Document:

Amendment to Employment Agreement

 Exhibit 10.26 
  
 AMENDMENT 
 TO 
 EMPLOYMENT AGREEMENT 
  
  
 This Amendment to the Employment Agreement (the “Amendment”) is
made as of the 20th day of May, 2003 between Premcor Inc. (the “Company”) and Thomas D. O’Malley (the “Executive”). 
  
  
 RECITALS 
  
 A.    The parties hereto are parties to an Employment Agreement dated January 30, 2002, as amended (the
“Employment Agreement”). 
  
 B.    The parties hereto desire to amend and modify certain provisions of the Employment Agreement as provided herein. 
  
  
 AGREEMENT 
  
 In consideration of the foregoing, the mutual covenants herein contained and other good and valuable consideration (the
receipt, adequacy and sufficiency of which are hereby acknowledged by the parties by their execution hereof), the parties agree as follows. 
  
 1.    Definitions.    For purposes of this Amendment, capitalized terms used herein have the same meanings
ascribed to them in the Employment Agreement. 
  
 2.    Amendments to the Employment Agreement. 
  
 2.1.    Section 8 of the Employment Agreement is amended by adding a new provision “g. Change of  
 Control” as follows: 
  
 “ g.    Change of Control. 
  
 (i)    Definitions. For purposes of this Agreement, the following definitions shall apply: 
  
 “Change of Control” shall mean (A) the consummation of (x) any consolidation, reorganization, merger or similar transaction involving Company, other than a
consolidation, reorganization, merger or similar transaction in which the shareholders immediately prior to such transaction own more than 50% of the combined voting power of the voting securities of the surviving corporation, (y) any sale, lease,
exchange or other transfer (in one transaction or a series of related transactions) of all or substantially all of the assets of the Company, or (z) the liquidation or dissolution of the Company; (B) when any person (as defined in Sections 13(d) and
14(d)(2) of the Exchange Act), other than an employee benefit plan or trust maintained by the Company or any of its subsidiaries, becomes the “beneficial owner” (as defined in Rule 13d-3 under the Exchange Act), directly or indirectly, of
more than 25% of the voting power of the Company outstanding at the time (in one or more related or unrelated transactions), but only if at such time such interest is greater than The Blackstone Group’s beneficial ownership (as defined in Rule
13d-3 under the Exchange Act) of the voting power of the Company; or (C) when, during any period of 24 months or less, the individuals who constituted the Board of Directors of the 

 Company at the beginning of such period shall cease for any reason to constitute at least a majority thereof, unless the
election or the nomination for election by the Company’s shareholders, as the case may be, of each new director during such period was approved by a vote of at least two-thirds of the directors then still in office who were directors at the
beginning of such period; and 
  
 “Target Level Annual Bonus” shall mean
that level established by the Board in its meeting of April 2, 2002, as it may be modified from time to time. 
  
 (ii)    upon a Change of Control Executive shall simultaneously receive a payment as follows: 
  
 (A)    In the event a Change of Control occurs in the
First Quarter of any year, the Executive shall receive one-half of the prior year’s Annual Bonus, but no less than one-half of the Executive’s Target Level Annual Bonus; 
  
 (B)    In the event a Change of Control occurs in the Second Quarter of any year, the Executive shall
receive a payment calculated upon the higher of three-quarters of the Annual Bonus based upon the First Quarter earnings per share annualized or three-quarters of the prior year’s Annual Bonus, but no less than three-quarters of the
Executive’s Target Level Annual Bonus; 
  
 (C)    In the event a Change of Control occurs in the Third Quarter of any year the Executive shall receive a payment calculated on one hundred percent of the Annual Bonus based upon earnings per share for the First and
Second Quarters annualized, but no less than the Executive’s Target Level Annual Bonus; 
  
 (D)    In the event a Change of Control occurs in the Fourth Quarter of any year the Executive shall receive a payment calculated on one hundred and twenty five percent of Annual Bonus based upon
the earnings per share for the First, Second and Third Quarters annualized, but no less than one hundred and twenty five percent of the Executive’s Target Level Annual Bonus; 
  
 (E)    A payment under this provision shall not change any payments otherwise due to Executive under any
other provisions of the Employment Agreement.” 
  
 2.2    Section 9.a. of the Employment Agreement is amended by adding a new subsection 4 as follows: 
  
 “(4)    In the event of a Change of Control, the restrictions on Executive contained in Section 9.a (1)(i) and 9.a (2) shall not
be applicable and shall be null and void.” 
  
 3.    No Other Modifications.    Nothing herein contained in any way impairs the Employment Agreement, or alters, waives, annuls, varies or affects any provision, condition or covenant therein,
except as specifically set forth in this Amendment. All other provisions of the Employment Agreement remain in full force and effect. 
  
 4.    Counterparts.    This Amendment may be signed in counterparts, each of which shall be an original,
with the same effect as if the signatures thereto and hereto were upon the same instrument. 
  

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 5.    Successors; Binding Agreement.    All provisions of
this Amendment shall inure to the benefit of and be binding upon personal or legal representatives, executors, administrators, successors, heirs, distributes, devises and legatees of the Executive. 
  
 IN WITNESS WHEREOF, the parties hereto have duly executed this Amendment as
of the date and year first above written. 
  

	 PREMCOR INC.
	  	EXECUTIVE
	 	  	 
	 	  	 
	 	  	 
	 By:

	  	

	 Print Name:  Richard Lappin
	  	Thomas D. O’Malley
	 Title:  Chairman of Compensation Committee
	  	 
	             Premcor Inc.
	  	 

  
  

 3Amended and Restated 1997 Stock Incentive Plan

 EXHIBIT 10.1 
  
 AMENDED AND RESTATED 
  
 1997 STOCK INCENTIVE PLAN OF 
  
 NANOGEN, INC. 
  

 TABLE OF CONTENTS 
  

	 	  	 	  	Page

	 ARTICLE 1.
	  	
INTRODUCTION	  	1
			
	 ARTICLE 2.
	  	
ADMINISTRATION.	  	1
	 2.1
	  	
Committee Composition	  	1
	 2.2
	  	
Committee Responsibilities	  	2
			
	 ARTICLE 3.
	  	
SHARES AVAILABLE FOR GRANTS	  	2
	 3.1
	  	
Basic Limitation	  	2
	 3.2
	  	
Additional Shares	  	2
	 3.3
	  	
Dividend Equivalents	  	2
			
	 ARTICLE 4.
	  	
ELIGIBILITY	  	2
	 4.1
	  	
General Rules	  	2
	 4.2
	  	
Outside Directors	  	2
	 4.3
	  	
Incentive Stock Options	  	2
			
	 ARTICLE 5.
	  	
OPTIONS	  	3
	 5.1
	  	
Stock Option Agreement	  	3
	 5.2
	  	
Number of Shares	  	3
	 5.3
	  	
Exercise Price	  	3
	 5.4
	  	
Exercisability and Term	  	3
	 5.5
	  	
Effect of Change in Control	  	3
	 5.6
	  	
Modification or Assumption of Options	  	3
	 5.7
	  	
Other Requirements Prior to Company’s Initial Public Offering	  	4
			
	 ARTICLE 6.
	  	
PAYMENT FOR OPTION SHARES	  	4
	 6.1
	  	
General Rule	  	4
	 6.2
	  	
Surrender of Stock	  	4
	 6.3
	  	
Exercise/Sale	  	4
	 6.4
	  	
Exercise/Pledge	  	4
	 6.5
	  	
Promissory Note	  	4
	 6.6
	  	
Other Forms of Payment	  	4
			
	 ARTICLE 7.
	  	
STOCK APPRECIATION RIGHTS	  	4
	 7.1
	  	
SAR Agreement	  	4
	 7.2
	  	
Number of Shares	  	5
	 7.3
	  	
Exercise Price	  	5
	 7.4
	  	
Exercisability and Term	  	5
	 7.5
	  	
Effect of Change in Control	  	5
	 7.6
	  	
Exercise of SARs	  	5
	 7.7
	  	
Modification or Assumption of SARs	  	5
			
	 ARTICLE 8.
	  	
RESTRICTED SHARES AND STOCK UNITS	  	5
	 8.1
	  	
Time, Amount and Form of Awards	  	5
	 8.2
	  	
Payment for Awards	  	5
	 8.3
	  	
Vesting Conditions	  	6
	 8.4
	  	
Form and Time of Settlement of Stock Units	  	6
	 8.5
	  	
Death of Recipient	  	6
	 8.6
	  	
Creditors’ Rights	  	6

  

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	 	  	 	  	Page

	 ARTICLE   9.
	  	
VOTING AND DIVIDEND RIGHTS	  	6
	 9.1
	  	
Restricted Shares	  	6
	 9.2
	  	
Stock Units	  	6
			
	 ARTICLE 10.
	  	
PROTECTION AGAINST DILUTION	  	7
	 10.1
	  	
Adjustments	  	7
	 10.2
	  	
Reorganizations	  	7
			
	 ARTICLE 11.
	  	
AWARDS UNDER OTHER PLANS	  	7
			
	 ARTICLE 12.
	  	
PAYMENT OF DIRECTOR’S FEES IN SECURITIES	  	7
	 12.1
	  	
Effective Date	  	7
	 12.2
	  	
Elections to Receive NSOs, Restricted Shares or Stock Units	  	7
	 12.3
	  	
Number and Terms of NSOs, Restricted Shares or Stock Units	  	7
			
	 ARTICLE 13.
	  	
LIMITATION ON RIGHTS	  	8
	 13.1
	  	
Retention Rights	  	8
	 13.2
	  	
Stockholders’ Rights	  	8
	 13.3
	  	
Regulatory Requirements	  	8
			
	 ARTICLE 14.
	  	
LIMITATION ON PAYMENTS	  	8
	 14.1
	  	
Gross-Up Payment	  	8
	 14.2
	  	
Determination by Accountant	  	8
	 14.3
	  	
Underpayments and Overpayments	  	9
	 14.4
	  	
Related Corporations	  	9
			
	 ARTICLE 15.
	  	
WITHHOLDING TAXES	  	9
	 15.1
	  	
General	  	9
	 15.2
	  	
Share Withholding	  	9
			
	 ARTICLE 16.
	  	
ASSIGNMENT OR TRANSFER OF AWARDS	  	9
	 16.1
	  	
General	  	9
	 16.2
	  	
Trusts	  	9
			
	 ARTICLE 17.
	  	
FUTURE OF THE PLAN	  	10
	 17.1
	  	
Term of the Plan	  	10
	 17.2
	  	
Amendment or Termination	  	10
			
	 ARTICLE 18.
	  	
DEFINITIONS	  	10
			
	 ARTICLE 19.
	  	
EXECUTION	  	13

  

 ii 

 AMENDED AND RESTATED 
 1997 STOCK INCENTIVE PLAN OF 
 NANOGEN, INC. 
  
  
 
ARTICLE 1.    INTRODUCTION 
  
 The Plan was adopted by the Board effective as of August 1, 1997, and was approved by the Company’s stockholders as of August 1, 1997. The Plan is effective as of August 1, 1997. However, Articles 7, 8 and 9
shall not apply prior to the Company’s initial public offering on April 14, 1998. The Plan was subsequently (a) amended and restated on June 30, 1999 to increase the number of shares available for issuance under the Plan in Section 3.1; (b)
amended on April 14, 2000 for options issued on and after that date, to increase the period during which such options may be exercised after the death or disability of a Plan Participant to twelve months in Section 5.4; (c) amended and restated on
June 6, 2000 to increase the number of shares available for issuance under the Plan in Section 3.1 to 4,508,760; (d) amended and restated on June 13, 2001 to increase the number of shares available for issuance under the Plan in Section 3.1 to
6,008,760; (e) amended and restated on April 26 to remove the ability of the Company in Section 5.6 to approve repricings of options issued pursuant to the Plan without stockholder approval; (f) amended and restated on June 14, 2002 to increase the
number of shares available for issuance under the Plan to 6,758,760; and (g) amended and restated on June 12, 2003 to increase the number of shares available for issuance under the Plan to its current number. 
  
 The purpose of the Plan is to promote the long-term success of the Company
and the creation of stockholder value by (a) encouraging Key Employees to focus on critical long-range objectives, (b) encouraging the attraction and retention of Key Employees with exceptional qualifications and (c) linking Key Employees directly
to stockholder interests through increased stock ownership. The Plan seeks to achieve this purpose by providing for Awards in the form of Restricted Shares, Stock Units, Options (which may constitute incentive stock options or nonstatutory stock
options) or stock appreciation rights. 
  
 The Plan shall be
governed by, and construed in accordance with, the laws of the State of California. 
  
  

ARTICLE 2.    ADMINISTRATION 
  
 
2.1 Committee Composition. The Plan shall be administered by the Committee. Except as provided below, the Committee shall consist exclusively of directors of the Company, who shall be appointed by the Board. In addition,
the composition of the Committee shall satisfy: 
  
 (a) Such requirements, if any, as the Securities and Exchange Commission may establish for administrators acting under plans intended to qualify for exemption under Rule 16b-3 (or its successor) under the Exchange Act; and 
  
 (b) Such requirements as the Internal Revenue Service may
establish for outside directors acting under plans intended to qualify for exemption under section 162(m)(4)(C) of the Code. 
  
 The Board may act on its own behalf with respect to Outside Directors and may also appoint one or more separate committees composed of one or more officers of the Company
who need not be directors of the Company and who need not satisfy the foregoing requirements, who may administer the Plan 
  

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 with respect to Key Employees who are not “covered employees” under section 162(m)(3) of the Code and who are
not required to report pursuant to § 16(a) of the Exchange Act. 
  
 
2.2 Committee Responsibilities. The Committee shall (a) select the Key Employees who are to receive Awards under the Plan, (b) determine the type, number, vesting requirements and other features and conditions of such
Awards, (c) interpret the Plan and (d) make all other decisions relating to the operation of the Plan. The Committee may adopt such rules or guidelines as it deems appropriate to implement the Plan. The Committee’s determinations under the
Plan shall be final and binding on all persons. 
  
  
 
ARTICLE 3.    SHARES AVAILABLE FOR GRANTS 
  
 
3.1 Basic Limitation. Common Shares issued pursuant to the Plan may be authorized but unissued shares or treasury shares. The aggregate number of Common Shares available for Restricted Shares, Stock Units, Options and
SARs awarded under the Plan shall not exceed 7,758,760. Of the Common Shares available hereunder, no more than 25% in aggregate shall be available with respect to Outside Directors. The limitation of this Section 3.1 shall be subject to adjustment
pursuant to Article 10. The number of Common Shares available under this Plan shall be increased by unexercised or forfeited Common Shares under the Company’s 1993 and 1995 Stock Plans. 
  
 
3.2 Additional Shares. If Stock Units, Options or SARs are forfeited or if Options or SARs terminate for any other reason before being exercised, then the corresponding Common Shares shall again become available for
Awards under the Plan. If Restricted Shares are forfeited before any dividends have been paid with respect to such Shares, then such Shares shall again become available for Awards under the Plan. If Stock Units are settled, then only the number of
Common Shares (if any) actually issued in settlement of such Stock Units shall reduce the number available under Section 3.1 and the balance shall again become available for Awards under the Plan. If SARs are exercised, then only the number of
Common Shares (if any) actually issued in settlement of such SARs shall reduce the number available under Section 3.1 and the balance shall again become available for Awards under the Plan. 
  
 
3.3 Dividend Equivalents. Any dividend equivalents distributed under the Plan shall not be applied against the number of Restricted Shares, Stock Units, Options or SARs available for Awards, whether or not such dividend
equivalents are converted into Stock Units. 
  
  
 
ARTICLE 4.    ELIGIBILITY 
  
 
4.1 General Rules. Only Key Employees (including, without limitation, independent contractors who are not members of the Board) shall be eligible for designation as Participants by the Committee. 
  
 
4.2 Outside Directors. The Committee may provide that the NSOs that otherwise would be granted to an Outside Director under this Plan shall instead be granted to an affiliate of such Outside Director. Such affiliate
shall then be deemed to be an Outside Director for purposes of the Plan, provided that the service-related vesting and termination provisions pertaining to the NSOs shall be applied with regard to the service of the Outside Director. 
  
 
4.3 Incentive Stock Options. Only Key Employees who are common-law employees of the Company, a Parent or a Subsidiary shall be eligible for the grant of ISOs. In addition, a Key Employee who owns more than 10% of the
total combined voting power of all classes of outstanding stock of the Company or any of its Parents or Subsidiaries shall not be eligible for the grant of an ISO unless the requirements set forth in section 422(c)(6) of the Code are satisfied.

  

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ARTICLE 5.    OPTIONS 
  
 
5.1 Stock Option Agreement. Each grant of an Option under the Plan shall be evidenced by a Stock Option Agreement between the Optionee and the Company. Such Option shall be subject to all applicable terms of the Plan and
may be subject to any other terms that are not inconsistent with the Plan. The Stock Option Agreement shall specify whether the Option is an ISO or an NSO. The provisions of the various Stock Option Agreements entered into under the Plan need not be
identical. Options shall be granted in consideration of services rendered to the Company or a Subsidiary. A Stock Option Agreement may provide that a new Option will be granted automatically to the Optionee when he or she exercises a prior Option
and pays the Exercise Price in the form described in Section 6.2. 
  
 
5.2 Number of Shares. Each Stock Option Agreement shall specify the number of Common Shares subject to the Option and shall provide for the adjustment of such number in accordance with Article 10. Options granted to any
Optionee in a single calendar year shall in no event cover more than 750,000 Common Shares, subject to adjustment in accordance with Article 10. 
  
 
5.3 Exercise Price. Each Stock Option Agreement shall specify the Exercise Price; provided that the Exercise Price under an ISO shall in no event be less than 100% of the Fair Market Value of a Common Share on the date
of grant and the Exercise Price under an NSO shall in no event be less than the par value of the Common Shares subject to such NSO. In the case of an NSO, a Stock Option Agreement may specify an Exercise Price that varies in accordance with a
predetermined formula while the NSO is outstanding, provided that prior to the Company’s initial public offering, the NSO Exercise Price shall be at least 85% (110% for 10% shareholders) of the Fair Market Value of a Common Share of Stock on
the date of grant. 
  
 
5.4 Exercisability and Term. Each Stock Option Agreement shall specify the date when all or any installment of the Option is to become exercisable, provided that prior to the Company’s initial public offering,
Options shall become exercisable pursuant to a schedule providing for at least 20% vesting per year over a five-year period (or, in the case of performance options, to the extent permitted under applicable regulations of the California Department of
Corporations). The Stock Option Agreement shall also specify the term of the Option; provided that the term of an ISO shall in no event exceed 10 years from the date of grant. A Stock Option Agreement may provide for accelerated exercisability in
the event of the Optionee’s death, disability or retirement or other events and may provide for expiration prior to the end of its term in the event of the termination of the Optionee’s service. 
  
 Options may be awarded in combination with SARs, and such an Award may
provide that the Options will not be exercisable unless the related SARs are forfeited. NSOs may also be awarded in combination with Restricted Shares or Stock Units, and such an Award may provide that the NSOs will not be exercisable unless the
related Restricted Shares or Stock Units are forfeited. 
  
 Options must be exercised within 90 days of the termination of employment (twelve months for termination on account of death or disability). 
  
 
5.5 Effect of Change in Control. The Committee may determine, at the time of granting an Option or thereafter, that such Option shall become fully exercisable as to all Common Shares subject to such Option in the event
that a Change in Control occurs with respect to the Company. 
  
 
5.6 Modification or Assumption of Options. Within the limitations of the Plan, the Committee may modify, extend or assume outstanding options or may accept the cancellation of outstanding options (whether granted by the
Company or by another issuer) in return for the grant of new options for the same or a different number of shares and at the same or a different exercise price. The Committee 
  

 3 

 may not, however, reprice any options without the consent of the stockholders of the Company. The foregoing
notwithstanding, no modification of an Option shall, without the consent of the Optionee, alter or impair his or her rights or obligations under such Option. 
  
 
5.7 Other Requirements Prior to Company’s Initial Public Offering. Prior to the Company’s initial public offering, Optionees shall receive Company financial statements at least annually. 
  
  
 
ARTICLE 6.    PAYMENT FOR OPTION SHARES 
  
 
6.1 General Rule. The entire Exercise Price of Common Shares issued upon exercise of Options shall be payable in cash at the time when such Common Shares are purchased, except as follows: 
  
 (a) In the case of an ISO granted under the Plan, payment
shall be made only pursuant to the express provisions of the applicable Stock Option Agreement. The Stock Option Agreement may specify that payment may be made in any form(s) described in this Article 6. 
  
 (b) In the case of an NSO, the Committee may at any time
accept payment in any form(s) described in this Article 6. 
  
 
6.2 Surrender of Stock. To the extent that this Section 6.2 is applicable, payment for all or any part of the Exercise Price may be made with Common Shares which have already been owned by the Optionee for more than six
months. Such Common Shares shall be valued at their Fair Market Value on the date when the new Common Shares are purchased under the Plan. 
  
 
6.3 Exercise/Sale. To the extent that this Section 6.3 is applicable, payment may be made by the delivery (on a form prescribed by the Company) of an irrevocable direction to a securities broker approved by the Company
to sell Common Shares and to deliver all or part of the sales proceeds to the Company in payment of all or part of the Exercise Price and any withholding taxes. 
  

6.4 Exercise/Pledge. To the extent that this Section 6.4 is applicable, payment may be made by the delivery (on a form prescribed by the Company) of an irrevocable direction to pledge Common Shares to a securities broker
or lender approved by the Company, as security for a loan, and to deliver all or part of the loan proceeds to the Company in payment of all or part of the Exercise Price and any withholding taxes. 
  
 
6.5 Promissory Note. To the extent that this Section 6.5 is applicable, payment may be made with a full-recourse promissory note; provided that the par value of the Common Shares shall be paid in cash. 
  
 
6.6 Other Forms of Payment. To the extent that this Section 6.6 is applicable, payment may be made in any other form that is consistent with applicable laws, regulations and rules. 
  
  
 
ARTICLE 7.    STOCK APPRECIATION RIGHTS 
  
 
7.1 SAR Agreement. Each grant of an SAR under the Plan shall be evidenced by an SAR Agreement between the Optionee and the Company. Such SAR shall be subject to all applicable terms of the Plan and may be subject to any
other terms that are not inconsistent with the Plan. The provisions of the various SAR Agreements entered into under the Plan need not be identical. SARs may be granted in consideration of a reduction in the Optionee’s other compensation.

  

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7.2 Number of Shares. Each SAR Agreement shall specify the number of Common Shares to which the SAR pertains and shall provide for the adjustment of such number in accordance with Article 10. SARs granted to any Optionee
in a single calendar year shall in no event pertain to more than 300,000 Common Shares, subject to adjustment in accordance with Article 10. 
  
 
7.3 Exercise Price. Each SAR Agreement shall specify the Exercise Price. An SAR Agreement may specify an Exercise Price that varies in accordance with a predetermined formula while the SAR is outstanding. 
  
 
7.4 Exercisability and Term. Each SAR Agreement shall specify the date when all or any installment of the SAR is to become exercisable. The SAR Agreement shall also specify the term of the SAR. An SAR Agreement may
provide for accelerated exercisability in the event of the Optionee’s death, disability or retirement or other events and may provide for expiration prior to the end of its term in the event of the termination of the Optionee’s service.
SARs may also be awarded in combination with Options, Restricted Shares or Stock Units, and such an Award may provide that the SARs will not be exercisable unless the related Options, Restricted Shares or Stock Units are forfeited. An SAR may be
included in an ISO only at the time of grant but may be included in an NSO at the time of grant or thereafter. An SAR granted under the Plan may provide that it will be exercisable only in the event of a Change in Control. 
  
 
7.5 Effect of Change in Control. The Committee may determine, at the time of granting an SAR or thereafter, that such SAR shall become fully exercisable as to all Common Shares subject to such SAR in the event that a
Change in Control occurs with respect to the Company. 
  
 
7.6 Exercise of SARs. The exercise of an SAR shall be subject to the restrictions imposed by Rule 16b-3 (or its successor) under the Exchange Act, if applicable. If, on the date when an SAR expires, the Exercise Price
under such SAR is less than the Fair Market Value on such date but any portion of such SAR has not been exercised or surrendered, then such SAR shall automatically be deemed to be exercised as of such date with respect to such portion. Upon exercise
of an SAR, the Optionee (or any person having the right to exercise the SAR after his or her death) shall receive from the Company (a) Common Shares, (b) cash or (c) a combination of Common Shares and cash, as the Committee shall determine. The
amount of cash and/or the Fair Market Value of Common Shares received upon exercise of SARs shall, in the aggregate, be equal to the amount by which the Fair Market Value (on the date of surrender) of the Common Shares subject to the SARs exceeds
the Exercise Price. 
  
 
7.7 Modification or Assumption of SARs. Within the limitations of the Plan, the Committee may modify, extend or assume outstanding SARs or may accept the cancellation of outstanding SARs (whether granted by the Company
or by another issuer) in return for the grant of new SARs for the same or a different number of shares and at the same or a different exercise price. The foregoing notwithstanding, no modification of an SAR shall, without the consent of the
Optionee, alter or impair his or her rights or obligations under such SAR. 
  
  
 
ARTICLE 8.    RESTRICTED SHARES AND STOCK UNITS 
  
 
8.1 Time, Amount and Form of Awards. Awards under the Plan may be granted in the form of Restricted Shares, in the form of Stock Units, or in any combination of both. Restricted Shares or Stock Units may also be awarded
in combination with NSOs or SARs, and such an Award may provide that the Restricted Shares or Stock Units will be forfeited in the event that the related NSOs or SARs are exercised. 
  
 
8.2 Payment for Awards. To the extent that an Award is granted in the form of newly issued Restricted Shares, the Award recipient, as a condition to the grant of such Award, shall be required to 
  

 5 

 pay the Company in cash an amount equal to the par value of such Restricted Shares. To the extent that an Award is
granted in the form of Restricted Shares from the Company’s treasury or in the form of Stock Units, no cash consideration shall be required of the Award recipients. 
  
 
8.3 Vesting Conditions. Each Award of Restricted Shares or Stock Units shall become vested, in full or in installments, upon satisfaction of the conditions specified in the Stock Award Agreement. A Stock Award Agreement
may provide for accelerated vesting in the event of the Participant’s death, disability or retirement or other events. The Committee may determine, at the time of making an Award or thereafter, that such Award shall become fully vested in the
event that a Change in Control occurs with respect to the Company. 
  
 
8.4 Form and Time of Settlement of Stock Units. Settlement of vested Stock Units may be made in the form of (a) cash, (b) Common Shares or (c) any combination of both, as determined by the Committee. The actual number of
Stock Units eligible for settlement may be larger or smaller than the number included in the original Award, based on predetermined performance factors. Methods of converting Stock Units into cash may include (without limitation) a method based on
the average Fair Market Value of Common Shares over a series of trading days. Vested Stock Units may be settled in a lump sum or in installments. The distribution may occur or commence when all vesting conditions applicable to the Stock Units have
been satisfied or have lapsed, or it may be deferred to any later date. The amount of a deferred distribution may be increased by an interest factor or by dividend equivalents. Until an Award of Stock Units is settled, the number of such Stock Units
shall be subject to adjustment pursuant to Article 10. 
  
 
8.5 Death of Recipient. Any Stock Units Award that becomes payable after the recipient’s death shall be distributed to the recipient’s beneficiary or beneficiaries. Each recipient of a Stock Units Award under
the Plan shall designate one or more beneficiaries for this purpose by filing the prescribed form with the Company. A beneficiary designation may be changed by filing the prescribed form with the Company at any time before the Award recipient’s
death. If no beneficiary was designated or if no designated beneficiary survives the Award recipient, then any Stock Units Award that becomes payable after the recipient’s death shall be distributed to the recipient’s estate. 

 
 
8.6 Creditors’ Rights. A holder of Stock Units shall have no rights other than those of a general creditor of the Company. Stock Units represent an unfunded and unsecured obligation of the Company, subject to the
terms and conditions of the applicable Stock Award Agreement. 
  
  
 
ARTICLE 9.    VOTING AND DIVIDEND RIGHTS 
  
 
9.1 Restricted Shares. The holders of Restricted Shares awarded under the Plan shall have the same voting, dividend and other rights as the Company’s other stockholders. A Stock Award Agreement, however, may require
that the holders of Restricted Shares invest any cash dividends received in additional Restricted Shares. Such additional Restricted Shares shall be subject to the same conditions and restrictions as the Award with respect to which the dividends
were paid. Such additional Restricted Shares shall not reduce the number of Common Shares available under Article 3. 
  
 
9.2 Stock Units. The holders of Stock Units shall have no voting rights. Prior to settlement or forfeiture, any Stock Unit awarded under the Plan may, at the Committee’s discretion, carry with it a right to dividend
equivalents. Such right entitles the holder to be credited with an amount equal to all cash dividends paid on one Common Share while the Stock Unit is outstanding. Dividend equivalents may be converted into additional Stock Units. Settlement of
dividend equivalents may be made in the form of cash, in the form of Common Shares, or in a combination of both. Prior to distribution, any dividend equivalents which are not paid shall be subject to the same conditions and restrictions as the Stock
Units to which they attach. 
  

 6 

 
ARTICLE 10.    PROTECTION AGAINST DILUTION 
  
 
10.1 Adjustments. In the event of a subdivision of the outstanding Common Shares, a declaration of a dividend payable in Common Shares, a declaration of a dividend payable in a form other than Common Shares in an amount
that has a material effect on the price of Common Shares, a combination or consolidation of the outstanding Common Shares (by reclassification or otherwise) into a lesser number of Common Shares, a recapitalization, a spinoff or a similar
occurrence, the Committee shall make such adjustments as it, in its sole discretion, deems appropriate in one or more of (a) the number of Options, SARs, Restricted Shares and Stock Units available for future Awards under Article 3, (b) the
limitations set forth in Sections 5.2 and 7.2, (c) the number of NSOs to be granted to Outside Directors under Section 4.2, (d) the number of Stock Units included in any prior Award which has not yet been settled, (e) the number of Common Shares
covered by each outstanding Option and SAR or (f) the Exercise Price under each outstanding Option and SAR. Except as provided in this Article 10, a Participant shall have no rights by reason of any issue by the Company of stock of any class or
securities convertible into stock of any class, any subdivision or consolidation of shares of stock of any class, the payment of any stock dividend or any other increase or decrease in the number of shares of stock of any class. 
  
 
10.2 Reorganizations. In the event that the Company is a party to a merger or other reorganization, outstanding Options, SARs, Restricted Shares and Stock Units shall be subject to the agreement of merger or
reorganization. Such agreement may provide, without limitation, for the assumption of outstanding Awards by the surviving corporation or its parent, for their continuation by the Company (if the Company is a surviving corporation), for accelerated
vesting and accelerated expiration (provided the Company has previously had its initial public offering), or for settlement in cash. 
  
  
 
ARTICLE 11.    AWARDS UNDER OTHER PLANS 
  
 The Company may grant awards under other plans or programs. Such awards may be settled in the form of Common Shares issued under this Plan. Such Common Shares shall be treated for all purposes under the Plan like
Common Shares issued in settlement of Stock Units and shall, when issued, reduce the number of Common Shares available under Article 3. 
  
  
 
ARTICLE 12.    PAYMENT OF DIRECTOR’S FEES IN SECURITIES 
  
 
12.1 Effective Date. No provision of this Article 12 shall be effective unless and until the Board has determined to implement such provision. 
  
 
12.2 Elections to Receive NSOs, Restricted Shares or Stock Units. An Outside Director may elect to receive his or her annual retainer payments and meeting fees from the Company in the form of cash, NSOs, Restricted
Shares, Stock Units, or a combination thereof, as determined by the Board. Such NSOs, Restricted Shares and Stock Units shall be issued under the Plan. An election under this Article 12 shall be filed with the Company on the prescribed form.

  
 
12.3 Number and Terms of NSOs, Restricted Shares or Stock Units. The number of NSOs, Restricted Shares or Stock Units to be granted to Outside Directors in lieu of annual retainers and meeting fees that would otherwise
be paid in cash shall be calculated in a manner determined by the Board. The terms of such NSOs, Restricted Shares or Stock Units shall also be determined by the Board. 
  

 7 

 
ARTICLE 13.    LIMITATION ON RIGHTS 
  
 
13.1 Retention Rights. Neither the Plan nor any Award granted under the Plan shall be deemed to give any individual a right to remain an employee, consultant or director of the Company, a Parent or a Subsidiary. The
Company and its Parents and Subsidiaries reserve the right to terminate the service of any employee, consultant or director at any time, with or without cause, subject to applicable laws, the Company’s certificate of incorporation and by-laws
and a written employment agreement (if any). 
  
 
13.2 Stockholders’ Rights. A Participant shall have no dividend rights, voting rights or other rights as a stockholder with respect to any Common Shares covered by his or her Award prior to the issuance of a stock
certificate for such Common Shares. No adjustment shall be made for cash dividends or other rights for which the record date is prior to the date when such certificate is issued, except as expressly provided in Articles 8, 9 and 10. 
  
 
13.3 Regulatory Requirements. Any other provision of the Plan notwithstanding, the obligation of the Company to issue Common Shares under the Plan shall be subject to all applicable laws, rules and regulations and such
approval by any regulatory body as may be required. The Company reserves the right to restrict, in whole or in part, the delivery of Common Shares pursuant to any Award prior to the satisfaction of all legal requirements relating to the issuance of
such Common Shares, to their registration, qualification or listing or to an exemption from registration, qualification or listing. 
  
  
 
ARTICLE 14.    LIMITATION ON PAYMENTS 
  
 
14.1 Gross-Up Payment. In the event that it is determined that any payment or transfer by the Company under the Plan to or for the benefit of (the “Payment”) would be subject to the excise tax imposed by
section 4999 of the Code or any interest or penalties with respect to such excise tax (such excise tax, together with any such interest or penalties, are collectively referred to as the “Excise Tax”), then the Participant shall be entitled
to receive an additional payment (a “Gross-Up Payment”) in an amount that shall fund the payment by the Participant of any Excise Tax on the Payment as well as all income taxes imposed on the Gross-Up Payment, any Excise Tax imposed on the
Gross-Up Payment and any interest or penalties imposed with respect to taxes on the Gross-Up Payment or any Excise Tax. 
  
 
14.2 Determination by Accountant. All mathematical determinations and all determinations of whether any of the Payments are “parachute payments” (within the meaning of section 280G of the Code) including all
determinations of whether a Gross-Up Payment is required, of the amount of such Gross-Up Payment and of amounts determined under § 14.3 shall be made by the independent auditors most recently selected by the Board (the “Auditors”),
which shall provide its determination (the “Determination”), together with detailed supporting calculations regarding the amount of any Gross-Up Payment and any other relevant matters, both to the Company and to the Participant within
seven business days of the Participant’s termination date, if applicable, or such earlier time as is requested by the Company or by the Participant (if the Participant reasonably believes that any of the Total Payments may be subject to the
Excise Tax). If the Accounting Firm determines that no Excise Tax is payable by the Participant, it shall furnish the Participant with a written statement that the Auditors have concluded that no Excise Tax is payable (including the reasons
therefor) and that the Participant has substantial authority not to report any Excise Tax on the Participant’s federal income tax return. If a Gross-Up Payment is determined to be payable, it shall be paid to the Participant within five
business days after the Determination is delivered to the Company or the Participant. Any determination by the Auditors shall be binding upon the Company and the Participant, absent manifest error. 
  

 8 

 
14.3 Underpayments and Overpayments. As a result of uncertainty in the application of section 4999 of the Code at the time of the initial determination by the Auditors hereunder, it is possible that Gross-Up Payments not
made by the Company should have been made (“Underpayments”) or that Gross-Up Payments will have been made by the Company which should not have been made (“Overpayments”). In either event, the Auditors shall determine the amount
of the Underpayment or Overpayment that has occurred. In the case of an Underpayment, the amount of such Underpayment shall promptly be paid by the Company to or for the benefit of the Employee. In the case of an Overpayment, the Employee shall, at
the direction and expense of the Company, take such steps as are reasonably necessary (including the filing of returns and claims for refund), follow reasonable instructions from, and procedures established by, the Company and otherwise reasonably
cooperate with the Company to correct such Overpayment; provided, however, that (i) the Employee shall in no event be obligated to return to the Company an amount greater than the net after-tax portion of the Overpayment that the Employee has
retained or has recovered as a refund from the applicable taxing authorities and (ii) this provision shall be interpreted in a manner consistent with the intent of this Article 14, which is to make the Employee whole, on an after-tax basis, for the
application of the Excise Tax, it being understood that the correction of an Overpayment may result in the Employee’s repaying to the Company an amount which is less than the Overpayment. 
  
 
14.4 Related Corporations. For purposes of this Article 14, the term “Company” shall include affiliated corporations to the extent determined by the Auditors in accordance with section 280G(d)(5) of the Code.

  
  
 
ARTICLE 15.    WITHHOLDING TAXES 
  
 
15.1 General. To the extent required by applicable federal, state, local or foreign law, a Participant or his or her successor shall make arrangements satisfactory to the Company for the satisfaction of any withholding
tax obligations that arise in connection with the Plan. The Company shall not be required to issue any Common Shares or make any cash payment under the Plan until such obligations are satisfied. 
  
 
15.2 Share Withholding. The Committee may permit a Participant to satisfy all or part of his or her withholding or income tax obligations by having the Company withhold all or a portion of any Common Shares that
otherwise would be issued to him or her or by surrendering all or a portion of any Common Shares that he or she previously acquired. Such Common Shares shall be valued at their Fair Market Value on the date when taxes otherwise would be withheld in
cash. Any payment of taxes by assigning Common Shares to the Company may be subject to restrictions, including any restrictions required by rules of the Securities and Exchange Commission. 
  
  
 
ARTICLE 16.    ASSIGNMENT OR TRANSFER OF AWARDS 
  
 
16.1 General. An Award granted under the Plan shall not be anticipated, assigned, attached, garnished, optioned, transferred or made subject to any creditor’s process, whether voluntarily, involuntarily or by
operation of law, except as approved by the Committee. Notwithstanding the foregoing, ISOs and, prior to the Company’s initial public offering, NSOs may not be transferable. However, this Article 16 shall not preclude a Participant from
designating a beneficiary who will receive any outstanding Awards in the event of the Participant’s death, nor shall it preclude a transfer of Awards by will or by the laws of descent and distribution. 
  
 
16.2 Trusts. Neither this Article 16 nor any other provision of the Plan shall preclude a Participant from transferring or assigning Restricted Shares to (a) the trustee of a trust that is revocable by such Participant
alone, both at the time of the transfer or assignment and at all times thereafter prior to such Participant’s death, or (b) the trustee of any other trust to the extent approved in advance by the 
  

 9 

 Committee in writing. A transfer or assignment of Restricted Shares from such trustee to any person other than such
Participant shall be permitted only to the extent approved in advance by the Committee in writing, and Restricted Shares held by such trustee shall be subject to all of the conditions and restrictions set forth in the Plan and in the applicable
Stock Award Agreement, as if such trustee were a party to such Agreement. 
  
  
 
ARTICLE 17.    FUTURE OF THE PLAN 
  
 
17.1 Term of the Plan. The Plan, as set forth herein, was adopted as of August 1, 1997, and became effective August 1, 1997, except that Articles 7, 8 and 9 shall not be effective prior to the date of the Company’s
initial public offering on April 14, 1998. The Plan shall remain in effect until it is terminated under Section 17.2, except that no ISOs shall be granted after July 31, 2007. 
  
 
17.2 Amendment or Termination. The Board may, at any time and for any reason, amend or terminate the Plan. An amendment of the Plan shall be subject to the approval of the Company’s stockholders only to the extent
required by applicable laws, regulations or rules. No Awards shall be granted under the Plan after the termination thereof. The termination of the Plan, or any amendment thereof, shall not affect any Award previously granted under the Plan.

  
  
 
ARTICLE 18.    DEFINITIONS 
  
 18.1 “Award” means any award of an Option, an SAR, a Restricted Share or a Stock Unit under the Plan. 
  
 18.2 “Board” means the Company’s Board of Directors, as constituted from time to time. 
  
 18.3 “Change in Control” shall mean the occurrence of any of the
following events: 
  
 (a) The consummation of a
merger or consolidation of the Company with or into another entity or any other corporate reorganization, if more than 50% of the combined voting power of the continuing or surviving entity’s securities outstanding immediately after such
merger, consolidation or other reorganization is owned by persons who were not stockholders of the Company immediately prior to such merger, consolidation or other reorganization; 
  
 (b) A change in the composition of the Board, as a result of which fewer than one-half of the incumbent
directors are directors who either: 
  
 (A) Had
been directors of the Company 24 months prior to such change; or 
  
 (B) Were elected, or nominated for election, to the Board with the affirmative votes of at least a majority of the directors who had been directors of the Company 24 months prior to such change and who were still in
office at the time of the election or nomination; or 
  
 (c) Any “person” (as such term is used in sections 13(d) and 14(d) of the Exchange Act) by the acquisition or aggregation of securities is or becomes the beneficial owner, directly or indirectly, of securities of the Company
representing 50% or more of the combined voting power of the Company’s then outstanding securities ordinarily (and apart from rights accruing under special circumstances) having the right to vote at elections of directors (the “Base
Capital Stock”); except that any change in the relative beneficial ownership of the Company’s securities by any person resulting solely from a reduction in the aggregate number of outstanding shares of Base Capital Stock, and any decrease
thereafter in such person’s ownership of securities, 
  

 10 

 shall be disregarded until such person increases in any manner, directly or indirectly, such
person’s beneficial ownership of any securities of the Company. Thus, for example, any person who owns less than 50% of the Company’s outstanding shares, shall cause a Change in Control to occur as of any subsequent date if such person
then acquires an additional interest in the Company which, when added to the person’s previous holdings, causes the person to hold more than 50% of the Company’s outstanding shares. 
  
 The term “Change in Control” shall not include the Company’s initial public
offering or a transaction, the sole purpose of which is to change the state of the Company’s incorporation. 
  
 18.4 “Code” means the Internal Revenue Code of 1986, as amended. 
  
 18.5 “Committee” means a committee of the Board, as described in Article 2. 
  
 18.6 “Common Share” means one share of the common stock of the
Company. 
  
 18.7 “Company” means Nanogen, Inc., a
Delaware corporation. 
  
 18.8 “Exchange Act” means the
Securities Exchange Act of 1934, as amended. 
  
 18.9
“Exercise Price,” in the case of an Option, means the amount for which one Common Share may be purchased upon exercise of such Option, as specified in the applicable Stock Option Agreement. “Exercise Price,” in the case of an
SAR, means an amount, as specified in the applicable SAR Agreement, which is subtracted from the Fair Market Value of one Common Share in determining the amount payable upon exercise of such SAR. 
  
 18.10 “Fair Market Value” means the market price of Common Shares,
determined by the Committee as follows: 
  
 (a)
If the Common Shares were traded over-the-counter on the date in question but was not traded on the Nasdaq Stock Market or the Nasdaq National Market, then the Fair Market Value shall be equal to the mean between the last reported representative bid
and asked prices quoted for such date by the principal automated inter-dealer quotation system on which the Common Shares are quoted or, if the Common Shares are not quoted on any such system, by the “Pink Sheets” published by the National
Quotation Bureau, Inc.; 
  
 (b) If the Common
Shares were traded over-the-counter on the date in question and were traded on the Nasdaq Stock Market or the Nasdaq National Market, then the Fair Market Value shall be equal to the last-transaction price quoted for such date by the Nasdaq Stock
Market or the Nasdaq National Market; 
  
 (c) If
the Common Shares were traded on a stock exchange on the date in question, then the Fair Market Value shall be equal to the closing price reported by the applicable composite transactions report for such date; and 
  
 (d) If none of the foregoing provisions is applicable, then
the Fair Market Value shall be determined by the Committee in good faith on such basis as it deems appropriate. 
  
 Whenever possible, the determination of Fair Market Value by the Committee shall be based on the prices reported in the Western Edition of The Wall Street Journal.
Such determination shall be conclusive and binding on all persons. 
  
 18.11 ”ISO” means an incentive stock option described in section 422(b) of the Code. 
  

 11 

 18.12 “Key Employee” means (a) a common-law employee of the Company, a Parent or a Subsidiary,
(b) an Outside Director and (c) a consultant or adviser who provides services to the Company, a Parent or a Subsidiary as an independent contractor. Service as an Outside Director or as an independent contractor shall be considered employment for
all purposes of the Plan, except as provided in Sections 4.2 and 4.3. 
  
 18.13 “NSO” means a stock option not described in sections 422 or 423 of the Code. 
  
 18.14 “Option” means an ISO or NSO granted under the Plan and entitling the holder to purchase one Common Share. 
  
 18.15 “Optionee” means an individual or estate who holds an Option
or SAR. 
  
 18.16 “Outside Director” shall mean a member
of the Board who is not a common-law employee of the Company, a Parent or a Subsidiary. 
  
 18.17 “Parent” means any corporation (other than the Company) in an unbroken chain of corporations ending with the Company, if each of the corporations other than the Company owns stock possessing 50% or
more of the total combined voting power of all classes of stock in one of the other corporations in such chain. A corporation that attains the status of a Parent on a date after the adoption of the Plan shall be considered a Parent commencing as of
such date. 
  
 18.18 “Participant” means an individual
or estate who holds an Award. 
  
 18.19 “Plan” means
this 1997 Stock Incentive Plan of Nanogen, Inc., as amended from time to time. 
  
 18.20 “Restricted Share” means a Common Share awarded under the Plan. 
  
 18.21 “SAR” means a stock appreciation right granted under the Plan. 
  
 18.22 “SAR Agreement” means the agreement between the Company and an Optionee which contains the terms, conditions
and restrictions pertaining to his or her SAR. 
  
 18.23
“Stock Award Agreement” means the agreement between the Company and the recipient of a Restricted Share or Stock Unit which contains the terms, conditions and restrictions pertaining to such Restricted Share or Stock Unit. 
  
 18.24 “Stock Option Agreement” means the agreement between the
Company and an Optionee which contains the terms, conditions and restrictions pertaining to his or her Option. 
  
 18.25 “Stock Unit” means a bookkeeping entry representing the equivalent of one Common Share, as awarded under the Plan. 
  
 18.26 “Subsidiary” means any corporation (other than the Company)
in an unbroken chain of corporations beginning with the Company, if each of the corporations other than the last corporation in the unbroken chain owns stock possessing 50% or more of the total combined voting power of all classes of stock in one of
the other corporations in such chain. A corporation that attains the status of a Subsidiary on a date after the adoption of the Plan shall be considered a Subsidiary commencing as of such date. 
  

 12 

 
ARTICLE 19.    EXECUTION 
  
 To record the adoption of the Plan by the Board, the Company has caused its duly authorized officer to affix the corporate name and seal hereto. 
  
  

	 NANOGEN, INC.
  
  

	 By:
	 	 /S/    WILLIAM FRANZBLAU

	 	 	 William Franzblau, Esq.
 Vice President,
Legal Affairs and Secretary

  

 13

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