Document:

exv10w53

Exhibit 10.53

THIS SECURITY HAS NOT BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES
COMMISSION OF ANY STATE IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF
1933, AS AMENDED (THE “SECURITIES ACT”), AND, ACCORDINGLY, MAY NOT BE OFFERED OR SOLD
EXCEPT PURSUANT TO AN EFFECTIVE REGISTRATION STATEMENT UNDER THE SECURITIES ACT OR PURSUANT TO AN
AVAILABLE EXEMPTION FROM, OR IN A TRANSACTION NOT SUBJECT TO, THE REGISTRATION REQUIREMENTS OF THE
SECURITIES ACT AND IN ACCORDANCE WITH APPLICABLE STATE SECURITIES LAWS AS EVIDENCED BY A LEGAL
OPINION OF COUNSEL TO THE TRANSFEROR TO SUCH EFFECT, THE SUBSTANCE OF WHICH SHALL BE REASONABLY
ACCEPTABLE TO THE COMPANY.

	 	 	 
	[                    ], 2009

	 	$[                    ]

[AMENDED AND RESTATED]

10% SENIOR SECURED DEBENTURE

     THIS [AMENDED AND RESTATED] 10% SENIOR SECURED DEBENTURE is one of a series of duly authorized
and issued 10% Senior Secured Debentures (the “Debentures”) of Intraop Medical Corporation,
a Nevada corporation, having a principal place of business at 570 Del Rey Avenue, Sunnyvale, CA
94085 (the “Company”).

     FOR VALUE RECEIVED, the Company promises to pay to [                                        ], or its
registered assigns (the “Holder”), to the extent not already repaid or converted in
accordance with the terms hereof, the principal sum of $[                    ] on the earlier of (i) June 30,
2009 or (ii) the date the Company closes an issuance, or series of issuances, of promissory notes
convertible into shares of its Common Stock with gross aggregate proceeds received by the Company
of not less than $4,000,000, or such earlier date as this Debenture is required or permitted to be
repaid as provided hereunder (the “Maturity Date”), and to pay interest to the Holder on
the then outstanding principal amount of this Debenture in accordance with the provisions hereof.
This Debenture is subject to the following additional provisions:

     Section 1. Definitions. For the purposes hereof, in addition to the terms
defined elsewhere in this Debenture: (a) capitalized terms not otherwise defined herein have the
meanings given to such terms in the Purchase Agreement, and (b) the following terms shall have the
following meanings:

     “Business Day” means any day except Saturday, Sunday and any day which shall be
a federal legal holiday in the United States or a day on which banking institutions in the
State of New York are authorized or required by law or other government action to close.

     “California Courts” shall have the meaning set forth in Section 8(e).

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     “Change of Control Transaction” means the occurrence after the date hereof of
any of (i) an acquisition after the date hereof by an individual or legal entity or “group”
(as described in Rule 13d-5(b)(1) promulgated under the Exchange Act), other than pursuant
to the Transaction Documents, of effective control (whether through legal or beneficial
ownership of capital stock of the Company, by contract or otherwise) of in excess of 40% of
the voting securities of the Company, (ii) the Company merges into or consolidates with any
other Person, or any Person merges into or consolidates with the Company and, after giving
effect to such transaction, the stockholders of the Company immediately prior to such
transaction own less than 60% of the aggregate voting power of the Company or the successor
entity of such transaction, (iii) the Company sells or transfers its assets, as an entirety
or substantially as an entirety, to another Person and the stockholders of the Company
immediately prior to such transaction own less than 60% of the aggregate voting power of the
acquiring entity immediately after the transaction, (iv) a replacement at one time or within
a three year period of more than one-half of the members of the Company’s board of directors
which is not approved by a majority of those individuals who are members of the board of
directors on the date hereof (or by those individuals who are serving as members of the
board of directors on any date whose nomination to the board of directors was approved by a
majority of the members of the board of directors who are members on the date hereof), or
(v) the execution by the Company of an agreement to which the Company is a party or by
which it is bound, providing for any of the events set forth above in (i) or (iv).

     “Common Stock” means the common stock, par value $0.001 per share, of the
Company and stock of any other class of securities into which such securities may hereafter
have been reclassified or changed into.

     “Debenture Register” shall have the meaning set forth in Section 2(c).

     “Event of Default” shall have the meaning set forth in Section 7.

     “Exchange Act” means the Securities Exchange Act of 1934, as amended, and the
rules and regulations promulgated thereunder.

     “Fundamental Transaction” shall mean (A) the Company effects any merger or
consolidation of the Company with or into another Person, (B) the Company effects any sale
of all or substantially all of its assets in one or a series of related transactions, (C)
any tender offer or exchange offer (whether by the Company or another Person) is completed
pursuant to which holders of Common Stock are permitted to tender or exchange their shares
for other securities, cash or property, or (D) the Company effects any reclassification of
the Common Stock or any compulsory share exchange pursuant to which the Common Stock is
effectively converted into or exchanged for other securities, cash or property.

     “Late Fees” shall have the meaning set forth in Section 2(d).

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     “Monthly Payment Amount” shall mean the interest to be paid on each Monthly
Payment Date in accordance with the terms of this Debenture.

     “Monthly Payment Date” means the last day of each month, commencing on the
first such date after the Original Issue Date and ending upon June 30, 2009.

     “Original Issue Date” shall mean October 3, 2008.

     “Permitted Indebtedness” shall mean the individual and collective reference to
the following: (a) up to, in the aggregate during the term of this Debenture, $2,000,000 of
new Indebtedness, (b) Indebtedness incurred in connection with the Purchase Agreement, (c)
Indebtedness existing on the date of the Purchase Agreement, (d) up to $6,000,000 in
connection with the Company’s revolving inventory and sales contract financing agreement
with E.U. Capital and (e) up to $1,040,000 of Indebtedness related to Mobetron S/N 28 to be
placed under lease to a customer in Fort Meyers, Florida.

     “Permitted Lien” shall mean the individual and collective reference to the
following: (a) Liens for taxes, assessments and other governmental charges or levies not yet
due or Liens for taxes, assessments and other governmental charges or levies being contested
in good faith and by appropriate proceedings for which adequate reserves (in the good faith
judgment of the management of the Company) have been established in accordance with GAAP;
(b) Liens imposed by law which were incurred in the ordinary course of business, such as
carriers’, warehousemen’s and mechanics’ Liens, statutory landlords’ Liens, and other
similar Liens arising in the ordinary course of business, and (x) which do not individually
or in the aggregate materially detract from the value of such property or assets or
materially impair the use thereof in the operation of the business of the Company or (y)
which are being contested in good faith by appropriate proceedings, which proceedings have
the effect of preventing the forfeiture or sale of the property or asset subject to such
Lien; and (c) Liens on Receivables and the Company’s “inventory” (as such term is used in
the Security Agreement) incurred solely in connection with a Permitted Indebtedness under
clause (a), (d) and (e) of the definition of Permitted Indebtedness.

     “Person” means a corporation, an association, a partnership, organization, a
business, an individual, a government or political subdivision thereof or a governmental
agency.

     “Purchase Agreement” means the Debenture Purchase Agreement, dated as of
September 30, 2008 and amended on or around the date hereof, to which the Company, the
original Holder and other investors signatory thereto are parties, as further amended,
modified or supplemented from time to time in accordance with its terms.

     “Trading Day” means a day on which the Common Stock is traded on a Trading
Market.

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     “Trading Market” means the following markets or exchanges on which the Common
Stock is listed or quoted for trading on the date in question: the Nasdaq SmallCap Market,
the American Stock Exchange, the New York Stock Exchange, the Nasdaq National Market or the
OTC Bulletin Board.

     “Transaction Documents” shall have the meaning set forth in the Purchase
Agreement.

     Section 2. Payments.

     a) Monthly Payment. On each Monthly Payment Date, the Company shall pay the
Monthly Payment Amount.

     b) Balloon Payment. On the Maturity Date, all outstanding principal, plus
accrued but unpaid interest thereon, plus all other outstanding amounts due to the Holder
shall be paid to the Holder (except that, if such date is not a Business Day, then such
payment shall be due on the next succeeding Business Day).

     c) Interest Calculations. Interest on the then outstanding principal amount of
this Debenture shall accrue at the rate of 10% per annum, payable on the Monthly Payment
Date and on the Maturity Date. Interest shall be calculated on the basis of a 360-day year
and shall accrue daily commencing on the Original Issue Date until payment in full of the
principal sum, together with all accrued and unpaid interest and other amounts which may
become due hereunder, has been made. Interest hereunder will be paid to the Person in whose
name this Debenture is registered on the records of the Company regarding registration and
transfers of this Debenture (the “Debenture Register”).

     d) Late Fee. All overdue accrued and unpaid interest to be paid hereunder
shall entail a late fee at the rate of 18% per annum (or such lower maximum amount of
interest permitted to be charged under applicable law) (“Late Fees”) which will
accrue daily, from the date such interest is due hereunder through and including the date of
payment.

     e) Prepayment. The Company may prepay all or any portion of the principal
amount of this Debenture without the prior written consent of the Holder at any time.

     Section 3. Conversion.

     a) Qualified Preferred Financing. In the event that (i) the Company closes an
issuance, or series of issuances, of shares of its Preferred Stock (the “New
Securities”)
with gross aggregate proceeds received by the Company of not less than $1,000,000 (a
“Qualified Preferred Financing”) and (ii) this Debenture has not been paid in full,
then the entire outstanding principal balance and all unpaid accrued interest of this
Debenture shall convert at the sole option of the Holder into the number of shares of the
New

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Securities at a conversion price equal to the price per share paid by the investors
purchasing the New Securities (the “Conversion Price”) on the same terms and
conditions as given to such investors.

     b) Hart-Scott-Rodino. Notwithstanding any provision to the contrary herein,
this Debenture shall convert only (i) if no filing is required in connection with the
conversion in order to comply with the Hart-Scott-Rodino Antitrust Improvements Act of 1976
(a “Required Filing”); (ii) after a Required Filing has been filed and upon the
expiration or termination of any waiting period required in connection with such Required
Filing; or (iii) with the prior written consent of the Holder (such prior written consent to
specifically waive the provisions of this Section 3(b)).

     c) Conversion Procedures. Upon conversion of this Debenture pursuant to
Section 3(a) above, the Holder shall surrender this Debenture, duly endorsed, at the
principal office of the Company, and the Company shall, at its expense, upon receipt of this
Debenture, duly endorsed, promptly deliver or cause to be delivered to the Holder a
certificate or certificates (bearing such legends as may be required) representing that
number of fully paid and non-assessable shares of New Securities into which this Debenture
may be converted, and any other securities or property to which the Holder may be entitled
to receive upon conversion of this Debenture, including a check payable to the Holder for
fractional shares as described in Section 3(d) below. The conversion of this Debenture
shall be deemed to have been made on the date of the closing of the Qualified Preferred
Financing pursuant to Section 3(a) above and the Holder shall be treated for all purposes as
the record holder of such shares of New Securities as of such date.

     d) Fractional Shares. No fractional shares shall be issued upon conversion of
this Debenture. In lieu thereof, the Company shall pay to the Holder an amount in cash
equal to the product obtained by multiplying the New Securities by the fraction of a share
not issued upon such conversion.

     Section 4. Warrant Coverage.

     a) Issuance of Warrant. Concurrently with the issuance of this Debenture, the
Company shall issue to the Holder (or an affiliate of the Holder designated in writing to
the Company), a warrant (the “Warrant”) exercisable for the number of shares of the
Company’s Common Stock as follows: twenty-five percent (25%) multiplied by the principal
balance of this Debenture then outstanding, divided by (b) $0.028.

     b) Exercise Price. The exercise price of the Warrant shall be $0.028 per
share.

     c) Agreement. The Company and the Holder, having adverse interests and as a
result of arm’s length bargaining, agree that:

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	 	i.	 	Neither the Holder nor any affiliate of the Holder
has rendered any services to the Company in connection with this
Debenture;
	 
	 	ii.	 	The Warrants are not to be issued as compensation;
	 
	 	iii.	 	The fair market value of this Debenture, if issued
apart from the Warrant is $[                                        ], and the aggregate fair
market value of the Warrant, if issued apart from this Debenture, is
$[                                        ]; and
	 
	 	iv.	 	All tax returns and other information return of the
Company and the Holder relative to this Debenture and the Warrant issued
pursuant hereto shall consistently reflect the matters agreed to in
clauses (i) through (iii) above.

     Section 5. Registration of Transfers and Exchanges.

     a) Different Denominations. This Debenture is exchangeable for an equal
aggregate principal amount of Debentures of different authorized denominations, as requested
by the Holder surrendering the same. No service charge will be made for such registration
of transfer or exchange; provided, however, the Company shall not be
required to exchange this Debenture for denominations of less than the greater of $50,000
and the principal amount of this Debenture then outstanding. No service charge will be made
for such registration of transfer or exchange.

     b) Investment Representations. This Debenture has been issued subject to
certain investment representations of the original Holder set forth in the Purchase
Agreement and may be transferred or exchanged only in compliance with the Purchase Agreement
and applicable federal and state securities laws and regulations.

     c) Reliance on Debenture Register. Prior to due presentment to the Company for
transfer of this Debenture, the Company and any agent of the Company may treat the Person in
whose name this Debenture is duly registered on the Debenture Register as the owner hereof
for the purpose of receiving payment as herein provided and for all other purposes, whether
or not this Debenture is overdue, and neither the Company nor any such agent shall be
affected by notice to the contrary.

Section 6. Negative Covenants. So long as any portion of this Debenture is
outstanding, the Company will not directly or indirectly:

     a) other than Permitted Indebtedness, enter into, create, incur, assume, guarantee or
suffer to exist any indebtedness for borrowed money of any kind, including but not limited
to, a guarantee, on or with respect to any of its property or assets now owned or hereafter
acquired or any interest therein or any income or profits therefrom;

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     b) other than Permitted Liens, enter into, create, incur, assume or suffer to exist any
liens of any kind, on or with respect to any of its property or assets now owned or
hereafter acquired or any interest therein or any income or profits therefrom;

     c) amend its certificate of incorporation, bylaws or other charter documents so as to
materially and adversely affect any rights of the Holder;

     d) repay, repurchase or offer to repay, repurchase or otherwise acquire more than a
de minimis number of shares of its Common Stock or Common Stock Equivalents;

     e) enter into any agreement with respect to any of the foregoing; or

     f) pay cash dividends or distributions on any equity securities of the Company.

     Section 7. Events of Default.

     a) “Event of Default”, wherever used herein, means any one of the following
events (whatever the reason and whether it shall be voluntary or involuntary or effected by
operation of law or pursuant to any judgment, decree or order of any court, or any order,
rule or regulation of any administrative or governmental body):

     i. any default in the payment of (A) the principal amount of any Debenture, or
(B) interest (including Late Fees) on, or liquidated damages in respect of, any
Debenture, as and when the same shall become due and payable (whether on the
Maturity Date or by acceleration or otherwise) which default, solely in the case of
an interest payment or other default under clause (B) above, is not cured, within 5
Trading Days;

     ii. the Company shall fail to observe or perform any other covenant or
agreement contained in (A) this Debenture or (B) any of the other Transaction
Documents, which failure is not cured, if possible to cure, within the earlier to
occur of (A) 15 Trading Days after notice of such default sent by the Holder or by
any other Holder and (B) 20 Trading Days after the Company shall become or should
have become aware of such failure;

     iii. a default or event of default (subject to any grace or cure period
provided for in the applicable agreement, document or instrument) shall occur under
(A) any of the Transaction Documents or (B) any other material agreement,
lease, document or instrument to which the Company is bound and which default
or event of default could have a Material Adverse Effect on the Company;

     iv. any representation or warranty made herein or in any other Transaction
Document shall be untrue or incorrect in any material respect as of the date when
made or deemed made;

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     v. (i) the Company shall commence a case, as debtor, under any applicable
bankruptcy or insolvency laws as now or hereafter in effect or any successor
thereto, or the Company commences any other proceeding under any reorganization,
arrangement, adjustment of debt, relief of debtors, dissolution, insolvency or
liquidation or similar law of any jurisdiction whether now or hereafter in effect
relating to the Company thereof or (ii) there is commenced a case against the
Company thereof, under any applicable bankruptcy or insolvency laws, as now or
hereafter in effect or any successor thereto which remains undismissed for a period
of 60 days; or (iii) the Company is adjudicated by a court of competent jurisdiction
insolvent or bankrupt; or any order of relief or other order approving any such case
or proceeding is entered; or (iv) the Company thereof suffers any appointment of any
custodian or the like for it or any substantial part of its property which continues
undischarged or unstayed for a period of 60 days; or (v) the Company thereof makes a
general assignment for the benefit of creditors; or (vi) the Company shall fail to
pay, or shall state that it is unable to pay, or shall be unable to pay, its debts
generally as they become due; or (vii) the Company thereof shall call a meeting of
its creditors with a view to arranging a composition, adjustment or restructuring of
its debts; or (viii) the Company thereof shall by any act or failure to act
expressly indicate its consent to, approval of or acquiescence in any of the
foregoing; or (ix) any corporate or other action is taken by the Company thereof for
the purpose of effecting any of the foregoing;

     vi. the Company shall default in any of its obligations under any mortgage,
credit agreement or other facility, indenture agreement, factoring agreement or
other instrument under which there may be issued, or by which there may be secured
or evidenced any indebtedness for borrowed money or money due under any long term
leasing or factoring arrangement of the Company in an amount exceeding $250,000,
whether such indebtedness now exists or shall hereafter be created and such default
shall result in such indebtedness becoming or being declared due and payable prior
to the date on which it would otherwise become due and payable.

     vii. the Company shall be a party to any Change of Control Transaction or
Fundamental Transaction, shall agree to sell or dispose of all or in excess of 33%
of its assets in one or more transactions (whether or not such sale would constitute
a Change of Control Transaction) or shall redeem or repurchase more than a de
minimis number of its outstanding shares of Common Stock or
other equity securities of the Company (other than repurchases of shares of
Common Stock or other equity securities of departing officers and directors of the
Company; provided such repurchases shall not exceed $250,000, in the aggregate, for
all officers and directors during the term of this Debenture);

     viii. the Company shall redeem more than a de minimis number of Common Stock
Equivalents; and

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     ix. other than Permitted Liens, the Company shall fail, at any time, to have a
perfected, first priority security interest in all Collateral (as defined in the
Security Agreement) and all other assets pledged to Holder as security for the loan
evidenced by this Debenture.

     b) Remedies Upon Event of Default. If any Event of Default occurs, the full
principal amount of this Debenture, together with interest and other amounts owing in
respect thereof, to the date of acceleration shall become, at the Holder’s election,
immediately due and payable in cash. Commencing 5 days after the occurrence of any Event
of Default that results in the eventual acceleration of this Debenture, the interest rate on
this Debenture shall accrue at the rate of 18% per annum, or such lower maximum amount of
interest permitted to be charged under applicable law. Upon the payment in full of all
amounts owing under this Debenture the Holder shall promptly surrender this Debenture to or
as directed by the Company. The Holder need not provide and the Company hereby waives any
presentment, demand, protest or other notice of any kind, and the Holder may immediately and
without expiration of any grace period enforce any and all of its rights and remedies
hereunder and all other remedies available to it under applicable law. Such declaration may
be rescinded and annulled by Holder at any time prior to payment hereunder and the Holder
shall have all rights as a Debenture holder until such time, if any, as the full payment
under this Section 7(b) shall have been received by it. No such rescission or annulment
shall affect any subsequent Event of Default or impair any right consequent thereon.

     Section 8. Miscellaneous.

     a) Notices. Any and all notices or other communications or deliveries to be
provided by the Holder hereunder, including, without limitation, any Notice of Conversion,
shall be in writing and delivered personally, by facsimile, sent by a nationally recognized
overnight courier service, addressed to the Company, at the address set forth above, Attn:
Chief Financial Officer or such other address or facsimile number as the Company may specify
for such purposes by notice to the Holder delivered in accordance with this Section 8(a).
Any and all notices or other communications or deliveries to be provided by the Company
hereunder shall be in writing and delivered personally, by facsimile, sent by a nationally
recognized overnight courier service addressed to each Holder at the facsimile telephone
number or address of such Holder appearing on the books of the Company, or if no such
facsimile telephone number or address appears, at the principal place of business of the
Holder. Any notice or other
communication or deliveries hereunder shall be deemed given and effective on the
earliest of (i) the date of transmission, if such notice or communication is delivered via
facsimile at the facsimile telephone number specified in this Section 8(a) prior to 5:30
p.m. (New York City time), (ii) the date after the date of transmission, if such notice or
communication is delivered via facsimile at the facsimile telephone number specified in this
Section 8(a) later than 5:30 p.m. (New York City time) on any date and earlier than 11:59
p.m. (New York City time) on such date, (iii) the second Business Day following the date of
mailing, if sent by nationally recognized overnight courier service, or (iv) upon actual
receipt by the party to whom such notice is required to be given.

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     b) Absolute Obligation. Except as expressly provided herein, no provision of
this Debenture shall alter or impair the obligation of the Company, which is absolute and
unconditional, to pay the principal of, interest and liquidated damages (if any) on, this
Debenture at the time, place, and rate, and in the coin or currency, herein prescribed.
This Debenture is a direct debt obligation of the Company. This Debenture ranks
pari passu with all other Debentures now or hereafter issued under the terms
set forth herein.

     c) Security Interest. This Debenture is a direct debt obligation of the
Company and, subject to Permitted Liens and pursuant to the Security Documents, is secured
by a first priority security interest in all of the assets of the Company and certain other
collateral for the benefit of the Holders.

     d) Lost or Mutilated Debenture. If this Debenture shall be mutilated, lost,
stolen or destroyed, the Company shall execute and deliver, in exchange and substitution for
and upon cancellation of a mutilated Debenture, or in lieu of or in substitution for a lost,
stolen or destroyed Debenture, a new Debenture for the principal amount of this Debenture so
mutilated, lost, stolen or destroyed but only upon receipt of evidence of such loss, theft
or destruction of such Debenture, and of the ownership hereof, and indemnity, if requested,
all reasonably satisfactory to the Company.

     e) Governing Law. All questions concerning the construction, validity,
enforcement and interpretation of this Debenture shall be governed by and construed and
enforced in accordance with the internal laws of the State of Delaware, without regard to
the principles of conflicts of law thereof. Each party agrees that all legal proceedings
concerning the interpretations, enforcement and defense of the transactions contemplated by
any of the Transaction Documents (whether brought against a party hereto or its respective
affiliates, directors, officers, shareholders, employees or agents) shall be commenced in
the courts of the State of California located in Santa Clara County and the United States
District Court for the Northern District of California (the “California Courts”).
Each party hereto hereby irrevocably submits to the exclusive jurisdiction of the California
Courts for the adjudication of any dispute hereunder or in connection herewith or with any
transaction contemplated hereby or discussed herein (including with respect to the
enforcement of any of the Transaction Documents), and hereby irrevocably waives, and agrees
not to assert in any suit, action or proceeding, any claim that it is not personally subject
to the jurisdiction of any such court, or such California Courts are
improper or inconvenient venue for such proceeding. Each party hereby irrevocably
waives personal service of process and consents to process being served in any such suit,
action or proceeding by mailing a copy thereof via registered or certified mail or overnight
delivery (with evidence of delivery) to such party at the address in effect for notices to
it under this Debenture and agrees that such service shall constitute good and sufficient
service of process and notice thereof. Nothing contained herein shall be deemed to limit in
any way any right to serve process in any manner permitted by law. Each party hereto hereby
irrevocably waives, to the fullest extent permitted by applicable law, any and all right to
trial by jury in any legal proceeding arising out of or relating to this Debenture or the
transactions contemplated hereby. If either party shall commence an

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action or proceeding to
enforce any provisions of this Debenture, then the prevailing party in such action or
proceeding shall be reimbursed by the other party for its attorneys fees and other costs and
expenses incurred with the investigation, preparation and prosecution of such action or
proceeding.

     f) Modification; Waiver. No modification or waiver of any provision of this
Debenture or consent to departure therefrom shall be effective without the written consent
of (i) the Company and (ii) the Holder. The failure of the Company or the Holder to insist
upon strict adherence to any term of this Debenture on one or more occasions shall not be
considered a waiver or deprive that party of the right thereafter to insist upon strict
adherence to that term or any other term of this Debenture. Any waiver must be in writing.

     g) Severability. If any provision of this Debenture is invalid, illegal or
unenforceable, the balance of this Debenture shall remain in effect, and if any provision is
inapplicable to any person or circumstance, it shall nevertheless remain applicable to all
other persons and circumstances. If it shall be found that any interest or other amount
deemed interest due hereunder violates applicable laws governing usury, the applicable rate
of interest due hereunder shall automatically be lowered to equal the maximum permitted rate
of interest. The Company covenants (to the extent that it may lawfully do so) that it shall
not at any time insist upon, plead, or in any manner whatsoever claim or take the benefit or
advantage of, any stay, extension or usury law or other law which would prohibit or forgive
the Company from paying all or any portion of the principal of or interest on this Debenture
as contemplated herein, wherever enacted, now or at any time hereafter in force, or which
may affect the covenants or the performance of this indenture, and the Company (to the
extent it may lawfully do so) hereby expressly waives all benefits or advantage of any such
law, and covenants that it will not, by resort to any such law, hinder, delay or impeded the
execution of any power herein granted to the Holder, but will suffer and permit the
execution of every such as though no such law has been enacted.

     h) Next Business Day. Whenever any payment or other obligation hereunder shall
be due on a day other than a Business Day, such payment shall be made on the next succeeding
Business Day.

     i) Headings. The headings contained herein are for convenience only, do not
constitute a part of this Debenture and shall not be deemed to limit or affect any of the
provisions hereof.

     j) Usury. To the extent it may lawfully do so, the Company hereby agrees not
to insist upon or plead or in any manner whatsoever claim, and will resist any and all
efforts to be compelled to take the benefit or advantage of, usury laws wherever enacted,
now or at any time hereafter in force, in connection with any claim, action or proceeding
that may be brought by any Purchaser in order to enforce any right or remedy under any
Transaction Document. Notwithstanding any provision to the contrary contained in any
Transaction Document, it is expressly agreed and provided that the total liability of the

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Company under the Transaction Documents for payments in the nature of interest shall not
exceed the Maximum Rate, and, without limiting the foregoing, in no event shall any rate of
interest or default interest, or both of them, when aggregated with any other sums in the
nature of interest that the Company may be obligated to pay under the Transaction Documents
exceed such Maximum Rate. It is agreed that if the maximum contract rate of interest
allowed by law and applicable to the Transaction Documents is increased or decreased by
statute or any official governmental action subsequent to the date hereof, the new maximum
contract rate of interest allowed by law will be the Maximum Rate applicable to the
Transaction Documents from the effective date of such increase or decrease forward, unless
such application is precluded by applicable law. If under any circumstances whatsoever,
interest in excess of the Maximum Rate is paid by the Company to any Purchaser with respect
to indebtedness, if any, evidenced by the Transaction Documents, such excess shall be
applied by such Purchaser to the unpaid principal balance of any such indebtedness or be
refunded to the Company, the manner of handling such excess to be at such Purchaser’s
election in the event any principal amount remains outstanding.

     k) Assumption. Any successor to the Company or surviving entity in a
Fundamental Transaction shall (i) assume in writing all of the obligations of the Company
under this Debenture and the other Transaction Documents pursuant to written agreements in
form and substance satisfactory to the Holder (such approval not to be unreasonably withheld
or delayed) prior to such Fundamental Transaction and (ii) to issue to the Holder a new
debenture of such successor entity evidenced by a written instrument substantially similar
in form and substance to this Debenture, including, without limitation, having a principal
amount and interest rate equal to the principal amounts and the interest rates of the
Debentures held by the Holder and having similar ranking to this Debenture, and satisfactory
to the Holder (any such approval not to be unreasonably withheld or delayed). The
provisions of this Section 8(k) shall apply similarly and equally to successive Fundamental
Transactions and shall be applied without regard to any limitations of this Debenture.

     l) [Amended and Restated Debenture. This Debenture is issued in substitution
and exchange for, and not in satisfaction or payment of, the 10% Senior Secured Debenture
Due December 31, 2008, dated October 3, 2008, payable to the order
of the Holder (the “Existing Debenture”), and the indebtedness originally
evidenced by the Existing Debenture which is now evidenced by this Debenture shall be a
continuing indebtedness, and nothing herein contained shall be construed to deem the
Existing Debenture paid, or to release or terminate any lien given to secure the Existing
Debenture, which liens shall continue to secure the indebtedness evidenced by this
Debenture; provided that the Holder acknowledges that any default that may have existed on
the Existing Debenture shall be deemed satisfied and waived upon the issuance of this
Debenture.]

12

 

     IN WITNESS WHEREOF, the Company has caused this Debenture to be duly executed by a duly
authorized officer as of the date first above indicated.

	 	 	 	 	 
	 	INTRAOP MEDICAL CORPORATION

 	 
	 	By:  	 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 
	 	[HOLDER]

 	 
	 	By:  	 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 

13exv10w54

Exhibit 10.54

NEITHER THIS SECURITY NOR THE SECURITIES INTO WHICH THIS SECURITY IS EXERCISABLE HAVE BEEN
REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE IN
RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE
"SECURITIES ACT”), AND, ACCORDINGLY, MAY NOT BE OFFERED OR SOLD EXCEPT PURSUANT TO AN EFFECTIVE
REGISTRATION STATEMENT UNDER THE SECURITIES ACT OR PURSUANT TO AN AVAILABLE EXEMPTION FROM, OR IN A
TRANSACTION NOT SUBJECT TO, THE REGISTRATION REQUIREMENTS OF THE SECURITIES ACT AND IN ACCORDANCE
WITH APPLICABLE STATE SECURITIES LAWS AS EVIDENCED BY A LEGAL OPINION OF COUNSEL TO THE TRANSFEROR
TO SUCH EFFECT, WHICH SHALL BE REASONABLY ACCEPTABLE TO THE COMPANY.

WARRANT TO PURCHASE

COMMON STOCK OF

INTRAOP MEDICAL CORPORATION

WARRANT #CC-[__]

     FOR VALUE RECEIVED, subject to the terms and conditions herein set forth, [                    ] (“Holder”)
is entitled to purchase from Intraop Medical Corporation, a Nevada corporation (the “Company”), at
any time after the date hereof and prior to the Expiration Date (as defined below), at a price per
share as set forth in Section 1 hereof, the number of fully paid and non-assessable shares of
Common Stock of the Company as set forth in Section 2 hereof (the “Shares”).

     1. Warrant Price. The Warrant Price for each of the Shares purchasable hereunder
shall be two cents and eight tenths of a cent ($0.028) (the “Warrant Price”), subject to adjustment
as provided in Section 10.

     2. Number of Shares. The number of Shares issuable upon exercise of this Warrant
shall be [                                        ] ([                    ]), subject to adjustment as provided in Section 10.

     3. Expiration of Warrant. Subject to earlier termination in accordance with Section 8
below, this Warrant shall expire and shall no longer be exercisable after April 8, 2014 (the
“Expiration Date”).

     4. No Fractional Shares. This Warrant may not be exercised as to fractional Shares.

     5. No Stockholder Rights. This Warrant shall not entitle Holder to any of the rights
of a stockholder of the Company.

     6. Reservation of Shares. The Company covenants that during the period this Warrant
is exercisable it will reserve from its authorized and unissued shares of Common Stock a sufficient
number of shares to provide for the issuance of the maximum number of shares of Common Stock
issuable upon the exercise of this Warrant. The Company agrees that its issuance of this Warrant
shall constitute full authority to its officers to instruct the Company’s
transfer agent to issue the necessary certificates for shares of Common Stock upon the
exercise of this Warrant.

1.

 

     7. Exercise of Warrant.

          (a) This Warrant may be exercised by Holder, in whole or in part, at any time after the date
hereof and prior to the Expiration Date by the surrender of this Warrant at the principal office of
the Company, together with the Subscription Form attached hereto duly completed and executed,
accompanied by payment in full of the aggregate Warrant Price for the Shares being purchased upon
such exercise. In the event of exercise of this Warrant in compliance with the provisions hereof,
certificates for the Shares so purchased shall be delivered to Holder promptly and, unless this
Warrant has been fully exercised or expired, a new Warrant representing that portion of the Shares,
if any, with respect to which this Warrant will not then have been exercised, shall be issued to
Holder. The Warrant shall be deemed to have been exercised immediately prior to the close of
business on the date of its surrender for exercise as provided above, and Holder shall be treated
for all purposes as the holder of record of such shares as of the close of business on such date.

          In lieu of exercising this Warrant pursuant to the first paragraph of this Section 7(a),
Holder may elect to receive Shares equal to the value of this Warrant (or any portion thereof
remaining unexercised) by surrender of this Warrant at the principal office of the Company together
with the Subscription Form, in which event the Company shall issue to Holder a number of Shares
computed using the following formula:

	 	 	 
	X =

	 	Y (A-B) 
	 

	 	A

     Where  X= the number of Shares to be issued to Holder.

		Y=	 	 the number of Shares for which this Warrant is then being
exercised (at the date of such exercise).
	 
	 	A=	 	 the fair market value of one Share (at the date of such exercise).
	 
	 	B=	 	 the Warrant Price (as adjusted to the date of such exercise).

     For purposes of this subsection fair market value of one Share shall mean:

(i) The average of the closing bid and asked prices of the Common Stock quoted in
the NASDAQ National Market System or the Over-the-Counter market or the closing
price quoted on any exchange on which the Common Stock is listed, whichever is
applicable, as published in the Western Edition of The Wall Street Journal for the
five (5) trading days prior to the date of determination of the fair market value;
or

(ii) If the Common Stock is not publicly traded, the per share fair market value of
the Common Stock shall be determined in good faith by the Company’s Board of
Directors. If Holder disagrees with the determination by the Board of

2.

 

Directors of the fair market value of the Common Stock then such fair market value
shall be determined by an independent appraiser selected jointly by the Company and
Holder. The cost of such appraisal shall be paid equally by the Company and Holder.

          (b) As promptly as practicable on or after such date, the Company shall cause to be issued and
delivered to Holder a certificate or certificates for the number of full Shares issuable upon such
exercise.

          (c) Issuance of certificates for the Shares upon the exercise of this Warrant shall be made
without charge to the registered holder hereof for any issue or transfer tax or other incidental
expense with respect to the issuance of such certificates, all of which taxes and expenses shall be
paid by the Company, and such certificates shall be issued in the name of the registered holder of
this Warrant or in such name or names as may be directed by the registered holder of this Warrant;
provided, however, that in the event certificates for the Shares are to be issued in a name other
than the name of the registered holder of this Warrant, this Warrant, when surrendered for
exercise, shall be accompanied by the Assignment Form attached hereto duly executed by Holder
hereof, and provided further, that any such transfer shall comply with Section 9 hereof.

     8. Automatic Termination. In the event of the sale of all or substantially all the
capital stock, or substantially all the assets, of the Company in a merger, business combination,
or other form of business transaction with or into a third party in which the Company’s
stockholders do not own at least a majority of the outstanding voting securities of the surviving
corporation or business entity after such transaction, then the Company shall give Holder of this
Warrant at least thirty (30) days written notice of the proposed effective date and terms of such
offering, transaction or agreements, and if the Warrant has not been exercised before the effective
date of such transaction, then this Warrant and the rights hereunder shall be automatically
terminated.

     9. Transfer or Assignment of Warrant.

          (a) This Warrant, and any rights hereunder, may not be assigned or transferred, except as
provided herein and in accordance with and subject to the provisions of (i) applicable state
securities laws, and (ii) the Securities Act of 1933, as amended, and the rules and regulations
promulgated thereunder (such Act and such rules and regulations being hereinafter collectively
referred to as the “Securities Act”). Any purported transfer or assignment made other than in
accordance with this Section 9 shall be null and void and of no force and effect.

          (b) This Warrant, and any rights hereunder, may be transferred or assigned only with the prior
written consent of the Company, which shall be granted only upon receipt by the Company of an
opinion of counsel satisfactory to the Company that (i) the transferee is a person to whom this
Warrant may be legally transferred without registration under the Securities Act, and (ii) such
transfer will not violate any applicable law or governmental rule or regulation, including, without
limitation, any applicable federal or state securities law.

3.

 

          (c) Any assignment permitted hereunder shall be made by surrender of this Warrant to the
Company at its principal office with the Assignment Form annexed hereto duly executed and funds
sufficient to pay any transfer tax, if any. In such event, the Company shall, without charge,
execute and deliver a new Warrant in the name of the assignee named in such instrument of
assignment and this Warrant shall be promptly canceled.

     10. Adjustments to Shares.

          (a) If the outstanding shares of the Company’s Common Stock shall be subdivided into a greater
number of shares or a dividend in Common Stock shall be paid in respect of Common Stock, the
Warrant Price in effect immediately prior to such subdivision or at the record date of such
dividend shall simultaneously with the effectiveness of such subdivision or immediately after the
record date of such dividend be proportionately reduced. If outstanding shares of Common Stock
shall be combined into a smaller number of shares, the Warrant Price in effect immediately prior to
such combination shall, simultaneously with the effectiveness of such combination, be
proportionately increased. When any adjustment is required to be made in the Warrant Price, the
number of shares of Common Stock purchasable upon the exercise of this Warrant shall be changed to
the number determined by dividing (i) an amount equal to the number of shares issuable upon the
exercise of this Warrant immediately prior to such adjustment, multiplied by the Warrant Price in
effect immediately prior to such adjustment, by (ii) the Warrant Price in effect immediately after
such adjustment.

          (b) In case of any reclassification or change of the outstanding securities of the Company or
of any reorganization of the Company (or any other corporation the stock or securities of which are
at the time receivable upon the exercise of this Warrant) or any similar corporate reorganization
on or after the date hereof, then and in each such case the holder of this Warrant, upon the
exercise hereof at any time after the consummation of such reclassification, change,
reorganization, merger or conveyance, shall be entitled to receive, in lieu of the stock or other
securities and property receivable upon the exercise hereof prior to such consummation, the stock
or other securities or property to which such holder would have been entitled upon such
consummation if such holder had exercised this Warrant immediately prior thereto, all subject to
further adjustment as provided in Section 10(a); and in each such case, the terms of this Section
10 shall be applicable to the shares of stock or other securities properly receivable upon the
exercise of this Warrant after such consummation.

          (c) When any adjustment is required to be made in the number of shares of Common Stock
purchasable hereunder or the Warrant Price pursuant to this Section 10, the Company shall promptly
mail to the Holder a certificate setting forth (i) a brief statement of the facts requiring such
adjustment, (ii) the Warrant Price after such adjustment and (iii) the kind and amount of stock or
other securities or property into which this Warrant shall be exercisable after such adjustment.

     11. Loss, Theft, Destruction or Mutilation of Warrant. Upon receipt by the Company of
evidence reasonably satisfactory to it of the loss, theft, destruction or mutilation of this
Warrant, and in case of loss, theft or destruction, of indemnity or security reasonably
satisfactory to it, and upon reimbursement to the Company of all reasonable expenses incidental
thereto, and

4.

 

upon surrender and cancellation of this Warrant, if mutilated, the Company will make and
deliver a new warrant identical in tenor and date in lieu of this Warrant.

     12. General. This Warrant shall be governed by and interpreted in accordance with the
laws of the State of Delaware, except for its principles of conflicts of laws. The headings in
this Warrant are for purposes of convenience and reference only and shall not be deemed to
constitute a part hereof. Neither this Warrant nor any term hereof may be changed, waived,
discharged or terminated orally but rather only by an instrument in writing signed by the Company
and Holder. All notices and other communications from the Company to Holder shall be mailed by
prepaid courier or first-class registered or certified mail, postage pre-paid, to the address
furnished to the Company in writing by the last holder who shall have furnished an address to the
Company in writing.

     13. Amendment and Waiver. Any provisions of this Warrant (including, without
limitation, termination of exercisability) may be amended or waived, and any and all such
amendments or waivers shall be binding upon Holder, only if approved in writing by the Company and
Holder.

     Issued this 9th day of April, 2009.

	 	 	 	 	 
	 	INTRAOP MEDICAL CORPORATION

 	 
	 	By:  	 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 

5.

 

	 	 	 	 	 

SUBSCRIPTION FORM

     The undersigned registered owner of the Warrant which accompanies this Subscription Form
hereby irrevocably (a) exercises such warrant for, and purchases                      shares of Common Stock (the
"Shares”) of Intraop Medical Corporation, a Nevada corporation (the “Company”), purchasable upon
the exercise of such Warrant, and herewith makes payment therefor, or (b) exercises such Warrant
for                      shares of Intraop Medical Corporation Common Stock purchasable under the Warrant
pursuant to the net exercise provisions of the second paragraph of Section 7(a) of such Warrant,
all at the price and on the terms and conditions specified in such Warrant.

          1.01 Authorization. This exercise constitutes a valid and legally binding obligation
of the undersigned, enforceable in accordance with its terms.

          1.02 Investment Representation. The undersigned acknowledges, represents, and
warrants that it (a) has a preexisting personal or business relationship with the Company, and/or
by reason of its business or financial experience has the capacity to protect its own interests in
connection with the transaction, and (b) is an “accredited investor” under Regulation D of the
Securities Act of 1933, as amended (the “Act”). The undersigned further acknowledges that it is
aware that the Shares have not been registered under the Act, or qualified under any state’s
securities laws. The Shares are being acquired for investment purposes only and not for sale or
with a view to distribution of all or any part thereof.

          1.03 Access to Information. The undersigned represents that it has or will have had
upon exercise of the Warrant an opportunity to ask questions of and receive answers from the
Company regarding the terms and conditions of its purchase of the Shares concerning the business,
financial affairs and other aspects of the Company, and it has further had the opportunity to
obtain any information (to the extent the Company possesses or can acquire such information without
unreasonable effort or expense) which it deems necessary to evaluate its investment or to verify
the accuracy of information otherwise provided to it. The undersigned acknowledges that it is not
relying upon any person, firm or corporation (other than the Company and its officers and
directors) in making its investment or decision to invest in the Company, and the undersigned
represents that it has been solely responsible for its own “due diligence” investigation of the
Company and its management and business, for its own analysis of the merits and risks of this
investment.

          1.04 Investment Experience. The undersigned represents and warrants that by reason of
its financial and business experience, it has the capacity to protect its interests in connection
with these transactions.

          1.05 Restricted Securities. The undersigned understands that the Shares will be
characterized as “restricted securities” under the federal securities laws inasmuch as they are
being acquired from the Company in a transaction not involving a public offering, and that under
such laws and applicable regulations such securities may be resold without registration under the
Act only in certain limited circumstances and that otherwise such securities must be held
indefinitely. In this connection, the undersigned represents that it is familiar with SEC Rule
144,

1

 

as presently in effect, and the conditions which must be met in order for that Rule to be
available for resale of “restricted securities,” and understands the resale limitations imposed by
the Act.

          1.06 Further Limitations on Disposition. Without in any way limiting the
representations set forth above, the undersigned further agrees not to make any disposition of all
or any portion of the Shares unless and until:

                    (a) There is then in effect a “Registration Statement” under the Act covering such proposed
disposition and such disposition is made in accordance with such Registration Statement and any
applicable requirements of state securities laws; or

                    (b) (i) the undersigned shall have notified the Company of the proposed disposition and shall
have furnished the Company with a detailed statement of the circumstances surrounding the proposed
disposition, and (ii) if reasonably requested by the Company, shall have furnished the Company with
an opinion of counsel at undersigned’s expense (except for dispositions pursuant to Rule 144 of the
Rules and Regulations under the Act which dispositions shall not so require an opinion of counsel)
reasonably satisfactory to the Company, that such disposition will not require registration of the
Shares under the Act or the consent of or permit from appropriate authorities under any applicable
state securities law.

                    (c) Notwithstanding the provisions of paragraphs (a) and (b) above, no such Registration
Statement or opinion of counsel shall be necessary for a transfer by the undersigned to a
constituent stockholder or constituent partner (including any constituent of a constituent) of the
undersigned, if the transferee or transferees agree in writing to be subject to the terms hereof to
the same extent as if they were the undersigned hereunder.

     2. RESTRICTIONS ON THE TRANSFER OF SECURITIES.

          2.01 Corporate Securities Law. The Shares shall be transferred only in compliance
with the conditions specified in Section 1.06, which conditions are intended to ensure compliance
with the provisions of the Act and state securities laws with respect to the transfer of any such
securities. Each certificate representing the Shares shall bear at least a legend substantially in
the following form until such time as the conditions of such legend have been met:

THE SECURITIES REPRESENTED HEREBY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED (“ACT”), NOR HAVE THEY BEEN REGISTERED OR QUALIFIED UNDER THE SECURITIES LAWS OF ANY STATE.
NO TRANSFER OF SUCH SECURITIES WILL BE PERMITTED UNLESS A REGISTRATION STATEMENT UNDER THE ACT IS
IN EFFECT AS TO SUCH TRANSFER, THE TRANSFER IS MADE IN ACCORDANCE WITH RULE 144 UNDER THE ACT OR AS
OTHERWISE PERMITTED BY THE COMPANY, OR IN THE OPINION OF COUNSEL SATISFACTORY TO THE COMPANY AND AT
HOLDER’S EXPENSE, REGISTRATION UNDER THE ACT IS UNNECESSARY IN ORDER FOR SUCH TRANSFER TO COMPLY
WITH THE ACT AND WITH APPLICABLE STATE SECURITIES LAWS.

2

 

The Company shall, within ten (10) days of the request of any holder of a certificate bearing the
foregoing legend and the surrender of such certificate, issue a new stock certificate in the name
of the transferee provided that there has been compliance with the provisions of subsection 1.06
above.

          2.02 Additional Legends. The Company may also impose any additional legend required
under applicable federal or state securities laws or permitted under its bylaws and shall be
entitled to issue stop transfer notices on its books with respect to any securities purchased
hereunder until the conditions set forth in the applicable legends have been met.

     Dated:                                         

	 	 	 
	 
	 	 
	 
	 	 
	 

	 	(Signature of Registered Owner)
	 
	 	 
	 
	 	 
	 
	 	 
	 

	 	(Name)
	 
	 	 
	 
	 	 
	 
	 	 
	 

	 	(Street Address)
	 
	 	 
	 
	 	 
	 
	 	 
	 

	 	(City, State, Zip Code)
	 
	 	 
	 
	 	 
	 
	 	 
	 

	 	Social Security or Tax Identification Number

     If the number of Shares issuable upon this exercise shall not be all of the Shares which the
undersigned is entitled to purchase in accordance with the enclosed Warrant, the undersigned
requests that a new warrant evidencing the right to purchase the Shares not issuable pursuant to
the exercise evidenced hereby be issued in the name of and delivered to:

 

(Please print name and address)

 

 

	 	 	 	 	 
	Date:                      	Name of Holder:
 	 
	 	(Print)

 	 
	 	(By)  	 	 
	 	 	(Name:)  	 	 
	 	 	(Title:)  	

	 
	 
	 	
(Signature must conform in all respects to name of
holder as specified on the face of the Warrant) 	 

3

 

	 	 	 	 	 

FORM OF ASSIGNMENT

(To be signed only upon assignment of Warrant)

FOR VALUE RECEIVED, the undersigned hereby sells, assigns and transfers unto:

 

 

 

(Name and address of assignee must be printed or typewritten)

                     shares of Intraop Medical Corporation Common Stock purchasable under the within
Warrant, hereby irrevocably constituting and appointing                                          Attorney to transfer
said Warrant on the books of the Company, with full power of substitution in the premises.

     Dated:                     

	 	 	 
	 

	 	 
	 

	 	(Signature of Registered Owner)

4

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