Document:

exv10w6

Exhibit
10.6

STOCKHOLDERS AGREEMENT

     THIS STOCKHOLDERS AGREEMENT (the “Agreement”) is made as of the 3rd day of July, 2008 (the
“Effective Date”), by and between Alon USA Energy, Inc., a Delaware corporation (“Alon USA”), Alon
Refining Louisiana, Inc., a Delaware corporation (the “Company”), Alon Louisiana Holdings, Inc., a
Delaware corporation (“Alon LA”), Alon Israel Oil Company, Ltd., an Israeli limited liability
company (“Alon Israel” and, together with Alon LA, the “Stockholders”), and any other stockholder
who from time to time becomes party to this Agreement by execution of a joinder agreement in form
and substance reasonably acceptable to the Stockholders.

RECITALS:

     A. On the date hereof, Alon Israel is purchasing 80,000 shares of the Company’s Series A
Preferred Stock, par value $1,000.00 per share (the “Preferred Stock”), pursuant to that certain
Series A Stock Purchase Agreement dated as of the date hereof by and between the Company and Alon
Israel (the “Purchase Agreement”);

     B. The Purchase Agreement contemplates that this Agreement be executed by the parties hereto
on even date therewith, and the parties are willing to execute this Agreement and be bound by the
provisions hereof; and

     C. The parties hereto desire to agree upon the terms on which the securities of the Company,
now or hereafter outstanding and held by them, will be held and transferred.

AGREEMENT:

     NOW, THEREFORE, in consideration of the foregoing and the mutual covenants and agreements
hereinafter set forth, the parties hereto agree as follows:

1. Definitions.

     1.1 Certain Interpretive Matters. When a reference is made in this Agreement to
Sections, such reference will be to a Section of this Agreement unless otherwise indicated.
Whenever the words “include,” “includes” or “including” are used in this Agreement, they will be
deemed to be followed by the words “without limitation.” Unless the context otherwise requires,
(i) “or” is disjunctive but not necessarily exclusive, (ii) words in the singular include the
plural and vice versa, (iii) the use in this Agreement of a pronoun in reference to a party hereto
includes the masculine, feminine or neuter, as the context may require, (iv) the use in this
Agreement of “day” will mean a calendar day unless indicated otherwise, (v) all references to $ or
dollar amounts will be to lawful currency of the United States, and (vi) the words “herein”,
“hereby”, “hereof”, and “hereunder” and other words of similar import refer to this Agreement as a
whole and not to any particular section, paragraph or other subdivision of this Agreement.

     1.2 Number of Shares of Stock. Whenever any provision of this Agreement calls for any
calculation based on a number of shares of capital stock issued and outstanding or held by a
Stockholder, the number of shares deemed to be issued and outstanding or held by that Stockholder,
unless specifically stated otherwise, as applicable, shall be the total number of

 

 

shares of the Company’s Common Stock, par value $0.01 per share (the “Common Stock”), or
Preferred Stock then issued and outstanding or owned by such Stockholder, as applicable.

     1.3 Defined Terms. The following capitalized terms, as used in this Agreement, shall
have the meanings set forth below.

     “Affiliate” shall mean with respect to any Person (as defined below), any Person who, directly
or indirectly, controls, is controlled by or is under common control with such Person, including
any partner, officer, director, member, manager or employee of such Person.

     “Change of Control” means either of the following events:

     (a) the failure, for any reason, of Alon USA to beneficially own, directly or indirectly, at
least a majority of the voting stock of the Company or, if applicable, any entity that succeeds to
all or substantially all of the assets of the Company by purchase, contribution, assignment,
merger, consolidation or otherwise; or

     (a) the failure, for any reason, of Alon Israel to beneficially own, directly or indirectly,
at least a majority of the voting stock of Alon USA or, if applicable, any entity that succeeds to
all or substantially all of the assets of Alon USA by purchase, contribution, assignment, merger,
consolidation or otherwise.

     “Alon Common Stock” shall mean the shares of common stock, par value $0.01 per share, of Alon
USA Energy, Inc., a Delaware corporation.

     “Alon Share Price” shall mean the greater of (i) the average of the daily closing sales prices
per share of the Alon Common Stock on the New York Stock Exchange for each trading day during the
period commencing on the day 90 days prior to the date of this Agreement and (ii) the closing sale
price per share of the Alon Common Stock on the New York Stock Exchange on the date of this
Agreement.

     “Business Day” means a day other than a Saturday, Sunday or other day on which commercial
banks in Dallas, Texas are not open for business.

     “Certificate” means the Company’s Amended and Restated Certificate of Incorporation, as in
effect from time to time.

     “Par Value” means $1,000 per share of Series A Preferred Stock.

     “Permitted Transferee” means any Person to which a Stockholder may Transfer Securities as
permitted by and in accordance with Sections 2.1 and 2.2 of this Agreement.

     “Person” means an individual, a corporation, an association, a joint venture, a partnership, a
limited liability company, an estate, a trust, an unincorporated organization and any other entity
or organization, governmental or otherwise.

     “Securities” means, at any time, any shares of capital stock of the Company, including Common
Stock and Preferred Stock now or hereafter issued by the Company, together with any

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options thereon and any other shares of stock directly or indirectly issued or issuable with
respect thereto, whether by way of a stock dividend, stock split or in exchange for or upon
conversion of such shares or otherwise in connection with a combination of shares,
recapitalization, merger, consolidation or other corporate reorganization, and any instrument
convertible into or exercisable or exchangeable for (in each case, directly or indirectly) shares
of capital stock of the Company, together with any shares of stock issued or issuable with respect
thereto.

     “Securities Act” means the Securities Act of 1933, as amended, and the rules and regulations
promulgated thereunder.

     “Series A Dividends” has the meaning set forth in the Certificate.

     “Share Exchange” means the issuance and delivery by Alon USA to Alon Israel and/or any of its
Permitted Transferees in exchange for all of the shares of Preferred Stock then held by Alon Israel
and/or any of its Permitted Transferees a number of duly authorized, fully paid and nonassessable
whole shares of Alon Common Stock as determined in accordance with Section 2.3(c) hereof.

     “Transfer” means any direct transfer, donation, sale, assignment, pledge, hypothecation, grant
of a security interest in or other disposal or attempted disposal of all or any portion of a
Security, any interest or rights in a Security, or any rights under this Agreement. “Transferred”
means the accomplishment of a Transfer, and “Transferee” means the recipient of a Transfer.

2. Restrictions on Transfer.

     2.1 Restrictions on Transfer. Each Stockholder agrees that such Stockholder will not,
without the prior written consent of the Company, not to be unreasonably withheld, Transfer all or
any portion of the Securities now owned or hereafter acquired by such Stockholder, except in
connection with, and strictly in compliance with this Article 2. Notwithstanding the foregoing, a
Transfer by a Stockholder to any Affiliate of such Stockholder shall not be subject to the prior
consent of the Company.

     2.2 Permitted Transfers. Notwithstanding the provisions of Section 2.1, no Transfer
shall be permitted or effected hereunder unless and until the Transferee shall have entered into a
joinder agreement in form and substance reasonably acceptable to the Stockholders providing that
all Securities so Transferred shall continue to be subject to all provisions of this Agreement as
if such Securities were still held by such Stockholder (“Joinder Agreement”). Notwithstanding
anything to the contrary in this Agreement or any failure by a Transferee under this Section 2.2 to
execute a Joinder Agreement, such Transferee shall take any Securities so Transferred subject to
all provisions of this Agreement as if such Securities were still held by the Stockholder making
such Transfer, whether or not they so agree in writing.

     2.3 Exchange Right.

          (a) Subject to the prior receipt by Alon USA of approval of holders of a majority of the Alon
Common Stock with respect to the issuance of the Exchange Shares (as defined below) pursuant to and
in compliance with Section 312.03 of the NYSE’s Listed Company Manual (“NYSE Stockholder
Approval”), prior to the consummation of a Change of

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Control (a “Change of Control Date”), each of Alon USA and Alon Israel shall have the option,
exercisable at each such party’s sole and absolute discretion, to require the other party to
consummate the Share Exchange by delivery to the other party at least 10 Business Days prior to the
Change of Control Date of a written notice (the “Exercise Notice”) setting forth such party’s
election to effectuate the Share Exchange. Any Share Exchange elected pursuant to this Section
2.3(a) shall be consummated effective as of the Business Day immediately preceding the Change of
Control Date (the “Change of Control Exchange Date”).

          (b) If a Share Exchange effected pursuant to Section 2.3(a) shall not have occurred prior to
5:00 p.m. (Dallas, Texas time) on July 1, 2011 (the “Mandatory Exchange Date”), then, subject to
the prior receipt by Alon USA of NYSE Stockholder Approval, Alon USA and Alon Israel and/or any of
its Permitted Transferees shall consummate the Share Exchange effective as of the Mandatory
Exchange Date.

          (c) Alon USA acknowledges and agrees that it shall include the NYSE Stockholder Approval (and
all required disclosures) as a matter to be voted upon in its proxy statement relating to its 2009
annual meeting of stockholders.

          (d) On the Change of Control Exchange Date or Mandatory Exchange Date, as applicable, Alon USA
shall issue and deliver to Alon Israel and/or any of its Permitted Transferees in exchange for all
of the shares of Preferred Stock then held by Alon Israel and/or any of its Permitted Transferees
(all of which shares shall be transferred and delivered to Alon USA free and clear of any lien,
claim, judgment, charge, mortgage, security interest, escrow, equity or other encumbrance), a
number of duly authorized, fully paid and nonassessable whole shares of Alon Common Stock equal to
the quotient obtained by dividing (i) the sum of (A) the aggregate Par Value of the shares of
Preferred Stock then held by Alon Israel and/or any of its Permitted Transferees, and (B) the
aggregate Series A Dividends accrued but unpaid on such shares of Preferred Stock, whether or not
declared, together with any other dividends declared but unpaid on such shares of Preferred Stock,
by (ii) the Alon Share Price (the “Exchange Shares”); provided that in lieu of any fractional share
of Alon Common Stock that would otherwise by payable by operation of this subsection, Alon USA
shall pay to the Person entitled thereto an amount in cash equal to such fraction multiplied by the
Alon Share Price.

          (e) As a condition precedent to delivery of the Exchange Shares, Alon Israel and/or any of its
Permitted Transferees shall surrender the certificate or certificates for all shares of Preferred
Stock then held by it and/or its Permitted Transferees (or, if Alon Israel and/or any of its
Permitted Transferees alleges that any such certificate has been lost, stolen or destroyed, a lost
certificate affidavit and agreement reasonably acceptable to Alon USA to indemnify Alon USA and the
Company against any claim that may be made against Alon USA or the Company on account of the
alleged loss, theft or destruction of such certificate) to Alon USA at its principal office. If so
required by Alon USA, certificates surrendered for exchange shall be endorsed or accompanied by
written instrument or instruments of transfer, in form reasonably satisfactory to Alon USA, duly
executed by the registered holder. All rights of Alon Israel and/or any of its Permitted
Transferees with respect to the Preferred Stock exchanged pursuant to Section 2.3, whether arising
under the Certificate, this Agreement or otherwise, including the rights, if any, to receive Series
A Dividends accrued on or after the Change of Control Exchange Date or Mandatory Exchange Date, as
applicable, will be deemed transferred and assigned by

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Alon Israel and its Permitted Transferees to Alon USA on the Change of Control Exchange Date
or Mandatory Exchange Date, as applicable, (notwithstanding the failure of Alon Israel and/or any
of its Permitted Transferees to surrender the certificates at or prior to such time), except only
the right of Alon Israel and/or any of its Permitted Transferees, upon surrender of the certificate
or certificates (or lost certificate affidavit and agreement) therefor, to receive the Exchange
Shares.

          (f) If there shall occur any reorganization, recapitalization, reclassification or other
similar event involving Alon USA in which the Alon Common Stock is reclassified as, converted into
or exchanged for new or different securities (the “Successor Securities”), then, following any such
reorganization, recapitalization, reclassification or other event, the shares of Preferred Stock
shall instead be exchangeable pursuant to this Section 2.3 for such Successor Securities and all
references in this Agreement to the Alon Common Stock shall be deemed to be references to such
Successor Securities, mutatis mutandis.

          (g) In connection with the Share Exchange, Alon USA will, upon request, enter into a customary
and reasonable registration rights agreement with a Permitted Transferee of Alon Israel with
respect to shares of Alon USA common stock issued to such Permitted Transferee pursuant to the
Share Exchange.

     2.4 Effect of Prohibited Transfers. If any Transfer by any Stockholder is made or
attempted contrary to the provisions of this Agreement, such purported Transfer shall be void ab
initio; the Company and the other parties hereto shall have, in addition to any other legal or
equitable remedies which they may have, the right to enforce the provisions of this Agreement by
actions for specific performance (to the extent permitted by law); and the Company shall have the
right to refuse to recognize any improper Transferee of any Stockholder for any purpose.

     2.5 Call Option. During the 18 month period following the date of issuance of the
Preferred Stock, each of Alon USA and Alon LA, shall have the option to purchase from Alon Israel
and/or its Permitted Transferees all or a portion of the Preferred Stock at a price per share
payable in cash equal to the Par Value plus accrued but unpaid dividends; provided, however, that
such call option shall be (1) subject to the prior release of the Letters of Credit (as hereinafter
defined) and (2) conditioned upon the approval of such purchase by the audit committee of Alon USA.

3. Letters of Credit.

     3.1 In accordance with the Purchase Agreement, Alon Israel shall cause to be issued and
delivered to Bank of America, N.A. (“Bank of America”) one or more irrevocable standby letters of
credit (each, a “Letter of Credit”) up to the aggregate amount of $55,000,000 in order to support
the borrowing base of Alon Refining Krotz Springs, Inc., a Delaware corporation (“Krotz Springs”),
under the Loan and Security Agreement by and among the Company, Krotz Springs, the banks and
financial institutions listed on the signature page thereof as “Lenders”, and Bank of America,
N.A., a national banking association, as administrative agent (the “Credit Agreement”).

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     3.2 In the event that Bank of America draws upon one or more Letters of Credit at any time
during which the Letters of Credit are outstanding, Alon LA shall issue and deliver to Alon Israel
within three days following each such draw a promissory note (each a “Promissory Note”) in a
principal amount equal to the aggregate amount of such draw under the Letter(s) of Credit (each an
“Repayment Amount”) and bearing interest at a rate of 10.75% per annum in full and final settlement
and discharge of any obligation or liability of the Company or any affiliate of the Company to Alon
Israel with respect to the Repayment Amount; provided, however, that no fees, bank charges or other
expenses shall be included in the determination of the Repayment Amount. The principal amount and
all accrued interest under each Promissory Note shall be due and payable on or before 12 months
following the date of issuance of such Promissory Note.

     3.3 From and after the date of the initial issuance of the Letters of Credit, Alon USA and the
Company shall, and shall cause their affiliates to, use their respective best efforts (subject to
the terms of their respective existing credit facilities and other binding obligations) to either
(i) replace the Letters of Credit with their own resources or by obtaining funds or other support,
including other letters of credit, through commercially reasonable arrangements with third party
financing sources or (ii) otherwise secure the release by Bank of America of the Letter of Credit
support requirement under the Credit Agreement. In addition, if the Letters of Credit remain
outstanding after the first anniversary of the original issuance of such Letters of Credit, the
Company shall, and shall cause Krotz Springs to, use its respective best efforts to prevent any
draw down on the Letters of Credit, including, without limitation, by reducing inventories and
throughput at Krotz Springs.

4 Miscellaneous Provisions.

     4.1 Reliance. Each of the parties hereto agrees that each covenant and agreement made
by it in this Agreement is material, shall be deemed to have been relied upon by the other parties
and shall remain operative and in full force and effect after the date hereof regardless of any
investigation. This Agreement shall not be construed so as to confer any right or benefit upon any
Person other than the parties hereto and their respective successors and permitted assigns to the
extent contemplated herein.

     4.2 Legend on Securities. The Company and the Stockholders acknowledge and agree that
in addition to any other legend on the certificates representing Securities held by them,
substantially the following legend shall be typed on each certificate evidencing any of the
Securities held at any time by any Stockholder:

THE SHARES REPRESENTED BY THIS CERTIFICATE HAVE BEEN ACQUIRED FOR INVESTMENT AND HAVE NOT BEEN
REGISTERED PURSUANT TO THE SECURITIES ACT OF 1933, AS AMENDED, OR THE SECURITIES LAWS OF ANY STATE
OR OTHER JURISDICTION. ABSENT SUCH REGISTRATION OR AN EXEMPTION FROM THE REQUIREMENT THEREFOR, NO
TRANSFER OF THESE SHARES OR ANY INTEREST THEREIN MAY BE MADE.

THE SECURITIES REPRESENTED HEREBY ARE SUBJECT TO THE PROVISIONS OF A CERTAIN STOCKHOLDERS
AGREEMENT, INCLUDING CERTAIN RESTRICTIONS ON TRANSFER SET FORTH THEREIN. A COMPLETE AND CORRECT
COPY OF SUCH AGREEMENT IS AVAILABLE FOR INSPECTION AT THE PRINCIPAL OFFICE OF THE

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COMPANY AND WILL BE FURNISHED UPON WRITTEN REQUEST AND WITHOUT CHARGE.

     4.3 Alon Common Stock.

          (a) Alon Israel understands that any shares of Alon Common Stock that may be issued pursuant
to this Agreement will not be registered under the Securities Act, and will be issued by reason of
a specific exemption from the registration provisions of the Securities Act which depends upon,
among other things, the bona fide nature of the investment intent and the accuracy of Alon Israel’s
representations as expressed herein. Alon Israel understands that such shares will be “restricted
securities” under applicable U.S. federal and state securities laws and that, pursuant to these
laws, Alon Israel must hold such shares indefinitely unless they are registered with the Securities
and Exchange Commission and qualified by state authorities, or an exemption from such registration
and qualification requirements is available. Alon Israel acknowledges that, except pursuant to the
terms of the Registration Rights Agreement, dated as of July 6, 2005, between Alon USA and Alon
Israel, Alon USA has no obligation to register or qualify such shares for resale. Alon Israel
further acknowledges that if an exemption from registration or qualification is available, it may
be conditioned on various requirements, including the time and manner of sale and the holding
period for such Shares, and on requirements relating to the Company which are outside of Alon
Israel’s control, and which Alon USA is under no obligation and may not be able to satisfy.

          (b) Alon Israel acknowledges that Alon USA’s agreement hereunder to issue shares of Alon
Common Stock is made in reliance upon Alon Israel’s representation to Alon USA, which by the its
execution of this Agreement, Alon Israel hereby confirms, that any shares of Alon Common Stock that
may be acquired by Alon Israel hereunder will be acquired for investment for Alon Israel’s own
account, not as a nominee or agent, and not with a view to the resale or distribution of any part
thereof. By executing this Agreement, Alon Israel further represents that it does not presently
have any contract, undertaking, agreement or arrangement with any Person to sell, transfer or grant
participations to such Person or to any third Person, with respect to any of such shares. Alon
Israel has not been formed for the specific purpose of acquiring the Shares.

          (c) Alon Israel represents to Alon USA that Alon Israel is an accredited investor as defined
in Rule 501(a) of Regulation D promulgated under the Securities Act.

          (d) Alon Israel acknowledges and agrees that any certificates representing shares of Alon
Common Stock will bear substantially the following legend:

THE SHARES REPRESENTED BY THIS CERTIFICATE HAVE BEEN ACQUIRED FOR INVESTMENT AND HAVE NOT BEEN
REGISTERED PURSUANT TO THE SECURITIES ACT OF 1933, AS AMENDED, OR THE SECURITIES LAWS OF ANY STATE
OR OTHER JURISDICTION. ABSENT SUCH REGISTRATION OR AN EXEMPTION FROM THE REQUIREMENT THEREFOR, NO
TRANSFER OF THESE SHARES OR ANY INTEREST THEREIN MAY BE MADE.

          (e) Alon Israel represents that, with respect to any issuance of shares of Alon Common Stock
pursuant to this Agreement, it will satisfy itself as to the full observance of the

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laws of Israel, including (i) the legal requirements within Israel for the acquisition of such
shares, (ii) any foreign exchange restrictions applicable to such acquisition, (iii) any
governmental or other consents that may need to be obtained, and (iv) the income tax and other tax
consequences, if any, that may be relevant to the acquisition, holding, redemption, sale, or
transfer of such shares. Alon Israel’s acquisition and continued beneficial ownership of such
shares will not violate any applicable securities or other laws of Israel.

     4.4 Successors and Assigns. The terms and conditions of this Agreement shall inure to
the benefit of and be binding upon the respective successors and permitted assigns of the parties.
Nothing in this Agreement, express or implied, is intended to confer upon any party other than the
parties hereto or their respective successors and assigns any rights, remedies, obligations, or
liabilities under or by reason of this Agreement, except as expressly provided in this Agreement.

     4.5 Governing Law. This Agreement shall be governed by, and construed in accordance
with, the laws of the State of Texas, regardless of the laws that might otherwise govern under
applicable principles of conflicts of law.

     4.6 Counterparts; Facsimile. This Agreement may be executed and delivered by
facsimile signature and in two or more counterparts, each of which shall be deemed an original, but
all of which together shall constitute one and the same instrument.

     4.7 Titles and Subtitles. The titles and subtitles used in this Agreement are used
for convenience only and are not to be considered in construing or interpreting this Agreement.

     4.8 Notices. All notices and other communications given or made pursuant to this
Agreement shall be in writing and shall be deemed effectively given: (a) upon personal delivery to
the party to be notified, (b) five business days after having been sent by certified mail, return
receipt requested, postage prepaid, or (d) two business days after deposit with an internationally
recognized express courier service, specifying same day or next business day delivery, with written
verification of receipt. All communications shall be sent to the respective parties at their
address as set forth on the signature page, or to such address as subsequently modified by written
notice given in accordance with this Section 4.8.

     4.9 Amendments and Waivers. Any term of this Agreement may be amended, terminated or
waived only with the written consent of Alon USA, the Company and the Stockholders.

     4.10 Severability. Whenever possible, each provision or portion of any provision of
this Agreement shall be interpreted in such manner as to be effective and valid under applicable
law, but if any provision or portion of any provision of this Agreement is held to be invalid,
illegal or unenforceable in any respect under any applicable law or rule in any jurisdiction, such
invalidity, illegality or unenforceability shall not affect the validity, legality or
enforceability of any other provision or portion of any provision in such jurisdiction, and this
Agreement shall be reformed, construed and enforced in such jurisdiction in such manner as will
effect as nearly as lawfully possible the purposes and intent of such invalid, illegal or
unenforceable provision.

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     4.11 Delays or Omissions. No delay or omission to exercise any right, power or remedy
accruing to any party under this Agreement, upon any breach or default of any other party under
this Agreement, shall impair any such right, power or remedy of such non-breaching or
non-defaulting party nor shall it be construed to be a waiver of any such breach or default, or an
acquiescence therein, or of or in any similar breach or default thereafter occurring; nor shall any
waiver of any single breach or default be deemed a waiver of any other breach or default
theretofore or thereafter occurring. Any waiver, permit, consent or approval of any kind or
character on the part of any party of any breach or default under this Agreement, or any waiver on
the part of any party of any provisions or conditions of this Agreement, must be in writing and
shall be effective only to the extent specifically set forth in such writing. All remedies, either
under this Agreement or by law or otherwise afforded to any party, shall be cumulative and not
alternative.

     4.12 Entire Agreement. This Agreement constitutes the full and entire understanding
and agreement between the parties with respect to the subject matter hereof, and any other written
or oral agreement relating to the subject matter hereof existing between the parties are expressly
canceled.

     4.13 Further Assurances. From and after the date of this Agreement, upon the request
of either Stockholder or the Company, the Company and each Stockholder shall execute and deliver
such instruments, documents and other writings as may be reasonably necessary or desirable to
confirm and carry out and to effectuate fully the intent and purposes of this Agreement and the
transactions contemplated hereby.

     4.14 After-Acquired Securities; New Parties. Whenever any Stockholder becomes the
record or beneficial owner of additional securities of the Company, such securities will be subject
to all of the terms and conditions of this Agreement. The Company will cause Persons not parties
to this Agreement who from time to time receive securities of the Company to be subject to the
terms and conditions of this Agreement.

[Signature Page Follows]

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     IN WITNESS WHEREOF, the parties hereto have caused this Stockholders Agreement to be duly
executed as of the date first set forth above.

	 	 	 	 	 
	 	ALON USA ENERGY, INC.

 	 
	 	By:  	/s/ Jeff D. Morris
 	 
	 	 	Name:  	Jeff D. Morris 	 
	 	 	Title:  	President and CEO 	 
	 

Address:

7616 LBJ Freeway, Suite 300

Dallas, Texas 75251

Attention: General Counsel

	 	 	 	 	 
	 	ALON REFINING LOUISIANA, INC.

 	 
	 	By:  	/s/ Jeff D. Morris
 	 
	 	 	Name:  	Jeff D. Morris 	 
	 	 	Title:  	President and CEO 	 
	 

Address:

7616 LBJ Freeway, Suite 300

Dallas, Texas 75251

Attention: General Counsel

	 	 	 	 	 
	 	STOCKHOLDERS:

ALON LOUISIANA HOLDINGS, INC.

 	 
	 	By:  	/s/ Jeff D. Morris
 	 
	 	 	Name:  	Jeff D. Morris 	 
	 	 	Title:  	President and CEO 	 
	 

Address:

7616 LBJ Freeway, Suite 300

Dallas, Texas 75251

Attention: General Counsel

10

 

	 	 	 	 	 
	 	ALON ISRAEL OIL COMPANY, LTD.

 	 
	 	By:  	/s/ Yizhak Bader
 	 
	 	 	Name:  	Yizhak Bader 	 
	 	 	Title:  	Chairman of the Board of Directors 	 
	 

Address:

Europark (France Building)

P.O.B. 10

Kibbutz Yakum, Israel 60972

Attention: General Counsel

11exv10w1

Exhibit 10.1

Penford Corporation

First Amendment to Second Amended and Restated Credit Agreement

     This First Amendment to Second Amended and Restated Credit Agreement (herein, the “Amendment”)
is entered into as of July 9, 2008, by and among Penford Corporation, a Washington
corporation (the “Borrower”), the direct and indirect Subsidiaries of the Borrower from time to
time party to the Credit Agreement, as Guarantors, the several financial institutions from time to
time party to this Agreement, as Lenders, and Harris N.A., as Administrative Agent as
provided herein.

Preliminary Statements

     A. The Borrower, the Guarantors, the Lenders and the Administrative Agent are parties to that
certain Second Amended and Restated Credit Agreement dated as of October 5, 2006, (the “Credit
Agreement”). All capitalized terms used herein without definition shall have the same meanings
herein as such terms have in the Credit Agreement.

     B. The Borrower and the Lenders have agreed to make certain amendments to the Credit
Agreement, in each case under the terms and conditions set forth in this Amendment.

     Now, Therefore, for good and valuable consideration, the receipt and sufficiency of
which is hereby acknowledged, the parties hereto agree as follows:

Section 1. Amendments to the Credit Agreement.

     Subject to the satisfaction of the conditions precedent set forth in Section 2 hereof, the
Credit Agreement shall be and hereby is amended as follows:

     1.1. The definition of the term “EBITDA” appearing in Section 5.1 of the Credit Agreement
shall be amended to read as follows:

     “EBITDA” means, with reference to any period, Net Income for such period plus the sum
of all amounts deducted in arriving at such Net Income amount in respect of (a) Interest
Expense for such period, (b) federal, state, and local income taxes for such period, (c)
depreciation of fixed assets and amortization of intangible assets for such period, plus
(minus) any non-cash losses (gains) but only to the extent such losses (gains) have not
become a cash loss (or gain), plus non-cash stock compensation charges incurred in such
period, plus (d) expenses (including without limitation inventory write-downs), continuing
costs incurred during the fiscal quarter ending August 31, 2008, and repair, restoration and
replacement costs and other costs reasonably acceptable to the Administrative Agent incurred
by the Borrower and its Subsidiaries as a result of the

 

 

flooding of the Borrower’s facilities in Cedar Rapids, Iowa during the month of June,
2008, net of the aggregate amount of all insurance proceeds (including, without limitation,
business interruption insurance) received by the Borrower and its Subsidiaries as a result
of such flooding, provided that the aggregate amount added to EBITDA pursuant to this clause
(d) shall not exceed $45,000,000 during the twelve consecutive months ending August 31,
2008, $20,000,000 during the twelve consecutive months ending November 30, 2008, and
$10,000,000 during each period of twelve consecutive months ending on the last day of each
fiscal quarter thereafter.

     1.2. The table appearing in Section 8.22(b) of the Credit Agreement shall be amended to read
as follows:

	 	 	 	 	 
	 	 	 	 	Fixed Charge Coverage
	 	 	 	 	Ratio shall not be Less
	From and Including	 	To and Including	 	than
	 	 	 	 	 
	August 31, 2006
	 	August 31, 2007
	 	1.50 to 1.0
	 	 	 	 	 
	September 1, 2007
	 	November 31, 2008
	 	1.25 to 1.0
	 	 	 	 	 
	December 1, 2008
	 	At all times thereafter
	 	1.50 to 1.0

     1.3. Section 8.22(d) of the Credit Agreement shall be amended to read as follows:

     (d) Capital Expenditures. The Borrower shall not, nor shall it permit any of its
Subsidiaries to, incur Capital Expenditures (but excluding (i) Capital Expenditures made
with the Net Cash Proceeds of any Event of Loss as permitted by Section 1.9(b)(i) hereof,
(ii) Capital Expenditures incurred in connection with the repair, restoration or replacement
of Property damaged or destroyed as a result of the flooding of the Borrower’s facilities in
Cedar Rapids, Iowa during the month of June, 2008, that the Borrower reasonably believes are
covered by insurance, for which at the time such expenditure is incurred the Borrower has
made or reasonably expects to make a written claim under the applicable insurance policy and
which claim has not been denied by the insurer, (iii) Capital Expenditures made with the
proceeds of grants from governmental entities and (iv) Capital Expenditures incurred in
connection with the Ethanol Facility that are financed with the proceeds of the Capital
Expansion Loans) in an amount in excess of $20,000,000 (or the Australian Dollar Equivalent
or NZ Dollar Equivalent) in the aggregate during any fiscal year; provided, however, for any
fiscal year when Total Funded Debt Ratio is less than 2.0 to 1.0 for each fiscal quarter of
such fiscal year, Capital Expenditures for such year shall not exceed $25,000,000 (or the
Australian Dollar Equivalent or NZ Dollar Equivalent) for such fiscal year.

     1.4. Schedule I attached to the form of Compliance Certificate attached to the Credit
Agreement as Exhibit E shall be replaced by Schedule I attached to this Amendment.

     1.5. The Required Lenders hereby agree that the Borrower and its Subsidiaries may use proceeds
of Revolving Loans obtained hereunder to pay expenses incurred by the Borrower and

-2-

 

its Subsidiaries as a result of the flooding of the Borrower’s facilities in Cedar Rapids, Iowa
during the month of June, 2008, prior to receiving any proceeds of insurance relating thereto and
that the Borrower and its Subsidiaries may use any proceeds of insurance relating thereto to pay
for costs incurred for the repair, restoration and replacement of Property damaged or destroyed as
a result of such floods without having to comply with the requirements of Section 9(d) of the
Mortgages but otherwise in compliance with the requirements of Section 1.9(b)(i) of the Credit
Agreement.

     1.6. The Borrower hereby agrees that commencing on the effective date of this Amendment and
until it delivers its financial statements for its fiscal quarter ending February 28, 2009, and the
related Compliance Certificate to the Administrative Agent and the Lenders pursuant to Section 8.5
hereof, the Applicable Margins shall be those set forth in Level V in the definition of the term
“Applicable Margin” contained in Section 5.1 of the Credit Agreement.

Section 2. Conditions Precedent.

     The effectiveness of this Amendment is subject to the satisfaction of all of the following
conditions precedent:

     2.1. The Borrower, the Guarantors, and the Required Lenders shall have executed and delivered
this Amendment.

     2.2. Each of the representations and warranties set forth in Section 6 of the Credit Agreement
shall be true and correct in all material respects, except that the representations and warranties
made under Section 6.5 shall be deemed to refer to the most recent financial statements of the
Borrower delivered to the Lenders and the June 2008 flooding at the Borrower’s Cedar Rapids, Iowa
facilities shall not be taken into account with respect to the representations and warranties made
under Section 6.6 of the Credit Agreement.

     2.3. Upon giving effect to this Amendment, (a) the Borrower shall be in full compliance with
all of the terms and conditions of the Loan Documents and (b) no Default or Event of Default shall
have occurred and be continuing thereunder or shall result after giving effect to this Amendment.

     2.4. The Borrower shall have paid to the Administrative Agent for the benefit of the Lender
that have executed this amendment a non-refundable fee in the amount of 0.05% of each such Lender’s
outstanding Term Loans, Capital Expansion Loans, Capital Expansion Loan Commitment and Revolving
Credit Commitment.

Section 3. Representations.

     In order to induce the Required Lenders to execute and deliver this Amendment, the Borrower
hereby represents to the Lenders that as of the date hereof, and after giving effect to the
amendments called for hereby, the representations and warranties set forth in Section 6 of the
Credit Agreement are and shall be and remain true and correct in all material respects (except that
for purposes of this paragraph the representations contained in Section 6.5 shall be deemed to
refer to the most recent financial statements of the Borrower delivered to the Lenders and the June
2008 flooding at the Borrower’s Cedar Rapids, Iowa facilities shall not be taken into

-3-

 

account with respect to the representations and warranties made under Section 6.6 of the
Credit Agreement) and after giving effect to this Amendment (a) the Borrower is in compliance with
all of the terms and conditions of the Loan Documents and (b) no Default or Event of Default exists
under the Credit Agreement or shall result after giving effect to this Amendment.

Section 4. Miscellaneous.

     4.1. The Borrower and the Guarantors heretofore executed and delivered to the Agent and the
Lenders the Collateral Documents to which it is a party. Each of the Borrower and the Guarantors
hereby acknowledges and agrees that the Liens created and provided for by the Collateral Documents
to which it is a party continue to secure, among other things, the indebtedness, obligations and
liabilities described therein; and the Collateral Documents to which it is a party and the rights
and remedies of the Agents and the Lenders thereunder, the obligations of the Borrower and the
Guarantors thereunder, and the Liens created and provided for thereunder remain in full force and
effect and shall not be affected, impaired or discharged hereby. Nothing herein contained shall in
any manner affect or impair the priority of the Liens created and provided for by the Collateral
Documents to which it is a party as to the indebtedness, obligations and liabilities which would be
secured thereby prior to giving effect to this Amendment.

     4.2. Except as specifically amended herein or waived hereby, the Credit Agreement shall
continue in full force and effect in accordance with its original terms. Reference to this
specific Amendment need not be made in the Credit Agreement, the other Loan Documents, or any other
instrument or document executed in connection therewith, or in any certificate, letter or
communication issued or made pursuant to or with respect to the Credit Agreement, any reference in
any of such items to the Credit Agreement being sufficient to refer to the Credit Agreement as
amended hereby.

     4.3. This Amendment may be executed in any number of counterparts, and by the different
parties on different counterpart signature pages, all of which taken together shall constitute one
and the same agreement. Any of the parties hereto may execute this Amendment by signing any such
counterpart and each of such counterparts shall for all purposes be deemed to be an original. This
Amendment shall be governed by the internal laws of the State of Illinois.

     4.4. The Borrower agrees to pay all reasonable out-of-pocket costs and expenses incurred by
the Administrative Agent in connection with the credit facilities and the preparation, execution
and delivery of this Amendment, and the documents and transactions contemplated hereby, including
the reasonable fees and expenses of counsel for the Administrative Agent with respect to the
foregoing.

-4-

 

     This First Amendment to Second Amended and Restated Credit Agreement is entered into as of the
date and year first above written.

	 	 	 	 	 
	 	“Borrower”

Penford Corporation

 	 
	 	By  	 	 
	 	 	Name 	 	 	 
	 	 	
Title
 	 	 	 
	 
	 	“Guarantors”

Penford Products Co.

 	 
	 	By  	 	 
	 	 	Name 	 	 	 
	 	 	
Title
 	 	 	 
	 

Penford Corporation

Signature Page to First Amendment

to Second Amended and Restated Credit Agreement

 

 

     Accepted and agreed to as of the date and year last above written.

	 	 	 	 	 
	 	“Lenders”
	 
	 
	 	Harris N.A., in its individual capacity
as a Lender, as L/C Issuer, and as
Administrative Agent

 
	 
	 	By  	 	 
	 	 	Name 	 	 	 
	 	 	
Title
 	 	 	 
	 
	 	U.S. Bank National Association

 	 
	 	By  	 	 
	 	 	Name 	 	 	 
	 	 	
Title
 	 	 	 
	 
	 	LaSalle Bank National Association

 	 
	 	By  	 	 
	 	 	Name 	 	 	 
	 	 	
Title
 	 	 	 
	 
	 	Cooperative Centrale

Raiffeisen-Boerenleenbank B.A., “Rabobank

Nederland,” New York Branch

 
	 
	 	By  	 	 
	 	 	Name 	 	 	 
	 	 	
Title
 	 	 	 
	 
	 	 	 
	 	By  	 	 
	 	 	Name 	 	 	 
	 	 	
Title
 	 	 	 
	 

Penford Corporation

Signature Page to First Amendment

to Second Amended and Restated Credit Agreement

 

 

	 	 	 	 	 
	 	Australia and New Zealand Banking Group
Limited

 
	 
	 	By  	 	 
	 	 	Name 	 	 	 
	 	 	
Title
 	 	 	 
	 

Penford Corporation

Signature Page to First Amendment

to Second Amended and Restated Credit Agreement

 

 

Schedule I

to Compliance Certificate

Penford Corporation

Compliance Calculations

for Second Amended and Restated Credit Agreement

dated as of October 5, 2006, as amended

Calculations as of                                         ,                     

	 	 	 	 	 	 	 	 	 	 	 
	A.	 	 	Total Funded Debt Ratio (Section 8.22(a))
	 
	 

	 	 	1.	 	 	Total Funded Debt
	 	$                    

	 

	 	 	2.	 	 	Net Income for past 4 quarters
	 	$                    

	 

	 	 	3.	 	 	Interest Expense for past 4 quarters
	 	$                    

	 

	 	 	4.	 	 	Income taxes for past 4 quarters
	 	$                    

	 

	 	 	5.	 	 	Depreciation and Amortization Expense for past 4
quarters
	 	$                    

	 

	 	 	6.	 	 	Non-cash Loss (Gain) realized on sale/disposition of
assets [Loss shall be identified by a positive number;
Gains shall be identified by a negative number]
	 	$                    

	 

	 	 	7.	 	 	Non-cash stock compensation charges for past 4 quarters
	 	$                    

	 

	 	 	8.	 	 	Flood-related charges for past 4 quarters
	 	$                    

	 

	 	 	9.	 	 	Sum of Lines A2, A3, A4, A5, A6, A7 and A8
	 	$                    

	 

	 	 	10.	 	 	Flood-related insurance proceeds received during past 4 quarters
	 	$                    

	 

	 	 	11.	 	 	Line A9 minus A10 (“EBITDA”)
	 	$                    

	 

	 	 	12.	 	 	Ratio of Line A1 to A11
	 	 	___:1.0	 
	 

	 	 	13.	 	 	Line A12 ratio must not exceed
	 	 	___:1.0	 
	 

	 	 	14.	 	 	The Borrower is in compliance (circle yes or no)
	 	yes/no

	 
	 	 	 	 	 	 	 	 	 	 
	B.	 	 	Fixed Charge Coverage Ratio (Section 8.22(b))
	 

	 	 	1.	 	 	EBITDA (Line A11 above)
	 	$                    

	 

	 	 	2.	 	 	Principal payments made in cash during past 4 quarters
	 	$                    

 

	 	 	 	 	 	 	 	 	 	 	 
	 

	 	 	3.	 	 	Interest Expense for past 4 quarters paid in cash
	 	$                    

	 

	 	 	4.	 	 	Restricted Payments for past 4 quarters made in cash
	 	$                    

	 

	 	 	5.	 	 	Income taxes for 4 quarters paid in cash
	 	$                    

	 

	 	 	6.	 	 	Sum of Lines B2, B3, B4, and B5
	 	$                    

	 

	 	 	7.	 	 	Ratio of Line B1 to Line B6
	 	 	___:1.0	 
	 

	 	 	8.	 	 	Line B7 ratio must not be less than
	 	 	1.50:1.0	 
	 

	 	 	9.	 	 	The Borrower is in compliance (circle yes or no)
	 	yes/no

	 
	 	 	 	 	 	 	 	 	 	 
	C.	 	 	Leverage Ratio (Section 8.22(c))
	 

	 	 	1.	 	 	Net Worth
	 	$                    

	 

	 	 	2.	 	 	Intangible Assets
	 	$                    

	 

	 	 	3.	 	 	Write-up of assets
	 	$                    

	 

	 	 	4.	 	 	Line C1 minus the sum of Lines C2 and C3
	 	$                    

	 

	 	 	5.	 	 	Line C4 ratio must not be less than
	 	$65,000,000

	 

	 	 	6.	 	 	The Borrower is in compliance (circle yes or no)
	 	yes/no

	 
	 	 	 	 	 	 	 	 	 	 
	D.	 	 	Capital Expenditures (Section 8.22(d))
	 

	 	 	1.	 	 	Year-to-date Capital Expenditures (net of permitted
exclusions other than for the Ethanol Facility)
	 	$                    

	 

	 	 	2.	 	 	Year-to-date Capital Expenditures for Ethanol Facility
	 	$                    

	 

	 	 	3.	 	 	Line D1 minus Line D2
	 	$                    

	 

	 	 	4.	 	 	Maximum permitted amount
	 	$                    

	 

	 	 	5.	 	 	The Borrower is in compliance (circle yes or no)
	 	yes/no

-2-

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