Document:

EX-4.16

 Exhibit 4.16 

JOINDER NO. 2 TO SECURITY AGREEMENT 

Joinder No. 2 (this “Joinder”), dated as of July 24, 2014, to the Security Agreement, dated as of December 21, 2012 (as
amended, restated, supplemented, or otherwise modified from time to time, the “Security Agreement”), by and among each of the parties listed on the signature pages thereto and those additional entities that thereafter become parties
thereto (collectively, jointly and severally, “Grantors” and each, individually, a “Grantor”) and Wells Fargo Bank, National Association, as trustee (in such capacity, together with its successors and assigns, the
“Trustee”) and as collateral agent (in such capacity, together with its successors and assigns, the “Collateral Agent”). 

W I T N E S S E T H: 
 Armstrong
Energy, Inc. (the “Issuer”), the other Grantors party from time to time thereto (the “Guarantors”), Wells Fargo Bank, National Association, as Trustee and Wells Fargo Bank, National Association, as the Collateral
Agent are parties to that certain Indenture, dated as of the date hereof (as amended, supplemented, amended and restated or otherwise modified from time to time, the “Indenture”), pursuant to which the Issuer has issued $200,000,000
of its 11.75% senior secured notes due 2019 (the “Initial Notes”) and may issue additional notes from time to time in accordance with the Indenture (the “Additional Notes” and, together with the Initial Notes, the
“Notes”); and 
 Initially capitalized terms used herein and not otherwise defined herein shall have the meanings assigned to such terms in
the Security Agreement or, if not defined therein, in the Indenture; and 
 Grantors have entered into the Security Agreement in order to induce the Holders
of the Notes to make certain financial accommodations to Issuer; and 
 Pursuant to the Indenture and Section 26 of the Security Agreement,
certain Subsidiaries of the Issuer, must execute and deliver certain Note Collateral Documents (as defined in the Intercreditor Agreement), including the Security Agreement, and the Joinder to the Security Agreement by the undersigned new Grantor
(the “New Grantor”) may be accomplished by the execution of this Joinder in favor of Collateral Agent, for the benefit of the Secured Parties; and 

The New Grantor (a) is a Subsidiary of Issuer and, as such, will benefit by virtue of the financial accommodations extended to Issuer by the Secured
Parties and (b) by becoming a Grantor will benefit from certain rights granted to the Grantors pursuant to the terms of the Note Documents; 
 NOW,
THEREFORE, for and in consideration of the foregoing and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the New Grantor hereby agrees as follows: 

1. In accordance with Section 26 of the Security Agreement, the New Grantor, by its signature below, becomes a “Grantor” under the
Security Agreement with the same force and effect as if originally named therein as a “Grantor” and the New Grantor hereby (a) agrees to all of the terms and provisions of the Security Agreement applicable to it as a
“Grantor” thereunder 

 
and (b) represents and warrants that the representations and warranties made by it as a “Grantor” thereunder are true and correct in all material respects (except that such
materiality qualifier shall not be applicable to any representations and warranties that are already qualified or modified by materiality in the text thereof) on and as of the date hereof. In furtherance of the foregoing, the New Grantor does hereby
unconditionally grant, assign, and pledge to Collateral Agent, for the benefit of the Secured Parties, to secure the Secured Obligations, a continuing security interest in and to all of the New Grantor’s right, title and interest in and to the
Collateral. Schedule A, “Security Interest Data Summary”, and Schedule B, “Commercial Tort Claims”, attached hereto, supplement Schedule A and Schedule B, respectively, to the Security Agreement and shall be deemed
a part thereof for all purposes of the Security Agreement. Each reference to a “Grantor” in the Security Agreement shall be deemed to include the New Grantor. The Security Agreement is incorporated herein by reference. The New Grantor
authorizes Collateral Agent at any time and from time to time to file, transmit, or communicate, as applicable, financing statements and amendments thereto (i) describing the Collateral as “all personal property of debtor” or
“all assets of debtor” or words of similar effect, (ii) describing the Collateral as being of equal or lesser scope or with greater detail, or (iii) that contain any information required by part 5 of Article 9 of the UCC for the
sufficiency or filing office acceptance. The New Grantor also hereby ratifies any and all financing statements or amendments previously filed by the Collateral Agent in any jurisdiction in connection with the Note Documents. 

2. The New Grantor represents and warrants to Collateral Agent and the Amended that this Joinder has been duly executed and delivered by the New Grantor and
constitutes its legal, valid, and binding obligation, enforceable against it in accordance with its terms, except as enforceability thereof may be limited by bankruptcy, insolvency, reorganization, fraudulent transfer, moratorium, or other similar
laws affecting creditors’ rights generally and general principles of equity (regardless of whether such enforceability is considered in a proceeding at law or in equity). 

3. This Joinder is a Senior Secured Note Document. This Joinder may be executed in any number of counterparts and by different parties on separate
counterparts, each of which, when executed and delivered, shall be deemed to be an original, and all of which, when taken together, shall constitute but one and the same Joinder. Delivery of an executed counterpart of this Joinder by telefacsimile
or other electronic method of transmission shall be equally as effective as delivery of an original executed counterpart of this Joinder. Any party delivering an executed counterpart of this Joinder by telefacsimile or other electronic method of
transmission also shall deliver an original executed counterpart of this Joinder but the failure to deliver an original executed counterpart shall not affect the validity, enforceability, and binding effect of this Joinder. 

4. The Security Agreement, as supplemented hereby, shall remain in full force and effect. 

5. This Agreement, and the rights and duties of the parties hereto, shall be construed and determined in accordance with the internal laws of the State of New
York. The headings in this Agreement are for convenience of reference only and shall not limit or otherwise affect the meaning of any provision hereof. 

 6. Each Guarantor hereby submits to the nonexclusive jurisdiction of any U.S. Federal or New York State court
sitting in New York, New York for purposes of all legal proceedings arising out of or relating to this Agreement or the transactions contemplated hereby. Each Grantor irrevocably waives, to the fullest extent permitted by law, any objection which it
may now or hereafter have to the laying of the venue of any such proceeding brought in such a court and any claim that any such proceeding brought in such a court has been brought in an inconvenient forum. EACH GRANTOR AND THE COLLATERAL AGENT
HEREBY IRREVOCABLY WAIVES ANY AND ALL RIGHT TO TRIAL BY JURY IN ANY LEGAL PROCEEDING ARISING OUT OF OR RELATING TO THIS AGREEMENT OR THE TRANSACTIONS CONTEMPLATED HEREBY. 

[REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK] 

 IN WITNESS WHEREOF, the parties hereto have caused this Joinder to the Security Agreement to be
executed and delivered as of the day and year first above written. 
  

							
	NEW GRANTOR:	 		 	THOROUGHFARE MINING, LLC
				
		 		 	By:	 	 /s/ Martin D. Wilson

		 		 	Name:	 	Martin D. Wilson
		 		 	Title:	 	Manager
			
	COLLATERAL AGENT:	 		 	WELLS FARGO BANK, NATIONAL ASSOCIATION as Collateral Agent
				
		 		 	By:	 	 /s/ Gregory S. Clarke

		 		 	Name:	 	Gregory S. Clarke
		 		 	Title:	 	Vice President

  

							
	TRUSTEE:	 		 	WELLS FARGO BANK, NATIONAL ASSOCIATION as Trustee
				
		 		 	By:	 	 /s/ Gregory S. Clarke

		 		 	Name:	 	Gregory S. Clarke
		 		 	Title:	 	Vice President

 SCHEDULE A 

to 
 SECURITY AGREEMENT

 Security Interest Data Summary 

1. The chief executive office of Thoroughfare Mining, LLC (the “Debtor”) is located at: 407 Brown Road, Madisonville, KY
42431. 
 2. The Debtor’s true and full name is as follows: Thoroughfare Mining, LLC. The Debtor uses no trade names or fictitious
names. 
 3. The Debtor’s form of organization is as follows: limited liability company. 

4. The Debtor’s state of organization is as follows: Delaware. 

5. The Debtor’s organization ID # (if any exists) is as follows: 5454575. 

6. All of the Debtor’s personal property which has not been delivered to the Administrative Agent pursuant to the terms of this Agreement
or the Credit Agreement is now, and will be at all future times, located at the Debtor’s chief executive office as described in Paragraph 1 above, except as specified below: 

Property that is located at the mining operations in Muhlenberg County, Ohio County, McLean County, Union County and/or Webster County,
Kentucky, or at the corporate office located at 7733 Forsyth Boulevard, Suite 1625, St. Louis, Missouri 63105. 
 7. All of the
Debtor’s books and records, including those relating to accounts payable and accounts receivable, are kept at the Debtor’s chief executive office as described in Paragraph 1 above, except as specified below: 

Books and records that are located at the corporate office located at 7733 Forsyth Boulevard, Suite 1625, St. Louis, Missouri 63105. 

8. All of the Debtor’s real property is located in the following counties: 

Muhlenberg County, McLean County 

 SCHEDULE B 

to 
 SECURITY AGREEMENT

 Commercial Tort Claims 

NoneEX-4.17

 Exhibit 4.17 

THIRD SUPPLEMENTAL INDENTURE 

This Third Supplemental Indenture (this “Supplemental Indenture”), dated as of August 14, 2014, is by and
among Armstrong Energy, Inc., a Delaware corporation (the “Company”), the Guarantors (as defined in the Indenture referred to below), and Wells Fargo Bank, National Association, as trustee under the Indenture referred to
below (the “Trustee”). 
 W I T N E S S E T H 

WHEREAS, the Company and the Guarantors have heretofore executed and delivered to the Trustee an indenture (as amended, supplemented or
otherwise modified, the “Indenture”), dated as of December 21, 2012 providing for the issuance of 11.75% Senior Secured Notes due 2019 (the “Notes”), as supplemented by a First Supplemental Indenture thereto,
dated September 19, 2013, and a Second Supplemental Indenture thereto, dated July 24, 2014; 
 WHEREAS, the Indenture currently
permits the Company and the Guarantors to make Permitted Reserve Transfers by transferring undivided fractional interests in the real property tracts designated in the Royalty Deferment and Option Agreement (the “Designated
Property”) to certain affiliates in lieu of paying cash royalties due to such affiliates; 
 WHEREAS, the Company desires to add
additional tracts of real property to the Designated Property and has requested the amendment of certain provisions of the Indenture as described below (the “Amendments”) to permit the inclusion of such additional Designated
Property; 
 WHEREAS, pursuant to Section 9.02 of the Indenture, the Company, the Guarantors and the Trustee may amend or supplement
the Indenture with the written consent of the Holders of not less than a majority in aggregate principal amount of the outstanding Notes; 

WHEREAS, the Company has obtained and delivered to the Trustee the written consent of the Holders of not less than a majority in aggregate
principal amount of the outstanding Notes to the Amendments upon the terms of the Indenture and has satisfied all other conditions required under Article 9 of the Indenture; 

WHEREAS, pursuant to Sections 9.02 and 9.08 of the Indenture, the Trustee is authorized to execute and deliver this Supplemental
Indenture; and 
 WHEREAS, the Amendments contemplated hereby shall become effective on the date hereof (the “Effective
Date”). 
 NOW, THEREFORE, in consideration of the foregoing and for other good and valuable consideration, the receipt and
sufficiency of which is hereby acknowledged, the Company and the Guarantors agree with the Trustee as follows: 

 ARTICLE I 

DEFINITIONS 

Section 1.01. Capitalized Terms. Capitalized terms used herein without definition shall have the meanings assigned to them
in the Indenture. 
 ARTICLE II 

AMENDMENT OF INDENTURE 

Section 2.01. Amendment of Indenture. The Indenture (including the exhibits thereto, including the Notes) is hereby amended
as follows (the amendments set forth below reflect additions in bolded underline and deletions in strikethrough): 

(a) The definition of “Permitted Reserve Transfers,” as set forth in Section 1.01 of the Indenture, is hereby amended and
restated as follows: 
 “Permitted Reserve Transfers” means transfers of interests in coal reserves to
Armstrong Resource Partners or a subsidiary thereof (1) to satisfy obligations in respect of the Royalty Deferment and Option Agreement or the Credit and Collateral Support Fee, Indemnification and Right of First Refusal Agreement, each
as in effect on the Issue Date or (2) to satisfy deferred royalty obligations owing to Armstrong Resource Partners or a subsidiary thereof relating to coal reserves acquired after the Issue Date pursuant to agreements that have been
entered into by the Company or a Restricted Subsidiary in compliance with clause (a) and (b) of Section 4.10. 
 (b) The
definition of “Royalty Deferment and Option Agreement,” as set forth in Section 1.01 of the Indenture, is hereby amended and restated as follows: 

“Royalty Deferment and Option Agreement” means that certain agreement, Royalty
Deferment and Option Agreement entered into on October 11, 2011 but effective February 9, 2011, as amended and restated by that certain First Amended and Restated Royalty Deferment and Option Agreement dated August 14,
2014 between by and among Armstrong Coal Company, Inc., Thoroughfare Mining, LLC, Western Diamond LLC, Western Land Company, LLC, Thoroughbred Resources,
L.P., Western Mineral Development, LLC and Ceralvo Holdings, LLC. as in effect on the Issue Date and described in the offering memorandum for the Notes issued on the Issue Date under “Certain Relationships and
Related Party Transactions.” 
 (c) The definition of “Armstrong Resource Partners,” as set forth in
Section 1.01 of the Indenture, is hereby amended and restated as follows: 
 “Armstrong Resource
Partners” means Thoroughbred Resources, L.P., a Delaware limited partnership formerly known (by name change only) as Armstrong Resource Partners, L.P., a Delaware limited partnership. 

  
 2 

 ARTICLE III 

MISCELLANEOUS 

Section 3.01. Governing Law. The internal law of the State of New York shall govern and be used to construe this Supplemental
Indenture, the Indenture and the Notes, without giving effect to applicable principles of conflict of law to the extent that the application of the laws of another jurisdiction would be required thereby. 

Section 3.02. Counterparts. The parties may sign any number of copies of this Supplemental Indenture. Each signed copy
shall be an original, but all of them together represent the same agreement. The exchange of copies of this Supplemental Indenture and of signature pages by facsimile or portable document format (“PDF”) transmission shall
constitute effective execution and delivery of this Supplemental Indenture as to the parties hereto and may be used in lieu of the original Supplemental Indenture for all purposes. Signatures of the parties hereto transmitted by facsimile or PDF
shall be deemed to be their original signatures for all purposes. 
 Section 3.03. Effect of Headings. The
Section headings herein are for convenience only and shall not affect the construction hereof. 
 Section 3.04. The Trustee and
Agent. Neither the Trustee nor the Paying Agent shall be responsible in any manner whatsoever for or in respect of the validity, sufficiency or adequacy of this Supplemental Indenture, or with respect to the solicitation of consents of the
Holders, or the consents of the Holders, or for or in respect of the recitals contained herein, all of which recitals are made solely by the Company and the Guarantors. All of the provisions contained in the Indenture in respect of the rights,
privileges, immunities, powers, and duties of the Trustee shall be applicable in respect of this Supplemental Indenture as fully and with like force and effect as though fully set forth in full herein. The Company hereby confirms to the Trustee that
this Supplemental Indenture has not resulted in a material modification of the Notes for Foreign Accounting Tax Compliance Act (“FATCA”) purposes. The Company shall give the Trustee prompt written notice of any material modification
of the Notes deemed to occur for FATCA purposes. The Trustee shall assume that no material modification for FATCA purposes has occurred regarding the Notes, unless the Trustee receives written notice of such modification from the Company. 

Section 3.05. Consents. The Company hereby represents, warrants, and certifies to the Trustee that the Holders of at least a
majority in aggregate principal amount of the Notes currently outstanding have provided consents to the execution of this Supplemental Indenture, and execution of this Supplemental Indenture is authorized and permitted by the Indenture and
constitutes the legal, valid and binding obligation of the Company and the Guarantors enforceable in accordance with its terms, subject to bankruptcy, insolvency, fraudulent conveyance, reorganization, moratorium and other similar laws relating to
or affecting creditors’ rights generally, general equitable principles (whether considered in a proceeding in equity or at law) and an implied covenant of good faith and fair dealing. 

  
 3 

 IN WITNESS WHEREOF, the parties hereto have caused this Supplemental Indenture to be duly
executed and attested, all as of the date first above written. 
 Dated: August 14, 2014 

 

			
	Armstrong Energy, Inc.
		
	By:	 	 /s/ Martin D. Wilson

	Name:	 	Martin D. Wilson
	Title:	 	President and Chief Commercial Officer
	
	 Thoroughfare Mining, LLC
 as a
Guarantor

		
	By:	 	 /s/ Martin D. Wilson

	Name:	 	Martin D. Wilson
	Title:	 	Manager
	
	 Armstrong Logistics Services, LLC

as a Guarantor

		
	By:	 	 /s/ Martin D. Wilson

	Name:	 	Martin D. Wilson
	Title:	 	Manager
	
	 Armstrong Air, LLC
 as a
Guarantor

		
	By:	 	 /s/ Martin D. Wilson

	Name:	 	Martin D. Wilson
	Title:	 	Manager
	
	 Armstrong Coal Company, Inc.
 as a
Guarantor

		
	By:	 	 /s/ Martin D. Wilson

	Name:	 	Martin D. Wilson
	Title:	 	President

			
	
	 Armstrong Energy Holdings, Inc.
 as
a Guarantor

		
	By:	 	 /s/ Martin D. Wilson

	Name:	 	Martin D. Wilson
	Title:	 	President
	
	 Western Diamond LLC
 as a
Guarantor

		
	By:	 	 /s/ Martin D. Wilson

	Name:	 	Martin D. Wilson
	Title:	 	Manager
	
	 Western Land Company, LLC
 as a
Guarantor

		
	By:	 	 /s/ Martin D. Wilson

	Name:	 	Martin D. Wilson
	Title:	 	Manager
	
	Wells Fargo Bank, National Association, as Trustee
		
	By:	 	 /s/ Gregory S. Clarke

	Name:	 	Gregory S. Clarke
	Title:	 	Vice President

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