Exhibit 10.6

CONTRIBUTION, CONVEYANCE AND ASSUMPTION

AGREEMENT

By and Among

ALON ASSETS INC.

ALON USA PARTNERS GP, LLC

ALON USA PARTNERS, LP

ALON USA ENERGY, INC.

ALON USA REFINING, LLC

ALON USA OPERATING, INC.

ALON USA, LP

and

ALON USA GP, LLC

Dated as of November 26, 2012

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CONTRIBUTION, CONVEYANCE AND ASSUMPTION

AGREEMENT

This Contribution, Conveyance and Assumption Agreement, dated as of November 26,
2012 (this “Agreement”), is by and among Alon USA Partners, LP, a Delaware
limited partnership (the “Partnership”), Alon USA Partners GP, LLC, a Delaware
limited liability company (the “General Partner”), Alon Assets, Inc., a Delaware
corporation (“Alon Assets”), Alon USA Energy, Inc., a Delaware corporation
(“Alon Energy”), Alon USA Refining, LLC, a Delaware limited liability company,
Alon USA Operating, Inc., a Delaware corporation (“Alon Operating”), Alon USA,
LP, a Texas limited partnership (“Alon USA, LP”), and Alon USA GP, LLC, a
Delaware limited liability company (“Alon USA GP, LLC”). The above-named
entities are sometimes referred to in this Agreement each as a “Party” and
collectively as the “Parties.” Capitalized terms used herein shall have the
meanings assigned to such terms in Article I.

RECITALS

WHEREAS, Alon Assets and the General Partner have formed the Partnership,
pursuant to the Delaware Revised Uniform Limited Partnership Act (the “Delaware
LP Act”), for the purpose of engaging in any business activity that is approved
by the General Partner and that lawfully may be conducted by a limited
partnership organized pursuant to the Delaware LP Act.

WHEREAS, in order to accomplish the objectives and purposes in the preceding
recital, each of the following actions has been taken prior to the date hereof:

 

  1. Alon Assets formed the General Partner under the terms of the Delaware
Limited Liability Company Act (the “Delaware LLC Act”) and contributed $1,000 in
exchange for all of the member interests in the General Partner.

 

  2. Alon Assets and the General Partner formed the Partnership under the terms
of the Delaware LP Act and contributed $1,000 and $0, respectively, in exchange
for a 100% limited partner interest and a non-economic general partner interest,
respectively, in the Partnership.

 

  3. Alon Energy refinanced its existing term loan facility with a term loan
facility that is guaranteed by its subsidiaries named therein, including Alon
Assets (the “New Term Loan Facility”).

 

  4. Alon USA Capital, Inc. (“Alon Capital”) acquired certain intercompany
receivables from Alon USA, LP and Alon Assets in exchange for an intercompany
obligation of Alon USA Capital, Inc. for an equivalent amount.

 

  5. Alon Refining, Inc. converted pursuant to the terms of the Delaware General
Corporation Law into Alon Refining, LLC, a limited liability company under the
terms of the Delaware LLC Act (as converted, “Alon Refining”).

 

  6. Alon Refining distributed 100% of the member interests in Alon Crude
Pipelines, LLC, a Texas limited liability company, to Alon Assets.

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  7. Alon Operating formed Alon USA Holdings, LLC (“Alon Holdings”) under the
terms of the Texas Limited Liability Company Act.

 

  8. Alon USA, LP amended its IDB Credit Facility.

 

  9. Alon Holdings and Alon USA, LP have undergone a multi-survivor merger
pursuant to which both entities survived and all of Alon USA, LP’s non-Big
Spring Refinery assets were transferred to Alon Holdings, LLC.

 

  10. Alon USA GP, LLC formed Alon USA GP II, LLC under the terms of the
Delaware LLC Act and contributed its general partner interest in Alon USA, LP to
Alon USA GP II, LLC.

 

  11. Alon Operating merged into Alon Assets.

WHEREAS, at the closing of the Partnership’s initial public offering of Common
Units, each of the following transactions shall occur in the following order:

 

  1. Alon USA GP, LLC distributes all of the interests in Alon USA GP II, LLC to
Alon Assets.

 

  2. Alon Assets contributes 100% of the member interests in each of Alon USA
Delaware, Alon USA GP II, LLC and Alon Refining to the Partnership in exchange
for 51,000,000 Common Units.

 

  3. The Partnership and all of its subsidiaries assign all of their remaining
intercompany receivables to Alon Assets, and Alon Assets assumes liability for
all of the remaining intercompany payables of the Partnership and all of its
subsidiaries other than the IPO Repayment Obligations.

 

  4. Alon Energy executes and delivers the Promissory Note as consideration for
Alon Assets’ assumption of the MLP Tranche of the New Term Loan Facility.

 

  5. The Partnership assumes the MLP Tranche of the New Term Loan Facility from
Alon Assets.

 

  6. The Underwriters contribute $171,120,000.00 in cash (which amount is less
the amount of $12,880,000.00 payable to the Underwriters after taking into
account the underwriting discount of 7.0% (the “Spread”) payable to the
Underwriters), in exchange for 11,500,000 Common Units (representing an
approximate 81.6% limited partner interest in the Partnership).

 

  7. The Partnership will repay $171,120,000.00 of its intercompany liabilities,
and Alon Energy, on behalf of the Partnership, will pay approximately $2,000,000
of offering expenses.

 

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NOW, THEREFORE, in consideration of the mutual covenants, representations,
warranties and agreements herein contained, the parties hereto agree as follows:

ARTICLE I

DEFINITIONS

The terms set forth below in this Article I shall have the meanings ascribed to
them below or in the part of this Agreement referred to below:

“Agreement” has the meaning assigned to such term in the preamble.

“Alon Assets” has the meaning assigned to such term in the preamble.

“Alon Capital” has the meaning assigned to such term in the recitals.

“Alon Energy” has the meaning assigned to such term in the preamble.

“Alon Holdings” has the meaning assigned to such term in the recitals.

“Alon USA, LP” has the meaning assigned to such term in the preamble.

“Alon USA GP, LLC” has the meaning assigned to such term in the preamble.

“Alon USA GP II, LLC” has the meaning assigned to such term in the recitals.

“Alon Operating” has the meaning assigned to such term in the preamble.

“Alon Refining” has the meaning assigned to such term in the recitals.

“Big Spring Refinery Assets” means the refinery and related crude oil and
refined product logistic assets of the Big Spring Refinery in Big Spring, Texas.

“Common Units” means the common units representing limited partner interests in
the Partnership.

“Commission” means the U.S. Securities and Exchange Commission.

“Delaware LLC Act” has the meaning assigned to such term in the recitals.

“Delaware LP Act” has the meaning assigned to such term in the recitals.

“Effective Time” means immediately prior to the closing of the initial public
offering pursuant to the Underwriting Agreement.

“General Partner” has the meaning assigned to such term in the preamble.

“IDB Credit Facility” means the Amended Revolving Credit Agreement by and among
Alon USA Partners, LP, Alon USA, LP and certain other guarantor companies and
Israel Discount Bank of New York, Bank Leumi USA and financial institutions from
time to time named therein, as amended.

 

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“IPO Repayment Intercompany Obligations” means (i) a subordinated intercompany
note receivable in the principal amount of $12,044,120, with interest accrued
and payable thereon in the amount of $14,857,996 payable by Alon Refining to
Alon Capital, (ii) a subordinated intercompany note receivable in the principal
amount of $33,423,000 with interest accrued and payable thereon in the amount of
$ 29,811,384 payable by Alon Refining to Alon USA, Inc., and (iii) a portion
equal to $80,983,500.00 of the principal amount on a subordinated intercompany
note receivable with the initial principal amount of $112,000,000 payable by
Alon USA, LP to Alon Capital.

“MLP Tranche” means the portion of the New Term Loan Facility that will be
assumed by the Partnership.

“New Term Loan Facility” has the meaning assigned to such term in the recitals.

“Option Units” means the common units that the Partnership will agree to issue
upon an exercise of the Over-Allotment Option.

“Original Partnership Agreement” means the Agreement of Limited Partnership of
the Partnership dated as of August 17, 2012.

“Over-Allotment Option” has the meaning assigned to such term in the Partnership
Agreement.

“Partnership” has the meaning assigned to such term in the preamble.

“Partnership Agreement” means the First Amended and Restated Agreement of
Limited Partnership of the Partnership dated as of November 26, 2012.

“Party” or “Parties” has the meaning assigned to such term in the preamble.

“Pricing” means the time at which that certain Underwriting Agreement is entered
into.

“Promissory Note” means that certain unsecured promissory note to be dated the
Closing Date issued by Alon Energy in favor of Alon Assets in the principal
amount of $250,000,000.

“Registration Statement” means the Registration Statement on Form S-1 filed with
the Commission (Registration No. 333-183671), as amended and effective at the
Effective Time.

“Securities Act” means the Securities Act of 1933, as amended.

“Spread” has the meaning assigned to such term in the recitals.

“Underwriters” means those underwriters listed in the Underwriting Agreement.

“Underwriting Agreement” means that certain Underwriting Agreement between Alon
Energy, Alon Assets, Alon USA GP, LLC, the Partnership, the General Partner and
the Underwriters, dated as of November 19, 2012.

 

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ARTICLE II

CONTRIBUTION, ACKNOWLEDGEMENTS AND DISTRIBUTIONS

Section 2.1 Alon USA GP’s Distribution of Alon USA GP II. Alon USA GP, as the
sole member of Alon USA GP II, hereby distributes, grants, bargains, conveys,
assigns, transfers, sets over and delivers to Alon Assets, its successors and
assigns, for its use forever, all right, title and interest in and to all of the
member interests in Alon USA GP II, and Alon Assets accepts such member
interests and shall be admitted as the sole member of Alon USA GP II.

Section 2.2 Alon Assets’ Contribution to the Partnership. Alon Assets, as the
sole member of each of Alon USA Delaware, Alon USA GP II and Alon Refining,
contributes 100% of the member interests in each of Alon USA Delaware, Alon USA
GP II and Alon Refining to the Partnership in exchange for 51,000,000 Common
Units, and the Partnership accepts such member interests and shall be admitted
as the sole member of each of Alon USA Delaware, Alon USA GP II and Alon
Refining.

Section 2.3 Elimination of Certain Intercompany Receivables and Payables. The
Partnership and all of its subsidiaries hereby assign, transfer, set over and
deliver to Alon Assets, its successors and assigns, for its use forever, all
right, title and interest to all of their remaining intercompany receivables,
and Alon Assets accepts such assignment and assumes all liability for all of the
remaining intercompany payables of the Partnership and all of its subsidiaries
other than the IPO Repayment Obligations.

Section 2.4 Alon Assets’ Assumption of New Term Loan Facility. The Parties
acknowledge that on or before the date hereof, Alon Energy has executed and
delivered the Promissory Note as consideration for Alon Assets’ assumption of
the MLP Tranche of the New Term Loan Facility.

Section 2.5 Execution of the Partnership Agreement. The Parties acknowledge that
the Partnership, the General Partner and Alon Energy have amended and restated
the Original Partnership Agreement by executing the Partnership Agreement in
substantially the form included in Appendix A to the Registration Statement,
with such changes as the Partnership, the General Partner and Alon Energy have
agreed.

Section 2.6 Partnership’s Assumption of New Term Loan Facility. The Partnership
hereby assumes the MLP Tranche of the New Term Loan Facility from Alon Assets.

Section 2.7 Underwriters’ Cash Contribution. The Parties acknowledge that the
Underwriters have made a contribution to the capital of the Partnership in the
amount of $171,120,000.00 in cash (which amount is less Spread payable to the
Underwriters), in exchange for 11,500,000 Common Units (representing an
approximate 81.6% limited partner interest in the Partnership).

Section 2.8 Payment of Intercompany Liabilities. The Parties acknowledge the
payment in full by the Partnership (on behalf of its subsidiaries Alon Refining
and Alon USA, LP), in connection with the transactions contemplated hereby, of
the $171,120,000 of IPO Repayment Intercompany Obligations to Alon Capital and
Alon USA, Inc.

 

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Section 2.9 Payment of Transaction Expenses. The Parties acknowledge the payment
by Alon Energy, on behalf of the Partnership, in connection with the
transactions contemplated hereby, of estimated transaction expenses in the
amount of approximately $2,000,000 (excluding the Spread).

ARTICLE III

DEFERRED ISSUANCE AND DISTRIBUTION

[Intentionally omitted to facilitate a simultaneous closing of the initial
public offering and the Over-Allotment Option.]

ARTICLE IV

FURTHER ASSURANCES

From time to time after the Effective Time, and without any further
consideration, the Parties agree to execute, acknowledge and deliver all such
additional deeds, assignments, bills of sale, conveyances, instruments, notices,
releases, acquittances and other documents, and to do all such other acts and
things, all in accordance with applicable law, as may be necessary or
appropriate (a) more fully to assure that the applicable Parties own all of the
properties, rights, titles, interests, estates, remedies, powers and privileges
granted by this Agreement, or which are intended to be so granted, (b) more
fully and effectively to vest in the applicable Parties and their respective
successors and assigns beneficial and record title to the interests contributed
and assigned by this Agreement or intended to be so and (c) more fully and
effectively to carry out the purposes and intent of this Agreement.

ARTICLE V

EFFECTIVE TIME

Notwithstanding anything contained in this Agreement to the contrary, none of
the provisions of Article II of this Agreement shall be operative or have any
effect until the Effective Time, at which time all the provisions of Article II
of this Agreement shall be effective and operative in accordance with Article
VI, without further action by any Party hereto.

ARTICLE VI

MISCELLANEOUS

Section 6.1 Order of Completion of Transactions. The transactions provided for
in Article II of this Agreement shall be completed immediately following the
Effective Time in the order set forth therein.

Section 6.2 Headings; References; Interpretation. All Article and Section
headings in this Agreement are for convenience only and shall not be deemed to
control or affect the meaning or construction of any of the provisions hereof.
The words “hereof,” “herein” and “hereunder” and words of similar import, when
used in this Agreement, shall refer to this Agreement as a whole, including,
without limitation, all Schedules and Exhibits attached hereto, and not to any
particular provision of this Agreement. All references herein to Articles,
Sections, Schedules and Exhibits shall, unless the context requires a different
construction, be deemed to be references to the Articles and Sections of this
Agreement and the Schedules and Exhibits

 

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attached hereto, and all such Schedules and Exhibits attached hereto are hereby
incorporated herein and made a part hereof for all purposes. All personal
pronouns used in this Agreement, whether used in the masculine, feminine or
neuter gender, shall include all other genders, and the singular shall include
the plural and vice versa. The use herein of the word “including” following any
general statement, term or matter shall not be construed to limit such
statement, term or matter to the specific items or matters set forth immediately
following such word or to similar items or matters, whether or not non-limiting
language (such as “without limitation,” “but not limited to,” or words of
similar import) is used with reference thereto, but rather shall be deemed to
refer to all other items or matters that could reasonably fall within the
broadest possible scope of such general statement, term or matter.

Section 6.3 Successors and Assigns. This Agreement shall be binding upon and
inure to the benefit of the Parties and their respective successors and assigns.

Section 6.4 No Third Party Rights. The provisions of this Agreement are intended
to bind the Parties as to each other and are not intended to and do not create
rights in any other person or confer upon any other person any benefits, rights
or remedies, and no person is or is intended to be a third party beneficiary of
any of the provisions of this Agreement.

Section 6.5 Counterparts. This Agreement may be executed in any number of
counterparts with the same effect as if all signatory Parties had signed the
same document. All counterparts shall be construed together and shall constitute
one and the same instrument.

Section 6.6 Choice of Law. This Agreement shall be subject to and governed by
the laws of the State of Delaware. Each Party hereby submits to the jurisdiction
of the state and federal courts of, and to venue in, the State of Delaware.

Section 6.7 Severability. If any of the provisions of this Agreement are held by
any court of competent jurisdiction to contravene, or to be invalid under, the
laws of any political body having jurisdiction over the subject matter hereof,
such contravention or invalidity shall not invalidate the entire Agreement.
Instead, this Agreement shall be construed as if it did not contain the
particular provisions or provisions held to be invalid and an equitable
adjustment shall be made and necessary provision added so as to give effect to
the intention of the Parties as expressed in this Agreement at the time of
execution of this Agreement.

Section 6.8 Amendment or Modification. This Agreement may be amended or modified
from time to time only by the written agreement of all the Parties. Each such
instrument shall be reduced to writing and shall be designated on its face as an
amendment to this Agreement.

Section 6.9 Integration. This Agreement and the instruments referenced herein
supersede all previous understandings or agreements among the Parties, whether
oral or written, with respect to the subject matter of this Agreement and such
instruments. This Agreement and such instruments contain the entire
understanding of the Parties with respect to the subject matter hereof and
thereof. No understanding, representation, promise or agreement, whether oral or
written, is intended to be or shall be included in or form part of this
Agreement unless it is contained in a written amendment hereto executed by the
parties hereto after the date of this Agreement.

 

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Section 6.10 Deed; Bill of Sale; Assignment. To the extent required and
permitted by applicable law, this Agreement shall also constitute a “deed,”
“bill of sale” or “assignment” of the assets and interests referenced herein.

[Signature Pages Follow]

 

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IN WITNESS WHEREOF, the parties to this Agreement have caused it to be duly
executed as of the date first above written.

 

ALON ASSETS INC. By:  

/s/ James Ranspot

Name:   James Ranspot Title:   Secretary ALON USA PARTNERS GP, LLC By:  

/s/ Michael Oster

Name:   Michael Oster Title:   Vice President ALON USA PARTNERS, LP By:   Alon
USA Partners GP, LLC, its   General Partner By:  

/s/ Michael Oster

Name:   Michael Oster Title:   Vice President ALON USA ENERGY, INC. By:  

/s/ Michael Oster

Name:   Michael Oster Title:   Senior Vice President

 

Signature Page to Contribution, Conveyance and Assumption Agreement

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ALON USA REFINING, LLC By:  

/s/ Michael Oster

Name:   Michael Oster Title:   Vice President ALON USA OPERATING, INC. By:  

/s/ Michael Oster

Name:   Michael Oster Title:   Vice President ALON USA, LP By:   Alon USA GP,
LLC, its General Partner By:  

/s/ Michael Oster

Name:   Michael Oster Title:   Vice President ALON USA GP, LLC By:  

/s/ Michael Oster

Name:   Michael Oster Title:   Vice President

 

Signature Page to Contribution, Conveyance and Assumption Agreement