Document:

Amendment, dated 5/30/06 to Metabolic Disorder Collaboration Agmt

			
	[presented on Bayer letterhead]	 	Exhibit 10.1

 May 30, 2006 
 CuraGen Corporation 
 322 East Main Street 
 Branford,
CT 06405 
 Attention: Executive Vice President, Business Development 
 Gentlemen: 
 Reference is made to the
Metabolic Disorder Collaboration Agreement dated January 12, 2001 between Bayer Corporation and CuraGen Corporation (as previously amended, the “Agreement”). Terms which are defined in the Agreement are used herein as so defined. This
letter will set forth our agreement with respect to the closing of the Qualified Target Production Phase of the Agreement and addresses issues not previously contemplated in the Agreement with respect to such closing. 
  

	1)	Bayer will not be exercising its option to extend CuraGen’s obligations under Section 2.5(b) of the Agreement to provide Qualified Targets into [***] and CuraGen has no
further obligations under Section 2.5. The Qualified Target Production Phase of the Agreement will be deemed closed as of the final meeting of the Metabolic Program Target Selection Team, which occurred on December 7, 2005.

  

	2)	In order to allow for the continued prosecution of the Qualified Targets, active projects on existing Qualified Targets shall continue to be prosecuted according to the terms of the
Agreement. To this accomplish this, we have agreed to the following: 

  

	 	a)	Biological Materials generated or acquired by Bayer and provided to CuraGen under the Agreement, as well as data derived by CuraGen from its use of those Biological Materials, shall
be made available by CuraGen to Bayer. 

  

	 	b)	Derivatives made by Bayer of constructs supplied by CuraGen to Bayer for target prosecution pursuant to Section 2.2(d) of the Agreement, including [***], shall become Joint
Know-How or Joint Inventions as the case may be, subject to Section 5.1(b) and 5.2(a) of the Agreement. 

  

	3)	CuraGen may, in its sole discretion, provide Bayer with access to GeneScape upon request of Bayer. If provided, any such access may be terminated by CuraGen at any time in its sole
discretion upon written notice to Bayer. . 

  

	4)	CuraGen has no further obligation to provide Bayer with access to GeneCalling or PathCalling. CuraGen may, in its sole discretion, provide Bayer with access to GeneCalling or
PathCalling or to other comparable technologies to the extent owned or controlled by CuraGen. If provided, any such access may be terminated by CuraGen at any time in its sole discretion upon written notice to Bayer. 

 Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 24b-2 of the Exchange Act. 

	5)	Neither Bayer nor CuraGen is restricted from the pursuit of any indication of any Qualified Target that has ceased screening or development under the Metabolic Program. If any such
Qualified Target is subsequently developed by a Party as a Non-CFA Product, such Party shall pay the other Party Royalty Payments under Section 4.2 with respect to such Non-CFA Product as follows: 

  

	 	•	 	[***]% of the first $[***] of Annual Sales Volume 

  

	 	•	 	[***]% of the next $[***] of Annual Sales Volume up to $[***] 

  

	 	•	 	[***]% of the next $[***] of Annual Sales Volume up to $[***] 

  

	 	•	 	[***]% of the next $[***] of Annual Sales Volume up to $[***] 

  

	 	•	 	[***]% of the next $[***] of Annual Sales Volume up to $[***] 

  

	 	•	 	[***]% of Annual Sales Volume over $[***] 

  

	6)	In all other aspects the Agreement remains unchanged and in full force and effect and is not modified hereby. 

 If the foregoing accurately sets forth our understanding, please so signify by signing and returning a duplicate of this letter, whereupon this letter shall take effect
as an amendment to the Agreement. 
  

			
	Sincerely,
	
	Bayer Pharmaceuticals Corporation
		
	By:	 	 /s/ Joseph J. Catino

		 	Joseph J. Catino, Ph.D.
		 	Senior Vice President, Research

 cc: Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, PC 
  

			
	Accepted and Agreed:
	
	CuraGen Corporation
		
	By:	 	 /s/ Frank M. Armstrong

	Title:	 	 Frank M. Armstrong, M.D.
 Chief Executive Officer and
President

 Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission
pursuant to the Company’s application requesting confidential treatment under Rule 24b-2 of the Exchange Act.Form of Non-Qualified Stock Option Agreement

 Exhibit 10.5 
 NON-QUALIFIED STOCK OPTION AGREEMENT (STANDARD) 
 CURAGEN CORPORATION 
 AGREEMENT made as of the XXth day of XXXX, 2006, between CuraGen Corporation (the “Company”), a Delaware corporation having a principal place of business in Branford, Connecticut, and EMPLOYEE NAME, (the “Participant”).

 WHEREAS, the Company desires to grant to the Participant an Option to purchase shares of its common stock, $.01 par value per share (the
“Shares”), under and for the purposes set forth in the Company’s 1997 Employee, Director and Consultant Stock Plan, as amended and restated (the “Plan”); 
 WHEREAS, the Company and the Participant understand and agree that any terms used and not defined herein have the same meanings as in the Plan; and

 WHEREAS, the Company and the Participant each intend that the Option granted herein shall be a Non-Qualified Option. 
 NOW, THEREFORE, in consideration of the mutual covenants hereinafter set forth and for other good and valuable consideration, the parties hereto agree as
follows: 
 1. GRANT OF OPTION. 
 The Company hereby grants to the Participant the right and option to purchase all or any part of an aggregate of WORD SHARES (# SHARES) Shares, on the terms and conditions and subject to all the limitations set forth herein and in
the Plan, which is incorporated herein by reference. The Participant acknowledges receipt of a copy of the Plan. 
 2. PURCHASE PRICE.

 The purchase price of the Shares covered by the Option shall be WORD PRICE ($PRICE) per Share, subject to adjustment, as provided in
the Plan, in the event of a stock split, reverse stock split or other events affecting the holders of Shares. Payment shall be made in accordance with Paragraph 8 of the Plan. 
 3. EXERCISABILITY OF OPTION. 
 Subject
to the terms and conditions set forth in this Agreement and the Plan, the Option granted hereby shall become vested and exercisable as follows: 
  

	 	•	 	# SHARES Shares on the first anniversary of the date of the Agreement; 

  

	 	•	 	# Qtrly Shares Shares (of # total “remaining balance”) each quarter end after the first anniversary through the fourth anniversary of the date of the
Agreement; 

 The foregoing rights are cumulative and are subject to the other terms and conditions of this Agreement
and the Plan. 
 The period of time set forth above over which the Option shall become exercisable may be extended during any period of time
in which the Participant’s pay as an employee of the Company or an Affiliate is reduced because such Participant’s scheduled work week at the Company or an Affiliate has been reduced to less than 40 hours per week (“Part Time
Employment”) unless the continuation of vesting on the schedule set forth above during such Part Time Employment shall be approved in writing by the Administrator. At the time of such Part Time Employment, the Option, to the extent not then
exercisable, shall become exercisable over a period of time as determined by the Administrator, based on the number of hours that such Participant continues to be scheduled to work at the Company or an Affiliate. Upon the Participant’s return
to the Company or an Affiliate at a scheduled workweek of 40 hours, the Option shall continue to become exercisable on such schedule as shall be determined by the Administrator at such time. 
 Notwithstanding the foregoing, the exercisability of the Option granted hereby shall toll during any period of time in which the Participant takes a
leave of absence as an employee, director, consultant or Scientific Advisory Board member of the Company or an Affiliate unless such leave of absence is pursuant to a statute in which the Participant’s right to reemployment is guaranteed or
unless the continuation of vesting during such leave of absence shall be approved in writing by the Administrator (a “Voluntary Leave”). At such time, the Option shall cease to vest and shall be exercisable only to the extent that the
Option has become exercisable and is in effect at the date of such Voluntary Leave. Upon the Participant’s return to the Company or an Affiliate, the Option shall continue to become exercisable on such schedule as shall be determined by the
Administrator at the time of the Participant’s return from Voluntary Leave. 
 4. TERM OF OPTION. 
 The Option shall terminate ten (10) years from the date of this Agreement, but shall be subject to earlier termination as provided herein or in the
Plan. 
 If the Participant ceases to be an employee, director or consultant of the Company or of an Affiliate (for any reason other than the
death or Disability of the Participant or termination of the Participant for “cause” (as defined in the Plan)), the Option may be exercised, if it has not previously terminated, within twelve (12) months after the date the Participant
ceases to be an employee, director or consultant of the Company or an Affiliate, or within the originally prescribed term of the Option, whichever is earlier, but may not be exercised thereafter. In such event, the Option shall be exercisable only
to the extent that the Option has become exercisable and is in effect at the date of such cessation of employment, directorship or consultancy. 
 Notwithstanding the foregoing, in the event of the Participant’s Disability or death within twelve (12) months after the termination of employment, directorship or consultancy, the Participant or the Participant’s Survivors
may exercise the Option within one (1) year after the date of the Participant’s termination of employment, directorship or consultancy, but in no event after the date of expiration of the term of the Option. 

 In the event the Participant’s employment, directorship or consultancy is terminated by the Company
or an Affiliate for “cause” (as defined in the Plan), the Participant’s right to exercise any unexercised portion of this Option shall cease as of such termination, and this Option shall thereupon terminate. Notwithstanding anything
herein to the contrary, if subsequent to the Participant’s termination, but prior to the exercise of the Option, the Board of Directors of the Company determines that, either prior or subsequent to the Participant’s termination, the
Participant engaged in conduct which would constitute “cause,” then the Participant shall immediately cease to have any right to exercise the Option and this Option shall thereupon terminate. 
 In the event of the Disability of the Participant, as determined in accordance with the Plan, the Option shall be exercisable within one (1) year
after the Participant’s termination of service or, if earlier, within the term originally prescribed by the Option. In such event, the Option shall be exercisable: 
  

	 	(a)	to the extent exercisable but not exercised as of the date of Disability; and 

  

	 	(b)	in the event rights to exercise the Option accrue periodically, to the extent of a pro rata portion of any additional rights to exercise the Option as would have accrued had the
Participant not become Disabled prior to the end of the accrual period which next ends following the date of Disability. The proration shall be based upon the number of days during the accrual period prior to the date of Disability.

 In the event of the death of the Participant while an employee, director or consultant of the Company or of an Affiliate,
the Option shall be exercisable by the Participant’s Survivors within one (1) year after the date of death of the Participant or, if earlier, within the originally prescribed term of the Option. In such event, the Option shall be
exercisable: 
  

	 	(x)	to the extent exercisable but not exercised as of the date of death; and 

  

	 	(y)	in the event rights to exercise the Option accrue periodically, to the extent of a pro rata portion of any additional rights to exercise the Option as would have accrued had the
Participant not died prior to the end of the accrual period which next ends following the date of death. The proration shall be based upon the number of days during the accrual period prior to the Participant’s death. 

5. METHOD OF EXERCISING OPTION. 
 Subject to the terms and conditions of this Agreement, the Option may be exercised by written notice to the Company or its designee. Such notice shall state the number of Shares with respect to which the Option is being exercised and shall
be signed by the person exercising the Option. Payment of the purchase price for such Shares shall be made in accordance with Paragraph 8 of the Plan. The Company shall deliver such Shares as soon as practicable after the notice shall be received,
provided, however, that the Company may delay issuance of such Shares until completion of any action or obtaining of any consent, which the Company deems necessary under any applicable law (including, without limitation, state securities or
“blue sky” laws). The Shares as to which the Option shall have been so exercised shall be registered in the name of the person or persons so exercising the Option (or, if the Option shall be exercised by the Participant 

 
and if the Participant shall so request in the notice exercising the Option, shall be registered in the Company’s share register in the name of the
Participant and another person jointly, with right of survivorship) and shall be delivered as provided above to or upon the written order of the person or persons exercising the Option. In the event the Option shall be exercised, pursuant to
Section 4 hereof, by any person or persons other than the Participant, such notice shall be accompanied by appropriate proof of the right of such person or persons to exercise the Option. All Shares that shall be purchased upon the exercise of
the Option as provided herein shall be fully paid and nonassessable. 
 6. PARTIAL EXERCISE. 
 Exercise of this Option to the extent above stated may be made in part at any time and from time to time within the above limits, except that no
fractional share shall be issued pursuant to this Option. 
 7. NON-ASSIGNABILITY. 
 The Option shall not be transferable by the Participant otherwise than by will or by the laws of descent and distribution or pursuant to a qualified
domestic relations order as defined by the Code or Title I of the Employee Retirement Income Security Act or the rules thereunder (a “QUADRO”). Except as provided in the previous sentence, the Option shall be exercisable, during the
Participant’s lifetime, only by the Participant (or, in the event of legal incapacity or incompetency, by the Participant’s guardian or representative) and shall not be assigned, pledged or hypothecated in any way (whether by operation of
law or otherwise) and shall not be subject to execution, attachment or similar process. Any attempted transfer, assignment, pledge, hypothecation or other disposition of the Option or of any rights granted hereunder contrary to the provisions of
this Section 7, or the levy of any attachment or similar process upon the Option shall be null and void. 
 8. NO RIGHTS AS
STOCKHOLDER UNTIL EXERCISE. 
 The Participant shall have no rights as a stockholder with respect to Shares subject to this Agreement
until registration of the Shares in the Company’s share register in the name of the Participant. Except as is expressly provided in the Plan with respect to certain changes in the capitalization of the Company, no adjustment shall be made for
dividends or similar rights for which the record date is prior to the date of such registration. 
 9. CAPITAL CHANGES AND BUSINESS
SUCCESSIONS. 
 The Plan contains provisions covering the treatment of Options in a number of contingencies such as stock splits and
mergers. Provisions in the Plan for adjustment with respect to stock subject to Options and the related provisions with respect to successors to the business of the Company are hereby made applicable hereunder and are incorporated herein by
reference. 

 10. TAXES. 
 The Participant acknowledges that upon exercise of the Option the Participant will be deemed to have taxable income measured by the difference between the then fair market value of the Shares received upon exercise
and the price paid for such Shares pursuant to this Agreement. The Participant acknowledges that any income or other taxes due from him or her with respect to this Option or the Shares issuable pursuant to this Option shall be the Participant’s
responsibility. 
 The Participant agrees that the Company may withhold from the Participant’s remuneration, if any, the minimum
statutory amount of federal, state and local withholding taxes attributable to such amount that is considered compensation includable in such person’s gross income. At the Company’s discretion, the amount required to be withheld may be
withheld in cash from such remuneration, or in kind from the Shares otherwise deliverable to the Participant on exercise of the Option. The Participant further agrees that, if the Company does not withhold an amount from the Participant’s
remuneration sufficient to satisfy the Company’s income tax withholding obligation, the Participant will reimburse the Company on demand, in cash, for the amount under-withheld. 
 11. PURCHASE FOR INVESTMENT. 
 Unless
the offering and sale of the Shares to be issued upon the particular exercise of the Option shall have been effectively registered under the Securities Act of 1933, as now in force or hereafter amended (the “1933 Act”), the Company shall
be under no obligation to issue the Shares covered by such exercise unless and until the following conditions have been fulfilled: 
  

	 	(a)	The person(s) who exercise the Option shall warrant to the Company, at the time of such exercise, that such person(s) are acquiring such Shares for their own respective accounts,
for investment, and not with a view to, or for sale in connection with, the distribution of any such Shares, in which event the person(s) acquiring such Shares shall be bound by the provisions of the following legend which shall be endorsed upon the
certificate(s) evidencing the Shares issued pursuant to such exercise: 

 “The shares represented by this certificate have
been taken for investment and they may not be sold or otherwise transferred by any person, including a pledgee, unless (1) either (a) a Registration Statement with respect to such shares shall be effective under the Securities Act of 1933,
as amended, or (b) the Company shall have received an opinion of counsel satisfactory to it that an exemption from registration under such Act is then available, and (2) there shall have been compliance with all applicable state securities
laws;” and 
  

	 	(b)	If the Company so requires, the Company shall have received an opinion of its counsel that the Shares may be issued upon such particular exercise in compliance with the 1933 Act
without registration thereunder. Without limiting the generality of the foregoing, the Company may delay issuance of the Shares until completion of any action or obtaining of any consent, which the Company deems necessary under any applicable law
(including without limitation state securities or “blue sky” laws). 

 12. NO OBLIGATION TO MAINTAIN RELATIONSHIP. 
 The Company is not by the Plan or this Option obligated to continue the Participant as an employee, director or consultant of the Company. 
 13. NOTICES. 
 Any notices required or
permitted by the terms of this Agreement or the Plan shall be given by recognized courier service, facsimile, registered or certified mail, return receipt requested, addressed as follows: 
 If to the Company: 
  

	
	CuraGen Corporation
	322 East Main Street
	Branford, CT 06405
	Attention: Corporate Secretary

 If to the Participant: 
  

	
	EMPLOYEE NAME

 or to such other address or addresses of which notice in the same manner has previously been given. Any such
notice shall be deemed to have been given upon the earlier of receipt, one business day following delivery to a recognized courier service or three business days following mailing by registered or certified mail. 
 14. GOVERNING LAW. 
 This Agreement
shall be construed and enforced in accordance with the law of the State of Delaware, without giving effect to the conflict of law principles thereof. 
 15. BENEFIT OF AGREEMENT. 
 Subject to the provisions of the Plan and the other provisions hereof,
this Agreement shall be for the benefit of and shall be binding upon the heirs, executors, administrators, successors and assigns of the parties hereto. 
 16. ENTIRE AGREEMENT. 
 This Agreement, together with the Plan, embodies the entire agreement and
understanding between the parties hereto with respect to the subject matter hereof and supersedes all prior oral or written agreements and understandings relating to the subject matter hereof. No statement, representation, warranty, covenant or
agreement not expressly set forth in this 

 
Agreement shall affect or be used to interpret, change or restrict, the express terms and provisions of this Agreement, provided, however, in any event, this
Agreement shall be subject to and governed by the Plan. 
 17. MODIFICATIONS AND AMENDMENTS. 
 The terms and provisions of this Agreement may be modified or amended as provided in the Plan. 
 18. WAIVERS AND CONSENTS. 
 Except as
provided in the Plan, the terms and provisions of this Agreement may be waived, or consent for the departure therefrom granted, only by written document executed by the party entitled to the benefits of such terms or provisions. No such waiver or
consent shall be deemed to be or shall constitute a waiver or consent with respect to any other terms or provisions of this Agreement, whether or not similar. Each such waiver or consent shall be effective only in the specific instance and for the
purpose for which it was given, and shall not constitute a continuing waiver or consent. 
 IN WITNESS WHEREOF, the Company has caused this
Agreement to be executed by its duly authorized officer, and the Participant has hereunto set his or her hand, all as of the day and year first above written. 
  

			
	CuraGen Corporation:
		
	By	 	  

	Name:	 	David M. Wurzer
	Title:	 	 Chief Financial Officer,
 Executive Vice President and
Treasurer

	
	Participant:
	
	  

	EMPLOYEE NAME

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