Document:

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EXHIBIT 10.1

MKS INSTRUMENTS, INC.

2004 STOCK INCENTIVE PLAN
(as amended October 25, 2006)

	1.	 	Purpose

     The purpose of this 2004 Stock Incentive Plan (the “Plan”) of MKS Instruments, Inc., a
Massachusetts corporation (the “Company”), is to advance the interests of the Company’s
stockholders by enhancing the Company’s ability to attract, retain and motivate persons who are
expected to make important contributions to the Company and by providing such persons with equity
ownership opportunities and performance-based incentives that are intended to better align their
interests with those of the Company’s stockholders. Except where the context otherwise requires,
the term “Company” shall include any of the Company’s present or future subsidiary corporations as
defined in Section 424(f) of the Internal Revenue Code of 1986, as amended, and any regulations
promulgated thereunder (the “Code”) and any other business venture (including, without limitation,
joint venture or limited liability company) in which the Company has a controlling interest, as
determined by the Board of Directors of the Company (the “Board”).

	2.	 	Eligibility

     All of the Company’s employees, officers, directors, consultants and advisors are eligible to
receive options, restricted stock awards, stock appreciation rights and other stock-based awards
(each, an “Award”) under the Plan. Each person who receives an Award under the Plan is deemed a
“Participant”.

	3.	 	Administration and Delegation

     (a) Administration by Board of Directors. The Plan will be administered by the Board. The
Board shall have authority to grant Awards and to adopt, amend and repeal such administrative
rules, guidelines and practices relating to the Plan as it shall deem advisable. The Board may
correct any defect, supply any omission or reconcile any inconsistency in the Plan or any Award in
the manner and to the extent it shall deem expedient to carry the Plan into effect and it shall be
the sole and final judge of such expediency. All decisions by the Board shall be made in the
Board’s sole discretion and shall be final and binding on all persons having or claiming any
interest in the Plan or in any Award. No director or person acting pursuant to the authority
delegated by the Board shall be liable for any action or determination relating to or under the
Plan made in good faith.

     (b) Appointment of Committees.

          (1) To the extent permitted by applicable law, the Board may delegate any or all of its powers
under the Plan to one or more committees or subcommittees of the Board (a “Committee”). During such
time as the common stock, no par value per share, of the Company (the “Common Stock”) is registered
under the Securities Exchange Act of 1934 (the “Exchange Act”), the Board shall appoint one such
Committee of not less than two members, each member of which shall be an “outside director” within
the meaning of Section 162(m) of the Code and a “non-employee director” as defined in Rule 16b-3
promulgated under the Exchange Act.

 

 

          (2) To the extent permitted by applicable law, the Board may delegate to one or more officers
of the Company, who, if required by law, are also members of the Board, the power to make Awards
and exercise such other powers under the Plan as the Board shall determine, provided that the Board
shall fix the maximum number of shares subject to Awards to be made by any such person and such
other terms as the Board may determine are appropriate.

          (3) All references in the Plan to the “Board” shall mean the Board, a Committee of the Board
or any person described in subsection (2) above, to the extent that the Board’s powers or authority
under the Plan have been delegated to such Committee or person.

	4.	 	Stock Available for Awards

     (a) Number of Shares. Subject to adjustment under Section 9, the number of shares of Common
Stock available for Awards under the Plan: (i) shall annually increase by 5% of the total shares of
the Company’s outstanding Common Stock on January 1 of each year; and (ii) in the event of an
increase in the total shares of the Company’s Common Stock after January 1 of any such year in
connection with the acquisition of any corporation, partnership or other business entity by the
Company (whether by merger, stock purchase or otherwise), shall increase by 5% of such increased
amount. Such increases shall occur until such time as the aggregate number of shares of Common
Stock which may be issued under the Plan is 15,000,000 shares, subject to adjustment under Section
9. If any Award expires or is terminated, surrendered or canceled without having been fully
exercised or is forfeited in whole or in part (including as the result of shares of Common Stock
subject to such Award being repurchased by the Company at the original issuance price pursuant to a
contractual repurchase right) or results in any Common Stock not being issued, the unused Common
Stock covered by such Award shall again be available for the grant of Awards under the Plan,
subject, however, in the case of Incentive Stock Options (as hereinafter defined), to any
limitations under the Code. Shares issued under the Plan may consist in whole or in part of
authorized but unissued shares or treasury shares.

     (b) Per-Participant Limit. Subject to adjustment under Section 9, the maximum number of shares
of Common Stock with respect to which Awards may be granted to any Participant under the Plan shall
be 900,000 per calendar year. The per-Participant limit described in this Section 4(b) shall be
construed and applied consistently with Section 162(m) of the Code.

	5.	 	Stock Options

     (a) General. The Board may grant options to purchase Common Stock (each, an “Option”) and
determine the number of shares of Common Stock to be covered by each Option, the exercise price of
each Option and the conditions and limitations applicable to the exercise of each Option, including
conditions relating to applicable federal or state securities laws, as it considers necessary or
advisable. An Option which is not intended to be an Incentive Stock Option (as hereinafter defined)
shall be designated a “Nonstatutory Stock Option”.

     (b) Incentive Stock Options. An Option that the Board intends to be an “incentive stock
option” as defined in Section 422 of the Code (an “Incentive Stock Option”) shall only be granted
to employees of MKS Instruments, Inc., any of MKS Instruments, Inc.’s present or future subsidiary
corporations as defined in Section 424(f) of the Code, and any other entities the

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employees of which are eligible to receive Incentive Stock Options under the Code, and shall be
subject to and shall be construed consistently with the requirements of Section 422 of the Code.
The Company shall have no liability to a Participant, or any other party, if an Option (or any part
thereof) that is intended to be an Incentive Stock Option is not an Incentive Stock Option or for
any action taken by the Board pursuant to Section 10(f), including without limitation the
conversion of an Incentive Stock Option to a Nonstatutory Stock Option.

     (c) Exercise Price. The Board shall establish the exercise price of each Option and specify
such exercise price in the applicable option agreement.

     (d) Duration of Options. Each Option shall be exercisable at such times and subject to such
terms and conditions as the Board may specify in the applicable option agreement; provided,
however, that no Option will be granted for a term in excess of 10 years.

     (e) Exercise of Option. Options may be exercised by delivery to the Company of a written
notice of exercise signed by the proper person or by any other form of notice (including electronic
notice) approved by the Board together with payment in full as specified in Section 5(f) for the
number of shares for which the Option is exercised.

     (f) Payment Upon Exercise. Common Stock purchased upon the exercise of an Option granted under
the Plan shall be paid for as follows:

(1) in cash or by check, payable to the order of the Company;

(2) except as the Board may otherwise provide in an option agreement, by (i) delivery of an
irrevocable and unconditional undertaking by a creditworthy broker to deliver promptly to the
Company sufficient funds to pay the exercise price and any required tax withholding or (ii)
delivery by the Participant to the Company of a copy of irrevocable and unconditional instructions
to a creditworthy broker to deliver promptly to the Company cash or a check sufficient to pay the
exercise price and any required tax withholding;

(3) to the extent permitted by applicable law and by the Board, by (i) delivery of a promissory
note of the Participant to the Company on terms determined by the Board, or (ii) payment of such
other lawful consideration as the Board may determine; or

(4) by any combination of the above permitted forms of payment.

	6.	 	Stock Appreciation Rights.

     (a) Nature of Stock Appreciation Rights. A Stock Appreciation Right, or SAR, is an Award
entitling the holder on exercise to receive an amount in cash or Common Stock or a combination
thereof (such form to be determined by the Board) determined in whole or in part by reference to
appreciation, from and after the date of grant, in the fair market value of a share of Common
Stock. SARs may be based solely on appreciation in the fair market value of Common Stock or on a
comparison of such appreciation with some other measure of market growth such as (but not limited
to) appreciation in a recognized market index. The date as of which such appreciation or other
measure is determined shall be the exercise date unless another date is specified by the Board in
the SAR Award.

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     (b) Grants. Stock Appreciation Rights may be granted in tandem with, or independently of,
Options granted under the Plan.

     (c) Exercise. Any exercise of a Stock Appreciation Right must be in writing, signed by the
proper person and delivered or mailed to the Company, accompanied by any other documents required
by the Board.

	7.	 	Restricted Stock.

     (a) Grants. The Board may grant Awards entitling recipients to acquire shares of Common Stock,
subject to the right of the Company to repurchase all or part of such shares at their issue price
or other stated or formula price (or to require forfeiture of such shares if issued at no cost)
from the recipient in the event that conditions specified by the Board in the applicable Award are
not satisfied prior to the end of the applicable restriction period or periods established by the
Board for such Award (each, a “Restricted Stock Award”).

     (b) Terms and Conditions. The Board shall determine the terms and conditions of a Restricted
Stock Award, including the conditions for repurchase (or forfeiture) and the issue price, if any.

     (c) Stock Certificates. Any stock certificates issued in respect of a Restricted Stock Award
shall be registered in the name of the Participant and, unless otherwise determined by the Board,
deposited by the Participant, together with a stock power endorsed in blank, with the Company (or
its designee). At the expiration of the applicable restriction periods, the Company (or such
designee) shall deliver the certificates no longer subject to such restrictions to the Participant
or if the Participant has died, to the beneficiary designated, in a manner determined by the Board,
by a Participant to receive amounts due or exercise rights of the Participant in the event of the
Participant’s death (the “Designated Beneficiary”). In the absence of an effective designation by a
Participant, “Designated Beneficiary” shall mean the Participant’s estate.

     (d) Deferred Delivery of Shares. The Board may, at the time any Restricted Stock Award is
granted, provide that, at the time Common Stock would otherwise be delivered pursuant to the Award,
the Participant shall instead receive an instrument evidencing the right to future delivery of
Common Stock at such time or times, and on such conditions, as the Board shall specify. The Board
may at any time accelerate the time at which delivery of all or any part of the Common Stock shall
take place.

	8.	 	Other Stock-Based Awards.

     Other Awards of shares of Common Stock, and other Awards that are valued in whole or in part
by reference to, or are otherwise based on, shares of Common Stock or other property, may be
granted hereunder to Participants (“Other Stock Unit Awards”), including without limitation Awards
entitling recipients to receive shares of Common Stock to be delivered in the future. Such Other
Stock Unit Awards shall also be available as a form of payment in the settlement of other Awards
granted under the Plan or as payment in lieu of compensation to which a Participant is otherwise
entitled. Other Stock Unit Awards may be paid in shares of Common Stock or cash, as the Board shall
determine. Subject to the provisions of the Plan, the Board shall determine the conditions of each
Other Stock Unit Award, including any purchase

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price applicable thereto. At the time any Award is granted, the Board may provide that, at the time
Common Stock would otherwise be delivered pursuant to the Award, the Participant will instead
receive an instrument evidencing the Participant’s right to future delivery of the Common Stock.

	9.	 	Adjustments for Changes in Common Stock and Certain Other Events.

     (a) Changes in Capitalization. In the event of any stock split, reverse stock split, stock
dividend, recapitalization, combination of shares, reclassification of shares, spin-off or other
similar change in capitalization or event, or any distribution to holders of Common Stock other
than an ordinary cash dividend, (i) the number and class of securities available under this Plan,
(ii) the per-Participant limit set forth in Section 4(b), (iii) the number and class of securities
and exercise price per share of each outstanding Option, (iv) the repurchase price per share
subject to each outstanding Restricted Stock Award and (v) the share- and per-share-related
provisions of each outstanding Stock Appreciation Right and Other Stock Unit Award, shall be
appropriately adjusted by the Company (or substituted Awards may be made, if applicable) to prevent enlargement or dilution of rights to the
extent determined by the Board.

     (b) Reorganization Events.

(1) Definition. A “Reorganization Event” shall mean: (a) any merger or consolidation of the Company
with or into another entity as a result of which all of the Common Stock of the Company is
converted into or exchanged for the right to receive cash, securities or other property, (b) any
exchange of all of the Common Stock of the Company for cash, securities or other property pursuant
to a share exchange transaction or (c) any liquidation or dissolution of the Company.

(2) Consequences of a Reorganization Event on Awards Other than Restricted Stock Awards. In
connection with a Reorganization Event, the Board shall take any one or more of the following
actions as to all or any outstanding Awards on such terms as the Board determines: (i) provide that
Awards shall be assumed, or substantially equivalent Awards shall be substituted, by the acquiring
or succeeding corporation (or an affiliate thereof), (ii) upon written notice to a Participant,
provide that the Participant’s unexercised Options or other unexercised Awards shall become
exercisable in full and will terminate immediately prior to the consummation of such Reorganization
Event unless exercised by the Participant within a specified period following the date of such
notice, (iii) provide that outstanding Awards shall become realizable or deliverable, or
restrictions applicable to an Award shall lapse, in whole or in part prior to or upon such
Reorganization Event, (iv) in the event of a Reorganization Event under the terms of which holders
of Common Stock will receive upon consummation thereof a cash payment for each share surrendered in
the Reorganization Event (the “Acquisition Price”), make or provide for a cash payment to a
Participant equal to (A) the Acquisition Price times the number of shares of Common Stock subject
to the Participant’s Options or other Awards (to the extent the exercise price does not exceed the
Acquisition Price) minus (B) the aggregate exercise price of all such outstanding Options or other
Awards, in exchange for the termination of such Options or other Awards, (v) provide that, in
connection with a liquidation or dissolution of the Company, Awards shall convert into the right to
receive liquidation proceeds (if applicable, net of the exercise price thereof) and (vi) any
combination of the foregoing.

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          For purposes of clause (i) above, an Option shall be considered assumed if, following
consummation of the Reorganization Event, the Option confers the right to purchase, for each share
of Common Stock subject to the Option immediately prior to the consummation of the Reorganization
Event, the consideration (whether cash, securities or other property) received as a result of the
Reorganization Event by holders of Common Stock for each share of Common Stock held immediately
prior to the consummation of the Reorganization Event (and if holders were offered a choice of
consideration, the type of consideration chosen by the holders of a majority of the outstanding
shares of Common Stock); provided, however, that if the consideration received as a result of the
Reorganization Event is not solely common stock of the acquiring or succeeding corporation (or an
affiliate thereof), the Company may, with the consent of the acquiring or succeeding corporation,
provide for the consideration to be received upon the exercise of Options to consist solely of
common stock of the acquiring or succeeding corporation (or an affiliate thereof) equivalent in
fair market value to the per share consideration received by holders of outstanding shares of
Common Stock as a result of the Reorganization Event.

          To the extent all or any portion of an Option becomes exercisable solely as a result of clause
(ii) above, the Board may provide that upon exercise of such Option the Participant shall receive
shares subject to a right of repurchase by the Company or its successor at the Option exercise
price; such repurchase right (x) shall lapse at the same rate as the Option would have become
exercisable under its terms and (y) shall not apply to any shares subject to the Option that were
exercisable under its terms without regard to clause (ii) above.

(3) Consequences of a Reorganization Event on Restricted Stock Awards. Upon the occurrence of a
Reorganization Event other than a liquidation or dissolution of the Company, the repurchase and
other rights of the Company under each outstanding Restricted Stock Award shall inure to the
benefit of the Company’s successor and shall apply to the cash, securities or other property which
the Common Stock was converted into or exchanged for pursuant to such Reorganization Event in the
same manner and to the same extent as they applied to the Common Stock subject to such Restricted
Stock Award. Upon the occurrence of a Reorganization Event involving the liquidation or dissolution
of the Company, except to the extent specifically provided to the contrary in the instrument
evidencing any Restricted Stock Award or any other agreement between a Participant and the Company,
all restrictions and conditions on all Restricted Stock Awards then outstanding shall automatically
be deemed terminated or satisfied.

	10.	 	General Provisions Applicable to Awards

     (a) Transferability of Awards. Except as the Board may otherwise determine or provide in an
Award, Awards shall not be sold, assigned, transferred, pledged or otherwise encumbered by the
person to whom they are granted, either voluntarily or by operation of law, except by will or the
laws of descent and distribution or, other than in the case of an Incentive Stock Option, pursuant
to a qualified domestic relations order, and, during the life of the Participant, shall be
exercisable only by the Participant. References to a Participant, to the extent relevant in the
context, shall include references to authorized transferees.

     (b) Documentation. Each Award shall be evidenced in such form (written, electronic or
otherwise) as the Board shall determine. Each Award may contain terms and conditions in addition to
those set forth in the Plan.

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     (c) Board Discretion. Except as otherwise provided by the Plan, each Award may be made alone
or in addition or in relation to any other Award. The terms of each Award need not be identical,
and the Board need not treat Participants uniformly.

     (d) Termination of Status. The Board shall determine the effect on an Award of the disability,
death, retirement, authorized leave of absence or other change in the employment or other status of
a Participant and the extent to which, and the period during which, the Participant, or the
Participant’s legal representative, conservator, guardian or Designated Beneficiary, may exercise
rights under the Award.

     (e) Withholding. Each Participant shall pay to the Company, or make provision satisfactory to
the Company for payment of, any taxes required by law to be withheld in connection with an Award to
such Participant. The Company may, to the extent permitted by law, deduct any such tax obligations
from any payment of any kind otherwise due to a Participant.

     (f) Amendment of Award. The Board may amend, modify or terminate any outstanding Award,
including but not limited to, substituting therefor another Award of the same or a different type,
changing the date of exercise or realization, and converting an Incentive Stock Option to a
Nonstatutory Stock Option, provided that the Participant’s consent to such action shall be required
unless the Board determines that the action, taking into account any related action, would not
materially and adversely affect the Participant.

     (g) Conditions on Delivery of Stock. The Company will not be obligated to deliver any shares
of Common Stock pursuant to the Plan or to remove restrictions from shares previously delivered
under the Plan until (i) all conditions of the Award have been met or removed to the satisfaction
of the Company, (ii) in the opinion of the Company’s counsel, all other legal matters in connection
with the issuance and delivery of such shares have been satisfied, including any applicable
securities laws and any applicable stock exchange or stock market rules and regulations, and (iii)
the Participant has executed and delivered to the Company such representations or agreements as the
Company may consider appropriate to satisfy the requirements of any applicable laws, rules or
regulations.

     (h) Acceleration. The Board may at any time provide that any Award shall become immediately
exercisable in full or in part, free of some or all restrictions or conditions, or otherwise
realizable in full or in part, as the case may be.

	11.	 	Miscellaneous

     (a) No Right To Employment or Other Status. No person shall have any claim or right to be
granted an Award, and the grant of an Award shall not be construed as giving a Participant the
right to continued employment or any other relationship with the Company. The Company expressly
reserves the right at any time to dismiss or otherwise terminate its relationship with a
Participant free from any liability or claim under the Plan, except as expressly provided in the
applicable Award.

     (b) No Rights As Stockholder. Subject to the provisions of the applicable Award, no
Participant or Designated Beneficiary shall have any rights as a stockholder with respect to any

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shares of Common Stock to be distributed with respect to an Award until becoming the record holder
of such shares. Notwithstanding the foregoing, in the event the Company effects a split of the
Common Stock by means of a stock dividend and the exercise price of and the number of shares
subject to such Option are adjusted as of the date of the distribution of the dividend (rather than
as of the record date for such dividend), then an optionee who exercises an Option between the
record date and the distribution date for such stock dividend shall be entitled to receive, on the
distribution date, the stock dividend with respect to the shares of Common Stock acquired upon such
Option exercise, notwithstanding the fact that such shares were not outstanding as of the close of
business on the record date for such stock dividend.

     (c) Effective Date and Term of Plan. The Plan shall become effective on the date on which it
is adopted by the Board, but no Award may be granted unless and until the Plan has been approved by
the Company’s stockholders. No Awards shall be granted under the Plan after the completion of 10
years from the earlier of (i) the date on which the Plan was adopted by the Board or (ii) the date
the Plan was approved by the Company’s stockholders, but Awards previously granted may extend
beyond that date.

     (d) Amendment of Plan. The Board may amend, suspend or terminate the Plan or any portion
thereof at any time; provided that, to the extent determined by the Board, no amendment requiring
stockholder approval under any applicable legal, regulatory or listing requirement shall become
effective until such stockholder approval is obtained. No Award shall be made that is conditioned
upon stockholder approval of any amendment to the Plan.

     (e) Provisions for Foreign Participants. The Board may modify Awards or Options granted to
Participants who are foreign nationals or employed outside the United States or establish subplans
or procedures under the Plan to recognize differences in laws, rules, regulations or customs of
such foreign jurisdictions with respect to tax, securities, currency, employee benefit or other
matters.

     (f) Governing Law. The provisions of the Plan and all Awards made hereunder shall be governed
by and interpreted in accordance with the laws of the Commonwealth of Massachusetts, without regard
to any applicable conflicts of law.

As approved by the Board of Directors on
March 4, 2004 and by the
stockholders on May 13, 2004; as amended by
the Board of Directors on October 25, 2006

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                            SECOND AMENDMENT OF LEASE

     THIS SECOND AMENDMENT OF LEASE is made this 7th day of September, 2006, by
and between RB KENDALL FEE, LLC ("Landlord") and IDENIX PHARMACEUTICALS, INC.,
having a mailing address at One Kendall Square, Building 1400, Cambridge,
Massachusetts 02139 ("Tenant").

                                    RECITALS:

     A. Reference is made to an Indenture of Lease dated June 8, 2005 by and
between One Kendall Square Associates, LLC, the predecessor in title to
Landlord, and Tenant, as amended by a First Amendment of Lease dated July 24,
2006, demising approximately 41,746 s.f. of rentable square feet of space on a
portion of the first, fourth, fifth and penthouse floors of Building No. 1400,
One Kendall Square, Cambridge, Massachusetts (the "Lease"). Capitalized terms
used but not defined herein shall have the same meaning as in the Lease.

     B. Landlord and Tenant are the current holders, respectively, of the
lessor's and lessee's interests in the Lease.

     C. Landlord and Tenant now desire to amend the Lease as set forth herein.

     D. Capitalized terms not defined herein shall have the meanings set forth
in the Lease.

                                   AGREEMENTS:

     NOW, THEREFORE, in consideration of the mutual covenants and agreements
herein contained, and for other good and valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, Landlord and Tenant hereby agree
to amend the Lease as follows:

     1. As of the earlier of (i) the date Tenant's contractor delivers to
Landlord a certificate stating that Tenant's Second Amendment Expansion Work (as
defined herein) has been substantially completed in accordance with plans
approved by Landlord, with the exception of minor items of incomplete work and
so-called "punchlist items"; (ii) October 1, 2006; or (iii) the date Tenant
occupies any portion of the Second Amendment Expansion Premises (as defined
herein) for purposes other than completion of the Tenant's Second Amendment
Expansion Work (the earlier to occur of (i), (ii) or (iii) being hereinafter
called the "Second Amendment Expansion Commencement Date"), Landlord hereby
leases to Tenant and Tenant hereby leases from Landlord approximately 7,501
rentable square feet of additional floor area on the third (3rd) floor the
Building as shown outlined in red on "Exhibit A" attached hereto and made a part
hereof (the "Second Amendment Expansion Premises"). Effective as of the Second
Amendment Expansion Commencement Date, all references in the Lease to the
Premises shall be deemed to include the Second Amendment Expansion Premises. At
the written request of either Landlord or Tenant, the parties shall, after the
occurrence of the Second Amendment Expansion Commencement Date, execute a
written agreement confirming the Second Amendment Expansion Commencement Date
and the date of expiration of the term of the Lease.

     2. Effective as of the Second Amendment Expansion Commencement Date, in
addition to the rent paid by Tenant in accordance with Article 6 of the Lease,
as amended, Tenant shall pay additional base rent for the balance of the term
for the Second Amendment Expansion Premises at the rate of $202,527.00 per
annum, payable in advance, in monthly installments of $16,877.25, and otherwise
in

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accordance with the Lease (the "Second Amendment Expansion Premises Rent").

     3. Effective as of the Second Amendment Expansion Commencement Date,
Tenant's Proportionate Building Share shall increase to 36.95% and Tenant's
Proportionate Common Area Share shall increase to 7.57%.

     4. Except as may otherwise be expressly set forth in this Amendment, Tenant
shall take the Second Amendment Expansion Premises "as is", in the condition in
which the Second Amendment Expansion Premises are in as of the date hereof.
Landlord shall deliver the Second Amendment Expansion Premises with the HVAC
system serving the premises in good working order.

     5. Tenant will be performing all work to prepare the Second Amendment
Expansion Premises for Tenant's occupancy (the "Tenant's Second Amendment
Expansion Work"). Landlord shall, in the manner set forth herein, contribute up
to One Hundred Fifty Thousand Twenty and 00/100 ($150,020.00) Dollars
("Landlord's Second Amendment Expansion Contribution") towards the costs of
completing construction of Tenant's Second Amendment Expansion Work including
design and engineering fees. All of the provisions relating to Tenant's Work as
set forth in Sections 4.2 (b), (c) and (d) and 4.3 of the Lease shall apply to
Landlord's Second Amendment Expansion Contribution and Tenant's Second Amendment
Expansion Work, except that Landlord shall have no obligation to pay Landlord's
Second Amendment Expansion Contribution in respect of any requisition submitted
more than four (4) months after the Second Amendment Expansion Commencement
Date.

     6. Subject to delay by causes beyond the reasonable control of Landlord or
caused by the action or inaction of Tenant or Tenant's employees, contractors,
representatives or agents, upon execution of this Amendment Tenant shall be
granted access to the Second Amendment Expansion Premises for the purposes of
commencing and completing Tenant's Second Amendment Expansion Work. The failure
to have the Second Amendment Expansion Premises available to Tenant by the date
of this Amendment shall in no way affect the validity of this Amendment or the
obligations of Tenant hereunder nor shall the same be construed in any way to
extend the term of the Lease, and Tenant shall not have any claim against
Landlord, and Landlord shall have no liability to Tenant, by reason thereof. It
is specifically understood and agreed that Landlord has no obligation and has
made no promises to alter, remodel, improve, renovate, repair, decorate or
otherwise prepare the Second Amendment Expansion Premises for Tenant's
occupation or use. However, the Second Amendment Expansion Commencement Date
shall be delayed one day for each day of delay in the delivery of the Second
Amendment Expansion Premises by Landlord to Tenant, provided such delay was not
caused by the action or inaction of Tenant or Tenant's employees, contractors,
representatives or agents.

     7. Prior to entering the Second Amendment Expansion Premises, Tenant shall
provide certificates of insurance evidencing that the Second Amendment Expansion
Premises are included under the policies of insurance required under the Lease.
Tenant shall coordinate such entry with Landlord's building manager, and such
entry shall be made in compliance with all terms and conditions of this
Amendment and the Rules and Regulations then in effect for the Building. Such
right of entry shall be deemed a license from Landlord to Tenant, and any entry
thereunder shall be at the risk of Tenant.

     8. The Tenant may occupy and use the Second Amendment Expansion Premises
only for general business offices.

     9. Section 29.18 of the Lease, as previously amended, is hereby further
amended to provide that as of the Second Amendment Expansion Commencement Date,
the Landlord shall make available to

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Tenant seven (7) additional monthly parking passes for use in the OKS Garage.
The additional parking passes shall be paid for by Tenant at the current
prevailing rate in the OKS Garage as such rate may vary as set forth in Section
29.18 of the Lease.

     10. The Landlord and Tenant each warrant and represent to the other that
they have dealt with no brokers in connection with the negotiation or
consummation of this Amendment other than Richard Barry Joyce & Partners and
Lincoln Property Company, and in the event of any brokerage claim against either
party by any person (other than the aforementioned brokers) claiming to have
dealt with either Landlord or Tenant in connection with this Amendment, the
party with whom such person claims to have dealt shall defend and indemnify the
other party against such claim. Any brokerage fees due Richard Barry Joyce &
Partners and Lincoln Property Company shall be the responsibility of Landlord
pursuant to separate agreements.

     11. In all other respects the Lease shall remain unmodified and shall
continue in full force and effect, as amended hereby. The parties hereby ratify,
confirm, and reaffirm all of the terms and conditions of the Lease, as amended
hereby.

                     SIGNATURES CONTAINED ON FOLLOWING PAGE

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<PAGE>

     IN WITNESS WHEREOF the parties hereto have executed this Second Amendment
of Lease on the date first written above in multiple copies, each to be
considered an original hereof, as a sealed instrument.

LANDLORD:                               TENANT:

RB KENDALL FEE, LLC,                    IDENIX PHARMACEUTICALS, INC.
a Delaware limited liability company

By: Beal Kendall LLC,                   By: Paul Fanning
    a Massachusetts limited liability       ------------------------------------
    company,                            Name: Paul Fanning
    its authorized signatory            Title: VP, Human Resources
                                               Hereunto duly authorized

By: Robert L. Beal
    ---------------------------------
Name: Robert L. Beal
Title: Manager

                                       4

<PAGE>

                                    EXHIBIT A

                PLAN SHOWING SECOND AMENDMENT EXPANSION PREMISES

                                       5

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