Document:

EX-10.15

 Exhibit 10.15 

ZAFGEN, INC. 
 2014
EMPLOYEE STOCK PURCHASE PLAN 
 The purpose of the Zafgen, Inc. 2014 Employee Stock Purchase Plan (“the Plan”) is to provide
eligible employees of Zafgen, Inc. (the “Company”) and each Designated Subsidiary (as defined in Section 11) with opportunities to purchase shares of the Company’s common stock, par value $0.001 per share (the “Common
Stock”). 1,664,200 shares of Common Stock in the aggregate have been approved and reserved for this purpose. The Plan is intended to constitute an “employee stock purchase plan” within the meaning of Section 423(b) of the
Internal Revenue Code of 1986, as amended (the “Code”), and shall be interpreted in accordance with that intent. 
 1.
Administration. The Plan will be administered by the person or persons (the “Administrator”) appointed by the Company’s Board of Directors (the “Board”) for such purpose. The Administrator has authority at any time
to: (i) adopt, alter and repeal such rules, guidelines and practices for the administration of the Plan and for its own acts and proceedings as it shall deem advisable; (ii) interpret the terms and provisions of the Plan; (iii) make
all determinations it deems advisable for the administration of the Plan; (iv) decide all disputes arising in connection with the Plan; and (v) otherwise supervise the administration of the Plan. All interpretations and decisions of the
Administrator shall be binding on all persons, including the Company and the Participants. No member of the Board or individual exercising administrative authority with respect to the Plan shall be liable for any action or determination made in good
faith with respect to the Plan or any option granted hereunder. 
 2. Offerings. The Company will make one or more offerings to
eligible employees to purchase Common Stock under the Plan (“Offerings”). Unless otherwise determined by the Administrator, an Offering will begin on the first business day occurring on or after each January 1st and July 1st and will end on the last business day occurring on or before the following June 30th and December 31st, respectively. The Administrator may, in its discretion, designate a different period for any Offering, provided
that no Offering shall exceed 12 months in duration or overlap any other Offering. 
 3. Eligibility. All individuals classified as
employees on the payroll records of the Company and each Designated Subsidiary are eligible to participate in any one or more of the Offerings under the Plan, provided that as of the first day of the applicable Offering (the “Offering
Date”) they are customarily employed by the Company or a Designated Subsidiary for more than 20 hours a week and have completed at least six months of employment. Notwithstanding any other provision herein, individuals who are not
contemporaneously classified as employees of the Company or a Designated Subsidiary for purposes of the Company’s or applicable Designated Subsidiary’s payroll system are not considered to be eligible employees of the Company or any
Designated Subsidiary and shall not be eligible to participate in the Plan. In the event any such individuals are reclassified as employees of the Company or a Designated Subsidiary for any purpose, including, without limitation, common law or
statutory employees, by any action of any third party, including, without limitation, any government agency, or as a result of any private lawsuit, action or administrative proceeding, 

 
such individuals shall, notwithstanding such reclassification, remain ineligible for participation. Notwithstanding the foregoing, the exclusive means for individuals who are not
contemporaneously classified as employees of the Company or a Designated Subsidiary on the Company’s or Designated Subsidiary’s payroll system to become eligible to participate in this Plan is through an amendment to this Plan, duly
executed by the Company, which specifically renders such individuals eligible to participate herein. 
 4. Participation. 

(a) Participants in Offering. An eligible employee who is not a Participant on any Offering Date may participate in such Offering by
submitting an enrollment form to his or her appropriate payroll location at least 15 business days before the Offering Date (or by such other deadline as shall be established by the Administrator for the Offering). 

(b) Enrollment. The enrollment form will (a) state a whole percentage to be deducted from an eligible employee’s Compensation
(as defined in Section 11) per pay period, (b) authorize the purchase of Common Stock in each Offering in accordance with the terms of the Plan and (c) specify the exact name or names in which shares of Common Stock purchased for such
individual are to be issued pursuant to Section 10. An employee who does not enroll in accordance with these procedures will be deemed to have waived the right to participate. Unless a Participant files a new enrollment form or withdraws from
the Plan, such Participant’s deductions and purchases will continue at the same percentage of Compensation for future Offerings, provided he or she remains eligible. 

(c) Notwithstanding the foregoing, participation in the Plan will neither be permitted nor be denied contrary to the requirements of the Code.

 5. Employee Contributions. Each eligible employee may authorize payroll deductions at a minimum of one percent (1%) up
to a maximum of ten percent (10%) of such employee’s Compensation for each pay period. The Company will maintain book accounts showing the amount of payroll deductions made by each Participant for each Offering. No interest will
accrue or be paid on payroll deductions. 
 6. Deduction Changes. Except as may be determined by the Administrator in advance of an
Offering, a Participant may not increase or decrease his or her payroll deduction during any Offering, but may increase or decrease his or her payroll deduction with respect to the next Offering (subject to the limitations of Section 5) by
filing a new enrollment form at least 15 business days before the next Offering Date (or by such other deadline as shall be established by the Administrator for the Offering). The Administrator may, in advance of any Offering, establish rules
permitting a Participant to increase, decrease or terminate his or her payroll deduction during an Offering. 
 7. Withdrawal. A
Participant may withdraw from participation in the Plan by delivering a written notice of withdrawal to his or her appropriate payroll location. The Participant’s withdrawal will be effective as of the next business day. Following a
Participant’s withdrawal, the Company will promptly refund such individual’s entire account balance under the Plan to him or her (after payment for any Common Stock purchased before the effective date of withdrawal). Partial withdrawals
are not permitted. Such an employee may not begin participation again during the remainder of the Offering, but may enroll in a subsequent Offering in accordance with Section 4. 

  
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 8. Grant of Options. On each Offering Date, the Company will grant to each eligible
employee who is then a Participant in the Plan an option (“Option”) to purchase on the last day of such Offering (the “Exercise Date”), at the Option Price (as defined herein) for, the lowest of (a) a number of shares of
Common Stock determined by dividing such Participant’s accumulated payroll deductions on such Exercise Date by the Option Price (as defined herein), (b) 2,500 shares; or (c) such other lesser maximum number of shares as shall have
been established by the Administrator in advance of the Offering; provided, however, that such Option shall be subject to the limitations set forth below. Each Participant’s Option shall be exercisable only to the extent of such
Participant’s accumulated payroll deductions on the Exercise Date. The purchase price for each share purchased under each Option (the “Option Price”) will be eighty-five percent (85%) of the Fair Market Value of the Common Stock
on the Offering Date or the Exercise Date, whichever is less. 
 Notwithstanding the foregoing, no Participant may be granted an Option
hereunder if such Participant, immediately after the Option was granted, would be treated as owning stock possessing five percent (5%) or more of the total combined voting power or value of all classes of stock of the Company or any Parent
or Subsidiary (as defined in Section 11). For purposes of the preceding sentence, the attribution rules of Section 424(d) of the Code shall apply in determining the stock ownership of a Participant, and all stock which the Participant has
a contractual right to purchase shall be treated as stock owned by the Participant. In addition, no Participant may be granted an Option which permits his or her rights to purchase stock under the Plan, and any other employee stock purchase plan of
the Company and its Parents and Subsidiaries, to accrue at a rate which exceeds $25,000 of the fair market value of such stock (determined on the Option grant date or dates) for each calendar year in which the Option is outstanding at any time. The
purpose of the limitation in the preceding sentence is to comply with Section 423(b)(8) of the Code and shall be applied taking Options into account in the order in which they were granted. 

9. Exercise of Option and Purchase of Shares. Each employee who continues to be a Participant in the Plan on the Exercise Date shall be
deemed to have exercised his or her Option on such date and shall acquire from the Company such number of whole shares of Common Stock reserved for the purpose of the Plan as his or her accumulated payroll deductions on such date will purchase at
the Option Price, subject to any other limitations contained in the Plan. Any amount remaining in a Participant’s account at the end of an Offering solely by reason of the inability to purchase a fractional share will be carried forward to the
next Offering; any other balance remaining in a Participant’s account at the end of an Offering will be refunded to the Participant promptly. 

10. Issuance of Certificates. Certificates representing shares of Common Stock purchased under the Plan may be issued only in the name
of the employee, in the name of the employee and another person of legal age as joint tenants with rights of survivorship, or in the name of a broker authorized by the employee to be his, her or their, nominee for such purpose. 

  
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 11. Definitions. 

The term “Compensation” means the amount of base pay, prior to salary reduction pursuant to Sections 125, 132(f) or 401(k) of
the Code, but excluding overtime, commissions, incentive or bonus awards, allowances and reimbursements for expenses such as relocation allowances or travel expenses, income or gains on the exercise of Company stock options, and similar items. 

The term “Designated Subsidiary” means any present or future Subsidiary (as defined below) that has been designated by the Board to
participate in the Plan. The Board may so designate any Subsidiary, or revoke any such designation, at any time and from time to time, either before or after the Plan is approved by the stockholders. 

The term “Fair Market Value of the Common Stock” on any given date means the fair market value of the Common Stock determined in
good faith by the Administrator; provided, however, that if the Common Stock is admitted to quotation on the NASDAQ Capital Market, the NASDAQ Global Market, the NASDAQ Global Select Market or another national securities exchange, the
determination shall be made by reference to the closing price on such date. If there is no closing price for such date, the determination shall be made by reference to the last date preceding such date for which there is a closing price. 

The term “Initial Public Offering” means the consummation of the first underwritten firm commitment public offering pursuant to an
effective registration statement under the Securities Act of 1933, as amended, covering the offer and sale by the Company of its Common Stock. 

The term “Parent” means a “parent corporation” with respect to the Company, as defined in Section 424(e) of the Code.

 The term “Participant” means an individual who is eligible as determined in Section 3 and who has complied with the
provisions of Section 4. 
 The term “Subsidiary” means a “subsidiary corporation” with respect to the Company, as
defined in Section 424(f) of the Code. 
 12. Rights on Termination of Employment. If a Participant’s employment terminates
for any reason before the Exercise Date for any Offering, no payroll deduction will be taken from any pay due and owing to the Participant and the balance in the Participant’s account will be paid to such Participant or, in the case of such
Participant’s death, to his or her designated beneficiary as if such Participant had withdrawn from the Plan under Section 7. An employee will be deemed to have terminated employment, for this purpose, if the corporation that employs him
or her, having been a Designated Subsidiary, ceases to be a Subsidiary, or if the employee is transferred to any corporation other than the Company or a Designated Subsidiary. An employee will not be deemed to have terminated employment for this
purpose, if the employee is on an approved leave of absence for military service or sickness or for any other purpose approved by the Company, if the employee’s right to reemployment is guaranteed either by a statute or by contract or under the
policy pursuant to which the leave of absence was granted or if the Administrator otherwise provides in writing. 

  
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 13. Special Rules. Notwithstanding anything herein to the contrary, the Administrator may
adopt special rules applicable to the employees of a particular Designated Subsidiary, whenever the Administrator determines that such rules are necessary or appropriate for the implementation of the Plan in a jurisdiction where such Designated
Subsidiary has employees; provided that such rules are consistent with the requirements of Section 423(b) of the Code. Any special rules established pursuant to this Section 13 shall, to the extent possible, result in the employees subject
to such rules having substantially the same rights as other Participants in the Plan. 
 14. Optionees Not Stockholders. Neither the
granting of an Option to a Participant nor the deductions from his or her pay shall constitute such Participant a holder of the shares of Common Stock covered by an Option under the Plan until such shares have been purchased by and issued to him or
her. 
 15. Rights Not Transferable. Rights under the Plan are not transferable by a Participant other than by will or the laws of
descent and distribution, and are exercisable during the Participant’s lifetime only by the Participant. 
 16. Application of
Funds. All funds received or held by the Company under the Plan may be combined with other corporate funds and may be used for any corporate purpose. 

17. Adjustment in Case of Changes Affecting Common Stock. In the event of a subdivision of outstanding shares of Common Stock, the
payment of a dividend in Common Stock or any other change affecting the Common Stock, the number of shares approved for the Plan and the share limitation set forth in Section 8 shall be equitably or proportionately adjusted to give proper
effect to such event. 
 18. Amendment of the Plan. The Board may at any time and from time to time amend the Plan in any respect,
except that without the approval within 12 months of such Board action by the stockholders, no amendment shall be made increasing the number of shares approved for the Plan or making any other change that would require stockholder approval in order
for the Plan, as amended, to qualify as an “employee stock purchase plan” under Section 423(b) of the Code. 
 19.
Insufficient Shares. If the total number of shares of Common Stock that would otherwise be purchased on any Exercise Date plus the number of shares purchased under previous Offerings under the Plan exceeds the maximum number of shares
issuable under the Plan, the shares then available shall be apportioned among Participants in proportion to the amount of payroll deductions accumulated on behalf of each Participant that would otherwise be used to purchase Common Stock on such
Exercise Date. 
 20. Termination of the Plan. The Plan may be terminated at any time by the Board. Upon termination of the Plan, all
amounts in the accounts of Participants shall be promptly refunded. 
 21. Governmental Regulations. The Company’s obligation to
sell and deliver Common Stock under the Plan is subject to obtaining all governmental approvals required in connection with the authorization, issuance, or sale of such stock. 

  
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 22. Governing Law. This Plan and all Options and actions taken thereunder shall be
governed by, and construed in accordance with, the laws of the State of Delaware, applied without regard to conflict of law principles. 

23. Issuance of Shares. Shares may be issued upon exercise of an Option from authorized but unissued Common Stock, from shares held in
the treasury of the Company, or from any other proper source. 
 24. Tax Withholding. Participation in the Plan is subject to any
minimum required tax withholding on income of the Participant in connection with the Plan. Each Participant agrees, by entering the Plan, that the Company and its Subsidiaries shall have the right to deduct any such taxes from any payment of any
kind otherwise due to the Participant, including shares issuable under the Plan. 
 25. Notification Upon Sale of Shares. Each
Participant agrees, by entering the Plan, to give the Company prompt notice of any disposition of shares purchased under the Plan where such disposition occurs within two years after the date of grant of the Option pursuant to which such shares were
purchased. 
 26. Effective Date and Approval of Shareholders. The Plan shall take effect on the date of the Company’s Initial
Public Offering, subject to approval by the holders of a majority of the votes cast at a meeting of stockholders at which a quorum is present or by written consent of the stockholders. 

DATE APPROVED BY BOARD OF DIRECTORS: June 4, 2014 
 DATE
APPROVED BY STOCKHOLDERS: June 5, 2014 

  
 6EX-10.16

 Exhibit 10.16 
  

 
 One Broadway, 8th Floor 

Cambridge, MA 02142 
 Confidential

 June 3, 2014 
 Patrick Loustau 

665 Dodds Lane 
 Gladwyne, PA 19035 

 

	Re:	Employment Offer 

 Dear Patrick: 

On behalf of Zafgen, Inc., a Delaware corporation (the “Company”), I am pleased to offer employment to you. The purpose of this
letter is to outline the terms for your employment. 
 Position: Your initial position with the Company will be President, reporting
to Zafgen’s Chief Executive Officer. This is a full-time role and it is understood and agreed that you will not engage in any other employment, consulting or other business activities (whether full-time or part-time) after the Start Date
without prior written consent from the CEO. 
 Work Location. You will be based at the Company’s headquarters, currently in
Cambridge, Massachusetts. You agree to travel as reasonably necessary to accomplish your job duties. 
 Start Date: Your first day of
employment will be June 16, 2014, unless another date is agreed to by you and the Company. The actual first day of your employment shall be referred to in this document as the “Start Date.” 

Salary: Effective on the Start Date, the Company will pay you a salary at the annual rate of $400,000 (a semi-monthly rate of
$16,666.67). Your salary shall be subject to periodic review and adjustment at the discretion of the Company. 
 Bonus: You
will be eligible to receive an annual performance bonus. The Company will target the bonus at up to 35% of your annual salary rate, pro-rated based on your Start Date for the first year. The actual bonus percentage is discretionary and will be
subject to the Company’s assessment of your performance, as well as business conditions at the Company. The bonus also will be subject to approval by and adjustment at the discretion of the Company’s Board of Directors (the
“Board”) and the terms of any applicable bonus plan. You must be employed on the date a bonus is paid to earn any part of the bonus. 

Benefits: You will be eligible to participate in the employee benefits and insurance programs generally made available to the
Company’s full-time employees, subject to the terms and conditions of those programs. Currently, the employee programs include health, life, disability and dental insurance. Details of these benefits programs, including mandatory employee
contributions, will be made available to you when you start. You also will be eligible for up to 15 days of paid vacation per year, which shall accrue on a prorated basis. Other provisions of the Company’s vacation policy are set forth in the
policy itself. 

 Stock Options: Subject to approval by the Board, you be granted an option (the
“Option”) to purchase 1,757,000 shares (pre-split) of the Company’s common stock (equal to approximately 1.6% of the outstanding shares of the Company’s common stock on a fully diluted basis). Assuming the Start Date is prior to
the Company’s IPO, which is expected to occur in June 2014, the exercise price for the Option will be the IPO share price as reported in the Company’s S-1. If the Option is issued after the IPO, the exercise price for the Option shall be
at least equal to the fair market value of the Company’s common stock on the date of grant, which we expect will be the closing price of the Company’s stock on the NASDAQ. The Option will be governed by the Company’s stock option plan
and associated stock option agreement (the “Equity Documents”) including with respect to vesting and exercise rights. The Option will vest over four years at the rate of 25% after twelve months of full time active employment and then 1/48th for each additional month of full time active employment after your Start Date until after four full years when the Option is fully vested. Notwithstanding the forgoing if a Change of Control (as
defined in the Equity Documents”) occurs within 12 months of your Start Date, 25% of your then unvested options shall vest, effective upon the consummation of such Change in Control. 

Relocation: The Company will provide reimburse you with up to seventy-five thousand dollars ($75,000) for moving costs from your home
in connection with Executive’s relocation of Executive’s principal residence from Pennsylvania to the Boston/Cambridge area (“Relocation Amount”). The Company will provide local real estate assistance in connection with your home
search and you must relocate by a date to be determined by the Chief Executive Officer after consultation with you (the “Date”). Acceptable uses of the Relocation Amount include temporary housing, moving expenses and trips from
Pennsylvania for you and your spouse to search for a home (collectively, the “Relocation Expenses”). Appropriate supporting documentation (i.e., itemized receipts) of the Relocation Expenses must be submitted within 30 days after the
Relocation Expenses were incurred and prior to reimbursement. The Company will determine in its reasonable, good faith judgment what, if any, of Executive’s reimbursed Relocation Expenses are for nondeductible expenses in accordance with
applicable law and will comply with associated withholding and tax reporting obligations. In addition, provided you relocate prior to the Date, the Company will provide you with a one-time relocation bonus of $20,000, less applicable deductions and
withholdings (the “Relocation Bonus”), payable on or before the Date. If you resign prior to the one year anniversary of the Start Date, you must repay all Relocation Expenses and the Relocation Bonus to the Company within ten
(10) days of the date of termination (defined below) (the “Relocation Reimbursement”). 
 At-will Employment;
Severance. Your employment is “at will,” meaning you or the Company may terminate it at any time for any or no reason. Similarly, the terms of employment outlined in this letter are subject to change at any time. In the event of the
termination of your employment for any reason, the Company shall pay you the Accrued Obligations, defined as (1) your base salary through the date of termination, (2) an amount equal to the value of your accrued unused vacation days, and
(3) the amount of any expenses properly incurred by you on behalf of the Company prior to any such termination and not yet reimbursed: In addition, if the Company terminates your employment without Cause or you resign for Good Reason, you shall
be entitled to the following Termination Benefits in addition to the Accrued Obligations: 
 i) Continuation of your then
base salary for a period of three (3) months from the date of termination a (“Salary Continuation Payments); 
 ii)
if you are participating in the Company’s health plan benefits as of the date of termination, continuation of group health plan benefits to the extent authorized by and consistent with 29 U.S.C. § 1161 et seq. (commonly known

 
as “COBRA”), with the cost of the regular premium for such benefits shared in the same relative proportion by the Company and you as in effect on the date of termination until the
earlier of (i) three (3) months from the termination date; and (ii) the date you become eligible for health benefits through another employer or otherwise become ineligible for COBRA (“Health Benefits Continuation
Payments”); and 
 Notwithstanding anything to the contrary in this letter agreement, you shall not be entitled to any Termination Benefits unless you
first (i) enter into, do not revoke, and comply with the terms of a separation agreement in a form acceptable to the Company which shall include a release against the Company and related persons and entities (the “Release”);
(ii) resign from any and all positions, including, without implication of limitation, as a director, trustee, and officer, that you then hold with the Company and any affiliate of the Company; and (iii) return all Company property and
comply with any instructions related to deleting and purging duplicates of such Company property. 
 For purposes of this letter agreement: 

“Cause” means any of the following: (i) dishonesty, embezzlement, misappropriation of assets or property of the Company;
(ii) gross negligence, misconduct, neglect of duties, theft, fraud, or breach of fiduciary duty to the Company; (iii) violation of federal or state securities laws; (iv) breach of an employment, consulting or other agreement with the
Company; (v) the conviction of a felony, or any crime involving moral turpitude, including a plea of guilty or nolo contendre; or (vi) continued non-performance or unsatisfactory performance of your responsibilities hereunder; and
 
 “Good Reason” means that you have complied with the “Good Reason Process” (hereinafter defined) following the
occurrence of any of the following actions undertaken by the Company without your express prior written consent: (i) the material diminution in your responsibilities, authority and function; (ii) a material reduction in your base salary,
provided, however, that Good Reason shall not be deemed to have occurred in the event of a reduction in your base salary that is pursuant to a salary reduction program affecting substantially all of the senior level employees of the Company and that
does not adversely affect you to a greater extent than other similarly situated employees; or (iii) a material change in the geographic location at which you must regularly report to work and perform services, except for required travel on the
Company’s business. “Good Reason Process” means that (i) you have reasonably determined in good faith that a “Good Reason” condition has occurred; (ii) you have notified the Company in writing of the first
occurrence of the Good Reason condition within 60 days of the first occurrence of such condition; (iii) you have cooperated in good faith with the Company’s efforts, for a period not less than 30 days following such notice (the “Cure
Period”), to remedy the condition; (iv) notwithstanding such efforts, the Good Reason condition continues to exist; and (v) you terminate your employment within 60 days after the end of the Cure Period. If the Company cures the Good
Reason condition during the Cure Period, Good Reason shall be deemed not to have occurred. 
 Representation Regarding Other
Obligations: This offer is conditioned on your representation that you are not subject to any confidentiality, non-competition agreement or any other similar type of restriction that may affect your ability to devote full time and attention to
your work at Company. If you have entered into any agreement that may restrict your activities on behalf of the Company, please provide me with a copy of the agreement as soon as possible. 

 Other Terms: As a condition of your employment, you will be required to sign the
Company’s Employee Non-Competition, Non-Solicitation, Confidentiality and Assignment Agreement. A copy of that Agreement is enclosed. This offer and Agreement shall be governed by the laws of the Commonwealth of Massachusetts. In
addition, as with all employees, our offer to you is contingent on your submission of satisfactory proof of your identity and your legal authorization to work in the United States. 

We are excited about you becoming a Zafgen employee. If you have any questions about this information, please do not hesitate to call.
Otherwise, please confirm your acceptance of this offer of employment by signing below and returning a copy to me no later than June 9, 2014. We are confident that with you background and skills, you will have an immediate positive impact on
our organization. 
 Very truly yours, 
  

	
	
	
	/s/ Thomas Hughes
	Thomas Hughes, President and CEO

  

	
	ACKNOWLEDGED AND AGREED:
	
	/s/ Patrick Loustau
	Patrick Loustau

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