EX-10.16



 Exhibit 10.16 

Achillion Pharmaceuticals, Inc. 

Incentive Stock Option Agreement 

Granted Under 2015 Stock Incentive Plan 
  

	1.	Grant of Option. 

 This Incentive Stock Option Agreement (this “Agreement”)
evidences the grant by Achillion Pharmaceuticals, Inc. a Delaware corporation (the “Company”), on [                     ],
20[    ] (the “Grant Date”) to [                    ], an employee of the Company (the
“Participant”), of an option to purchase, in whole or in part, on the terms provided herein and in the Company’s 2015 Stock Incentive Plan (as amended and/or restated from time to time, the “Plan”), a total of
[             ] shares (the “Shares”) of common stock, $0.001 par value per share, of the Company (“Common Stock”) at
$[        ] per Share. Unless earlier terminated, this option shall expire at 5:00 p.m., Eastern time, on
[                ] (the “Final Exercise Date”). 

It is intended that the option evidenced by this Agreement shall be an incentive stock option as defined in Section 422 of the Internal
Revenue Code of 1986, as amended, and any regulations promulgated thereunder (the “Code”). Except as otherwise indicated by the context, the term “Participant”, as used in this option, shall be deemed to include any person who
acquires the right to exercise this option validly under its terms. 
  

	2.	Vesting Schedule. 

 (a) This option will become exercisable (“vest”) as to
[    ]% of the original number of Shares on the first anniversary of the Grant Date and as to an additional [    ]% of the original number of Shares at the end of each successive [three-month] period following
the [first] anniversary of the Grant Date until the [fourth] anniversary of the Grant Date. 
 (b) The right of exercise shall be cumulative
so that to the extent the option is not exercised in any period to the maximum extent permissible it shall continue to be exercisable, in whole or in part, with respect to all Shares for which it is vested until the earlier of the Final Exercise
Date or the termination of this option under Section 3 hereof or the Plan. 
  

	3.	Exercise of Option. 

 (a) Form of Exercise. Each election to exercise this
option shall be in writing in the form of Notice of Stock Option Exercise attached hereto as Exhibit A, signed by the Participant, and received by the Company at its principal office, accompanied by this Agreement, and payment in full in the
manner provided in the Plan. The Participant may purchase less than the number of Shares covered hereby, provided that no partial exercise of this option may be for any fractional share or for fewer than ten whole shares. 

(b) Continuous Relationship with the Company Required. Except as otherwise provided in this Section 3, this option may not be
exercised unless the Participant, at the time he or she exercises this option, is, and has been at all times since the Grant Date, an employee or officer of, or consultant or advisor to, the Company or any parent or subsidiary of the Company as
defined in Section 424(e) or (f) of the Code (an “Eligible Participant”). 







 (c) Termination of Relationship with the Company. If the Participant ceases to be an
Eligible Participant for any reason, then, except as provided in paragraphs (d) and (e) below, the right to exercise this option shall terminate three months after such cessation (but in no event after the Final Exercise Date),
provided that this option shall be exercisable only to the extent that the Participant was entitled to exercise this option on the date of such cessation. Notwithstanding the foregoing, if the Participant, prior to the Final
Exercise Date, violates the non-competition or confidentiality provisions of any employment contract, confidentiality and nondisclosure agreement or other agreement between the Participant and the Company, the right to exercise this option shall
terminate immediately upon written notice to the Participant from the Company describing such violation. 
 (d) Exercise Period
Upon Death or Disability. If the Participant dies or becomes disabled (within the meaning of Section 22(e)(3) of the Code) prior to the Final Exercise Date while he or she is an Eligible Participant and the Company has not terminated
such relationship for “Cause” as specified in paragraph (e) below, this option shall be exercisable, within the period of one year following the date of death or disability of the Participant, by the Participant (or in the case of death by
an authorized transferee), provided that this option shall be exercisable only to the extent that this option was exercisable by the Participant on the date of his or her death or disability, and further provided that this option shall
not be exercisable after the Final Exercise Date. 
 (e) Termination for Cause. If, prior to the Final Exercise Date, the
Participant’s employment is terminated by the Company for Cause, the right to exercise this option shall terminate immediately upon the effective date of such termination of employment. If, prior to the Final Exercise Date, the Participant is
given notice by the Company of the termination of his or her employment by the Company for Cause, and the effective date of such employment termination is subsequent to the date of the delivery of such notice, the right to exercise this option shall
be suspended from the time of the delivery of such notice until the earlier of (i) such time as it is determined or otherwise agreed that the Participant’s employment shall not be terminated for Cause as provided in such notice or (ii) the
effective date of such termination of employment (in which case the right to exercise this option shall, pursuant to the preceding sentence, terminate immediately upon the effective date of such termination of employment). If the Participant is
party to an employment or severance agreement with the Company that contains a definition of “cause” for termination of employment, “Cause” shall have the meaning ascribed to such term in such agreement. Otherwise,
“Cause” shall mean willful misconduct by the Participant or willful failure by the Participant to perform his or her responsibilities to the Company (including, without limitation, breach by the Participant of any provision of any
employment, consulting, advisory, nondisclosure, non-competition or other similar agreement between the Participant and the Company), as determined by the Company, which determination shall be conclusive. The Participant’s employment shall be
considered to have been terminated for “Cause” if the Company determines, within 30 days after the Participant’s resignation, that termination for Cause was warranted. 








	4.	Tax Matters. 

 (a) Withholding. No Shares will be issued pursuant to the
exercise of this option unless and until the Participant pays to the Company, or makes provision satisfactory to the Company for payment of, any federal, state or local withholding taxes required by law to be withheld in respect of this option. 

(b) Disqualifying Disposition. If the Participant disposes of Shares acquired upon exercise of this option within two years from
the Grant Date or one year after such Shares were acquired pursuant to exercise of this option, the Participant shall notify the Company in writing of such disposition. 
  

	5.	Transfer Restrictions. 

 This option may not be sold, assigned, transferred, pledged or
otherwise encumbered by the Participant, either voluntarily or by operation of law, except by will or the laws of descent and distribution, and, during the lifetime of the Participant, this option shall be exercisable only by the Participant. 

 

	6.	Provisions of the Plan. 

 This option is subject to the provisions of the Plan (including
the provisions relating to amendments to the Plan), a copy of which is furnished to the Participant with this option. 
 [Remainder of Page
Intentionally Left Blank] 







 IN WITNESS WHEREOF, the Company has caused this option to be executed under its corporate seal by
its duly authorized officer. This option shall take effect as a sealed instrument. 
  

											
		 		 		 	 Achillion Pharmaceuticals, Inc.

					
	 Dated:
	 	 	 		 	By:	 	  

						
		 		 		 		 	      Name:	 	
		 		 		 		 	      Title:	 	








 PARTICIPANT’S ACCEPTANCE 

The Participant hereby accepts the foregoing option and agrees to the terms and conditions thereof. The Participant hereby acknowledges
receipt of a copy of the Plan. 
  

			
	PARTICIPANT:
	
	  

		
	Address:	 	  

		
		 	  

		
	Date:	 	  










 Exhibit A 

NOTICE OF STOCK OPTION EXERCISE 

Date:
[                    ] 
 Achillion Pharmaceuticals,
Inc. 
 300 George Street 
 New Haven, CT 06511 

Attention: Treasurer 
 Dear Sir or Madam: 

I am the holder of an Incentive Stock Option granted to me under the Achillion Pharmaceuticals, Inc. (the “Company”) 2015 Stock
Incentive Plan, as amended and/or restated from time to time, on [                     ] for the purchase of [
            ] shares of Common Stock of the Company at a purchase price of $[        ] per share. 

I hereby exercise my option to purchase [            ] shares of Common Stock (the
“Shares”), for which I have enclosed [            ] in the amount of [            ]. Please register my stock
certificate as follows: 

Name(s):                      
                                     

 
  

Address:                      
                                      

Tax
I.D.#:                                        
                 
 I represent, warrant and covenant as
follows: 
 1. I am purchasing the Shares for my own account for investment only, and not with a view to, or for sale in connection with, any distribution of
the Shares in violation of the Securities Act of 1933, as amended (the “Securities Act”), or any rule or regulation under the Securities Act. 

2. I have had such opportunity as I have deemed adequate to obtain from representatives of the Company such information as is necessary to permit me to
evaluate the merits and risks of my investment in the Company. 
 3. I have sufficient experience in business, financial and investment matters to be able
to evaluate the risks involved in the purchase of the Shares and to make an informed investment decision with respect to such purchase. 
 4. I can afford a
complete loss of the value of the Shares and am able to bear the economic risk of holding such Shares for an indefinite period. 








 Exhibit A 

 


	
	 Very truly yours,

	
	 
	 (Signature)

Name: