalysts, the sum of the following
(a-e); provided that to the extent that a particular cost could be counted in
more than one of the following sections, such cost shall only be counted once:

 

  a. The amounts paid by Codexis and/or its Affiliates to a Third Party for
(i) providing the chemical and biological substances required for the
manufacture of such Biocatalyst (for purposes of this definition, collectively,
the “Raw Materials”) and packaging materials for producing such Biocatalyst,
(ii) formulation, manufacturing and/or finishing such Biocatalyst or any
component thereof, (iii) distributing, transporting, storing, and insuring such
Biocatalyst, and (iv) testing such Biocatalyst, including with respect to the
foregoing, all sales and excise taxes and customs duty charges imposed by
Government Authority with respect thereto to the extent actually paid by Codexis
and/or its Affiliates and not reimbursed, credited, or refunded by a Third
Party.

 

  b. Direct Expenses shall mean those Direct Material Expenses, Direct Labor
Expenses, and Direct Service Expenses captured in time sheets and invoices that
are specific for such Biocatalyst.

 

  i. Direct Material Expenses shall mean the actual cost of Raw Materials,
filters, manufacturing supplies, unrecoverable solvent, containers, container
components, packaging, labels, and other printed materials actually consumed in
the production of such Biocatalyst;

 

  ii. Direct Labor Expenses shall mean that portion of salaries and benefits
actually paid for the labor hours of personnel directly involved in the
manufacturing of such Biocatalyst, to the extent such labor hours are directly
attributable to the manufacture of such Biocatalyst, and such labor hours have
been properly documented by batch record and time sheets.

 

  iii. Direct Service Expenses shall mean actual out-of-pocket payments to Third
Parties for services and/or license rights related to the manufacture of such
Biocatalyst;

 

  c. Indirect Expenses shall mean production overhead costs such as a reasonable
allocation of expenses associated with line supervisory personnel overseeing the
direct manufacturing of such Biocatalyst. Indirect Expenses can include labor
and out-of-pocket costs for quality control, quality assurance, microbiology,
document control, calibration/validation, and non-research and development
expenses for process development and analytical methods development supporting
manufacturing. The above expenses will also include interest expenses
apportioned on such fixed assets used to manufacture Biocatalysts. However, any
capital expenditures for facilities and equipment used to manufacture
Biocatalysts will not be included; and

--------------------------------------------------------------------------------

  d. Overhead Expenses shall mean manufacturing costs with respect to such
Biocatalyst that cannot be identified in a practical manner with specific units
of production and, therefore, cannot be included as Direct Material Expenses or
Direct Labor Expenses. Overhead Expenses include:

 

  i. Specific manufacturing overhead allocations, including but not limited to
facilities support costs, utilities (including electricity, water, sewer, waste
disposal), indirect materials and supplies, consumables (including maintenance
and repair materials, tools, spare parts), plant management, engineering and
development support, maintenance and repair of the production plant and
production equipment, property taxes (excluding income taxes), materials
management, inventory storage, information management services, and insurance,
but shall exclude underutilized capacity; and

 

  ii. Depreciation and lease costs over the expected life of buildings and
equipment specifically attributable to the actual pro rata use of such equipment
to manufacture such Biocatalyst.

 

  e. Delivery costs will be a component of “Costs” to the extent such delivery
costs are not borne by a Third Party.

--------------------------------------------------------------------------------

SCHEDULE B

Dyadic Agreement Provisions

To the extent that any rights granted by Codexis to Shell under Section 4.2(a)
constitute a sublicense of any rights granted by Dyadic to Codexis under the
Dyadic License:

 

  1. In accordance with Section 2.1(c)(3), Shell acknowledges and agrees that:

 

  a. Shell shall not transfer any Dyadic Materials (as such term is defined in
the Dyadic License), or any derivative or modification thereof, to any to
permitted sublicensee under Section 4.2(a), other than under the terms of a
sublicense agreement between Shell and such permitted sublicensee; and

 

  b. Shell and each of its permitted sublicensees hereunder shall not (A) make
any derivatives or modifications of (1) any Production Strain (as such term is
defined in the Dyadic License) transferred by Codexis to Shell or (2) any Dyadic
Materials incorporated in such Production Strain, or (B) reverse engineer
(1) any Production Strain transferred by Codexis to Shell or (2) any Dyadic
Materials incorporated in such Production Strain. In addition, Shell
acknowledges and agrees that, with respect to any Dyadic Material that is
transferred by Codexis, directly or indirectly, to Shell, the terms of this
Agreement are subordinate to the terms of the Dyadic License.

 

  c. For purposes of this Schedule B, “reverse engineering” means the
identification, modification, derivatization or other manipulation of genetic
material included in a Production Strain, including for example any gene,
portion of any gene, promoter, regulator, inducer, metabolic pathway,
metabolomics, trancriptomics, secretion signal, vector, plasmid, protein,
compound, or other material in or of such Production Strain.

 

  2. In accordance with Section 2.7(b) of the Dyadic License, Shell hereby
covenants and agrees not to commence, aid, prosecute or cause to be commenced or
prosecuted any legal action or other proceeding against Dyadic or any of its
affiliates, or any of its or their successors and assigns, licensees,
sublicensees, distributors or customers, wherein Shell alleges infringement
(direct or contributory) or inducement of infringement of any Patent (as such
term is defined in the Dyadic License) claiming any Improvement (as such term is
defined in the Dyadic License) that was made by, or under the authority of
Shell.

 

  3. In accordance with Section 2.7(c) of the Dyadic License, Shell hereby
acknowledges and agrees that Dyadic is a third party beneficiary with respect to
Shell’s covenant in subpart (2) of this Schedule B.

--------------------------------------------------------------------------------

  4. In the event that Dyadic requests that a copy of this Agreement, or any
sublicense agreement entered into by Shell or its permitted sublicensees
hereunder, be provided to an independent law firm pursuant to Section 2.1(c) of
the Dyadic License, Codexis shall promptly notify Shell in writing. Codexis
agrees not to use any law firm for this purpose that is objected to by Shell
that Shell identifies in writing within two (2) business days of receipt of such
notification from Codexis, provided that in such notice, Shell provides a
reasonable basis for each such objection.

--------------------------------------------------------------------------------

SCHEDULE C

Expenditures and Payments

The value of Assignee’s expenditure on development of the Cellulase Technology
shall be calculated by multiplying the number of FTEs dedicated to the
development of Cellulase Technology by the Assignee and/or its Associated
Companies by [***] United States Dollars ($[***]) per year for each FTE
dedicated to such development after the effective date of the Assignment;

(a) If the Assignment occurs prior to the [***] anniversary of the Effective
Date, Assignee will have a [***] period after the date of the Assignment to
expend [***] United States Dollars ($[***]) on the development of Cellulase
Technology; provided, however, that in the event Codexis, its Affiliates and/or
Third Parties (i) have expended at least [***] United States Dollars ($[***]) as
of the date of the Assignment, or (ii) at the time of the Assignment are on a
pace to expend at least [***] United States Dollars ($[***]) by the [***]
anniversary of the Effective Date, and in each case of (i) and (ii), to develop
the Cellulase Technology, the Assignee’s expenditure requirement will be reduced
by an amount equivalent to the cumulative expenditure by Codexis, its Affiliates
and/or Third Parties to develop the Cellulase Technology during the period
beginning on the Effective Date and ending on the effective date of the
Assignment, where such expenditure will be calculated by multiplying the number
of FTEs assigned by Codexis and/or its Affiliates to develop the Cellulase
Technology by [***] United States Dollars ($[***]) per year;

(b) If the Assignment occurs after the [***], and before the [***], anniversary
of the Effective Date, the Assignee will have until the [***] anniversary of the
Effective Date to expend [***] United States Dollars ($[***]) on the development
of Cellulase Technology, provided, however, that in the event Codexis, its
Affiliates and/or Third Parties have expended at least [***] United States
Dollars ($[***]) to develop the Cellulase Technology within [***] after the
Effective Date, the Assignee’s expenditure requirement will be reduced by an
amount equivalent to the cumulative expenditure by Codexis, its Affiliates
and/or Third Parties to develop the Cellulase Technology during the period
beginning on the Effective Date and ending on the effective date of the
Assignment, where such expenditure will be calculated by multiplying the number
of FTEs assigned by Codexis and/or its Affiliates to develop the Cellulase
Technology during such period by [***] United States Dollars ($[***]) per year;

(c) If the Assignment occurs after the [***] anniversary of the Effective Date,
the Assignee will be obligated to pay Shell [***] United States Dollars
($[***]); provided, however, that in the event Codexis, its Affiliates and/or
Third Parties have expended at least [***] United States Dollars ($[***]) to
develop the Cellulase Technology within [***] after the Effective Date, the
Assignee’s payment to Shell will be reduced by an amount equivalent to the
cumulative expenditures by Codexis, its Affiliates and/or Third Parties to
develop the Cellulase Technology during the period beginning on the Effective
Date and ending on the effective date of the Assignment, where such expenditure
will be calculated by multiplying the number of FTEs assigned by Codexis and/or
its Affiliates to develop the Cellulase Technology during such period by [***]
United States Dollars ($[***]) per year;

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

--------------------------------------------------------------------------------

For the avoidance of doubt, the table below describes the obligations of the
Assignee pursuant to Section 7.1(a); provided, however, that in the event of a
conflict between the table below and the provisions of sections (a), (b) or
(c) in this Schedule C above, the provisions of sections (a), (b) or (c) in this
Schedule C above shall control:

 

TIMING OF THIRD
PARTY ASSIGNMENT
(POST- EFFECTIVE
DATE)    ASSIGNEE OBLIGATION UNDER SECTION 7.1(a) [***]   

$[***] towards Cellulase Technology development (calculated at $[***] per FTE
per year) over the [***] period following the Assignment, minus any expenditure
by Codexis, its Affiliates and/or Third Parties on development of Cellulase
Technology (calculated at $[***] per FTE per year), provided Codexis, its
Affiliates and/or Third Parties have spent or, at the time of Assignment, are on
a pace to spend, [***] prior to the [***] anniversary of the Effective Date.

 

[***]   

$[***] towards Cellulase Technology development (calculated at $[***] per FTE
per year) prior to the [***] anniversary of the Effective Date minus any
expenditure by Codexis, its Affiliates and/or Third Parties on development of
Cellulase Technology (calculated at $[***] per FTE per year), provided Codexis,
its Affiliates and/or Third Parties have spent $[***] prior to the [***]
anniversary of the Effective Date.

 

[***]    $[***] payment to Shell minus any expenditure by Codexis, its
Affiliates and/or Third Parties (calculated at $[***] per FTE per year) on
development of Cellulase Technology that occurs between the Effective Date and
the [***] anniversary of the Effective Date, provided Codexis, its Affiliates
and/or Third Parties have spent $[***] prior to the [***] anniversary of the
Effective Date.

By way of examples, not intended to be limiting, to further clarify the
obligations of the Assignee pursuant to Section 7.1(a) and this Schedule C (all
examples assume an Effective Date of August 31, 2012):

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

--------------------------------------------------------------------------------

Example 1: Assignment During [***] Where Codexis Expenditure Offsets Assignee’s
Obligation. If an Assignment were to occur on [***] and Codexis and/or its
Affiliates had employed [***] FTEs, self-funded by Codexis, on the development
of the Cellulase Technology beginning on the Effective Date, Codexis would have
been deemed to have been spent $[***] FTEs [***] Year [***] $[***] on the
development of the Cellulase Technology. This would qualify as Codexis being on
pace to spend $[***] over a [***] period following the Effective Date, allowing
the expenditure to offset the development obligation of an Assignee. Therefore,
an Assignee would be obligated to spend $[***] minus Codexis’ $[***]
expenditure, or $[***], by employing a total of [***] FTEs ($[***] $[***]) on
further development of the Cellulase Technology by [***] following the date of
Assignment, or [***].

Example 2: Assignment During [***] Where Codexis Expenditure Does Not Offset
Assignee’s Obligation. If an Assignment were to occur on [***] and Codexis
and/or its Affiliates had employed [***] FTEs, self-funded by Codexis, on the
development of the Cellulase Technology beginning on the Effective Date, Codexis
would have been deemed to have been spent $[***] FTEs [***] Year × $[***] on the
development of the Cellulase Technology. This would not qualify Codexis being on
pace to spend $[***] over a [***] period following the Effective Date, in which
case an Assignee would be obligated to spend $[***] by employing a total of
[***] FTEs ($[***] $[***]) on further development of the Cellulase Technology by
[***] following the date of Assignment, or [***].

Example 3: Assignment During [***] Where Codexis Expenditure Offsets Assignee’s
Obligation. If an Assignment were to occur on [***] and Codexis and/or its
Affiliates had employed [***] FTEs, funded by a Third Party at a rate of $[***]
per FTE, on the development of the Cellulase Technology since the Effective
Date, Codexis would have been deemed to have been spent $[***] FTEs [***] Years
× $[***] on the development of the Cellulase Technology, of which $[***] FTEs
[***] Years x $[***] is applicable towards the Codexis spending threshold of
$[***] over a [***] period following the Effective Date. Because this is above
Codexis’ $[***] spending threshold, Codexis’ full $[***] expenditure would be
subtracted against the development obligation of an Assignee. Therefore, an
Assignee would be obligated to spend $[***] minus Codexis’ $[***] expenditure,
or $[***], by employing a total of [***] FTEs ($[***] / $[***] on further
development of the Cellulase Technology by [***] following the Effective Date,
or [***].

Example 4: Assignment During [***] Where Codexis Expenditure Does Not Offset
Assignee’s Obligation. If an Assignment were to occur on [***] and Codexis
and/or its Affiliates had employed [***] FTEs, funded by a Third Party at a rate
of $[***] per FTE, on the development of the Cellulase Technology beginning on
the Effective Date, Codexis would have been deemed to have been spent $[***]
FTEs [***] Years × $[***] on the development of the Cellulase Technology, of
which $[***] FTEs [***] Years × $[***] is applicable towards the Codexis
spending threshold of $[***] a [***] period following the Effective Date.
Because this is below Codexis’ $[***] spending threshold, an Assignee would be
obligated to spend the full $[***] by employing a total of [***] FTEs ($[***] /
$[***] on further development of the Cellulase Technology by [***] following the
Effective Date, or [***].

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

--------------------------------------------------------------------------------

Example 5: Assignment After [***] Where Codexis Expenditure Offsets Assignee’s
Obligation. If an Assignment were to occur on [***] and Codexis and/or its
Affiliates had employed [***] FTEs, funded by a Third Party at a rate of $[***]
per FTE, on the development of the Cellulase Technology beginning on the
Effective Date and ending on [***] with no expenditures thereafter, Codexis
would have been deemed to have been spent $[***] FTEs [***] Year × $[***] on the
development of the Cellulase Technology. This would be over the threshold of
Codexis spending $[***] over a [***] period following the Effective Date,
allowing the expenditure to be offset against the development obligation of an
Assignee, however it would not be sufficient to satisfy an Assignee’s
obligations to Shell under Article 7. Therefore, an Assignee would be obligated
to pay directly to Shell $[***] minus Codexis’ $[***] expenditure, or $[***],
within 90 days after Assignment, or [***].

Example 6: Assignment After [***] Where Codexis Expenditure Entirely Offsets
Assignee’s Obligation. If an Assignment were to occur on [***] and Codexis
and/or its Affiliates had employed [***] FTEs, funded by a Third Party at a rate
of $[***] per FTE, on the development of the Cellulase Technology beginning on
the Effective Date and ending on [***], with no expenditures thereafter, Codexis
would have been deemed to have been spent $[***] FTEs [***] Years × $[***] on
the development of the Cellulase Technology. This would be above the threshold
of Codexis spending $[***] over a [***] period following the Effective Date,
allowing the expenditure to be offset against the development obligation of an
Assignee. Moreover, Codexis and/or its Affiliates would have been deemed to have
expended $[***] by [***], (assuming consistent employment of [***] FTEs since
the Effective Date) allowing Codexis to deliver notice that the obligations of
Article 7 have been fulfilled pursuant to Section 7.4.

Example 7: Assignment After [***] Where Codexis Expenditure Does Not Offset
Assignee’s Obligation. If an Assignment were to occur on [***] and Codexis
and/or its Affiliates had not employed any FTEs on the development of the
Cellulase Technology beginning on the Effective Date, Codexis would have been
deemed to have been spent $[***] FTEs [***] Years × $[***] on the development of
the Cellulase Technology. This would be below the threshold of Codexis spending
$[***] over a [***] period following the Effective Date, in which case an
Assignee would be obligated to pay directly to Shell $[***] within 90 days after
Assignment, or [***].

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

--------------------------------------------------------------------------------

SCHEDULE D

Example Calculations of Royalties Payments

By way of examples, not intended to be limiting, to further clarify Codexis’
obligation to pay royalty payments to Shell pursuant to Section 8.1(a):

 

  •  

If Codexis, [***] after the Effective Date and after the First Commercial Sale,
sells [***] tons of Biocatalyst for use in the Intermediate Field of Use to
Third Parties in the Territory for Net Sales amounting to $[***], Codexis is
obliged to pay Shell a [***] % royalty on such sales in the amount of $[***].

 

  •  

If Codexis, [***] after the Effective Date and after the First Commercial Sale,
sells [***] tons of Biocatalyst for use in the Intermediate Field of Use to
Third Parties in the Territory for Net Sales amounting to $[***] and utilizes
[***] tons of Biocatalyst for its own Intermediate Field of Use, Codexis is
obliged to pay Shell a [***] % royalty on such sales to Third Parties in the
amount of $[***] and a [***] % royalty on its own use in the amount of $[***],
indicated by the Third Party Net Sales price of $[***] per ton of Biocatalyst.

 

  •  

In the case of a valid assignment of this agreement to a third-party Assignee 3
years after the Effective Date, if such Assignee utilizes [***] tons of
Biocatalyst for its own Intermediate Field of Use but does not sell Biocatalyst
for use in the Intermediate Field of Use to Third Parties in the Territory,
Codexis is obliged to pay Shell a [***] % royalty on its own use, informed by a
mutually agreed upon price per ton of Biocatalyst at that point in time.

 

  •  

If Codexis, [***] after the Effective Date, forms a joint venture with a Third
Party where Codexis is a [***] equity participant and the Third Party is a [***]
equity participant, the joint venture will be considered a Codexis Affiliate,
owing Shell a [***] % royalty obligation from a sale of any Biocatalyst for use
in the Intermediate Field of Use in the Territory after the First Commercial
Sale. If the Third Party involved in such a joint venture, with such [***]
equity stake, is also obliged to pay Shell a [***] % royalty on from a sale of
the same Biocatalyst from a separate agreement, then the joint venture would be
deemed to owe Shell a weighted average royalty from the parties to the Other
Agreement. This weighted average royalty would be calculated by adding the sum
of [***] multiplied by [***] % and [***] multiplied by [***] %, equaling a [***]
% royalty that the joint venture would owe to Shell upon a sale of any
Biocatalyst for use in the Intermediate Field of Use in the Territory after the
First Commercial Sale.

 

  •  

If Codexis, [***] after the Effective Date, forms a joint venture with a Third
Party where Codexis is a [***] equity participant and the Third Party is a [***]
equity participant, the joint venture will be considered a Codexis Affiliate,
owing Shell a [***] % royalty obligation from a sale of any Biocatalyst for use
in the Intermediate Field of Use in the Territory after the First Commercial
Sale. If the Third Party involved in such a joint venture, with such [***]
equity stake, is also obliged to pay Shell a [***] % royalty on

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

--------------------------------------------------------------------------------

from a sale of the same Biocatalyst from a separate agreement, then the joint
venture would be deemed to owe Shell a weighted average royalty from the parties
to the Other Agreement. This weighted average royalty would be calculated by
adding the sum of [***] multiplied by [***] % and [***] multiplied by [***] %,
equaling a [***] % royalty that the joint venture would owe to Shell upon a sale
of any Biocatalyst for use in the Intermediate Field of Use in the Territory
after the First Commercial Sale

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.

--------------------------------------------------------------------------------

SCHEDULE E

Most Favored Nation Pricing

The examples below, which are not intended to be limiting, assume that the Cost
of manufacturing and sales price for Biocatalysts in the Intermediate Field of
Use in the Territory are representative of the preceding 12 month period to any
date indicated.

 

  •  

Assume that Codexis, [***] after the Effective Date, manufactures its
Biocatalysts for a [***] $[***] and that no individual Third Party customer of
Codexis pays less than $[***] for the same Biocatalysts. In this scenario, [***]
the [***] will provide Shell with a lower purchase price - $[***] - than [***]
lower than the lowest price paid by [***] for a BioCatalyst in the Intermediate
Field of Use in the Territory – $[***]. The purchase price is calculated by
determining [***] that will result in Codexis’ [***] with a Cost of $[***] per
ton of Biocatalyst. In this scenario, [***] $[***] can be calculated by dividing
the Cost of $[***] per ton by [***] minus a [***]. In this case the [***] $[***]
divided by [***] $[***] would equal [***].

 

  •  

Assume that Codexis, [***] after the Effective Date, manufactures its
Biocatalysts for a [***] $[***] per ton and that the lowest price paid by [***]
is $[***] per ton for the same Biocatalysts. If Codexis was to enter into a
supply agreement with Shell for the same Biocatalysts in the Intermediate Field
of Use in the Territory, Shell’s purchase price would be equal to $[***] per ton
because that would be [***] lower than the lowest price paid by [***] for a
BioCatalyst in the Intermediate Field of Use in the Territory. In this scenario
[***] would be equal to approximately $[***] per ton, calculated by setting the
[***] per ton, divided by [***]. Shell would thus obtain a lower purchase price
through opting for a price [***] lower than the lowest price paid by [***] than
for [***].

 

[***] Certain information in this document has been omitted and filed separately
with the Securities and Exchange Commission. Confidential treatment has been
requested with respect to the omitted portions.