Amendment to Agreement and Plan of Merger



 Exhibit 10.1 
 AMENDMENT TO AGREEMENT AND PLAN OF MERGER 
 THIS AMENDMENT TO AGREEMENT AND PLAN OF MERGER (this “Amendment”) is made and
entered into as of September 18, 2009, by and among LIGAND PHARMACEUTICALS INCORPORATED, a Delaware corporation (“Parent”); NEON SIGNAL, LLC, a Delaware
limited liability company and a wholly-owned Subsidiary of Parent (“Merger Sub”); and NEUROGEN CORPORATION, a Delaware corporation (the “Company”). This Amendment is made with regard to
the Agreement and Plan of Merger dated August 23, 2009, by and among Parent, Merger Sub and the Company (the “Agreement”). 
 1. The Agreement is hereby amended by changing the definition of “Target Net Cash Amount” in Article I of the Agreement to read in full as follows: 
 “Target Net Cash Amount” shall mean $7,900,000 if the Determination Date occurs on any date during the month
of September 2009, with a $5,000 decrease for each calendar day thereafter if the Determination Date occurs on any date thereafter. 
 2. Except as expressly set forth herein, the Agreement remains unchanged and in full force and effect. 
 3. This
Amendment may be executed in counterparts, each of which shall be deemed to be an original, and all of which taken together shall be deemed to constitute one and the same instrument. The parties agree that delivery of an executed counterpart of a
signature page of this Amendment electronically or by facsimile shall be effective as delivery of a manually executed counterpart of this Amendment. 
 [Remainder of page left intentionally blank. Signature page follows.] 







 IN WITNESS WHEREOF, Parent, Merger Sub and the Company have caused this Amendment to be
executed as of the date first written above. 
  

					
	LIGAND PHARMACEUTICALS INCORPORATED
		
	By:	 	 /s/ John Sharp

	Name:	 	 John Sharp

	Title:	 	 CFO

	
	NEON SIGNAL, LLC
		
	By:	 	 Ligand Pharmaceuticals Incorporated,
 its Member-Manager

			
		 	By:	 	 /s/ John Sharp

		 	Name:	 	 John Sharp

		 	Title:	 	 CFO

	
	NEUROGEN CORPORATION 
		
	By:	 	 /s/ Steve Davis

	Name:	 	 Steve Davis

	Title:	 	 President & CEO



 (Signature Page to Amendment to Merger Agreement) 







 ACKNOWLEDGED AND AGREED: 
  

							
	WARBURG PINCUS PRIVATE EQUITY VIII, L.P. 	 		 	STEPHEN R. DAVIS
				
	By:	 	 Warburg Pincus Partners, LLC,
 its General Partner
	 		 	 /s/ Stephen R. Davis

				
	By:	 	 Warburg Pincus & Co.,
 its Managing Member
	 		 	JULIAN BAKER
				
	 By:
	 	 /s/ Jonathan Leff
	 		 	 /s/ Julian Baker

	Name:	 	 Jonathan Leff
	 		 	
	Title:	 	 Partner
	 		 	
	Date:	 	 9/10/09
	 		 	

  

					
	 FBB ASSOCIATES
 /s/ Julian Baker
 JULIAN BAKER, A
GENERAL PARTNER
	 		 	 BAKER BROTHERS LIFE SCIENCES, L.P.
 BY: BAKER BROTHERS LIFE SCIENCES
 CAPITAL, L.P., (GENERAL PARTNER)
 BY: BAKER BROTHERS LIFE SCIENCES
 CAPITAL (GP), LLC, (GENERAL PARTNER)
 BY: JULIAN
BAKER, MANAGING MEMBER

		 		 	 /s/ Julian Baker

			
	 BAKER/TISCH INVESTMENTS, L.P.
 BY: BAKER/TISCH CAPITAL, L.P.,
 (GENERAL
PARTNER)
 BY: BAKER/TISCH CAPITAL (GP), LLC,
(GENERAL PARTNER)
 BY: JULIAN BAKER, MANAGING
MEMBER
	 		 	 BAKER BROS. INVESTMENTS, L.P.
 BY: BAKER BROS. CAPITAL, L.P., (GENERAL PARTNER)
 BY: BAKER BROS. CAPITAL (GP), LLC,
 (GENERAL PARTNER)
 BY: JULIAN BAKER,
MANAGING MEMBER

	 /s/ Julian Baker
	 		 	 /s/ Julian Baker

			
	 BAKER BROS. INVESTMENTS II, L.P.
 BY: BAKER BROS. CAPITAL, L.P.,
 (GENERAL
PARTNER)
 BY: BAKER BROS. CAPITAL (GP), LLC,
 (GENERAL PARTNER)
 BY: JULIAN BAKER, MANAGING MEMBER
	 		 	 BAKER BIOTECH FUND I, L.P.
 BY: BAKER BIOTECH CAPITAL, L.P.,
 (GENERAL
PARTNER)
 BY: BAKER BIOTECH CAPITAL (GP), LLC,

(GENERAL PARTNER)
 BY: JULIAN BAKER, MANAGING MEMBER

	 /s/ Julian Baker
	 		 	 /s/ Julian Baker


 (Signature Page to Amendment to Merger Agreement)