EXHIBIT 10.1

ALNYLAM PHARMACEUTICALS, INC.

AMENDED AND RESTATED 2004 EMPLOYEE STOCK PURCHASE PLAN, AS AMENDED

 

The purpose of this Amended and Restated Employee Stock Purchase Plan, as
amended (the “Plan”) is to provide eligible employees of Alnylam
Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and certain of
its subsidiaries with opportunities to purchase shares of the Company’s common
stock, $0.01 par value (the “Common Stock”). This Plan includes two components:
a Code Section 423 Component (the “423 Component”) and a Non-Code Section 423
Component (the “Non-423 Component”). It is the intention of the Company to have
the 423 Component qualify as an “employee stock purchase plan” as defined in
Section 423 of the Internal Revenue Code of 1986, as amended (the “Code”), and
the regulations promulgated thereunder, and shall be interpreted consistent
therewith. The provisions of the 423 Component, accordingly, shall be construed
so as to extend and limit participation in a uniform and non-discriminatory
basis consistent with the requirements of Section 423 of the Code. In addition,
this Plan authorizes the grant of share purchase rights under the Non-423
Component that do not qualify as an “employee stock purchase plan” under Section
423 of the Code. The share purchase rights granted under the Non-423 Component
are granted pursuant to rules, procedures or sub-plans adopted by the Company’s
Board of Directors (the “Board”) or by a Committee appointed by the Board (the
“Committee”) designed to achieve tax, securities laws or other objectives for
eligible employees and the Company. Except as otherwise provided herein, the
Non-423 Component will be operated and administered in the same manner as the
423 Component.

 

An aggregate of 1,215,789 shares of Common Stock have been approved for this
Plan. This aggregate limit will apply to purchases of Common Stock under either
the 423 Component or the Non-423 Component.

 

1.Administration. The Plan will be administered by the Board or by the
Committee. The Board or the Committee has authority to make rules and
regulations for the administration of the Plan and its interpretation and
decisions with regard thereto shall be final and conclusive. The Board and the
Committee will have full and discretionary authority to construe, interpret and
apply the terms of the Plan, to adjudicate all disputed claims made under the
Plan, to designate separate Plan Periods (as defined below), to designate
subsidiaries as participating in the Plan, to determine eligibility, including
which subsidiaries shall be Designated Subsidiaries (as defined below) and
whether the employees of the Designated Subsidiary shall participate in the 423
Component or the Non-423 Component. Notwithstanding any provision in this Plan
to the contrary, the Board or Committee may adopt rules or procedures relating
to the operation and administration of the Plan to accommodate the specific
requirements of local laws and procedures for jurisdictions outside of the
United States. Without limiting the generality of the foregoing, the Board or
the Committee specifically is authorized to adopt rules, procedures and
sub-plans, which, for purposes of the Non-423 Component, may be outside the
scope of Section 423 of the Code, regarding, without limitation, eligibility to
participate, the definition of Compensation (defined in Section 4), handling of
payroll deductions, making of contributions to the Plan (including, in forms
other than payroll deductions), establishment of bank or trust accounts to hold
payroll deductions, payment of interest, conversion of local currency,
obligations to pay payroll tax, withholding procedures and handling of Common
Stock issuances, which may vary according to local requirements.

 

2.Eligibility. All employees of the Company and all employees of any subsidiary
of the Company (as defined in Section 424(f) of the Code) designated by the
Board or the Committee from time to time (a “Designated Subsidiary”), are
eligible to participate in any one or more of the offerings of Purchase Rights
(as defined in Section 9) to purchase Common Stock under the Plan provided that:

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(a)they are customarily employed by the Company or a Designated Subsidiary for
more than twenty (20) hours a week and for more than five (5) months in a
calendar year if they are participating in the 423 Component;

 

(b)they have been employed by the Company or a Designated Subsidiary for at
least thirty (30) days prior to enrolling in the Plan;

(c)they are employees of the Company or a Designated Subsidiary on the first day
of the applicable Plan Period; and

(d)for purposes of the 423 Component, in the case of an executive officer of the
Company or a Designated Subsidiary, they are not considered a “highly
compensated individual” within the meaning of Section 414(q) of the Code).

No employee may be granted a Purchase Right hereunder if such employee,
immediately after the Purchase Right is granted, owns 5% or more of the total
combined voting power or value of the stock of the Company or any subsidiary.
For purposes of the preceding sentence, the attribution rules of Section 424(d)
of the Code shall apply in determining the stock ownership of an employee, and
all stock which the employee has a contractual right to purchase shall be
treated as stock owned by the employee.

3.Offerings. The Company will make one or more offerings (“Offerings”) to
employees to purchase Common Stock under this Plan. Offerings will begin each
November 1 or the first business day thereafter (the “Offering Commencement
Dates”). Each Offering Commencement Date will begin a twelve-month period (a
“Plan Period”) during which payroll deductions will be made and held for the
purchase of Common Stock at the end of the Plan Period. The Committee may, at
its discretion, decide that an employee may contribute to the Plan by means
other than payroll deductions, provided that contributions other than payroll
deductions will be permissible only for employees participating in the Non-423
Component. The Board or the Committee also may, at its discretion, choose a
different Plan Period of twelve (12) months or less for subsequent Offerings.
Notwithstanding any provision in this Plan to the contrary, the first Plan
Period shall begin on the later of November 1, 2004 or the first date that the
Common Stock is publicly traded following the Company’s IPO (the “IPO Date”),
and shall end on October 31, 2005.

4.Participation. An employee eligible on the Offering Commencement Date of any
Offering may participate in such Offering by completing (electronically or
otherwise) and forwarding a payroll deduction authorization form or other direct
contribution form to the employee’s appropriate payroll office at least five (5)
business days prior to the applicable Offering Commencement Date (or other
period of time determined by the Company).  The payroll deduction authorization
form or other direct contribution form will designate the percentage of
Compensation withheld or contributed during the Plan Period. Unless an employee
files a new form or withdraws from the Plan, his deductions or contributions and
purchases will continue at the same rate for future Offerings under the Plan as
long as the Plan remains in effect. For the 423 Component, the term
“Compensation” means the amount of money reportable on the employee’s Wage and
Tax Statement (the "Form W-2"). For the 423 Component, Compensation shall
exclude overtime, shift premium, incentive or bonus awards, allowances and
reimbursements for expenses such as relocation allowances for travel expenses,
income or gains on the exercise of Company stock options or stock appreciation
rights, amounts imputed in respect of benefit programs and similar items,
whether or not shown on the employee’s Form W-2, but including, in the case of
salespersons, sales commissions to the extent determined by the Company.

 

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5.Deductions or Contributions. The Company will maintain payroll deduction or
contribution accounts for all participating employees. With respect to any
Offering made under this Plan, an employee may authorize a payroll deduction or
contribution in any dollar amount up to a maximum of 15% of the Compensation he
or she receives during the Plan Period or such shorter period during which
deductions or contributions are made. The minimum payroll deduction is such
percentage of Compensation as may be established from time to time by the
Company.

6.Deduction or Contribution Changes. An employee may decrease or discontinue his
payroll deductions or contributions once during any Plan Period, by filing a new
payroll deduction authorization form or other direct contribution form
(electronically or otherwise). However, an employee may not increase his payroll
deductions or contributions during a Plan Period. If an employee elects to
discontinue his payroll deductions or contributions during a Plan Period but
does not elect to withdraw his funds pursuant to Section 8 hereof, funds
deducted or contributed prior to his election to discontinue will be applied to
the purchase of Common Stock on the Purchase Date (as defined below).

 

7.Interest. Interest will not be paid on any employee accounts unless otherwise
required by local law.

 

8.Withdrawal of Funds. An employee may at any time prior to the close of
business on the last business day in a Plan Period (or other date set by the
Company) and for any reason withdraw the balance accumulated in the employee’s
account and thereby withdraw from participation in an Offering. Partial
withdrawals are not permitted. The employee may not begin participation again
during the remainder of the Plan Period. The employee may participate in any
subsequent Offering in accordance with terms and conditions established by the
Company.

 

9.Purchase of Shares. On the Offering Commencement Date of each Plan Period, the
Company will grant to each eligible employee who is then a participant in the
Plan a purchase right (“Purchase Right”) to purchase on the last business day of
such Plan Period (the “Purchase Date”), at the Purchase Price (as defined below)
hereinafter provided for, the largest number of whole shares of Common Stock of
the Company as does not exceed the number of shares determined by dividing
$25,000 by the closing price (as defined below) on the Offering Commencement
Date of such Plan Period.

Notwithstanding the above, no employee may be granted a Purchase Right which
permits his rights to purchase Common Stock under this Plan and any other
employee stock purchase plan (as defined in Section 423(b) of the Code) of the
Company and its subsidiaries, to accrue at a rate which exceeds $25,000 of the
fair market value of such Common Stock (determined at the Offering Commencement
Date of the Plan Period) for each calendar year in which the Purchase Right is
outstanding at any time.

The purchase price for each share of Common Stock purchased will be 85% of the
closing price of the Common Stock on (i) the Offering Commencement Date of such
Plan Period or (ii) the Purchase Date, whichever closing price shall be less
(the “Purchase Price”). Such closing price shall be (a) the closing price on any
national securities exchange on which the Common Stock is listed, (b) the
closing price of the Common Stock on the NASDAQ Stock Market or (c) the average
of the closing bid and asked prices in the over-the-counter-market, whichever is
applicable, as published in The Wall Street Journal; provided that, with respect
to the first Plan Period, if the first day of such Plan Period is the IPO Date,
the closing price of the Common Stock on the first business day of such Plan
Period shall be deemed to be the initial public offering price for the Common
Stock, as set forth in the final prospectus relating to the IPO. If no sales of
Common Stock were made on such a day, the price of the Common Stock for purposes
of clauses (a) and (b)

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above shall be the reported price for the next preceding day on which sales were
made.

Each employee who continues to be a participant in the Plan on the Purchase Date
shall be deemed to have exercised his Purchase Right at the Purchase Price on
such date and shall be deemed to have purchased from the Company the number of
full shares of Common Stock reserved for the purpose of the Plan that his
accumulated payroll deductions or contributions on such date will pay for, but
not in excess of the maximum number determined in the manner set forth above.

Any balance remaining in an employee’s payroll deduction or contribution account
at the end of a Plan Period will be automatically refunded to the employee,
except that any balance which is less than the Purchase Price of one share of
Common Stock will be carried forward into the employee’s payroll deduction or
contribution account for the following Offering, unless the employee elects not
to participate in the following Offering under the Plan, in which case the
balance in the employee’s account shall be refunded.

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 Company’s sole discretion) in the name of a
brokerage firm, bank or other nominee holder designated by the employee.  The
Company may, in its sole discretion and in compliance with applicable laws,
authorize the use of book entry registration of shares in lieu of issuing stock
certificates.

11.Rights on Retirement, Death or Termination of Employment. In the event of a
participating employee’s termination of employment prior to the last business
day of a Plan Period, no payroll deduction or contribution shall be taken from
any pay or contribution due and owing to an employee and the balance in the
employee’s account shall be paid to the employee or, in the event of the
employee’s death, (a) to a beneficiary previously designated in a manner
specified by the Company) or (b) in the absence of such a designated
beneficiary, to the executor or administrator of the employee’s estate or (c) if
no such executor or administrator has been appointed to the knowledge of the
Company, to such other person(s) as the Company may, in its discretion,
designate. If, prior to the last business day of the Plan Period, the Designated
Subsidiary by which an employee is employed shall cease to be a subsidiary of
the Company, or if the employee is transferred to a subsidiary of the Company
that is not a Designated Subsidiary, the employee shall be deemed to have
terminated employment for the purposes of this Plan.

12.No Stockholder Rights. Neither the granting of a Purchase Right to an
employee nor the payroll deductions or contributions shall constitute such
employee a stockholder of the shares of Common Stock covered by a Purchase Right
under this Plan until such shares have been purchased by and issued to him.

13.Rights Not Transferable. Rights under this Plan are not transferable by a
participating employee other than under the laws of descent and distribution,
and are exercisable during the employee’s lifetime only by the employee.

14.Application of Funds. All funds received or held by the Company under this
Plan may be combined with other corporate funds and may be used for any
corporate purpose unless otherwise required by local law.

15.Adjustment in Case of Changes Affecting Common Stock. In the event of a
subdivision of outstanding shares of Common Stock, or the payment of a dividend
in Common Stock, the number of shares approved for this Plan, and the share
limitation set forth in Section 9, shall be increased proportionately, and

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such other adjustment shall be made as may be deemed equitable by the Board or
the Committee. In the event of any other change affecting the Common Stock, such
adjustment shall be made as may be deemed equitable by the Board or the
Committee to give proper effect to such event.

16.Merger. If the Company shall at any time merge or consolidate with another
corporation and the holders of the capital stock of the Company immediately
prior to such merger or consolidation continue to hold at least a majority by
voting power of the capital stock of the surviving corporation (“Continuity of
Control”), the holder of each Purchase Right then outstanding will thereafter be
entitled to receive at the next Purchase Date upon the exercise of such Purchase
Right for each share as to which such Purchase Right shall be exercised the
securities or property which a holder of one share of the Common Stock was
entitled to upon and at the time of such merger or consolidation, and the Board
or the Committee shall take such steps in connection with such merger or
consolidation as the Board or the Committee shall deem necessary to assure that
the provisions of Section 15 shall thereafter be applicable, as nearly as
reasonably may be, in relation to the said securities or property as to which
such holder of such Purchase Right might thereafter be entitled to receive
thereunder.

In the event of a merger or consolidation of the Company with or into another
corporation which does not involve Continuity of Control, or of a sale of all or
substantially all of the assets of the Company while unexercised Purchase Rights
remain outstanding under the Plan, (a) subject to the provisions of clauses (b)
and (c), after the effective date of such transaction, each holder of an
outstanding Purchase Right shall be entitled, upon exercise of such Purchase
Right, to receive in lieu of shares of Common Stock, shares of such stock or
other securities as the holders of shares of Common Stock received pursuant to
the terms of such transaction; or (b) all outstanding Purchase Rights may be
cancelled by the Board or the Committee as of a date prior to the effective date
of any such transaction and all payroll deductions shall be paid out to the
participating employees; or (c) all outstanding Purchase Rights may be cancelled
by the Board or the Committee as of the effective date of any such transaction,
provided that notice of such cancellation shall be given to each holder of a
Purchase Right, and each holder of a Purchase Right shall have the right to
exercise such Purchase Right in full based on payroll deductions then credited
to his account as of a date determined by the Board or the Committee, which date
shall not be less than ten (10) days preceding the effective date of such
transaction.

 

17.Amendment of the Plan. The Board may at any time, and from time to time,
amend this Plan in any respect, except that (a) if the approval of any such
amendment by the stockholders of the Company is required by Section 423 of the
Code, such amendment shall not be effected without such approval, and (b) in no
event may any amendment be made which would cause the 423 Component of the Plan
to fail to comply with Section 423 of the Code.

18.Insufficient Shares. In the event that the total number of shares of Common
Stock specified in elections to be purchased under any Offering plus the number
of shares of Common Stock purchased under previous Offerings under this Plan
exceeds the maximum number of shares of Common Stock issuable under this Plan,
the Board or the Committee will allot the shares of Common Stock then available
on a pro rata basis.

19.Termination of the Plan. This Plan may be terminated at any time by the
Board. Upon termination of this Plan all amounts in the accounts of
participating employees shall be promptly refunded.

20.Governmental Regulations. The Company’s obligation to sell and deliver Common
Stock under this Plan is subject to listing on a national stock exchange or
quotation on the NASDAQ (to the extent the Common Stock is then so listed or
quoted) and the approval of all governmental authorities required in

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connection with the authorization, issuance or sale of such Common Stock.

21.Governing Law. The Plan shall be governed by Delaware law except to the
extent that such law is preempted by federal law.

22.Issuance of Shares. Common Stock may be issued upon exercise of a Purchase
Right from authorized but unissued Common Stock, from Common Stock held in the
treasury of the Company, or from any other proper source.

23.Notification upon Sale of Shares. Each employee agrees, by entering the Plan,
to promptly give the Company notice of any disposition of Common Stock purchased
under the Plan where such disposition occurs within two (2) years after the date
of grant of the Purchase Right pursuant to which such Common Stock was
purchased.

24.Special Provisions for First Plan Period. If the first day of the first Plan
Period is the IPO Date, the following provisions of this Section 24 shall apply
with respect to the first Plan Period notwithstanding any provision of the Plan
to the contrary:

(a)Every eligible employee shall automatically become a participant in the Plan
for the first Plan Period at the highest percentage of Compensation permitted
under Section 5. No payroll deductions or contributions shall be required for
the first Plan Period; however, a participant may, at any time after the
effectiveness of the Plan’s Registration Statement on Form S-8, elect to have
payroll deductions or contributions up to the aggregate amount which would have
been credited to his account if a deduction or contribution of fifteen percent
(15%) of the Compensation which he received on each pay day during the first
Plan Period had been made (the “Maximum Amount”) or decline to participate by
filing an appropriate subscription agreement.

(b)Upon the automatic exercise of a participant’s Purchase Right on the Purchase
Date for the first Plan Period, a participant shall be permitted to purchase
Common Stock with (i) the accumulated payroll deductions or contributions in his
account, if any, (ii) a direct payment from the participant, or (iii) a
combination thereof; provided, however that the total amount applied to the
purchase may not exceed the Maximum Amount.

25.Withholding. Each employee shall, no later than the date of the event
creating the tax liability, make provision satisfactory to the Board for payment
of any taxes required by law to be withheld in connection with any transaction
related to Purchase Rights granted to or Common Stock acquired by such employee
pursuant to the Plan. The Company or Designated Subsidiary may, to the extent
permitted by law, deduct any such taxes from any payment of any kind otherwise
due to an employee.

26.Effective Date and Approval of Stockholders. The Plan originally took effect
on the IPO Date. The Board amended and restated the Plan on March 6, 2017. The
amended and restated Plan became effective on May 2, 2017 following approval by
the stockholders of the Company. The Plan was further amended on December 4,
2018.