Document:

exv10w5

Exhibit 10.5

SciQuest, Inc.

Second Amended and Restated

Exit Event Bonus Plan

 

 

SCIQUEST, INC.

SECOND AMENDED AND RESTATED EXIT EVENT BONUS PLAN

     THIS PLAN, sponsored and made effective as of the day and date noted on the last page
hereof, by SciQuest, Inc., a Delaware corporation (the “Corporation”), is intended to be an
unfunded deferred compensation plan maintained by the Corporation primarily for the purpose of
providing deferred and incentive-based compensation to only a select group of management or highly
compensated employees (within the meaning of ERISA §§201(2), 301(a)(3), 401(a)(1) and 4021(b)(6)).
However, this Plan is not intended to provide retirement income, or result in a deferral of income,
for employees, and is therefore not intended to be an employee benefit plan within the meaning of
ERISA §3(3) and is not intended to be subject to ERISA.

WITNESSETH:

     WHEREAS, the Corporation believes that the services of certain selected management or highly
compensated employees are of great value and that such individuals should be compensated for
careful and loyal service to all shareholders of the Corporation; and

     WHEREAS, the Corporation established that certain SciQuest, Inc. Exit Event Bonus Plan,
effective as of April 28, 2005 (the “Original Plan”) to provide a mechanism for motivating and
creating an incentive for such employees to accomplish an Exit Event (as defined below) for the
Corporation; and

     WHEREAS, the Corporation amended and restated the Original Plan in the form of the SciQuest,
Inc. Amended and Restated Exit Event Bonus Plan, effective as of September 19, 2007 (the “Existing
Plan”), which amended, restated and superseded in its entirety the Original Plan.

     NOW, THEREFORE, the Corporation does hereby amend and restate in its entirety the Existing
Plan as set forth herein.

ARTICLE 1

DEFINITIONS

     The following words and phrases as used in this Plan shall have the meanings set forth in this
Article unless a different meaning is clearly required by the context:

     1.1 Applicable Percentage shall mean, with respect to an Exit Event, the applicable percentage
as derived from the following formulas, as applicable:

     If the Exit Event occurs on or before the fourth anniversary of the Effective Date, then:

AP = (X/$40,000,000) x 3%

Where,

AP = the Applicable Percentage; and

X = the Exit Event Valuation minus $200,000,000.

     If the Exit Event occurs after the fourth anniversary of the Effective Date, then:

AP = (X/$40,000,000) x 3%

Where,

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AP = the Applicable Percentage; and

X = the Exit Event Valuation minus $210,000,000.

     In no event shall the Applicable Percentage exceed 3%. The Applicable Percentage shall be
subject to adjustment pursuant to Section 3.5 hereof.

     1.2 Beneficiary shall mean, with respect to a Participant, the individual to whom the
Participant’s Bonus Benefit, if any, shall be paid upon the Participant’s death, and shall be
determined in accordance with the following provisions:

     (a) Designation of Beneficiary. A Participant’s Beneficiary shall be the individual
who is last designated in writing by the Participant as such Participant’s Beneficiary under
this Plan in accordance with this subsection. A Participant shall designate the initial
Beneficiary in writing on a Beneficiary Election Form. Any subsequent modification of the
Participant’s Beneficiary shall be in a written executed and notarized letter addressed to
the Corporation or in a subsequently executed and notarized Beneficiary Election Form, and
such shall be effective only when it is received and accepted by the Board, determined in
the Board’s sole discretion.

     (b) No Designated Beneficiary. If, at any time, no Beneficiary has been validly
designated by an Participant, or the Beneficiary designated by the Participant is no longer
living at the time of the Participant’s death, then the Participant’s Beneficiary shall be
deemed to be the Participant’s spouse, and in the absence thereof, the Participant’s estate.

     (c) Designation of Multiple Beneficiaries or Entities. A Participant may not designate
more than one individual as a Beneficiary. A Participant may not designate an entity as a
Beneficiary. To the extent that a designation purports to designate more than one
individual as a Beneficiary and/or an entity as a Beneficiary, the entire designation shall
be null and void.

     (d) Contingent Beneficiaries. An Participant may designate a contingent Beneficiary to
receive the Participant’s Accrued Benefit in the event that the Participant’s currently
designated Beneficiary should predecease the Participant; otherwise, in the event a
Beneficiary predeceases the Participant, then the Participant’s spouse or estate, determined
in accordance with subsection (b) above, shall be the Participant’s Beneficiary.

     1.3 Beneficiary Election Form shall mean the written document (the form of which is attached
to this Plan as Exhibit B) by which a Participant may make his initial designation of a
Beneficiary to receive his Bonus Benefit, if any, in the event of the Participant’s death.

     1.4 Benefiting Participant shall mean, with respect to an Exit Event, a Participant who is
employed by the Corporation on the day immediately prior to the Exit Event or a Participant who
incurred a Qualified Termination of Employment at any time prior to the day immediately prior to
the Exit Event.

     1.5 Board shall mean the Board of Directors of the Corporation.

     1.6 Bonus Pool shall mean (i) with respect to an Exit Event that is a Merger Event, the
product of the Applicable Percentage multiplied by the difference of (A) the Merger Event
Consideration less (B) the amount that the holders of the Preferred Stock would be entitled to
receive pursuant to Section 4.02(C) of the Corporation’s Amended and Restated Certificate of
Incorporation, as in effect on the date hereof, and (ii) with respect to an Exit Event that is a
Public Offering, the product of the Applicable Percentage multiplied by the difference of (A) the
number of Fully Diluted Shares of Common Stock immediately after giving effect to the Public
Offering less (B) and the number of shares of Common Stock sold by the Corporation pursuant to the
Public Offering.

     1.7 Bonus Benefit shall mean, with respect to an Exit Event and with respect to a particular
Participant, the product of “A” multiplied by “B”, with such product divided by “C”, denoted
mathematically as follows:

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Bonus Benefit = [(A*B)/C]

where “A”, “B”, and “C” are defined as follows:

A = the Bonus Pool with respect to such Exit Event

B = the Units of the Participant with respect to such Exit Event

C = the aggregate Units of all Benefiting Participants as of such Exit Event

However, the above notwithstanding, the Bonus Benefit of any Participant with respect to an Exit
Event occurring after the fifth anniversary of the Effective Date shall be zero.

     1.8 Cause, with respect to any Participant who has a written employment agreement with the
Corporation that defines “Cause”, shall have the meaning set forth in such written employment
agreement, and with respect to any Participant who does not have a written employment agreement
with the Corporation that defines “Cause”, then Cause shall mean any act or acts by such
Participant involving (a) the use for profit or disclosure to unauthorized persons of confidential
information or trade secrets of the Corporation, (b) the continuing, material breach of any
contract with the Corporation after a reasonable opportunity to cure, (c) the violation of any
fiduciary obligation to the Corporation, (d) the unlawful trading in the securities of the
Corporation, or of another corporation based on information gained as a result of the performance
of services for the Corporation, (e) a felony conviction or the failure to contest prosecution of a
felony, or (f) willful misconduct, dishonesty, embezzlement, fraud, deceit or civil rights
violations.

     1.9 Code shall mean the Internal Revenue Code of 1986, as amended from time to time.

     1.10 Committee shall mean any committee appointed by the Board to administer the Plan, as
specified in Section 5.2 hereof. Any such committee shall be comprised entirely of Directors.

     1.11 Common Stock shall mean the common stock, par value $0.001 per share, of the Corporation.

     1.12 Corporation shall mean SciQuest, Inc., a Delaware corporation, and its successors and
assigns, and any other corporation, partnership or sole proprietorship into which the Corporation
may be merged or consolidated unless such organization indicates in writing that it does not
approve of such automatic succession.

     1.13 Disability shall mean, with respect to a Participant, that the Participant is disabled
within the meaning of the Corporation’s long term disability plan, if any, and if no such plan is
in existence, then Disability shall mean that the Participant has a physical or mental impairment
that substantially limits one or more of the major life activities of the Participant such that the
Participant can no longer perform the essential functions of the position or job which the
Participant had immediately prior to the occurrence of the impairment. The Board shall determine
whether a Participant has incurred a Disability in its sole and absolute discretion based upon the
definition of the preceding sentence.

     1.14 Effective Date shall mean April 28, 2005.

     1.15 Eligible Individual shall mean an individual who is involved with management of the
Corporation and/or who is a highly compensated employee (within the meaning of ERISA §§201(2),
301(a)(3), 401(a)(1) and 4021(b)(6)).

     1.16 ERISA shall mean the Employee Retirement Income Security Act of 1974, as amended from
time to time.

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     1.17 Exit Event shall mean either (i) a “Merger Event” (as defined in Section 4.02(C) of the
Corporation’s Amended and Restated Certificate of Incorporation in effect as of the date hereof) or
(ii) a Public Offering; provided, however, in no event shall an Exit Event be deemed to occur under
this Plan unless such Exit Event constitutes a “change in the ownership or effective control of,”
or “in the ownership of a substantial portion of the assets of” the Corporation, as defined in Code
§409A(a)(2)(A)(v) and any applicable guidance or regulations issued thereunder.

     1.18 Exit Event Valuation shall mean (i) with respect to an Exit Event that is a Merger Event,
the Merger Event Consideration and (ii) with respect to an Exit Event that is a Public Offering,
the Public Offering Valuation. However, the above notwithstanding:

     (a) In the case of a Merger Event resulting from the sale by the Corporation of all or
substantially all of its assets, the Exit Event Valuation shall be the Merger Event
Consideration plus the amount of any debt assumed by the acquiring entity (other than any
liability pursuant to this Plan); and

     (b) In the case of a Merger Event resulting from the acquisition by a Person of less
than all of the capital stock of the Corporation, the Exit Event Valuation shall be the
Merger Event Consideration divided by percentage of the capital stock of the Corporation so
acquired in such Merger Event.

     1.19 Fair Market Value of the Common Stock or any other securities constituting a part of the
Exit Event Consideration as of a date of determination shall mean the following:

     (a) Stock Listed and Shares Traded. If the Common Stock or other securities are listed
and traded on a national securities exchange (as such term is defined by the Securities
Exchange Act of 1934) or on the NASDAQ National Market System on the date of determination,
the Fair Market Value per share shall be the average of the closing prices of the securities
on such national securities exchange or on the National Market System, over the thirty (30)
day period ending three (3) business days prior to the date of determination. If the Common
Stock is traded in the over-the-counter market, the Fair Market Value per share shall be the
average of the closing bid and asked prices on the date of determination.

     (b) Stock Listed But No Shares Traded. If the Common Stock or other securities are
listed on a national securities exchange or on the National Market System but no shares of
the Common Stock or other securities are traded on the date of
determination but there were
shares traded on dates within a reasonable period before the date of determination, the Fair
Market Value shall be the closing price of the Common Stock or other securities on the most
recent date before the date of determination. If the Common Stock or other securities are
regularly traded in the over-the-counter market but no shares of the Common Stock or other
securities are traded on the date of determination (or if records of such trades are
unavailable or burdensome to obtain) but there were shares traded on dates within a
reasonable period before the date of determination, the Fair Market Value shall be the
average of the closing bid and asked prices of the Common Stock or other securities on the
most recent date before the date of determination.

     (c) Stock Not Listed. If the Common Stock or other securities are not listed on a
national securities exchange or on the National Market System and are not regularly traded
in the over-the-counter market, then the Board shall determine the Fair Market Value of the
Common Stock or other securities from all relevant available facts, which may include the
average of the closing bid and ask prices reflected in the over-the-counter market on a date
within a reasonable period either before or after the date of determination, or opinions of
independent experts as to value and may take into account any recent sales and purchases of
such Common Stock or other securities to the extent they are representative.

The Board’s determination of Fair Market Value, which shall be made pursuant to the foregoing
provisions, shall be final and binding for all purposes of this Plan.

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     1.20 Fully Diluted Shares of Common Stock shall mean, as of the date of determination, all
issued and outstanding shares of the Common Stock and all shares of Common Stock reserved for
issuance pursuant to the exercise of stock options, warrants or any other convertible securities or
other rights to acquire Common Stock of the Corporation.

     1.21 Merger Event Consideration shall mean the Fair Market Value of all cash, debt or equity
securities and other property paid or issued by the acquiring entity to the Corporation and/or its
shareholders in consideration of such Merger Event, less any expenses or liabilities incurred by
the Corporation’s shareholders in connection with the Merger Event. The Fair Market Value of any
debt securities constituting a part of the Merger Event Consideration shall be equal to the
discounted present value of such debt securities. The Fair Market Value of any Common Stock or
other securities shall be determined in accordance with Section 1.19 herein; the Fair Market Value
of any other property other than Common Stock or other securities or debt securities constituting a
part of the Merger Event Consideration shall be determined by the Board in good faith based upon
all relevant facts and circumstances. The Board’s determination of the Fair Market Value of the
Merger Event Consideration, which shall be made pursuant to the foregoing provisions, shall be
final and binding for all purposes of this Plan. For purposes of this Plan, the Merger Event
Consideration shall be determined without any deductions for the payment of the Bonus Pool pursuant
hereto.

     1.22 Participant shall mean an Eligible Individual (1) who has met the requirements for
participation in this Plan by being selected by the Board to be a Participant hereunder, (2) who
has received an executed Participation Form from the Board, and (3) who has a right to a benefit
under this Plan.

     1.23 Participation Form shall mean the written document (the form of which is attached to this
Plan as Exhibit A), which is given to an Eligible Individual to evidence such Eligible
Individual’s status as a Participant in this Plan. A Participant’s Participation Form shall set
forth the name of the Eligible Individual who is a Participant, the number of Units awarded to such
Eligible Individual, the date on which such Units are awarded, and any other information, which the
Board deems desirable. A Participation Form shall only be effective when validly executed by the
Board, and shall be deemed validly executed by the Board only when it has been executed by at least
two members of the Board.

     1.24 Person shall mean any individual, organization, corporation, partnership or other entity.

     1.25 Public Offering shall mean a firmly committed underwritten public offering of Common
Stock by the Corporation pursuant to an effective registration statement under the Securities Act
other than pursuant to a registration statement on Form S-4 or Form S-8 or any similar or successor
form, provided that the proceeds of such public offering amounts to at least $30,000,000, net of
underwriting discounts, commissions, costs and expenses.

     1.26 Public Offering Price shall mean the price at which shares of Common Stock are sold to
the public pursuant to the Public Offering (excluding underwriting discounts, commissions, costs
and expenses).

     1.27 Public Offering Valuation shall mean the sum of (x) the product of (i) the number of
Fully Diluted Shares of Common Stock of the Company immediately prior to giving effect to the
Public Offering multiplied by (ii) the Public Offering Price and (y) the aggregate amount, if any,
that is paid to the holders of the Preferred Stock of the Corporation in respect of such shares in
connection with the Public Offering (whether in respect of accrued dividends on such shares, in
redemption of such shares or otherwise).

     1.28 Plan shall mean this SciQuest, Inc. Exit Event Bonus Plan, as contained herein, as the
same shall be from time to time amended.

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     1.29 Qualified Termination of Employment shall mean, with respect to a Participant, a
termination of the employment of a Participant because of (1) the death of the Participant, (2) the
Disability of the Participant, or (3) the involuntary termination of employment of the Participant
by the Corporation other than for Cause.

     1.30 Units shall mean units or shares of the Bonus Pool awarded to a Participant by the Board
as shown on the Participant’s Participation Form, and shall determine a Participant’s portion of
the Bonus Pool in accordance with Section 1.6 and Article 3 hereof.

ARTICLE 2

ELIGIBILITY AND PARTICIPATION

     2.1 Attainment of Participant Status. Any Eligible Individual may become a Participant in
this Plan by (1) being selected to be a Participant hereunder by the Board and (2) receiving an
executed Participation Form evidencing such status. The Board shall have complete and absolute
discretion to decide which Eligible Individuals shall be become Participants in this Plan, and the
Board’s decisions regarding Participant status shall be final and binding on all individuals. In
no event may any Eligible Individual become a Participant after the occurrence of an Exit Event.

     2.2 Continued Participation. After having become a Participant in this Plan, an Eligible
Individual shall continue to be a Participant in this Plan until the earlier of (1) his termination
of employment (other than a Qualified Termination of Employment), (2) the complete payment of his
Bonus Benefit, if any, or (3) termination of this Plan in accordance with Section 6.3 below.
However, whether a Participant shall actually receive or be entitled to a Bonus Benefit under this
Plan at any time shall be determined pursuant to Article 3 below.

ARTICLE 3

BONUS BENEFITS

     3.1 Authorized Number of Units. The maximum number of Units that may be issued under this
Plan is one hundred (100).

     3.2 Initial Award of Units. Each Participant shall, upon being admitted as a Participant to
this Plan pursuant to Article 2 above, be granted by the Board a number of Units, subject to
Section 3.3 below. Such Units shall determine the Participant’s Bonus Benefit, if any, under this
Plan, as provided in this Article 3, and shall be indicated on the Participant’s Participation
Form.

     3.3 Additional Award of Units. Subsequent to a Participant’s initial participation date, the
Board may decide to award the Participant an additional number of Units. If such an award is
granted by the Board, the Board shall execute a new Participation Form for the Participant, which
indicates the new total aggregate number of Units of the Participant. If a Participant has
received two or more Participation Forms, the number of Units of the Participant shall always be
equal to the number of Units shown on the Participation Form of the Participant, which has the
largest number of Units. Once Units are awarded, they may not be decreased with respect to a
Participant.

     3.4 Accrual of Bonus Benefits. No Participant in this Plan shall accrue any Bonus Benefit
under this Plan unless and until the day immediately preceding the date of an Exit Event. Upon the
day immediately preceding the date of an Exit Event, each Participant who is a Benefiting
Participant with respect to such Exit Event shall immediately accrue a Bonus Benefit. Such Bonus
Benefit shall be paid to the Participant as described in Article 4, and each Participant who is not
a Benefiting Participant with respect to such Exit Event shall not accrue any Bonus Benefit.

     3.5 Adjustment of Applicable Percentage. In the event that the number of Fully Diluted Shares
of Common Stock immediately prior to the Exit Event is not equal to 28,237,815 (which number shall
be adjusted to reflect stock dividends, stock splits or recapitalizations with respect to the
Common

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Stock occurring subsequent to the Effective Date), the Applicable Percentage shall be adjusted
by multiplying the otherwise applicable Applicable Percentage by the quotient of 28,237,815 (which
number shall be adjusted to reflect subsequent stock dividends, stock splits or recapitalizations
with respect to the Common Stock occurring subsequent to the Effective Date) divided by the number
of Fully Diluted Shares of Common Stock immediately prior to the Exit Event.

ARTICLE 4

PAYMENT OF BONUS BENEFITS

     4.1 General Liability for Payment. All payment obligations to Participants created under this
Plan shall be the sole responsibility, liability and obligation of the Corporation.

     4.2 Timing of Payment of Benefit. In the case of an Exit Event that is a Merger Event, a
Participant shall receive his or her Bonus Benefit, if any, at the same time and on the same terms
and conditions as the Company’s stockholders receive their Merger Event Consideration. For
purposes of clarity, and without limiting the generality of the foregoing, (i) to the extent that
the Merger Event Consideration is paid in installments, the Bonus Benefit shall be paid in like
installments and (ii) to the extent that the Merger Event Consideration is subject to any escrow
holdbacks, earn-outs or other contingencies, the Bonus Benefit shall be subject to such escrow
holdbacks, earn-outs or other contingencies in a like manner, and (iii) to the extent that any
portion of the Merger Event Consideration is not actually paid, a proportionate amount of a
Participant’s Bonus Benefit shall not actually be paid. It is the intent of the foregoing that
Participants shall receive their Bonus Benefits in a manner that is timed to correspond
proportionately to the payment of the Merger Event Consideration, and that the deferral of
compensation set for in this Plan shall meet the requirements of Prop. Treas. Reg.
§1.409A-3(g)(5)(iv) and the corresponding provisions of any future guidance or regulations issued
under Code §409A relating to delayed payments pursuant to a change of control event. Thus, to
satisfy this intent, to the extent that a portion of a Bonus Benefit has not been paid within five
(5) years of the date of the Merger Event, then such portion of the Bonus Benefit shall nonetheless
be paid in a single lump sum payment on the fifth (5th) anniversary of the date of the
Merger Event. In the case of an Exit Event that is a Public Offering, a Participant shall receive
his or her Bonus Benefit, if any, no later than thirty (30) days following the consummation of the
Public Offering.

     4.3 Form of Payment of Benefit. In the event of an Exit Event that is a Merger Event, then a
Participant shall generally receive his Bonus Benefit, if any, in the same type or form of property
as the Merger Event Consideration. In the event of an Exit Event that is a Public Offering, the
Bonus Benefit, if any, shall be paid in the form of Common Stock. For purposes of calculating the
number of shares to be so issued, the shares of shares of Common Stock shall be valued at the
Public Offering Price.

     4.4 Death of Participant. In the event of the death of a Participant following the accrual of
the Bonus Benefit, if any, but prior to the payment of such Participant’s Bonus Benefit, if any,
pursuant to this Plan, such Participant’s Bonus Benefit shall instead be paid to the Participant’s
Beneficiary in the same form and manner as if the Participant had not died, with such Beneficiary
determined as of the date on which such subsequently payable amounts are paid and not on the date
of the Participant’s death.

     4.5 Additional Conditions to Payment of Bonus Benefit.

     (a) If the Exit Event is a Public Offering, payment of the Bonus Benefit to a Participant
shall be conditioned upon the execution by such Participant, to the extent requested by the
Corporation and the managing underwriter of the Public Offering, of an agreement (in the form
provided by such managing underwriter) to not sell or otherwise transfer or dispose of any
securities of the Corporation (excluding securities acquired in the Public Offering or in the
public market after such offering) held by such Participant for a period of 180 days following the
effective date of the registration statement for the Public Offering; provided, that all
stockholders of the Corporation then holding at least five percent of the outstanding Common Stock
shall enter into similar agreements.

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     (b) If the Exit Event is a Merger Event and the payment of the Merger Event Consideration is
subject to any transfer or other restrictions or contractual obligations that apply to all
stockholders of the Corporation then holding at least five percent of the outstanding Common Stock,
then the payment of the Bonus Benefit to a Participant shall be conditioned upon such Participant
executing an agreement to be bound by all such transfer or other restrictions or contractual
obligations.

ARTICLE 5

ADMINISTRATION

     5.1 Powers and Responsibility. The Board shall have complete control of the administration of
the Plan hereunder, with all powers necessary to enable it to properly carry out its duties as set
forth in this Plan. The Board shall have the following duties and responsibilities:

     (a) to construe the Plan and to determine all questions that shall arise thereunder;

     (b) to have all powers elsewhere herein conferred upon it;

     (c) to provide procedures for determination of claims for benefits;

     (d) to determine the benefits of the Plan to which any Participant may be entitled;

     (e) to maintain and retain records relating to Participants;

     (f) to prepare and furnish to Participants all information required under federal law
or provisions of the Plan to be furnished to them;

     (g) to prepare and file or publish with appropriate government officials all reports
and other information required under law to be so filed or published;

     (h) to engage assistants and professional advisers.

     5.2 Delegation of Authority. The Board may delegate its authority under the Plan, in whole or
in part, to a Committee appointed by the Board consisting of not less than one (1) Director or to
one or more other persons to whom the powers of the Board hereunder may be delegated in accordance
with applicable law. The members of the Committee and any other persons to whom authority has been
delegated shall be appointed from time to time by, and shall serve at the discretion of, the Board.
The Committee or other delegate (if appointed) shall act according to the policies and procedures
set forth in the Plan and to those policies and procedures established by the Board, and the
Committee or other delegate shall have such powers and responsibilities as are set forth by the
Board. Reference to the Board in this Plan shall specifically include reference to the Committee
or other delegate where the Board has delegated its authority to the Committee or other delegate,
and any action by the Committee or other delegate pursuant to a delegation of authority by the
Board shall be deemed an action by the Board under the Plan. Notwithstanding the above, the Board
may assume the powers and responsibilities granted to the Committee or other delegate at any time,
in whole or in part.

     5.3 Records of Board. All acts and determinations of the Board shall be duly recorded, and
all such records, together with such other documents as may be necessary for the administration of
the Plan, shall be preserved in the custody of the Board.

     5.4 Reporting and Disclosure. The Board shall keep all individual and group records relating
to Participants and all other records necessary for the proper operation of the Plan. Such records
shall be made available to the Corporation and to any other person or entity which the Corporation
authorizes to see such records. The Board shall prepare and shall file as required by law or
regulation all reports, forms, documents and other items required by the Code and every other
relevant statute, each as amended, and any regulations thereunder. This provision shall not be
construed as imposing upon the Board the responsibility or authority for the preparation,
preservation, publication or filing of any

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document required to be prepared, preserved or filed by any other person or entity to whom
such responsibilities are delegated by law or by the Plan.

     5.5 Construction of the Plan. The Board shall take such steps as are considered necessary and
appropriate to remedy any inequity that results from incorrect information received or communicated
in good faith or as the consequence of an administrative error. The Board shall interpret the Plan
and shall determine the questions arising in the administration, interpretation and application of
the Plan. The Board shall correct any defect, reconcile any inconsistency or supply any omission
with respect to the Plan.

     5.6 Assistants and Advisors.

     (a) The Board shall have the right to hire, at the expense of the Corporation, such
professional assistants and consultants as it, in its sole discretion, deems necessary or
advisable.

     (b) The Board and the Corporation shall be entitled to rely upon all certificates and reports
made by an accountant or attorney selected pursuant to this section; the Board and the Corporation
shall be fully protected in respect to any action taken or suffered by them in good faith in
reliance upon the advice or opinion of any such actuary, accountant or attorney; and any action so
taken or suffered shall be conclusive upon each of them and upon all other persons interested in
the Plan.

     5.7 Indemnification. The Board and each member thereof shall be indemnified by the
Corporation against judgment amounts, settlement amounts (other than amounts paid in settlement to
which the Corporation does not consent) and expenses reasonably incurred by the Board or him in
connection with any action to which the Board or he may be a party (by reason of his service as a
member of a Board) except in relation to matters as to which the Board or he shall be adjudged in
such action to be personally guilty of gross negligence or willful misconduct in the performance of
its or his duties. The foregoing right to indemnification shall be in addition to such other
rights as such Board or each Board member may enjoy as a matter of law or by reason of insurance
coverage of any kind. Rights granted hereunder shall be in addition to and not in lieu of any
rights to indemnification to which such Board or each Board member may be entitled pursuant to the
by-laws of the Corporation.

ARTICLE 6

AMENDMENT OR TERMINATION

     6.1 Continuation of Plan. The Board reserves and retains the right to amend and/or terminate
this Plan as set forth in this Article.

     6.2 Right to Amend Plan.

     (a) Amendment by the Board. Subject to the provisions of subsection (b) below, the
Board reserves the right, at any time, to modify or amend, in whole or in part, any or all
of the provisions of the Plan, including specifically the right to make such amendments
effective retroactively, if necessary or desirable in the opinion of the Board in its sole
discretion.

     (b) Restrictions on Amendments. Except as follows, or as may be otherwise required by
law, there shall be no restrictions or limitations on the Board’s power to amend this Plan;
provided, however, the Board (i) may not amend this Plan to reduce the number of Units
previously awarded to a Participant without the written consent of such Participant and (ii)
may not amend this Plan in any way that materially and adversely affects the rights of
Participants under this Plan without the written approval of Participants holding at least a
majority of the Units then awarded and outstanding under the Plan.

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     6.3 Termination of Plan.

     (a) Termination by the Board. Subject to the provisions of subsection (b) below, the
Board reserves the right, at any time, to wholly or partially terminate the Plan if
necessary or desirable in the opinion of the Board in its sole discretion; provided,
however, the Board may only terminate this Plan with the written approval of Participants
holding at least a majority of the Units then awarded and outstanding under the Plan.

     (b) Automatic Termination of Plan Upon an Exit Event. Upon the occurrence of an Exit
Event, this Plan shall automatically terminate and no Participant shall accrue any Bonus
Benefit under this Plan after such Exit Event. However, such automatic termination shall
not affect the accrual of a Bonus Benefit pursuant to Article 3 hereof upon such Exit Event,
and any such accrual of a Bonus Benefit may not, after the occurrence of such Exit Event, be
reduced or eliminated. Bonus Benefits which become payable upon an Exit Event pursuant to
Article 3 hereof are not affected by such automatic termination, and the provisions of
Article 4 shall survive such automatic termination.

     (c) Automatic Termination of Plan Upon Passage of Time. As of the fifth anniversary of
the Effective Date, this Plan shall automatically terminate and no Participant shall accrue
any Bonus Benefit under this Plan after such date; provided, however, in the event that such
fifth anniversary occurs at a time that the Corporation either (i) is a party to a duly
executed and in effect term sheet for a Merger Event or (ii) has filed a registration
statement under the Securities Act with respect to a Public Offering, then this Plan shall
remain in effect for a period of ninety (90) days following such fifth anniversary and shall
automatically terminate on the ninety-first (91st) day thereafter.

ARTICLE 7

MISCELLANEOUS

     7.1 Participant’s Rights to Employment, Etc. Nothing contained in the Plan or any modification
thereof, or the creation of any fund, or the payment of any benefits, shall be construed to give
any individual or employee, whether or not a Participant, any rights to continued employment or
continued performance of services for the Corporation or any affiliate, any legal or equitable
right against the Corporation or an affiliate, or any officer, director or employee thereof, except
as herein provided.

     7.2 Claims Procedures.

     (a) Filing a Claim. All claims and requests for benefits under the Plan shall be
directed to the attention of the Board in writing. The writing must be reasonably calculated
to bring the claim to the attention of the Board.

     (b) Notification of Denial. If the Board determines that any individual who has claimed
a right to receive benefits under the Plan (the “claimant”) is not entitled to receive all
or any part of the benefits claimed, the claimant shall be informed in writing of the
specific reason or reasons for the denial, with specific reference to pertinent Plan
provisions on which the denial is based, a description of any additional material or
information necessary for the claimant to perfect the claim and an explanation of why said
material or information is necessary and a description of the review procedures set forth in
subsection (d) below.

     (c) Timing of Notification. The claimant shall be so notified of the Board’s decision
within 90 days after the receipt of the claim, unless special circumstances require an
extension of time for processing the claim. If such an extension of time for processing is
required, the Board shall furnish the claimant written notice of the extension prior to the
termination of the initial 90-day period. In no event shall said extension exceed a period
of 90 days from the end of said initial period. The extension notice shall indicate the
special circumstances requiring an extension of time and the date by which the Board expects
to render a final decision. If for any reason, the claimant is not notified within the
period described above, the claim shall be deemed

SciQuest, Inc. Second Amended and Restated Exit Event Bonus Plan

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denied and the claimant may then request review of said denial, subject to the
provisions of subsection (d) below.

     (d) Review Procedures. The claimant or his duly authorized representative may, within
60 days after notice of the Board’s decision, request a review of said decision, review
pertinent documents and submit to the Board such further information as will, in the
claimant’s opinion, establish his rights to such benefits. If upon receipt of this further
information, the Board determines that the claimant is not entitled to the benefits claimed,
it shall afford the claimant or his representative reasonable opportunity to submit issues
and comments in writing and to review pertinent documents. If the claimant wishes, he may
request in writing that the Board hold a hearing. The Board may, in its discretion,
schedule an opportunity for a full and fair hearing on the issue as soon as is reasonably
possible under the circumstances. The Board shall render its final decision with the
specific reasons therefor in writing and in a manner calculated to be understood by the
claimant.

     (e) Timing of Final Decision. The Board’s final decision shall include specific
references to the pertinent Plan provisions on which the decision is based, and shall be
transmitted to the claimant by certified mail within 60 days of receipt of claimant’s
request for such review, unless special circumstances require a further extension of time
for processing, in which case a decision shall be rendered as soon as possible, but not
later than 120 days after receipt of a request for review. If such an extension of time for
review is required because of special circumstances, written notice of the extension shall
be furnished to the claimant prior to the commencement of the extension. If the Board holds
regularly scheduled meetings at least quarterly, in lieu of the time period described above,
the Board’s decision on review shall be made by no later than the date of the meeting of the
Board which immediately follows its receipt of the request for review, unless said request
is filed within 30 days preceding the date of said meeting in which case a decision shall be
made no later than the date of the second meeting following its receipt of said request for
review. If special circumstances require a further extension of time for processing, a
decision shall be rendered not later than the third meeting of the Board following its
receipt of the request for review. If a decision on review is not furnished within the time
period described above, the claim shall be deemed denied on review.

     7.3 Arbitration of Disputed Claims. In the event that after a claimant has filed a claim for
benefits and has appealed his claim to the Board pursuant to the provisions of Section 7.2 above,
the Board and the claimant do not agree to the proper amount payable to the claimant under this
Plan, the claimant and the Board shall first attempt in good faith amicably to settle the matter by
mutual negotiations. If such negotiations are unsuccessful, such claim must be settled by final
and binding arbitration to be held in Raleigh, North Carolina, in accordance with the Commercial
Arbitration Rules, as amended from time to time, and in effect (the “Rules”) of the American
Arbitration Association. The procedure and law applicable during the arbitration of any claim
shall be both the Rules and the internal laws of the State of North Carolina, without giving effect
to principles of conflicts of laws, except that in the arbitration, the arbitrator must either
decide for the claimant’s position or for the Board’s position, and may not render any other
decision. Furthermore, the losing party shall pay to the winning party an amount equal to all
costs of the winning party which are associated with the arbitration, including the reasonable fees
of any attorney, accountant or other third party used to support the position of the winning party.

     7.4 Nonalienation or Assignment. Except as otherwise provided by applicable law, none of the
benefits under this Plan is subject to the claims of creditors of Participants, and will not be
subject to attachment, garnishment, or any other legal process whatsoever. A Participant may not
assign, sell, borrow on, or otherwise encumber any of his interest in the Plan, nor shall any such
benefits be in any manner liable for or subject to the deeds, contracts, liabilities, engagements,
or torts of any Participant.

     7.5 Payments to Others on Behalf of the Participant. In making any distribution to or for the
benefit of any incompetent Participant, or any other Participant who, in the opinion of the Board,
is incapable of properly using, expending, investing, or otherwise disposing of such distribution,
the Board, in its sole and complete discretion may, but need not, have the Corporation make such
distribution to a

SciQuest, Inc. Second Amended and Restated Exit Event Bonus Plan

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legal or natural guardian or other relative of any incompetent, or to any adult with whom such
person temporarily or permanently resides; and any such guardian, relative, or other person shall
have full authority and discretion to expend such distribution for the use and benefit of such
person; and the receipt of such guardian, relative, or other person shall be a complete discharge
to the Corporation, the Board and this Plan, without any responsibility on the part of the
Corporation or the Board to see to the application of amounts so distributed.

     7.6 Location of Payee; Unclaimed Benefits. In the event that all, or any portion, of the
distribution payable to a Participant hereunder shall, at the expiration of a reasonable time after
it has become payable, remain unpaid solely by reason of the inability of the Board, after sending
a registered letter, return receipt requested, to the last known address of such person, and after
further diligent effort, to ascertain the whereabouts of such person, the amount so distributable
shall be paid to a federally-insured financial institution in the name of the Participant.

     7.7 Governing Law. This Plan shall be administered in the United States of America, and its
validity, construction, and all rights hereunder shall be governed by the laws of the State of
Delaware. If any provision of the Plan shall be held invalid or unenforceable, the remaining
provisions hereof shall continue to be fully effective.

     7.8 Correction of Participants’ Bonus Benefits. If an error or omission is discovered in the
Bonus Benefit payable to a Participant, or in the amount distributed to a Participant, the Board
will make such equitable adjustments in the records of the Plan as may be necessary or appropriate
to correct such error or omission as of the date on which such error or omission is discovered, and
the Corporation shall, as directed by the Board, make such additional payment(s) to the Participant
as are necessary to equitably account for the error or omission.

     7.9 Recovery of Mistaken Payments. If any benefit is paid to a Participant in an amount that
is greater than the amount payable under the terms of the Plan, the Corporation shall recover the
excess benefit amount by eliminating or reducing the Participant’s future payments, if any, from
the Corporation. Whether or not further payments are payable to the Participant, the Board, in its
discretion, may employ such means as are available under applicable law to recover the excess
benefit amount on behalf of the Corporation from the Participant.

     7.10 Action of Corporation and Board. Except as may be specifically provided, any action
required or permitted to be taken by the Corporation or the Board may be taken on behalf of such
person by any entity or individual who has been delegated the proper authority.

     7.11 Corporation Records. Records of the Corporation as to an employee’s or individual’s
period(s) of employment or service and Compensation will be conclusive on all persons, unless
determined by the Board to be incorrect.

     7.12 Gender and Number. Wherever applicable, the masculine pronoun shall include the feminine
pronoun, and the singular shall include the plural.

     7.13 Headings. The titles in this Plan are inserted for convenience of reference; they
constitute no part of the Plan, and are not to be considered in the construction hereof.

     7.14 Liability Limited. To the extent permitted by applicable law, neither the Board, nor any
member thereof, nor the Corporation shall be liable for any acts of omission or commission in
administering the Plan, except for his or its own individual, willful misconduct. The Corporation
and each member of the Board shall be entitled to rely conclusively on all tables, valuations,
certificates, opinions and reports which shall be furnished by an actuary, accountant, insurance
company, counsel or other expert who shall be employed or engaged by the Board or the Corporation.

     7.15 Withholding. The Corporation shall have the power and the right to deduct or withhold an
amount sufficient to satisfy federal, state or local taxes, domestic or foreign, required by law or

SciQuest, Inc. Second Amended and Restated Exit Event Bonus Plan

Page 12

 

 

regulation to be withheld (“tax obligations”) with respect to payment of any Bonus Benefit.
To the extent that any portion of a Participant’s Bonus Benefit is to be paid in the form of
property and the Corporation must deduct or withhold an amount sufficient to satisfy tax
obligations, the Corporation shall satisfy such tax obligations by withholding a portion of such
property sufficient to satisfy such amount based upon the Fair Market Value of the property as of
the date on which such federal, state or local taxes are paid, and satisfying the tax obligations
in cash.

     7.16 Supersedes Existing Plan. This Plan amends, restates and supersedes in its entirety the
Existing Plan.

SciQuest, Inc. Second Amended and Restated Exit Event Bonus Plan

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     IN WITNESS WHEREOF, the Corporation has caused this Plan to be executed by its duly authorized
officers and its corporate seal to be affixed hereto, all as of this 29th day of April, 2009.

	 	 	 	 	 
	 	CORPORATION:

SciQuest, Inc.

 	 
	 	By:  	/s/ Stephen J. Wiehe 	 
	 	 	Stephen J. Wiehe,  Chief Executive Officer 	 
	 

SciQuest, Inc. Second Amended and Restated Exit Event Bonus Plan

Page 14exv10w6

Exhibit 10.6

AMENDMENT NO. 1

TO THE

SCIQUEST, INC.

SECOND AMENDED AND RESTATED EXIT EVENT BONUS PLAN

     The SciQuest, Inc. Second Amended and Restated Bonus Plan (the “Plan”) is hereby
amended as of the Effective Date (as defined herein) as follows:

     1. Section 6.3(c) of the Plan is hereby amended to read in its entirety as follows:

     (c) Automatic Termination of Plan Upon Passage of Time. As of October 28, 2010 (the
“Automatic Termination Date”), this Plan shall automatically terminate and no Participant
shall accrue any Bonus Benefit under this Plan after such date; provided, however, in the
event that the Automatic Termination Date occurs at a time that the Corporation either (i)
is a party to a duly executed and in effect term sheet for a Merger Event or (ii) has filed
a registration statement under the Securities Act with respect to a Public Offering, then
this Plan shall remain in effect for a period of ninety (90) days following the Automatic
Termination Date and shall automatically terminate on the ninety-first (91st) day
thereafter.

     2. Effective Date. The effective date of this Amendment is March 24, 2010 (the
“Effective Date”).

     3. Miscellaneous.

          (a) Capitalized terms not otherwise defined herein shall have the meanings given them in the
Plan.

          (b) Except as specifically amended hereby, the Plan shall otherwise remain in full force and
effect in accordance with its terms.

     IN WITNESS WHEREOF, the Company has caused this Amendment No. 1 to the SciQuest, Inc. Second
Amended and Restated Exit Event Bonus Plan to be executed as of the Effective Date.

	 	 	 	 	 
	 	SCIQUEST, INC.

 	 
	 	By:  	/s/ Stephen J. Wiehe
 	 
	 	 	Stephen J. Wiehe, Chief Executive Officer

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