Document:

EX-10.7 SECOND AMENDMENT TO LEASE DATED 2-27-07

 

EXHIBIT 10.7

SECOND AMENDMENT TO LEASE AGREEMENT

     THIS SECOND AMENDMENT TO LEASE AGREEMENT (this “Second Amendment”), made and entered into as
of the 27th day of February, 2007, by and between 2300 WINDY RIDGE PARKWAY INVESTORS
LLC, a Delaware limited liability company (“Landlord”), and MANHATTAN ASSOCIATES, INC., a Georgia
corporation (“Tenant”);

W I T N E S S E T H         T H A T:

     WHEREAS, Wildwood Associates, a Georgia general partnership (“Original Landlord”) and Tenant
entered into that certain Lease Agreement June 25, 2001, as amended by that certain First Amendment
to Lease Agreement (the “First Amendment”) dated June 10, 2002 (collectively, as amended, the
"Lease”), for certain premises in the building located at 2300 Windy Ridge Parkway, Atlanta,
Georgia 30339 (the “Building”), consisting of approximately 137,868 square feet of Rentable Floor
Area in the Building being Floor 1 North (22,719 rsf), Floor 3 North (23,776 rsf), Floor 3 South
(9,021 rsf), Floor 6 South (13,608 rsf), Floor 7 (63,296 rsf), and Floor 8 (5,448 rsf)
(collectively, the “Original Demised Premises”);

     WHEREAS, Landlord acquired all of the right, title and interest of Original Landlord, in and
to the Lease;

     WHEREAS, Landlord and Tenant have agreed that Tenant will surrender a portion of the Original
Demised Premises and then lease additional premises in the Building and, in connection therewith,
extend the Lease Term by one hundred thirty five (135) months; and

     WHEREAS, Landlord and Tenant desire to evidence such reconfiguration of the Original Demised
Premises and extension of the Lease Term and to amend certain other terms and conditions of the
Lease and evidence their agreements and other matters by means of this Second Amendment;

     NOW THEREFORE, in consideration of the mutual covenants contained herein, and other good and
valuable consideration, the receipt, adequacy and sufficiency of which are hereby acknowledged, the
Lease is hereby amended and the parties hereto do hereby agree as follows:

     1. Relocation and Expansion of Original Demised Premises. As of July 1, 2007 (the
"Effective Date”), Landlord hereby leases to Tenant and Tenant hereby leases from Landlord certain
new premises in the Building, the exact location and Rentable Floor Area of which shall be
determined during space planning (all of such space, when determined, shall be known as the “Second
Expansion Space”). As of the Effective Date, the Second Expansion Space will be subject to all the
terms and conditions of the Lease, as amended herein. In connection with such expansion, Tenant
will also retain certain portions of the Original Demised Premises, the exact location and Rentable
Floor Area of which shall be determined during space planning (collectively, the “Retained
Premises”). Further and in conjunction with such expansion and as of the Effective Date, Tenant
will surrender, remise and release unto Landlord certain portions of the Original Demised Premises,
which portions will also be determined during space planning (collectively, the “Surrendered
Premises”). As of the Effective Date, all references in the Lease and this Second Amendment to the
“Demised Premises” shall be deemed to mean the Second Expansion Space and the Retained Premises and
shall consist of approximately 160,000 square feet of Rentable Floor Area, which square footage may
increase or decrease by up to ten percent (10%) during the space planning process.

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     In addition to the foregoing, the parties acknowledge that International Paper (“IP”) is
currently leasing approximately 9,133 rentable square feet of space being Suite 850 North (the “IP
Premises”) in the Building, the lease for which expires June 30, 2007. Tenant hereby covenants
that it will lease a portion of the IP Premises, which portion will be determined during the space
planning process. That portion of the IP Premises that is leased by Tenant will be deemed a part
of the Second Expansion Space for all purposes under this Amendment and the Lease. Tenant’s
payment of Base Rental for the IP Premises, or portion thereof, will commence ninety (90) days
after the IP Premises or portion thereof leased by Tenant is delivered to Tenant for Tenant to
commence construction therein. Landlord agrees to give Tenant at least ten (10) business days
prior written notice of the date that the portion of the IP Premises leased by Tenant will be
delivered to Tenant.

     Subject to the foregoing paragraph, Tenant acknowledges that its obligations with respect to
the Demised Premises will commence on the Effective Date and that Tenant will use its best efforts
to vacate and surrender the Surrendered Premises in accordance with the terms of the Lease no later
than the Effective Date. Notwithstanding the foregoing, if, due to construction matters, Tenant is
unable to completely vacate and surrender the Surrendered Premises by the Effective Date, it will
be permitted to remain in the Surrendered Premises or portions thereof and continue to pay Base
Rental and Additional Rental at the then existing rate under the Lease for the portion it continues
to occupy until such time as it does vacate and surrender same. In any event, Tenant covenants
that it will vacate and surrender the Surrendered Space no later than August 31, 2007 so that
Landlord may manage and coordinate the re-leasing of same.

     After the Rentable Floor Area of the Demised Premises has been determined and agreed to by
Landlord and Tenant, Landlord will deliver a Second Amendment Memorandum to Tenant. Within ten
(10) days after receipt of same, Tenant agrees to execute the Second Amendment Memorandum (the
"Memorandum”) confirming the Effective Date, the Expiration Date, the exact number of square feet
of Rentable Floor Area within the Demised Premises and the locations thereof, and Tenant’s
proportionate share of the Building. Such Memorandum shall be in the form attached hereto as
Exhibit A and by this reference incorporated herein. Upon full execution of the Memorandum
by both parties, Landlord will deliver the Second Expansion Space (other than Floor 9, Floor 10,
and the IP Premises) to Tenant for purposes of performing Tenant’s Work (as defined in Section 6
herein) therein. Landlord agrees to deliver Floor 9 and Floor 10 to Tenant upon full execution by
both parties hereto of a mutually agreeable indemnity letter pertaining to Tenant’s demolition work
to be performed within Floor 9 and Floor 10.

     2. Extension of Lease Term. Notwithstanding that the Lease Term expires March 31,
2008, the parties desire to extend the Lease Term early; therefore, the Lease Term is hereby
extended for a period of one hundred thirty-five (135) months (the “Extension Term”) commencing on
the Effective Date and expiring on September 30, 2018 (the “Expiration Date”). Tenant shall remain
subject to all terms and conditions of the Lease, as amended herein, during the Extension Term.

     3. Base Rental and Abatement; Tenant’s Additional Rental.

     (a) Base Rental. During the Extension Term, Base Rental for the Demised Premises
shall be paid on a monthly basis in accordance with the Lease at the initial rate during the first
Lease Year (which shall mean for purposes of this Second Amendment, the twelve [12] month period
commencing on the Effective Date and each successive twelve month period thereafter during the
Extension Term) of the Extension Term of $22.50 per square foot of Rentable Floor Area times the
final determination of the total Rentable Floor Area of the Demised Premises. Thereafter,
commencing on the first day of the second Lease Year of the Extension Term and each anniversary
thereafter through the remainder of the Extension Term, Base Rental for the Demised Premises shall
escalate at the rate of 1.475% per year and shall no longer be based on any increases in CPI as
previously provided in Section 7 of the Lease. The Base Rental shall be due and payable by Tenant
in accordance with the terms of the Lease. Notwithstanding the foregoing, Tenant shall be entitled
to an abatement of Base Rental for the entire Demised Premises for the six (6) month period from
April 1, 2008 through September 30, 2008. Tenant’s proportionate share for the payment of

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Tenant’s
Additional Rental shall be revised to reflect the Rentable Floor Area of the Demised Premises as
revised herein.

     (b) Additional Rental. Section 8 (Additional Rental) of the Lease is hereby amended to
reflect that during the Extension Term and commencing in calendar year 2008, Tenant will pay its
proportionate share of Tenant’s Additional Rental based on the excess of Landlord’s projected
Operating Expenses in each calendar year over the Base Year Operating Expenses. For purposes of
this Second Amendment, the “Base Year” shall mean calendar year 2007. In the event the average
occupancy level of the Building or the Project for any calendar year, including the Base Year, is
not ninety-five percent (95%) or more of full occupancy, then the Operating Expenses for such year
shall be apportioned among the tenants by the Landlord to reflect those costs which would have
occurred had the Building or the Project, as applicable, been ninety-five percent (95%) occupied
during such year. For each calendar year after the Base Year, Landlord shall provide Tenant with a
comparison of the Base Year Operating Expenses and the projected Operating Expenses for such
current calendar year. Such projected increase in Operating Expenses shall be payable in advance
on a monthly basis by paying one-twelfth (1/12th) of such projected increase during each month of
such respective calendar year. If Landlord has not furnished Tenant such comparison by January 1
of a calendar year, Tenant shall continue to pay on the basis of the prior year’s estimate until
the month after such comparison is given. The statement provided by Landlord to Tenant as set
forth in Section 8(c) of the Lease shall set forth such year’s actual Operating Expenses compared
to Base Year Operating Expenses and a statement comparing Tenant’s proportionate share of projected
increases in Operating Expenses which Tenant paid throughout such calendar year with Tenant’s
proportionate share of actual Operating Expense increases (the “Final Annual Statement of Operating
Expenses”). If Tenant’s proportionate share of increases in actual Operating Expenses are greater
than as shown in the statement delivered pursuant to Section 8(c) or greater than the amount of
Tenant’s Additional Rental actually paid by Tenant pursuant thereto, Tenant shall pay Landlord,
within thirty (30) days of such statement’s receipt, such additional sum owed by Tenant. If the
amount of Tenant’s Additional Rental actually paid by Tenant pursuant to Landlord’s estimate of
Tenant’s proportionate share of increases in Operating Expenses is greater than Tenant’s share of
increases in actual Operating Expenses as shown on the Final Annual Statement of Operating
Expenses, Landlord shall credit Tenant, within thirty (30) days of such statement issuance, such
overpaid amount, or if the Lease has expired, will issue a check to Tenant for such overpaid amount
within thirty (30) days of such statement issuance.

     4. Right of First Offer. Subject to the rights of existing tenants in the Building,
Landlord hereby grants Tenant a right of first offer (“Right of First Offer”) on any available
space in the Building, the Rentable Floor Area of which is at least 15,000 square feet if such
space is not contiguous to the Demised Premises (the “First Offer Space”) (i.e., if the space is
contiguous to the Demised Premises [on the same floor], then such space may be less than 15,000
square feet of Rentable Floor Area). When the First Offer Space, or portion thereof is to become
available and so long as Tenant is not then in default under the Lease and has not been in default
under the Lease during the prior 12-month period, in either event beyond any applicable notice and
cure periods, Landlord will notify Tenant (“Landlord’s Notice”) of the terms and conditions upon
which it would be willing to lease the First Offer Space to Tenant. The terms shall be as follows:

     (a) On Then Existing Terms. The lease of the First Offer Space will be on all of the
same terms and conditions as then exist for the Demised Premises, including without limitation, the
then current per square foot rate of Base Rental and shall be coterminous with the lease for the
Demised Premises (i.e., will expire on the Expiration Date), if either (i) the commencement date of
the lease of the First Offer Space will occur prior to June 30, 2010, or (ii) the Rentable Floor
Area of the First Offer Space then subject to the Right of First Offer when combined with any other
First Offer Space previously leased by Tenant pursuant to this Paragraph 4 and any other expansion
space leased to Tenant after the Effective Date, is less than twenty percent (20%) of the total
Rentable Floor Area of the Second Expansion Space and the Retained Premises (the “20% Threshold”)
(i.e., if Tenant has previously leased 10,000 rsf pursuant to this Right of First Offer and
the total rsf of the Second Expansion Space and the Retained Premises is 160,000 rsf, then the
remaining

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expansion space Tenant may lease under this Paragraph 4(a) or otherwise must be less than
22,000 rsf). In addition to the foregoing, if the 20% Threshold has not been met and the
commencement date of the lease for the First Offer Space will occur between July 1, 2010 and June
30, 2012, then the lease of the First Offer Space will be on all of the same terms and conditions
as then exist for the Demised Premises, including without limitation, the then current per square
foot rate of Base Rental, and shall be coterminous with the lease for the Demised Premises (i.e.,
will expire on the Expiration Date), except that the allowance for improvements will be $35.00 per
rentable square foot only and there shall be no Discretionary Allowance, as defined in Section 6
below. Any allowance for improvements or rental concession provided to Tenant under this
subsection (a) shall be an amount equal to the product of multiplying such allowance or rental
concession, if any, times a fraction, the numerator of which is the number of full calendar months
remaining in the Extension Term as of the commencement date of Tenant’s lease of the First Offer
Space and the denominator of which is 135 but in no event will such fraction exceed 1; or

     (b) On Market Terms. The lease of the First Offer Space will be as set forth in
Landlord’s Notice, which will be the then Expansion Market Rate (as defined below), will have a
term of at least three (3) years and will be coterminous with the Lease Term of the Demised
Premises, if (i) the commencement date of the lease of the First Offer Space will occur after June
30, 2012, or (ii) the Rentable Floor Area of the First Offer Space then subject to the
Right of First Offer when combined with any other First Offer Space previously leased by Tenant
pursuant to this Paragraph 4 and any other expansion space leased to Tenant after the Effective
Date, equals or exceeds the 20% Threshold. If Tenant exercises this Right of First Offer at any
time during the last three (3) Lease Years of the Extension Term, then Tenant agrees that the Lease
Term for the entire Demised Premises will be further extended so that it will expire coterminously
with the term of the First Offer Space (which will, as aforesaid, have a minimum 3-year term). If
the Lease Term is extended as aforesaid, then the economic terms for the Demised Premises during
the extended portion of the Lease Term shall be at the then Market Rate (as defined and determined
in accordance with Special Stipulation No. 1 [Renewal Option] in Exhibit “G” attached to the
Lease).

     (c) Tenant’s Notice. Tenant shall have ten (10) business days after receipt of
Landlord’s Notice, to notify Landlord in writing (“Tenant’s Notice”) whether Tenant will lease the
First Offer Space in accordance with the terms as set forth above, as applicable. If Tenant elects
to lease the First Offer Space, Landlord and Tenant will execute an amendment to the Lease adding
the First Offer Space to the Demised Premises within ten (10) business days after the later of (i)
Landlord’s receipt of Tenant’s Notice or (ii) the date the parties agree upon the Expansion Market
Rate, if applicable, or (iii) receipt by both parties of a mutually acceptable amendment. If
Tenant does not, within such 10-business day period, deliver Tenant’s Notice or elects not to lease
the First Offer Space, then this Right of First Offer to lease the First Offer Space then subject
to this Right of First Offer will lapse and be of no further effect and Landlord will have the
right to lease such First Offer Space to any third party on terms that are not materially more
favorable than those in Landlord’s Notice without re-submitting such changed terms to Tenant in
accordance with this Right of First Offer in which case Tenant shall have five (5) business days
after its receipt of such resubmitted offer to exercise the Right of First Offer on such terms as
to all of the space contained in the changed terms (which may be in excess of the square footage of
the First Offer Space). The term “materially more favorable” shall mean the net effective rental
rates and terms, such as the length of the term and the amount of any concessions such as the
tenant improvement allowance and any free rent, with respect to such proposal are less than 94% of
the net effective rental rates and terms originally offered to Tenant. If Landlord has not
negotiated a lease or amendment for the First Offer Space with a third party within one hundred
eighty (180) days after Tenant has elected not to, or has been deemed to have elected not to, lease
the First Offer Space, then this Right of First Offer will once again apply to the First Offer
Space. The right granted to Tenant under this paragraph is personal to Tenant, and in the event of
any assignment of this Lease or sublease by Tenant, this Right of First Offer to lease the First
Offer Space shall thenceforth be void and of no further force and effect.

     (d)
Defined Terms.

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          (i) “Expansion Market Rate” shall mean a rental rate equal to the effective rental rate on
transactions being executed by landlords with tenants desiring to lease comparable space of
comparable height and view that is the size of or comparable to the First Offer Space then subject
to the Right of First Offer, in other comparable first-class buildings with comparable amenities
and facilities in the area of the Building, taking into account any abatements, costs, allowances,
commissions or other concessions then being offered to such comparable tenants, seeking comparable
space, and any rights, privileges and allowances Tenant has with respect to the term for the First
Offer Space under, pursuant to or in connection with the Lease, as amended herein. If the parties
cannot agree upon the Expansion Market Rate, then such rate will be determined in accordance with
the procedure set forth in paragraph (c) of Special Stipulation No. 1 in Exhibit “G” attached to
the Lease.

          (ii) “Available” space means that no other third-party is in occupancy of such space or has
any rights therein or thereto, including, but not limited to, rights of expansion, rights of first
offer, rights of first refusal, right of extension, renewal or other option or right.
Notwithstanding anything contained herein to the contrary, the Surrendered Premises will not be
subject to this Right of First Offer until July 1, 2008.

     5. Acceptance of Demised Premises. Tenant hereby accepts the Demised Premises (other
than Floor 8) “AS IS” as of the date hereof and acknowledges that Landlord will have no obligation
to make any tenant improvements or alterations to the Demised Premises or to provide any credit,
abatement or adjustment of Rent or other sum payable under the Lease, as amended herein, except as
expressly set forth in this Second Amendment. Landlord will deliver the Second Expansion Space to
Tenant in accordance with Section 3 of Exhibit “D” to the Lease. Notwithstanding the foregoing,
once the location and dimensions of the space leased by Tenant on Floor 8 has been finally
determined, prior to Landlord delivering such space to Tenant, Landlord acknowledges and agrees
that it will perform certain work on Floor 8 in order to prepare it for Tenant’s Work therein,
including, without limitation, possible reconfiguration of the common corridors and relocation of
certain demising walls.

     6. Tenant Improvements. Tenant will be responsible for all design and construction of
the Demised Premises (“Tenant’s Work”), which will be performed in accordance with the terms of
Exhibit “D” attached to the Lease, as amended herein. Notwithstanding anything contained in the
Lease or Exhibit “D” to the contrary, the “Construction Allowance” for purposes of this Second
Amendment and Exhibit “D” is an amount equal to the product of (i) the total Rentable Floor Area of
the Demised Premises multiplied by (ii) $45.00 per square foot of Rentable Floor Area. Tenant
acknowledges that up to $35.00 per square foot of Rentable Floor Area of the Demised Premises of
the Construction Allowance must be utilized for the costs of design and construction of Tenant’s
Work (the “TI Allowance”). The remaining $10.00 per square foot of Rentable Floor Area of the
Demised Premises of the Construction Allowance may be utilized by Tenant in its sole discretion
(the “Discretionary Allowance”). The TI Allowance shall be applied solely to the cost of Tenant’s
Work, including preparation of design drawings, space planning and engineering, preparation of
electrical engineering and plans, cabling and telecommunications wiring, and signage (as set forth
in Section 8 below). Any move-related costs must be paid for out of the Discretionary Allowance.
If any portion of the Construction Allowance has not been paid by Landlord within six (6) months
following the Effective Date nor has a request for such funds been made by Tenant within such
period, such remaining portion shall be paid to Tenant and Tenant may apply it to Rent under the
Lease, as amended hereby. Exhibit “D” is hereby further amended as follows:

     Section 8A. and Section 8B. of Exhibit “D” are hereby deleted in their entirety and replaced
with the following new Section 8A.:

	 	“A.	 	In lieu of funding the Construction Allowance directly to Tenant, Landlord
agrees to pay Tenant’s general contractor and other contractors and vendors out of the
Construction Allowance directly in accordance with the following procedures: No more
often than once per month, Tenant may request a draw from the Construction Allowance by providing
Landlord (i) a letter containing each invoice number, invoice date, vendor name, and
dollar

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	 	 	 	amount of each invoice, the total amount being requested in such draw, whether
such payments are to be paid from the TI Allowance or the Discretionary Allowance,
and the total amount as of such date that has been requested and paid from the TI
Allowance and Discretionary Allowance, (ii) a copy of each invoice, (iii) partial
lien waivers from each contractor or vendor for which payment is requested and (iv)
such other information or documentation as Landlord may reasonably request. The
final draw request must also be accompanied by final lien waivers from all of
Tenant’s contractors and vendors. Landlord will pay such invoices within thirty (30)
days of its receipt of the draw request containing all of the foregoing required
documentation. Landlord will provide a copy of the checks therefore to Tenant as
proof of payment. If Tenant requests Landlord to process more than four (4) checks
in any month, then each additional check beyond the initial four (4) checks in such
month written by Landlord through this process will be subject to a $100
administrative charge, the total charges for which will be billed to Tenant after
completion of construction.
	 
	 	 	 	With respect to the Discretionary Allowance, Tenant may draw down any remaining
balance of the Discretionary Allowance in up to three (3) draws, at any time from and
after the date of the Second Amendment to Lease Agreement, but before December 31,
2007.
	 
	 	 	 	Tenant agrees that costs not covered by the Construction Allowance shall be paid
directly by Tenant.”

     Section 8C. of Exhibit “D” is hereby amended by deleting such section in its entirety and
replacing it with the following new section 8B.:

	 	“B.	 	Landlord’s property manager will be entitled to receive a construction
management or oversight fee of ten cents (10¢) per square foot of Rentable Floor Area
of the Demised Premises for the services it will be providing to Landlord and Tenant
during the design and construction of Tenant’s Work. Such fee will be paid by Landlord
out of the Construction Allowance.”

     7. Reserved Parking Spaces. As of the Effective Date, Special Stipulation No. 7,
Reserved Parking Spaces, of Exhibit “G” to the Lease shall be amended to provide that Tenant shall
be entitled to one (1) additional reserved parking space at no cost during the Extension Term for
every 7,500 square feet of Rentable Floor Area of additional premises that Tenant leases hereunder
in excess of 137,868 square feet of Rentable Floor Area.

     8. Signage. As of the Effective Date, Landlord agrees to re-orient the existing
monument sign granted to Tenant in Special Stipulation No. 5 of Exhibit “G” to the Lease to
increase the visibility and readability in both directions along Windy Ridge Parkway.
Additionally, as of the Effective Date, Landlord also agrees to allow Tenant to have an additional
small sign, plaque, or panel near the Building entrance or on the Building at its entrance
identifying Manhattan Associates. The size, design, color, material, font style and size, and all
other elements of the sign, plaque, or panel must be approved by Landlord and will be maintained
and removed in accordance with the terms of Special Stipulation No. 5 of Exhibit “G” to the Lease.
The costs for said signage improvements and additions will be paid from the TI Allowance.

     9. Electrical Capacity. The parties acknowledge that in furtherance of Section (f) of
Exhibit “E” (Building Standard Services) of the Lease and notwithstanding anything contained to the
contrary in the Lease, Tenant will be billed only for electrical usage in excess of 5 watts per
square foot of Rentable Floor Area of the Demised Premises. Separate meters will be installed by
Tenant for such excess consumption.

     10. 7th Floor Space. During the space planning process, Tenant
acknowledges that it might desire to retain a minimum of approximately 425 square feet of Rentable
Floor Area on the 7th floor of the

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Building (the “Wire Closet”) as a part of the Demised
Premises if it elects to otherwise vacate the 7th floor. If Tenant elects to do so, and
if such relocation causes Landlord (due to Building life safety or other code requirements) to
install additional corridors on the 7th floor of the Building in order to provide two
(2) means of egress from Tenant’s space in the event Landlord leases the 7th floor to a
full floor tenant, Landlord will allow Tenant to retain the Wire Closet provided that Tenant’s
square feet of Rentable Floor Area for the Demised Premises will include a combination of the
square feet of Rentable Floor Area for the Wire Closet and the square feet of Rentable Floor Area
in any corridors that Landlord is required to build specifically in order to maintain code if
Landlord leases the 7th floor to another full floor tenant. The square feet of Rentable
Floor Area in that case will be calculated with a single tenant add-on factor. If Landlord leases
the 7th floor in a multi-tenant configuration and no additional corridors are required
to be built as a result of Tenant retaining at least the Wire Closet on the 7th floor,
then Tenant will be required to pay only for the square feet of Rentable Floor Area of the Wire
Closet that it retains, calculated with a multi-tenant add-on factor.

     11. Termination Option. Notwithstanding anything to the contrary contained in the
Lease, provided Tenant is not in monetary default under the Lease beyond any applicable notice
and/or cure period, Tenant shall have the option (the “Termination Option”) to terminate the Lease
effective on the last day of the sixty-ninth (69th) month of the Extension Term (the
"Termination Date”), by providing Landlord with written notice of such option election (the
"Termination Notice”). The Termination Notice shall be effective only if it is given to Landlord
at least twelve (12) months prior to the Termination Date (the “Termination Notice Deadline”);
accordingly, if Tenant has not given the Termination Notice to Landlord prior to the Termination
Notice Deadline, the Termination Option shall expire and be of no further force or effect, and
Tenant shall have no right or option to terminate the Lease pursuant to this Paragraph 11 at any
time after the Termination Notice Deadline.

     As a condition precedent to any termination of the Lease pursuant to the provisions of this
Paragraph 11, Tenant must have delivered to Landlord within thirty (30) days after Landlord advises
Tenant in writing of the calculation of the Termination Fee (defined below) an amount as a
termination fee equal to the sum of (i) six (6) months of Base Rental and Tenant’s Additional
Rental in the amounts that would have been paid for the next six (6) months of the Extension Term
following the Termination Date had the Termination Option not been exercised, plus an amount equal
to the unamortized portion (amortized on a straight-line basis at ten percent (10%) per annum) of
the Construction Allowance, free rent and leasing commissions (the “Termination Fee”). It is
hereby acknowledged that any such amount required to be paid by Tenant in connection with such
early termination is not a penalty but a reasonable pre-estimate of the damages which would be
incurred by Landlord as a result of such early termination of the Lease (which damages are
impossible to calculate more precisely) and, in that regard, constitutes liquidated damages with
respect to such loss and shall be paid to Landlord as Additional Rent. Tenant shall continue to be
liable for its obligations under the Lease to and through the Termination Date, including, without
limitation, Tenant’s Additional Rental that accrues pursuant to the terms of the Lease, with all of
such obligations surviving the early termination of the Lease. The rights granted to Tenant under
this Paragraph 11 are personal to Tenant, and in the event of any assignment of the Lease by Tenant
prior to the Termination Notice Deadline, the Termination Option shall thenceforth be void and of
no further force or effect.

     12. Renewal Options. Special Stipulation No. 1, Renewal Option, of Exhibit “G” to the
Lease is hereby amended by deleting the words “one (1) option to renew” and replace them with the
words “two (2) options to renew” such that Tenant will have two (2) options to further renew the
Lease in accordance with the terms of Special Stipulation No. 1 as of the expiration of the
Extension Term.

     13. Other Amendments. Since such option has expired, Special Stipulation No. 2, Right
of First Refusal, of Exhibit “G” to the Lease has no further relevancy or application and is of no
further force and effect and is hereby deleted and replaced with the words “Intentionally Omitted”.

     14. Brokers. Each party represents and warrants to the other that neither it nor its
officers or agents nor anyone acting on its behalf has dealt with any real estate broker other than
Hines Properties, Inc.

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who represented Landlord and CB Richard Ellis, Inc. who represented Tenant
in the negotiating or making of this Second Amendment, and each party agrees to indemnify and hold
the other party, its agents, employees, partners, directors, shareholders and independent
contractors harmless from all liabilities, costs, demands, judgments, settlements, claims, and
losses, including reasonable attorneys’ fees and costs, incurred by the other party in conjunction
with any such claim or claims of any other broker or brokers purportedly acting on behalf of the
indemnifying party claiming to have interested Tenant in the Building or the Demised Premises, or
claiming to have caused such party to enter into this Second Amendment. Landlord will pay CB
Richard Ellis, Inc. a separate commission pursuant to the commission agreement attached hereto as
Exhibit B and incorporated herein by this reference.

     15. Notices. Article 1(b) and Article 33 of the Lease regarding the address and
notice to Landlord, shall be amended to provide that the address of Landlord is, and all notices to
Landlord shall be sent as follows:

          (a)     Notices to Landlord (other than rent payments):

2300 Windy Ridge Parkway Investors LLC

c/o UBS Realty Investors LLC

242 Trumbull Street

Hartford, Connecticut 06103-1212

Attention: General Counsel

                and

Cousins Properties

Wildwood Office Park

Management Office

2300 Windy Ridge Parkway

Suite 75

Atlanta, Georgia 30339

Attention: Property Manager

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          (b)       Rent Payments:

2300 Windy Ridge Parkway Investors LLC

c/o Cousins Properties Incorporated,

2500 Windy Ridge Parkway

Suite 1600

Atlanta, Georgia 30339

Attention: Treasury Department

     16. No Defaults. Each party hereby agrees that there are, as of the date hereof,
regardless of the giving of notice or the passage of time, or both, no defaults or breaches on the
part of Landlord or Tenant under the Lease.

     17. Capitalized Terms. All capitalized terms used herein and not otherwise defined
herein shall have the meanings ascribed to them in the Lease.

     18. Headings. The headings used herein are provided for convenience only and are not
to be considered in construing this Second Amendment.

     19. Entire Agreement. This Second Amendment represents the entire agreement between
the parties with respect to the subject matter hereto. Landlord and Tenant agree that there are no
collateral or oral agreements or understandings between them with respect to the Demised Premises,
the Second Expansion Space or the Building other than the Lease and this Second Amendment. This
Second Amendment supersedes all prior negotiations, agreements, letters or other statements with
respect to Tenant’s expansion of the Demised Premises and the extension of the Lease Term.

     20. Binding Effect. This Second Amendment shall not be valid and binding on Landlord
and Tenant unless and until it has been completely executed by and delivered to both parties.

     EXCEPT AS expressly amended and modified hereby, the Lease shall otherwise remain in full
force and effect, the parties hereto hereby ratifying and confirming the same. To the extent of
any inconsistency between the Lease and this Second Amendment, the terms of this Second Amendment
shall control.

[END OF PAGE]

- 9 -

 

     IN WITNESS WHEREOF, the undersigned parties have duly executed this Second Amendment under
seal as of the day and year first above written.

	 	 	 	 	 	 	 	 	 	 	 
	LANDLORD:	 	 	 	TENANT:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	2300 WINDY RIDGE PARKWAY INVESTORS	 	MANHATTAN ASSOCIATES, INC.,	 	 
	LLC, a Delaware limited liability company  	 	a Georgia corporation	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	UBS Realty Investors LLC,	 	 	 	 	 	 	 	 
	 

	 	a Massachusetts limited liability company,
	 	 	 	By:
	 	/s/Peter F. Sinisgalli
 

	 	 
	 	 	Its Manager	 	 	 	Print Name: Peter F. Sinisgalli
	 	 
	 	 	 	 	 	 	Its: President & CEO	 	 

	 	 	 	 	 	 	 	 	 	 	 
	 	 	By: /s/ James M. Fishman	 	 	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	 	 	Print Name: James M. Fishman	 	(CORPORATE SEAL)	 	 
	 	 	Title: Executive Director	 	 	 	 

- 10 -

 

EXHIBIT A

SECOND AMENDMENT MEMORANDUM

	 	 	 
	LANDLORD:

	 	2300 WINDY RIDGE PARKWAY INVESTORS

LLC
	 
	 	 
	TENANT:

	 	MANHATTAN ASSOCIATES, INC.
	 
	 	 
	SECOND AMENDMENT TO 

LEASE AGREEMENT DATE:

	 	February                    , 2007
	 
	 	 
	DEMISED PREMISES:

	 	Located at 2300 Windy Ridge Parkway, Atlanta,

Georgia 30339

     Tenant hereby accepts the Demised Premises in accordance with the Second Amendment to Lease
Agreement.

     The Effective Date as set forth in the Second Amendment to Lease Agreement is hereby
established as July 1, 2007 and the Expiration Date of the Lease is September 30, 2018.

     The Demised Premises consists of approximately                      square feet of Rentable Floor Area
of the Building consisting of the following:

Floor                       —                       rsf

Floor                       —                        rsf

Floor                       —                        rsf

Floor                       —                        rsf

Floor                       —                        rsf

     Tenant’s proportionate share of the Building is                     , subject to adjustment based on
future expansions/contractions of the Demised Premises.

	 	 	 	 	 	 	 	 	 	 	 
	TENANT:	 	 	 	MANHATTAN ASSOCIATES, INC.,
	 	 	 	 	a Georgia corporation
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By: 	 
	 

	 	 	 	 	 	 	 	 	 
	 	 	 	 	Print Name: 	 
	 

	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	Its:
	 

	 	 	 	 	 	 	 	 	 

A-1

 

A-1

Approved and Agreed:

2300 WINDY RIDGE PARKWAY INVESTORS LLC,

a Delaware limited liability company

	 	 	 	 	 	 	 
	By:	 	UBS Realty Investors LLC,

a Massachusetts limited liability company,

Its Manager
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 	 	 	 	 	 
	 	 	Print Name: 	 
	 	 	 	 	 	 	 
	 

	 	Its:	 	 	 	 
	 	 	 	 	 	 

A-2

 

EXHIBIT B

COMMISSION AGREEMENT

February 9, 2007

Mr. Sam Holmes

Mr. John Shlesinger

CB Richard Ellis, Inc.

3348 Peachtree Road

Suite 900

Atlanta, GA 30326

	 	 	 	 	 
	 

	 	Re:
	 	Proposed Second Amendment to Lease Agreement (“Amendment”) which amends that
certain Lease Agreement dated June 25, 2001, as amended (the “Lease”) by and between
2300 WINDY RIDGE PARKWAY INVESTORS LLC, a Delaware limited liability company (“Owner”),
successor to Wildwood Associates, and MANHATTAN ASSOCIATES, INC., a Georgia corporation
(“Tenant”) relating to certain premises at 2300 Windy Ridge Parkway, Atlanta, Georgia
30339 (“Property”)

Gentlemen:

     This letter is intended to confirm our agreement (“Agreement”) that in the event of the
execution and consummation of the above Amendment, Owner shall pay you in consideration for your
brokerage services rendered and subject to the other provisions hereof, a commission computed and
payable in accordance as described below. Capitalized terms used but not defined herein shall have
the meanings given to them in the Amendment.

     1. Commission Payable. Owner shall pay you a commission equal to a Procurement Fee
(“Procurement Fee") equal to the first full months “gross” rental payable by Tenant under the
Amendment for any additional space leased pursuant to the Amendment and subsequent space leased
prior to the Effective Date that exceeds 137,868 rentable square feet. Landlord shall also pay you
a commission equal to the product of Aggregate Rent (as defined on Attachment I hereto) less the
Procurement Fee payable during the Extension Term, times four percent (4%). Aggregate Rent shall
be calculated in accordance with Attachment I.

     2. Time of Payment. The amount payable pursuant to Section 1 above shall be deemed
earned upon execution of the Amendment by both Tenant and Landlord and shall be paid in two
separate installments. Owner shall pay 50% of such amount upon full execution of the Amendment by
Tenant and Owner and receipt by both Tenant and Owner of an original thereof, and the remaining 50%
will be paid within thirty (30) days of the Effective Date. In the event a default by Tenant
occurs under the Lease, as amended, beyond applicable notice and cure periods, such that the Lease
is terminated prior to Tenant taking possession of the Demised Premises and the second installment
of the commission being paid, then you shall forfeit the second half of the commission. If the
default is later cured, you will receive the second half of the commission. Since the exact square
footage of the Second Expansion Space and Retained Premises (as both are defined in the Amendment)
will not be known at the time the first (1st) installment is paid to you, the first
installment will be paid based on an estimate of 160,000 rentable square feet, with such amount
being reconciled at the time the 2nd installment is paid, based then on the exact amount
of square footage of the Second Expansion Space and Retained Premises which will then have been
determined.

B-1

 

     3. Renewals, Extensions or Expansions. If the Lease is renewed or extended, whether
pursuant to an option contained in the Lease or Amendment or otherwise, any commission payable to
you in connection with such renewal or extension shall be governed by the terms of a new agreement
between you and Owner, provided Tenant confirms in writing to Owner that you are representing them
with respect to such renewal or extension. If after the Effective Date, the Demised Premises is
expanded, whether pursuant to an option contained in the Lease or Amendment or otherwise, Owner
will pay you a commission provided Tenant confirms in writing to Owner that you are representing
them with respect to such expansion equal to the product of Aggregate Rent (as defined on
Attachment I hereto) payable for the expansion space, times four percent (4%). Aggregate Rent
shall be calculated in accordance with Attachment I. In the event of any such expansion, the
commission shall be deemed earned when the amendment reflecting such expansion is executed and
delivered by both Landlord and Tenant and shall be paid in two separate installments. Owner shall
pay 50% of such amount upon full execution of the amendment by Tenant and Owner and receipt by both
Tenant and Owner of an original thereof, and the remaining 50% will be paid following the
commencement date of such expansion. In the event a default by Tenant occurs under the Lease, as
amended, such that the Lease is terminated prior to Tenant taking possession of the expansion space
and the second installment of the commission being paid, then you shall forfeit the second half of
the commission. If the default is later cured, you will receive the second half of the commission.

     4. Exclusive Representation of Tenant; No Other Brokers. By signing this Agreement,
you represent and warrant that (a) you hold a valid real estate broker’s license, (b) you have
caused Tenant to give Owner written notice that it is being represented exclusively by you, and (c)
Tenant has not withdrawn such exclusive representation or notified you that it is being represented
by another broker. In the event that any person makes a claim that any of the foregoing items are
not true or Owner has a reasonable belief that any of such items are not true or if any other
person claims any commission from Owner respecting the Lease or Amendment (other than the Owner’s
leasing broker), Owner may elect to withhold payment of the commission hereunder until presented
with a duly executed valid and binding agreement between you and such other person or with a final,
valid court order setting forth how the commission will be divided or who is entitled to receive
the commission (and you agree that Owner shall be authorized to pay in accordance with the same).
Upon Owner’s payment of the commission owed pursuant to Section 1 above, you shall be responsible
for all other fees or commissions owing to or claimed to be owing by any other broker or other
person for services rendered or claimed to have been rendered to Tenant in connection with the
Lease or Amendment, except for any amounts which may be claimed, or due, pursuant to an agreement
between Owner and Owner’s leasing broker or any other person. You shall indemnify, defend and hold
Owner harmless from any and all claims, losses, demands, judgments, orders, settlements or decrees
(including any and all costs and expenses and reasonable attorneys’ fees and disbursements) arising
as a result of or which are attributable to any misrepresentation or breach of any warranty set
forth in this Section or any breach of your obligations under this Section. This Section shall
survive expiration or termination of this Agreement.

     5. Confidentiality. By execution of this Agreement, you agree after the date hereof
not to divulge to any other person or entity any of the terms or conditions of the Lease or
Amendment between Tenant and Owner, except you shall have the right to provide such information (a)
if compelled by law or court order and (b) as and when required in connection with your application
for the Atlanta Board of Realtors “Million Dollar Club” or similar designation and (c) internally
for either audit purposes or for purposes of payment. It is further agreed that all proposals,
discussions, terms and conditions pertaining to Tenant’s potential or actual lease of space in the
Building shall be treated by you in a strictly confidential manner and not disclosed in any fashion
or context to anyone other than Tenant or its designees. Any
material breach of the confidentiality provisions of this Agreement will terminate your rights and
Owner’s obligations under this Agreement.

B-2

 

     6. No Assignments. You shall not assign or encumber your rights hereunder nor
delegate your duties hereunder, without Owner’s prior written consent (which Owner may withhold in
its sole discretion). Any attempted assignment, encumbrance or delegation without Owner’s consent
shall be null and void and of no force or effect. Notwithstanding the foregoing, this Agreement
may be assigned without Owner’s consent if same is assigned in connection with the sale of the
assets or stock of CB Richard Ellis, Inc. so long as Tenant confirms in writing to the Owner that
the successor to CB Richard Ellis, Inc. is still representing Tenant in connection with the Lease,
as amended.

     7. Owner’s Right to Reject Lease Agreement; No Authority to Represent Owner. Owner,
in its sole and absolute discretion, may withhold its approval or decline to enter into the
Amendment for any reason whatsoever or for no reason, without incurring an obligation to you for
the payment of a commission or any other amounts to you. No binding agreement shall exist unless
and until the Amendment has been approved, executed and delivered by authorized representatives of
Tenant and Owner and all conditions and contingencies have been satisfied. You have no authority to
enter into any agreement on behalf of Owner and you are not authorized to make any representations
on behalf of Owner.

     8. Termination of this Agreement; Sale of Property. This Agreement and Owner’s
obligations hereunder shall terminate upon the sale or other transfer of Owner’s interest in the
Property and Owner shall be released automatically from any obligations hereunder so long as Owner
or the transferee has paid you all amounts then due hereunder and has caused the transferee to
assume the obligation to pay any future amounts due hereunder.

     9. Owner’s Liability. Owner’s liability under this Agreement shall be limited to
Owner’s interest in the Property, and no personal liability shall at any time be asserted or
enforceable against Owner or its manager, members, partners, officers, directors, shareholders, or
employees or their respective heirs, legal representatives, successors and assigns on account of
this Agreement. In addition, if Owner has entered into this Agreement on behalf of one or more
separate accounts (as such term is defined in Section 3(17) of ERISA), then Owner’s liability shall
be further limited to the assets of such separate account.

     10. Miscellaneous. This Agreement is the entire agreement and understanding of the
parties hereto, superseding and canceling all other agreements between the parties, whether written
or oral, relative to the subject matter hereof. This Agreement may not be modified except by
written instrument hereafter executed by the parties hereto. This Agreement shall not be valid or
binding unless and until signed and delivered by all of the parties hereto.

     11. Anti-Terrorism. Broker is not a person or entity described by Sec. 1 of the
Executive Order (No. 13,224) Blocking Property and Prohibiting Transactions With Persons Who
Commit, Threaten to Commit, or Support Terrorism, 66 Fed. Reg. 49,079 (Sept. 24, 2001), and does
not engage in any dealings or transactions, and is not otherwise associated, with any such persons
or entities.

[SIGNATURES COMMENCE ON NEXT PAGE]

B-3

 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	BROKER:	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	OWNER:	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	CB RICHARD ELLIS, INC.	 	 	 	 	 	  2300 WINDY RIDGE PARKWAY	 	 	 	 	 	 
	A Delaware corporation                                                                 INVESTORS LLC, a Delaware limited	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	liability company	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	     By:	 	UBS Realty Investors LLC,
	By:

	 	 

	 	 	 	 	 	a Massachusetts limited liability
	Name:

	 	 

	 	 	 	 	 	company, its Manager
	Title:

	 	 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	By:
	 	 

	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	Name:
	 	 

	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	Title:
	 	 

	 	 	 	 	 	 	 	 	 	 

B-4

 

Attachment I

[Definition of Aggregate Rent]

As used herein, the term “Aggregate Rent” shall mean the aggregate base fixed rent plus fixed
stated escalations plus Estimated Operating Expenses as defined hereinafter payable during the
Extension Term; provided, that, no commissions will be paid on, and Aggregate Rent shall not
include:

          (i) any percentage rent of any type, kind or character, including, without limitation,
any rent payable based on the tenant’s sales or income;

          (ii) implied rent during free rent periods or other periods during which the tenant has
no rent payment obligations;

          (iii) rent payable in connection with any future renewal, extension or expansion option
that the tenant may have;

          (iv) rent payable during month-to-month, holdover or statutory tenancy periods;

          (v) rent payable during portions of the term of the lease that can be cancelled or
terminated by the tenant unless the tenant’s termination option requires tenant to pay the
unamortized leasing commissions as a part of any termination fee;

          (vi) any amount payable by the tenant in connection with any cancellation or
termination of the lease or any exercise of any purchase option, right of first refusal to
purchase or similar right;

          (vii) reimbursement to Owner for any parking, decorations, improvements, space planning
or moving, or any security deposits;

          (viii) amounts payable by the tenant pursuant to the lease that constitute or are
considered in the ordinary course of business to be a payment of anything other than
Aggregate Rent, including, without limitation, payments in the form of warrants or other
equity interests in the tenant;

          (ix) any free rent periods or rent concessions, cash credits, payment deferments or
other concession items, and any amounts payable by the tenant to reimburse Owner for amounts
paid by Owner to take-over, buy- out or take-back another lease;

          (x) any amounts payable by the tenant (whether denominated as rent or not) that are
attributable to amortizing or defraying the cost of special or above-standard tenant
improvements or special services being provided by Owner to tenant; and

          (xi) in that the Amendment effects an early renewal of the Lease term (term currently
expires March 31, 2008), that portion of the Aggregate Rent applicable to the Retained
Premises for the period of July 1, 2007 through March 31, 2008, as a commission has
previously been paid on the Retained Premises in connection with the Lease.

For purposes hereof, the term “Estimated Operating Expenses” shall mean the amount equal to the
operating expenses and taxes that are passed through to tenants generally which Owner reasonably

B-5

 

estimates would be incurred with respect to the first full calendar year following the Effective
Date under the Amendment if the Property were ninety-five percent (95%) occupied throughout such
calendar year.

B-6EX-10.12 AMENDED & RESTATED EMPLOYMENT AGREEMENT

 

EXHIBIT 10.12

February 14, 2007

Jon Stonehouse

7 Pine Top Place

Durham, NC 27705

Dear Mr. Stonehouse:

     This amended and restated letter agreement (the “Agreement”) will serve to confirm our
agreement with respect to the terms and conditions of your employment with BioCryst
Pharmaceuticals, Inc. (“BioCryst” or the “Company”). As you know, this Agreement is identical in
all respects to the agreement originally executed on January 5, 2007, except that it reflects the
fact that all of the initial equity awards under Section 3 were issued under the BioCryst
Pharmaceuticals, Inc. Stock Incentive Plan.

1. Term of Employment. Subject to the terms and conditions of this Agreement, BioCryst hereby
employs Jon Stonehouse (the “Employee”), effective January 5, 2007, as Chief Executive Officer of
BioCryst, and Employee hereby accepts such employment. During the term of this Agreement, BioCryst
shall use its best efforts to provide that the Employee shall be elected as a member of the Board
of Directors of BioCryst (the “Board”). The Employee shall not, during the term of his employment,
engage in any other business activity that would interfere with, or prevent him from carrying out,
his duties and responsibilities under this Agreement. Employee represents that he currently serves
on the Board of Directors of River West Health Care, LLC (a start-up company the business of which
is not competitive with that of the Company) as well as on an advisory council at Duke University,
and that neither activity will interfere materially with his duties as contemplated hereunder.
BioCryst hereby acknowledges and approves such activities. BioCryst further agrees and
acknowledges that any compensation which the Employee receives from participation in any such
allowable activities shall be outside the scope of this Agreement and in addition to any
compensation received hereunder. The term of employment of Employee under this Agreement shall
commence as of the effective date set forth above and shall continue for a period of one year,
subject to earlier termination as provided herein; provided, however that the term shall be
automatically extended by one additional year on each anniversary of the effective date of this
Agreement, unless one party to this Agreement provides written notice of non-renewal to the other
party at least 30 days prior to the date of such automatic extension.

2. Basic Full-Time Compensation and Benefits.

     (a) As basic compensation for services rendered under this Agreement, Employee shall be
entitled to receive from BioCryst, a salary of $33,333 per month ($400,000 per annum)
payable in arrears on the first business day of each month during the term of this
Agreement, beginning on February 1, 2007 for the month of January 2007. This salary will be
reviewed annually by the Board of Directors and may be raised at the discretion of the
Board.

     (b) In addition to the basic compensation set forth in (a) above, Employee shall be
eligible to earn a cash bonus of up to $300,000, payable as soon as reasonably practicable
in calendar year 2008, based on the Company’s achievement of performance related goals
proposed by management and approved by the Board for the Company’s fiscal year ending
December 31, 2007. The bonus actually earned, if any, shall be based on a target amount of
$200,000 for achievement of the performance goals, and shall be pro-rated or increased, as
applicable, based on the degree to which the performance goals have or have not been
achieved or have been exceeded, subject to a minimum level of achievement proposed by
management and approved by the Board. The amount of the bonus earned in accordance with the
achievement of the performance goals, as described above, shall be prorated according to the
percentage of the calendar year that Employee is employed by the Company. The Company shall
provide Employee with similar annual bonus opportunities for future fiscal years during the
term of this Agreement, in amounts that are commensurate with the performance of the Company
and of Employee.

77

 

     (c) In addition to the basic compensation set forth in (a) and (b) above, Employee
shall be entitled to receive benefits and perquisites at least as favorable as those
provided to other executive officers of BioCryst, which benefits shall include, without
limitation, reasonable vacation, sick leave, payment of fees for Employee’s participation in
the advisory council at Duke University, medical benefits, $1,000,000 of life insurance
during the term of Employee’s employment, and participation in profit sharing or retirement
plans. Notwithstanding the foregoing, the Company’s obligation to provide $1,000,000 of
life insurance for Employee shall be subject to Employee’s insurability at rates customary
for an individual of Employee’s age who is in average physical condition. In addition, the
Company shall reimburse Employee for his reasonable attorneys fees incurred in connection
with the negotiation of this Agreement.

     (d) In addition to the compensation set forth in paragraphs 2(a), (b) and (c) above,
the Board of Directors of BioCryst may from time to time, in its discretion, also grant such
other cash or stock bonuses to the Employee either as an award or as an incentive as it
shall deem desirable or appropriate.

3. Initial Equity Awards. In connection with Employee’s execution of this Agreement, Employee shall
be issued initial equity incentive awards as follows:

     (a) The Company shall, on the effective date hereof, grant to Employee an option to
purchase 450,000 shares of the Company’s common stock (“Common Stock”), with an exercise
price equal to the fair market value of the Common Stock on the date of the grant. The
option shall vest and become exercisable contingent on Employee’s continued provision of
services to the Company on each respective vesting date, over a period of 4 years as
follows: one year after Employee’s start date, 25% of the awards will vest; thereafter, the
remaining shares will vest on a monthly schedule of 1/48 of the total number of shares
subject to the grants upon the completion of each month of service. The option will be an
“incentive stock option” to the maximum extent allowed by the tax code.

     (b) The Company shall grant to Employee 50,000 shares of its Common Stock, which shall
vest in two equal installments as follows: the first installment shall vest two years after
the Employee’s start date; the second installment shall vest four years after the Employee’s
start date. Employee understands and acknowledges that prior to vesting, the shares may not
be transferred and will be subject to forfeiture.

     (c) All awards will be issued under and shall be subject to the terms of the BioCryst
Pharmaceuticals, Inc. Stock Incentive Plan and specific award agreements between the
Employee and the Company, which award agreements shall provide that Employee be entitled to
exercise any vested incentive stock option or any non qualified stock option for a period of
two years subsequent to the termination or expiration of Employee’s employment with the
Company. All shares issuable pursuant to the awards in this Section 3 have been registered
on Form S-8.

4. Termination.

     (a) If Employee’s employment is terminated (i) as a result of the Employee’s
resignation or non-renewal of the term, (ii) as a result of the Employee’s death, or (iii)
by the Company for Cause, Employee will receive base salary, as well as any accrued but
unused vacation (if applicable) and other compensation, earned through the effective
termination date, and no additional compensation; provided, however, that in the event
Employee’s employment is terminated as a result of the Employee’s death, and the Company has
failed to procure and maintain $1,000,000 in life insurance on the life of Employee in
violation of its obligation pursuant to paragraph 3(c), the Company shall pay to the
Employee’s personal representative $1,000,000.

     For all purposes under this Agreement, a termination for “Cause” shall mean a
determination by the Board that Employee’s employment be terminated for any of the following
reasons: (i) a violation of a federal or state law or regulation that materially and
adversely impacts the business of the Company, (ii) conviction or plea of no contest to a
felony under the laws of the United States or any state, (iii) a breach of the terms of any
confidentiality, invention assignment or proprietary information agreement with the Company
or with a former employer that materially and adversely impacts the Company, (iv) fraud or
misappropriation of property belonging to the Company or its affiliates, or (v) willful
misconduct or gross negligence in connection with the performance of Employee’s duties;
provided, however, that no act or failure to act on the part of the Employee

78

 

shall be considered “willful” unless it is done, or omitted to be done, by the Employee
in bad faith or without reasonable belief that the Employee’s action or omission was in the
best interests of the Company.

     (b) If Employee’s employment is terminated (i) by the Company without Cause, (ii) upon
non-renewal of the term by the Company, (iii) as a result of a Constructive Termination, or
(iv) by the Company as a result of Disability, the Company shall provide written notice of
termination to Employee, along with any base salary and accrued but unused vacation or other
compensation earned through the effective termination date.

     In addition, and subject to the Employee (a) signing and not revoking a release of any
and all claims against the Company, its officers, directors and employees, (b) resigning
from the Board (if applicable) on the date that employment terminates, and (c) returning to
the Company all of its property and confidential information that is in Employee’s
possession, the Employee will receive:

     (I) severance in an amount equal to the product of (x) two, except in the event
the effective date of termination occurs within one year of the effective date of
this Agreement, in which case the severance multiplier shall be one, and (y) the sum
of (1) Employee’s annual base salary in effect immediately prior to the effective
date of termination, and (2) Executive’s target bonus in effect for the fiscal year
of termination, which severance amount shall be paid in equal installments over the
regularly scheduled payroll periods of the Company for the two years following the
effective date of termination, and

     (II) if Employee elects to continue health insurance coverage under COBRA
following termination of employment, the Company shall pay the monthly premium under
COBRA until the earlier of (1) twelve months following the effective date of
termination, or (2) the date upon which COBRA continuation coverage ceases.

     “Disability” shall mean the inability of Employee to perform his duties hereunder by
reason of physical or mental incapacity for ninety (90) days, whether consecutive or not,
during any consecutive twelve (12) month period.

     “Constructive Termination” shall mean a resignation of employment within 30 days of the
occurrence of any of: (i) a reduction in Employee’s responsibilities or any change in the
status or title of Employee with regard to his employment; (ii) a reduction in Employee’s
base salary, unless such reduction occurs prior to a Change in Control (as defined below)
and is made in connection with a fiscal downturn of the Company pursuant to which the base
salaries of all executive officers of the Company are reduced by a comparable percentage; or
(iii) a relocation of Employee’s principal office to a location more than 50 miles from the
location of Employee’s then-current principal office.

     (c) If, during Employee’s employment with the Company, there is a Change of Control,
all equity awards granted to Employee under paragraph 3 and otherwise shall vest in full.
In addition, if Employee’s employment is terminated following the Change in Control, the
provisions of paragraph (a) or (b) above shall apply, as applicable; provided, however, that
in the event the Employee’s employment is terminated pursuant to paragraph (b) above
following a Change in Control and within one year of the effective date of this Agreement,
the severance multiplier in paragraph 4(b)(I) above shall be two as opposed to one.

     “Change of Control” shall be defined as (i) a merger or consolidation in which the
Company is not the surviving entity, except for a transaction the principal purpose of which
is to change the State of the Company’s incorporation, (ii) the sale, transfer or other
disposition of all or substantially all of the assets of the Company in liquidation or
dissolution of the Company, (iii) any reverse merger in which the Company is the surviving
entity but in which securities possessing more than fifty percent (50%) of the total
combined voting power of the Company’s outstanding securities are transferred to a person or
persons different from the persons holding those securities immediately prior to such
merger, or (iv) any person or related group of persons (other than the Company or a person
that directly or indirectly controls, is controlled by, or is under common control with, the
Company) directly or indirectly acquires beneficial ownership (within the meaning of Rule
13d-3 of the 1934 Act) of securities possessing more than fifty percent (50%) of the total
combined voting power of the

79

 

Company’s outstanding securities pursuant to a tender or exchange offer made directly
to the Company’s stockholders.

     (d) In the event (i) any payments described in this paragraph 4 would be “deferred
compensation” subject to Section 409A of the Internal Revenue Code of 1986, as amended (the
“Code”), and (ii) Employee is a “specified employee” (as defined in Code Section
409A(2)(B)(i)), such payments shall, to the extent required by Code Section 409A, be delayed
for the minimum period and in the minimum manner necessary to avoid the imposition of the
tax required by Code Section 409A.

5. Non-Competition; Proprietary Information and Inventions.

     (a) Proprietary Information and Inventions Agreement. As a condition precedent
to the employment of Employee by the Company, Employee shall execute the Company’s standard
Proprietary Information and Inventions Agreement, attached hereto as Exhibit A.

     (b) Non-Competition Agreement. The Employee agrees that for one (1) year
following the termination of this Agreement, the Employee shall not become the Chief
Executive Officer or become a key executive of another for-profit business enterprise whose
activities are at such time directly competitive with BioCryst.

     (c) Equitable Remedies. Employee acknowledges and recognizes that a violation
of this paragraph by Employee may cause irreparable and substantial damage and harm to
BioCryst or its affiliates, could constitute a failure of consideration, and that money
damages will not provide a full remedy for BioCryst for such violations. Employee agrees
that in the event of his breach of this paragraph, BioCryst will be entitled, if it so
elects, to institute and prosecute proceedings at law or in equity to obtain damages with
respect to such breach, to enforce the specific performance of this paragraph by Employee,
and to enjoin Employee from engaging in any activity in violation hereof.

6. Golden Parachute Provisions. If it is determined that any payment or benefit provided by the
Company to or for the benefit of the Employee, whether paid or payable or distributed or
distributable pursuant to the terms of this Agreement or otherwise, including, by example and not
by way of limitation, acceleration by the Company or otherwise of the date of vesting or payment
under any plan, program, arrangement or agreement of the Company would be subject to the excise tax
imposed by Code section 4999 or any interest or penalties with respect to such excise tax (such
excise tax together with any such interest and penalties, shall be referred to as the “Excise
Tax”), then the Company shall first make a calculation under which such payments or benefits
provided to the Employee are reduced to the extent necessary so that no portion thereof shall be
subject to the Excise Tax (the “4999 Limit”). The Company shall then compare (a) the Employee’s
Net After-Tax Benefit (as defined below) assuming application of the 4999 Limit with (b) the
Employee’s Net After-Tax Benefit without application of the 4999 Limit. The Employee shall be
entitled to the greater of (a) or (b). “Net After-Tax Benefit” shall mean the sum of (i) all
payments that Employee receives or is entitled to receive that are contingent on a change in the
ownership or effective control of the Company or in the ownership of a substantial portion of the
assets of the Company within the meaning of Code section 280G(b)(2), less (ii) the amount of
federal, state, local, employment, and Excise Tax (if any) imposed with respect to such payments.
If the Employee is required to reduce payments to which he is otherwise entitled such that no
portion thereof is subject to the Excise Tax, the Employee shall choose which payments shall be
reduced and the amount of the reduction of each payment.

7. Miscellaneous.

     (a) Entire Agreement. This Agreement, including the exhibits hereto,
constitutes the entire agreement between the parties relating to the employment of the
Employee by BioCryst and there are no terms relating to such employment other than those
contained in this Agreement. No modification or variation hereof shall be deemed valid
unless in writing and signed by the parties hereto. No waiver by either party of any
provision or condition of this Agreement shall be deemed a waiver of similar or dissimilar
provisions or conditions at any time.

     (b) Assignability. This Agreement may not be assigned without prior written
consent of the parties hereto. To the extent allowable pursuant to this Agreement, this
Agreement shall be binding upon and

80

 

shall inure to the benefit of each of the parties hereto and their respective
executors, administrators, personal representatives, heirs, successors and assigns.

     (c) Notices. Any notice or other communication given or rendered hereunder by
any party hereto shall be in writing and delivered personally or sent by registered or
certified mail, postage prepaid, at the respective addresses of the parties hereto as set
forth below.

     (d) Captions. The section headings contained herein are inserted only as a
matter of convenience and reference and in no way define, limit or describe the scope of
this Agreement or the intent of any provision hereof.

     (e) Taxes. All amounts to be paid to Employee hereunder are in the nature of
compensation for Employee’s employment by BioCryst, and shall be subject to withholding,
income, occupation and payroll taxes and other charges applicable to such compensation.

     (f) Governing Law. This Agreement is made and shall be governed by and
construed in accordance with the laws of the State of Alabama without respect to its
conflicts of law principles.

     (g) Date. This Agreement is effective as of January 5, 2007.

     (h) Counterparts. This Agreement may be executed in one or more counterparts,
each of which will be deemed to be an original copy of this Agreement and all of which, when
taken together, will be deemed to constitute one and the same agreement. The exchange of
copies of this Agreement and of signature pages by facsimile or other electronic
transmission shall constitute effective execution and delivery of this Agreement as to the
parties and may be used in lieu of the original Agreement for all purposes. Signatures of
the parties transmitted by facsimile or other electronic means shall be deemed to be their
original signatures for all purposes.

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     If the foregoing correctly sets forth our understanding, please signify your acceptance of
such terms by executing this Agreement, thereby signifying your assent, as indicated below.

	 	 	 	 	 
	 	Yours very truly,

BIOCRYST PHARMACEUTICALS, INC.

COMPENSATION COMMITTEE

 	 
	 	By:  	/s/ Beth C. Seidenberg
 	 
	 	 	Beth C. Seidenberg, MD 	 
	 	 	Chairman 	 
	 
	 	 	 
	 	By:  	     /s/ Steve Biggar
 	 
	 	 	Steve Biggar, MD, PhD 	 
	 	 	 	 
	 
	 	 	 
	 	By:  	     /s/ William W. Featheringill
 	 
	 	 	William W. Featheringill 	 
	 	 	 	 
	 
	 	Address:

2190 Parkway Lake Drive

Birmingham, Alabama 35244

 	 
	 	 	 
	 	 	 
	 	 	 
	 

     AGREED AND ACCEPTED, as of this 14 day of February, 2007.

	 	 	 	 	 
	 	 	 
	 	     /s/ Jon Stonehouse
 	 
	 	Jon Stonehouse 	 
	 	

Address:	 
	 
	 	7 Pine Top Place

Durham, NC 27705 	 

82

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