EX-10.1



 Exhibit 10.1 

August 12, 2014 
  

			
	To:	  	Ligand Pharmaceuticals Incorporated
		  	11119 North Torrey Pines Rd
		  	Suite 200
		  	La Jolla, CA 92037
		  	Attn: Charles S. Berkman
		  	Telephone: 858-550-7835
		  	Facsimile: 858-550-7272
		
	From:	  	Bank of America, N.A.
		  	c/o Merrill Lynch, Pierce, Fenner & Smith Incorporated
		  	 One Bryant Park
 New York, NY
10036

		  	Attn: Peter Tucker, Assistant General Counsel
		  	Telephone: 646-855-5821
		  	Facsimile: 646-822-5633
		
	Re:	  	 Base Convertible Bond Hedge Transaction

(Transaction Reference Number: 148477473)


 Ladies and Gentlemen: 

The purpose of this communication (this “Confirmation”) is to set forth the terms and conditions of the
above-referenced transaction entered into on the Trade Date specified below (the “Transaction”) between Bank of America, N.A. (“Dealer”) and Ligand Pharmaceuticals Incorporated (“Counterparty”).
This communication constitutes a “Confirmation” as referred to in the ISDA Master Agreement specified below.  
 1. This
Confirmation is subject to, and incorporates, the definitions and provisions of the 2006 ISDA Definitions (the “2006 Definitions”) and the definitions and provisions of the 2002 ISDA Equity Derivatives Definitions (the
“Equity Definitions” and, together with the 2006 Definitions, the “Definitions”), in each case as published by the International Swaps and Derivatives Association, Inc. (“ISDA”). In the event of any
inconsistency between the 2006 Definitions and the Equity Definitions, the Equity Definitions will govern. Certain defined terms used herein have the meanings assigned to them in the Indenture to be dated as of the closing date for the initial
issuance of the Convertible Securities described below between Counterparty and Wilmington Trust, National Association as trustee (the “Indenture”) relating to the USD 225,000,000 principal amount of 0.75% convertible senior notes
due 2019 (the “Base Convertible Securities”) together with any 0.75% convertible senior notes due 2019 that may be issued pursuant to the Initial Purchasers’ option under the Purchase Agreement (as defined below) (the
“Optional Convertible Securities” and, together with the Base Convertible Securities, the “Convertible Securities”). In the event of any inconsistency between the terms defined in the Indenture and this
Confirmation, this Confirmation shall govern. For the avoidance of doubt, references herein to sections of the Indenture are based on the draft of the Indenture most recently reviewed by the parties at the time of execution of this Confirmation. If
any relevant sections of the Indenture are changed, added or renumbered following execution of this Confirmation but prior to the execution of the Indenture, the parties will amend this Confirmation in good faith to preserve the economic intent of
the parties based on the draft of the Indenture so reviewed. The parties further acknowledge that references to the Indenture herein are references to the Indenture as in effect on the date of its execution and if the Indenture is, or the
Convertible Securities are, amended, supplemented or modified following their execution, any such amendment, supplement or modification (other than a Merger Supplemental Indenture (as defined below)) will be disregarded for purposes of this
Confirmation (other than (i) as provided in Section 8(a) below and (ii) any amendment, supplement or modification pursuant to Section 9.01(b) of the Indenture that, as determined by the Calculation Agent, conforms the Indenture
to the description of the Convertible Securities in the preliminary offering memorandum, as supplemented by the pricing term sheet related to the Convertible Securities) unless the parties agree otherwise in writing. 







 This Confirmation evidences a complete and binding agreement between Dealer and Counterparty as
to the terms of the Transaction to which this Confirmation relates. This Confirmation shall be subject to an agreement (the “Agreement”) in the form of the ISDA 2002 Master Agreement (the “ISDA Form”) as if Dealer
and Counterparty had executed an agreement in such form (without any Schedule except for the elections set forth in this Confirmation and the election that the “Cross Default” provisions of Section 5(a)(vi) of the Agreement shall
apply to Counterparty with a “Threshold Amount” of USD 15 million and to Dealer with a “Threshold Amount” of 3% of the stockholders’ equity of Bank of America Corporation, in each case, as if (x) the phrase “,
or becoming capable at such time of being declared,” were deleted from Section 5(a)(vi)(1) of the Agreement, (y) the term “Specified Indebtedness” had the meaning specified in Section 14 of the Agreement, except that
such term did not include obligations in respect of deposits received in the ordinary course of a party’s banking business and (z) the following language shall be added to the end of such Section 5(a)(vi): “Notwithstanding the
foregoing, a default under subsection (2) hereof shall not constitute an Event of Default if (i) the default was caused solely by error or omission of an administrative or operational nature; (ii) funds were available to enable the
party to make the payment when due; and (iii) the payment is made within two Local Business Days of such party’s receipt of written notice of its failure to pay.”). For the avoidance of doubt, the Transaction shall be the only
transaction under the Agreement. 
 All provisions contained in, or incorporated by reference to, the Agreement will govern this
Confirmation except as expressly modified herein. In the event of any inconsistency between this Confirmation and either the Definitions or the Agreement, this Confirmation shall govern. For the avoidance of doubt, except to the extent of an express
conflict, the application of any provision of this Confirmation, the Agreement or the Equity Definitions shall not be construed to exclude or limit the application of any other provision of this Confirmation, the Agreement or the Equity Definitions.

 2. The Transaction constitutes a Share Option Transaction for purposes of the Equity Definitions. The terms of the particular Transaction
to which this Confirmation relates are as follows: 
 General Terms: 
  

			
	 Trade Date:
	  	August 12, 2014
		
	 Effective Date:
	  	The closing date of the initial issuance of the Convertible Securities.
		
	 Option Type:
	  	Call
		
	 Seller:
	  	Dealer
		
	 Buyer:
	  	Counterparty
		
	 Shares:
	  	The common stock of Counterparty, par value USD 0.001 per share (Ticker Symbol: “LGND”).
		
	 Number of Options:
	  	The number of Base Convertible Securities in denominations of USD 1,000 principal amount issued by Counterparty.
		
	 Applicable Percentage:
	  	50%
		
	 Number of Shares:
	  	As of any date, the product of the Number of Options and the Conversion Rate.
		
	 Conversion Rate:
	  	As of any date, the “Conversion Rate” (as defined in the Indenture) as of such date, but without regard to any adjustments to the “Conversion Rate” pursuant to Sections 10.05(l) or 10.07 of the Indenture (the
“Excluded Provisions”).
		
	 Premium:
	  	As provided in Annex A to this Confirmation.
		
	 Premium Payment Date:
	  	The Effective Date
		
	 Exchange:
	  	NASDAQ Global Market
		
	 Related Exchange:
	  	All Exchanges


  
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	Procedures for Exercise:	  	
		
	 Exercise Dates:
	  	Each Conversion Date.
		
	 Conversion Date:
	  	Each “Conversion Date”, as defined in the Indenture, occurring during the period from and excluding the Trade Date to and including the Expiration Date, for Convertible Securities, each in denominations of USD 1,000
principal amount, that are submitted for conversion on such Conversion Date in accordance with the terms of the Indenture (such Convertible Securities, other than Excluded Convertible Securities (as defined below), the “Relevant Convertible
Securities” for such Conversion Date).
		
	 Excluded Convertible Securities:
	  	Convertible Securities with a Conversion Date prior to the Final Conversion Period Start Date (as defined below). Counterparty shall, within one Scheduled Trading Day of the “Conversion Date” (as defined in the Indenture)
relating to any Excluded Convertible Securities, provide written notice (an “Excluded Conversion Notice”) to Dealer specifying (i) the number of Excluded Convertible Securities converted on such “Conversion Date”
(including, if applicable, whether all or any portion of the Excluded Convertible Securities are Make-Whole Convertible Securities (as defined below), (ii) the scheduled settlement date under the Indenture for such Excluded Convertible Securities
and (iii) the “Cash Percentage” (as defined in the Indenture); provided that, notwithstanding the foregoing, such notice in connection with any conversion of Excluded Convertible Securities shall be effective if given prior to 5:00
P.M., New York City time, on the sixth Exchange Business Day following the “Conversion Date” (as defined in the Indenture) relating to such Excluded Convertible Securities, in which event the Calculation Agent shall have the right to make
adjustments as appropriate to reflect the additional costs (including, but not limited to, hedging mismatches and market losses) and expenses incurred by Dealer in connection with its hedging activities (including the unwinding of any hedge
position) as a result of Dealer not having received such notice within one Scheduled Trading Day of the “Conversion Date” (as defined in the Indenture) relating to such Excluded Convertible Securities. Counterparty acknowledges its
responsibilities under applicable securities laws, and in particular Section 9 and Section 10(b) of the Exchange Act (as defined below) and the rules and regulations thereunder, in respect of any election of a settlement method with respect to the
Excluded Convertible Securities and the delivery of such Excluded Conversion Notice.
		
	 Required Exercise on Conversion Dates:
	  	On each Conversion Date, a number of Options equal to the number of Relevant Convertible Securities for such Conversion Date in denominations of USD 1,000 principal amount shall be automatically exercised.
		
	 Expiration Date:
	  	The second “Scheduled Trading Day” immediately preceding the “Maturity Date” (each as defined in the Indenture).
		
	 Automatic Exercise:
	  	As provided above under “Required Exercise on Conversion Dates”.
		
	 Exercise Notice Deadline:
	  	In the case of any exercise of Options hereunder in connection


  
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		  	with the conversion of any Relevant Convertible Securities on any Conversion Date occurring during the period starting on and including May 15, 2019 (the “Final Conversion Period Start Date”) and ending on and
including the second “Scheduled Trading Day” immediately preceding the “Maturity Date” (each as defined in the Indenture) (the “Final Conversion Period”), the Exercise Notice Deadline shall be the “Scheduled
Trading Day” immediately preceding such “Maturity Date”.
		
	 Notice of Exercise:
	  	Notwithstanding anything to the contrary in the Equity Definitions, Dealer shall have no obligation to make any payment or delivery in respect of any exercise of Options hereunder unless Counterparty notifies Dealer in writing prior
to 5:00 P.M., New York City time, on the Exercise Notice Deadline in respect of such exercise of the number of Options being exercised on the relevant Exercise Date (including, if applicable, whether all or any portion of the Relevant Convertible
Securities are Convertible Securities as to which additional Shares would be added to the “Conversion Rate” (as defined in the Indenture) pursuant to Section 10.07 of the Indenture (the “Make-Whole Convertible
Securities”)). Counterparty acknowledges its responsibilities under applicable securities laws, and in particular Section 9 and Section 10(b) of the Exchange Act (as defined below) and the rules and regulations thereunder, in respect of any
election of a settlement method with respect to the Convertible Securities. For the avoidance of doubt, if Counterparty fails to give such notice when due in respect of any exercise of Options hereunder, Dealer’s obligation to make any payment
or delivery in respect of such exercise shall be permanently extinguished, and late notice shall not cure such failure; provided that notwithstanding the foregoing, such notice (and the related exercise of Options) in connection with any
conversion of Relevant Convertible Securities shall be effective if given after the Exercise Notice Deadline, but prior to 5:00 P.M., New York City time, on the fifth Exchange Business Day following the Exercise Notice Deadline, in which event the
Calculation Agent shall have the right to adjust the Delivery Obligation as appropriate to reflect the additional costs (including, but not limited to, hedging mismatches and market losses) and expenses incurred by Dealer in connection with its
hedging activities (including the unwinding of any hedge position) as a result of Dealer not having received such notice on or prior to the Exercise Notice Deadline.
		
	 Notice of Cash Percentage:
	  	Counterparty shall notify Dealer in writing before 5:00 P.M., New York City time, on the Final Conversion Period Start Date of the irrevocable election by Counterparty, in accordance with Section 10.03(b) of the Indenture, of the
“Cash Percentage” (as defined in the Indenture) applicable to Relevant Convertible Securities with a Conversion Date occurring during the Final Conversion Period. If Counterparty fails timely to provide such notice, Counterparty shall be
deemed to have notified Dealer of a “Cash Percentage” (as defined in the Indenture) of zero for all conversions occurring during the Final Conversion Period. Counterparty agrees that it shall settle any Relevant Convertible Securities with
a Conversion Date occurring during the Final Conversion Period in the same manner as provided in the Notice of Cash Percentage it provides or is deemed to have provided hereunder.


  
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	 Dealer’s Telephone Number and Telex and/or Facsimile Number and Contact Details for purpose of Giving Notice:
	  	To be provided by Dealer.
		
	Settlement Terms:	  	
		
	 Settlement Date:
	  	In respect of an Exercise Date occurring in respect of a Conversion Date, the settlement date for the cash and/or Shares (if any) to be delivered in respect of the Relevant Convertible Securities converted on such Conversion Date
pursuant to Section 10.03(a) of the Indenture; provided that the Settlement Date will not be prior to the latest of (i) the date one Settlement Cycle following the final day of the relevant “Observation Period”, as defined in the
Indenture, (ii) the Exchange Business Day immediately following the date on which Counterparty gives notice to Dealer of such Settlement Date prior to 5:00 P.M., New York City time, and (iii) the Exchange Business Day immediately following the date
Counterparty provides the Notice of Delivery Obligation prior to 5:00 P.M., New York City time.
		
	 Delivery Obligation:
	  	In lieu of the obligations set forth in Sections 8.1 and 9.1 of the Equity Definitions, and subject to “Notice of Exercise” above, in respect of an Exercise Date occurring in respect of a Conversion Date, Dealer will
deliver to Counterparty, on the related Settlement Date, a number of Shares and/or amount of cash in USD equal to the Applicable Percentage of the aggregate number of Shares, if any, that Counterparty would be obligated to deliver to the holder(s)
of the Relevant Convertible Securities converted on such Conversion Date pursuant to Sections 10.03(a) of the Indenture and/or the Applicable Percentage of the aggregate amount of cash, if any, in excess of USD 1,000 per Convertible Security (in
denominations of USD 1,000) that Counterparty would be obligated to deliver to holder(s) pursuant to Section 10.03(b) of the Indenture, as determined by the Calculation Agent by reference to such Section of the Indenture (except that such aggregate
number of Shares shall be determined without taking into consideration any rounding pursuant to Section 10.03(d) of the Indenture and shall be rounded down to the nearest whole number) and cash in lieu of fractional Shares, if any, eliminated by
such rounding (the “Convertible Obligation”); provided that such obligation shall be determined (i) excluding any Shares and/or cash that Counterparty is obligated to deliver to holder(s) of the Relevant Convertible
Securities as a result of any adjustments to the Conversion Rate pursuant to any of the Excluded Provisions and (ii) without regard to the election, if any, by Counterparty to adjust the Conversion Rate (and, for the avoidance of doubt, the Delivery
Obligation shall not include any interest payment on the Relevant Convertible Securities that the Counterparty is (or would have been) obligated to deliver to holder(s) of the Relevant Convertible Securities for such Conversion Date); and
provided further that if such exercise relates to the conversion of Relevant Convertible Securities in connection with which holders thereof are entitled to receive additional Shares and/or cash pursuant to the adjustment to the Conversion
Rate set forth in Section 10.07 of the Indenture, then, notwithstanding the foregoing, the Delivery Obligation shall include the Applicable Percentage of such additional Shares and/or


  
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		  	cash (as determined by the Calculation Agent by reference to such Section of the Indenture), except that the Delivery Obligation shall be capped so that the value of the Delivery Obligation (with the value of any Shares included in
the Delivery Obligation determined by the Calculation Agent using the VWAP Price on the last day of the relevant “Observation Period”) does not exceed the amount as determined by the Calculation Agent that would be payable by Dealer
pursuant to Section 6 of the Agreement if such Conversion Date were an Early Termination Date resulting from an Additional Termination Event with respect to which the Transaction (except that, for purposes of determining such amount (x) the Number
of Options shall be deemed to be equal to the number of Options exercised on such Exercise Date and (y) such amount payable will be determined as if Section 10.07 of the Indenture were deleted) was the sole Affected Transaction and Counterparty was
the sole Affected Party (determined without regard to Section 8(b) of this Confirmation). Notwithstanding the foregoing, and in addition to the cap described in the further proviso to the preceding sentence, in all events the Delivery Obligation
shall be capped so that the value of the Delivery Obligation does not exceed the Applicable Percentage of the value of the Convertible Obligation (with the value of any Shares included in either the Delivery Obligation or such Convertible Obligation
determined by the Calculation Agent using the opening price as displayed under the heading “Op” on Bloomberg page LGND <equity> (or any successor thereto) on the applicable Settlement Date).
		
	 Notice of Delivery Obligation:
	  	No later than the second Scheduled Trading Day immediately following the last day of the relevant “Observation Period”, as defined in the Indenture, Counterparty shall give Dealer notice of the final number of Shares
and/or cash comprising the Convertible Obligation; provided that, with respect to any Exercise Date occurring during the Final Conversion Period, Counterparty may provide Dealer with a single notice of an aggregate number of Shares and/or
cash comprising the Convertible Obligations for all Exercise Dates occurring in such period (it being understood, for the avoidance of doubt, that the requirement of Counterparty to deliver such notice shall not limit Counterparty’s obligations
with respect to Notice of Exercise or Notice of Cash Percentage or Dealer’s obligations with respect to Delivery Obligation, each as set forth above, in any way).
		
	 Other Applicable Provisions:
	  	To the extent Dealer is obligated to deliver Shares hereunder, the provisions of Sections 1.27, 9.1(c), 9.8, 9.9 and 9.11 (except that the Representation and Agreement contained in Section 9.11 of the Equity Definitions shall be
modified by excluding any representations therein relating to restrictions, obligations, limitations or requirements under applicable securities laws arising as a result of the fact that Counterparty is the Issuer of the Shares) of the Equity
Definitions will be applicable as if “Physical Settlement” applied to the Transaction.
		
	 Restricted Certificated Shares:
	  	Notwithstanding anything to the contrary in the Equity Definitions, Dealer may, in whole or in part, deliver Shares required to be delivered to Counterparty hereunder in certificated form in lieu of delivery through the Clearance
System. With respect to such


  
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		  	certificated Shares, the Representation and Agreement contained in Section 9.11 of the Equity Definitions shall be modified by deleting the remainder of the provision after the word “encumbrance” in the fourth line
thereof.
		
	Share Adjustments:	  	
		
	 Method of Adjustment:
	  	 Notwithstanding Section 11.2 of the Equity Definitions (which shall not apply with respect to the Transaction), upon the occurrence of any
event or condition set forth in Sections 10.05(a)-(e) of the Indenture that the Calculation Agent determines would result in an adjustment under the Indenture by reference to such Sections thereof (any such event or condition, an “Adjustment
Event”), the Calculation Agent shall make a corresponding adjustment to the terms relevant to the exercise, settlement, payment or other terms of the Transaction, subject to “Discretionary Adjustments” below. Promptly following
the occurrence of any Adjustment Event, Counterparty shall notify the Calculation Agent of such Adjustment Event; and once the adjustments to be made to the terms of the Indenture and the Convertible Securities in respect of such Adjustment Event
have been determined, Counterparty shall promptly notify the Calculation Agent in writing of the details of such adjustments.
  

In addition, the Calculation Agent shall, to the extent the Calculation Agent determines practicable in good faith and in its commercially reasonable
discretion to preserve the economic intent of the parties, make an adjustment to the terms relevant to the exercise, settlement or payment of the Transaction (to the extent not already covered by, and without duplication of any adjustment pursuant
to the foregoing paragraph) corresponding to any adjustment made pursuant to Sections 10.05(g) or 10.05(h) of the Indenture; provided that the Calculation Agent may limit or alter any such adjustment referenced in this sentence so that the
fair value of the Transaction to Dealer is not reduced as a result of such adjustment.
  

For the avoidance of doubt, Dealer shall not have any payment or delivery obligation hereunder in respect of, and no adjustment shall be made to the terms of
the Transaction on account of, (x) any distribution of cash, property or securities by Counterparty to the holders of Convertible Securities (upon conversion or otherwise) or (y) any other transaction in which holders of Convertible Securities are
entitled to participate, in each case, in lieu of an adjustment under Section 10.05 of the Indenture in respect of an Adjustment Event (including, without limitation, under the introductory paragraph of Section 10.05 of the Indenture, under the
third to last sentence of Sections 10.05(c)(i) and 10.05(d) of the Indenture or under Section 10.05(f) of the Indenture).

		
	 Discretionary Adjustments:
	  	Notwithstanding anything to the contrary herein or in the Equity Definitions, if the Calculation Agent in good faith disagrees with any adjustment under the Indenture that involves an exercise of discretion by Counterparty or its
board of directors (including, without limitation, pursuant to Section 10.05(g) or Section 10.05(h) or pursuant to Section 10.06 of the Indenture or any supplemental indenture entered into thereunder (a “Merger


  
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		  	Supplemental Indenture”) or in connection with any proportional adjustment or the determination of the fair value of any securities, property, rights or other assets), then the Calculation Agent will determine the
adjustment to be made to any one or more of the Strike Price, Number of Options, Option Entitlement and any other variable relevant to the exercise, settlement, payment or other terms of or under the Transaction in a commercially reasonable
manner.
		
	Extraordinary Events:	  	
		
	 Merger Events:
	  	Notwithstanding Section 12.1(b) of the Equity Definitions (which shall not apply with respect to the Transaction), a “Merger Event” means the occurrence of any event or condition set forth in the definition of “Merger
Event” in Section 10.06(a) of the Indenture.
		
	 Consequences of Merger Events:
	  	Notwithstanding Sections 12.2 and 12.3 of the Equity Definitions (which shall not apply with respect to the Transaction), upon the occurrence of a Merger Event that the Calculation Agent determines by reference to Section 10.06(a)
of the Indenture would result in an adjustment under the Indenture, the Calculation Agent shall make a corresponding adjustment to the terms relevant to the exercise, settlement, payment or other terms of the Transaction, subject to
“Discretionary Adjustments” above; provided that such adjustment shall be made without regard to any adjustment to the Conversion Rate pursuant to the Excluded Provisions and the election, if any, by Counterparty to adjust the
Conversion Rate; and provided further that if, with respect to a Merger Event, (i) the consideration for the Shares includes (or, at the option of a holder of Shares, may include) shares (or depositary receipts evidencing interests in shares)
of an entity or person that is not a corporation organized under the laws of the United States, any State thereof or the District of Columbia or (ii) Counterparty following such Merger Event will not be a corporation organized under the laws of the
United States, any State thereof or the District of Columbia or will not be the Issuer following such Merger Event, Dealer may elect in its reasonable discretion that Cancellation and Payment (Calculation Agent Determination) shall apply.
		
	 Notice of Merger Consideration:
	  	Upon the occurrence of a Merger Event that causes the Shares to be converted into the right to receive more than a single type of consideration (determined based in part upon any form of stockholder election), Counterparty shall
reasonably promptly (but, in any event prior to the effective time of such Merger Event) notify the Calculation Agent of (i) the weighted average of the types and amounts of consideration to be received by the holders of Shares entitled to receive
cash, securities or other property or assets with respect to or in exchange for such Shares in any Merger Event who affirmatively make such an election or, if no holders of Shares affirmatively make such an election, the types and amounts of
consideration actually received by holders of Shares and (ii) the details of the adjustment made under the Indenture in respect of such Merger Event.
		
	 Nationalization, Insolvency or Delisting:
	  	Cancellation and Payment (Calculation Agent Determination); provided that, in addition to the provisions of Section 12.6(a)(iii) of the Equity Definitions, it shall also constitute a Delisting if the


  
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		  	Exchange is located in the United States and the Shares are not immediately re-listed, re-traded or re-quoted on any of the New York Stock Exchange, The NASDAQ Global Select Market or The NASDAQ Global Market (or their respective
successors); if the Shares are immediately re-listed, re-traded or re-quoted on any such exchange or quotation system, such exchange or quotation system shall thereafter be deemed to be the Exchange.
		
	Additional Disruption Events:	  	
		
	 (a) Change in Law:
	  	Applicable; provided that Section 12.9(a)(ii) of the Equity Definitions is hereby amended by (x) adding the words “(including, for the avoidance of doubt and without limitation, adoption or promulgation of new
regulations authorized or mandated by existing statute)” after the word “regulation” in the second line thereof, (y) adding the words “or any Hedge Positions” after the word “Shares” in the clause (X) thereof and
(z) adding the words “, or holding, acquiring or disposing of Shares or any Hedge Positions relating to,” after the words “obligations under” in clause (Y) thereof.
		
	 (b) Failure to Deliver:
	  	Applicable
		
	 (c) Insolvency Filing:
	  	Applicable
		
	 (d) Hedging Disruption:
	  	Applicable; provided that:
		
		  	(i) Section 12.9(a)(v) of the Equity Definitions is hereby amended by (a) inserting the following words at the end of clause (A) thereof: “in the manner contemplated by the Hedging Party on the Trade Date” and (b)
inserting the following two phrases at the end of such Section:
		
		  	“For the avoidance of doubt, the term “equity price risk” shall be deemed to include, but shall not be limited to, stock price and volatility risk. And, for the further avoidance of doubt, any such transactions or
assets referred to in phrases (A) or (B) above must be available on commercially reasonable pricing terms.”; and
		
		  	(ii) Section 12.9(b)(iii) of the Equity Definitions is hereby amended by inserting in the third line thereof, after the words “to terminate the Transaction”, the words “or a portion of the Transaction affected by such
Hedging Disruption”.
		
	 (e) Increased Cost of Hedging:
	  	Not Applicable
		
	Hedging Party:	  	For all applicable Potential Adjustment Events and Extraordinary Events, Dealer
		
	Determining Party:	  	For all applicable Extraordinary Events, Dealer
		
	Non-Reliance:	  	Applicable
		
	Agreements and Acknowledgments	  	Applicable
	Regarding Hedging Activities:	  	
		
	Additional Acknowledgments:	  	Applicable


  
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	 3. Calculation Agent:
	  	Dealer, whose judgments, determinations and calculations shall be made in good faith and in a commercially reasonable manner. Following any determination or calculation by the Calculation Agent hereunder, upon a written request by
Counterparty, the Calculation Agent shall promptly (but in any event within five Scheduled Trading Days) provide to Counterparty by email to the email address provided by Counterparty in such request a report (in a commonly used file format for the
storage and manipulation of financial data) displaying in reasonable detail the basis for such determination or calculation (including any assumptions used in making such determination or calculation), it being understood that the Calculation Agent
shall not be obligated to disclose any proprietary or confidential data or information or any proprietary or confidential models used by it for such determination or calculation.
		
	 4. Account Details:
	  	
		
	 Dealer Payment Instructions:
	  	Bank of America, N.A.
		  	New York, NY
		  	SWIFT: BOFAUS3N
		  	Bank Routing: 026-009-593
		  	Account Name: Bank of America
		  	Account No.: 0012334-61892
		
	 Counterparty Payment Instructions:
	  	To be provided by Counterparty.
		
	 5. Offices:
	  	
	
	 The Office of Dealer for the Transaction is: New York

	
	 The Office of Counterparty for the Transaction is: Not applicable

	
	 6. Notices: For purposes of this Confirmation:

	
	 Address for notices or communications to Counterparty:



 

			
	To:	  	Ligand Pharmaceuticals Incorporated
		  	11119 North Torrey Pines Rd
		  	Suite 200
		  	La Jolla, CA 92037
	Attn:	  	Charles S. Berkman
	Telephone :	  	858-550-7835
	Facsimile:	  	858-550-7272

 Address for notices or communications to Dealer: 

 

			
	To:	  	Bank of America, N.A.
		  	c/o Merrill Lynch, Pierce, Fenner & Smith Incorporated
		  	One Bryant Park
		  	New York, NY 10036
	Attn:	  	Peter Tucker, Assistant General Counsel
	Telephone:	  	646-855-5821
	Facsimile:	  	646-822-5633


  
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 7. Representations, Warranties and Agreements: 

(a) In addition to the representations and warranties in the Agreement and those contained elsewhere herein, Counterparty represents and
warrants to and for the benefit of, and agrees with, Dealer as follows: 
 (i) On the Trade Date and any date on which
Counterparty makes an election hereunder, (A) Counterparty is not aware of any material nonpublic information regarding Counterparty or the Shares and (B) all reports and other documents filed by Counterparty with the Securities and
Exchange Commission pursuant to the Securities Exchange Act of 1934, as amended (the “Exchange Act”) when considered as a whole (with the more recent such reports and documents deemed to amend inconsistent statements contained in
any earlier such reports and documents), do not contain any untrue statement of a material fact or any omission of a material fact required to be stated therein or necessary to make the statements therein, in the light of the circumstances in which
they were made, not misleading. 
 (ii) (A) On the Trade Date, the Shares or securities that are convertible into, or
exchangeable or exercisable for Shares, are not, and shall not be, subject to a “restricted period,” as such term is defined in Regulation M under the Exchange Act (“Regulation M”) and (B) Counterparty shall not
engage in any “distribution,” as such term is defined in Regulation M, other than a distribution meeting the requirements of the exceptions set forth in sections 101(b)(10) and 102(b)(7) of Regulation M, until the second Exchange Business
Day immediately following the Trade Date. 
 (iii) On the Trade Date, neither Counterparty nor any “affiliated
purchaser” (each as defined in Rule 10b-18 under the Exchange Act (“Rule 10b-18”)) shall directly or indirectly (including, without limitation, by means of any cash-settled or other derivative instrument) purchase, offer to
purchase, place any bid or limit order that would effect a purchase of, or commence any tender offer relating to, any Shares (or an equivalent interest, including a unit of beneficial interest in a trust or limited partnership or a depository share)
or any security convertible into or exchangeable or exercisable for Shares, except (i) through Dealer or (ii) up to $45.0 million of purchases from purchasers of the Convertible Securities, as described under “Use of Proceeds” in
the preliminary offering memorandum relating to the Convertible Securities. 
 (iv) Without limiting the generality of
Section 13.1 of the Equity Definitions, Counterparty acknowledges that Dealer is not making any representations or warranties or taking any position or expressing any view with respect to the treatment of the Transaction under any accounting
standards including ASC Topic 260, Earnings Per Share, ASC Topic 815, Derivatives and Hedging, or ASC Topic 480, Distinguishing Liabilities from Equity and ASC 815-40, Derivatives and Hedging – Contracts in Entity’s
Own Equity (or any successor issue statements) or under FASB’s Liabilities & Equity Project. 
 (v) Without
limiting the generality of Section 3(a)(iii) of the Agreement, the Transaction will not violate Rule 13e-1 or Rule 13e-4 under the Exchange Act. 

(vi) On or reasonably promptly following the Trade Date, Counterparty shall deliver to Dealer a resolution of
Counterparty’s board of directors or any committee thereof (together with a resolution of Counterparty’s board of directors authorizing such committee to take such actions) authorizing the Transaction and such other certificate or
certificates as Dealer shall, prior to the Trade Date, reasonably request. 
 (vii) Counterparty is not entering into this
Confirmation nor making any election hereunder or under the Convertible Securities to create actual or apparent trading activity in the Shares (or any security convertible into or exchangeable for Shares) or to raise or depress or otherwise
manipulate the price of the Shares (or any security convertible into or exchangeable for Shares) or otherwise in violation of the Exchange Act. 

(viii) Counterparty is not, and after giving effect to the transactions contemplated hereby will not be, required to register
as an “investment company” as such term is defined in the Investment Company Act of 1940, as amended. 
 (ix) On
each of the Trade Date and the Premium Payment Date, Counterparty is not, or will not be, “insolvent” (as such term is defined under Section 101(32) of the U.S. Bankruptcy Code (Title 11 of the United States Code) (the
“Bankruptcy Code”)) and Counterparty would be able to purchase the Number of Shares hereunder in compliance with the laws of the jurisdiction of its incorporation. 

(x) To Counterparty’s actual knowledge, no state or local (including non-U.S. jurisdictions) or non-U.S. federal law,
rule, regulation or regulatory order applicable to the Shares would give rise to any reporting, consent, registration or other requirement (including without limitation a requirement to obtain prior approval from any person or entity) as a result of
Dealer or its affiliates owning or holding (however defined) Shares. 

  
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 (xi) The representations and warranties of Counterparty set forth in
Section 3 of the Agreement and Section 1 of the Purchase Agreement dated as of the Trade Date, between Counterparty and Merrill Lynch, Pierce, Fenner & Smith Incorporated and Deutsche Bank Securities Inc., as representatives of
the several Initial Purchasers party thereto (the “Purchase Agreement”) are true and correct and are hereby deemed to be repeated to Dealer as if set forth herein. 

(xii) Counterparty understands no obligations of Dealer to it hereunder will be entitled to the benefit of deposit insurance
and that such obligations will not be guaranteed by any affiliate of Dealer or any governmental agency. 
 (b) Each of Dealer and
Counterparty agrees and represents that it is an “eligible contract participant” as defined in Section 1a(18) of the U.S. Commodity Exchange Act, as amended. 

(c) Each of Dealer and Counterparty acknowledges that the offer and sale of the Transaction to it is intended to be exempt from registration
under the Securities Act of 1933, as amended (the “Securities Act”), by virtue of Section 4(a)(2) thereof. Accordingly, Counterparty represents and warrants to Dealer that (i) it has the financial ability to bear the
economic risk of its investment in the Transaction and is able to bear a total loss of its investment, (ii) it is an “accredited investor” as that term is defined in Regulation D as promulgated under the Securities Act, (iii) it
is entering into the Transaction for its own account and without a view to the distribution or resale thereof and (iv) the assignment, transfer or other disposition of the Transaction has not been and will not be registered under the Securities
Act and is restricted under this Confirmation, the Securities Act and state securities laws. 
 (d) Counterparty agrees and acknowledges
that Dealer is a “financial institution” and “financial participant” within the meaning of Sections 101(22) and 101(22A) of the Bankruptcy Code. The parties hereto further agree and acknowledge that it is the intent of the
parties that (A) this Confirmation is a “securities contract,” as such term is defined in Section 741(7) of the Bankruptcy Code, with respect to which each payment and delivery hereunder or in connection herewith is a
“termination value,” “payment amount” or “other transfer obligation” within the meaning of Section 362 of the Bankruptcy Code and a “settlement payment” within the meaning of Section 546 of the
Bankruptcy Code, with respect to which each payment and delivery hereunder or in connection herewith is a “termination value,” “payment amount” or “other transfer obligation” within the meaning of Section 362 of
the Bankruptcy Code and a “transfer,” as such term is defined in Section 101(54) of the Bankruptcy Code and a “termination value, payment amount, or other transfer obligation” within the meaning of Section 362 of the
Bankruptcy Code, and (B) Dealer is entitled to the protections afforded by, among other sections, Sections 362(b)(6), 362(b)(27), 362(o), 546(e), 546(j), 548(d)(2), 555 and 561 of the Bankruptcy Code. 

(e) Counterparty shall deliver to Dealer an opinion of counsel, dated as of the Effective Date and reasonably acceptable to Dealer in form and
substance, with respect to the matters set forth in Section 3(a) of the Agreement, Section 7(a)(viii) hereof and such other matters as Dealer may, prior to the Trade Date, reasonably request; provided that any such opinion of
counsel may contain customary exceptions and qualifications, including, without limitation, exceptions and qualifications relating to indemnification provisions. 

8. Other Provisions: 
 (a)
Additional Termination Events. 
 The occurrence of (i) an “Event of Default” with respect to
Counterparty under the terms of the Convertible Securities as set forth in Section 6.01(a) of the Indenture that results in the Convertible Securities becoming or being declared due and payable pursuant to the terms of the Indenture or
(ii) an Amendment Event shall be an Additional Termination Event with respect to which the Transaction is the sole Affected Transaction and Counterparty is the sole Affected Party and Dealer shall be the party entitled to designate an Early
Termination Date pursuant to Section 6(b) of the Agreement. 
 “Amendment Event” means that
Counterparty amends, modifies, supplements, waives or obtains a waiver in respect of any term of the Indenture or the Convertible Securities governing the principal amount, maturity, repurchase obligation of Counterparty, lack of a redemption right
of Counterparty, any term relating to conversion of the Convertible Securities (including changes to the conversion rate, conversion rate adjustment provisions, conversion settlement dates or conversion conditions), or any term that would require
consent of the holders of not less than 100% of the principal amount of the Convertible Securities to amend (other than 

  
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pursuant to Sections 9.02(b) or (g) of the Indenture), in each case without the consent of Dealer, such consent not to be unreasonably withheld, conditioned or delayed. For the avoidance of
doubt, the application of the conversion rate adjustment provisions of the Indenture shall not constitute an Amendment Event. 

(ii) The receipt by Dealer from Counterparty of any Excluded Conversion Notice shall constitute an Additional Termination Event
as provided in this paragraph; provided that the Transaction shall be subject to termination only in respect of a number of Options equal to the number of Relevant Conversion Options (as defined below). For the avoidance of doubt, in
determining the amount payable in respect of such Affected Transaction pursuant to Section 6 of the Agreement in connection with an Excluded Conversion Notice, the Calculation Agent shall assume that the relevant Excluded Convertible Securities
shall not have been converted and remain outstanding and that any adjustments, agreements, payments, deliveries or acquisitions by or on behalf of Counterparty leading thereto had not occurred. Upon receipt of any such Notice of Excluded Conversion,
Dealer shall designate a Scheduled Trading Day following such Additional Termination Event as an Early Termination Date (and Dealer shall use commercially reasonable efforts (taking into account any commercially reasonable unwind activity by Dealer
or its affiliates in respect of the Transaction and the “Cash Percentage” elected (or deemed to be elected) by Counterparty under the Indenture with respect to such Excluded Convertible Securities) to designate such Early Termination Date
so that the related payment or delivery, as the case may be, hereunder in respect of the Relevant Conversion Options will occur on (or as promptly as reasonably practicable after) the related settlement for the conversion of the relevant Excluded
Convertible Securities) with respect to the portion of the Transaction corresponding to a number of Options (the “Relevant Conversion Options”) equal to the lesser of (A) the aggregate principal amount of Excluded Convertible
Securities specified in such Notice of Excluded Conversion, divided by USD 1,000, and (B) the Number of Options as of the date Dealer designates such Early Termination Date and, as of such date, the Number of Options shall be reduced by
the number of Relevant Conversion Options. Any payment hereunder with respect to such termination (the “Conversion Unwind Payment”) shall be calculated pursuant to Section 6 of the Agreement as if (1) an Early Termination
Date had been designated in respect of a Transaction having terms identical to the Transaction (except that, for purposes of this Section 8(a)(ii), the last sentence of the provisions opposite the caption “Delivery Obligation” above
shall be deemed to be deleted from this Confirmation) and a Number of Options equal to the number of Relevant Conversion Options, (2) Counterparty were the sole Affected Party with respect to such Additional Termination Event and (3) the
terminated portion of the Transaction were the sole Affected Transaction (and, in determining the amount payable pursuant to Section 6 of the Agreement, the Calculation Agent shall not take into account any adjustments to the “Conversion
Rate” (as defined in the Indenture) pursuant to the Excluded Provisions); provided that the Conversion Unwind Payment shall not be greater than the product of (x) the number of Relevant Conversion Options, (y) the Applicable
Percentage, and (z) the excess of (I) the “Conversion Rate” (as defined in the Indenture after taking into account any adjustments thereto pursuant to the Excluded Provisions), multiplied by the opening price as displayed
under the heading “Op” on Bloomberg page LGND <equity> (or any successor thereto) on the applicable Settlement Date, as commercially reasonably determined by the Calculation Agent in good faith, over (II) the principal amount per
Convertible Security of the relevant Excluded Convertible Securities. 
 (iii) By the fifth Scheduled Trading Day following
any Repayment Event (as defined below), Counterparty shall notify Dealer of such Repayment Event and the aggregate principal amount of Convertible Securities subject to such Repayment Event (any such notice, a “Repayment Notice”).
The receipt by Dealer from Counterparty of any Repayment Notice shall constitute an Additional Termination Event as provided in this paragraph. Upon receipt of any such Repayment Notice, Dealer shall designate a Scheduled Trading Day following
receipt of such Repayment Notice as an Early Termination Date with respect to the portion of the Transaction corresponding to a number of Options (the “Repayment Options”) equal to the lesser of (A) the aggregate principal
amount of Convertible Securities specified in such Repayment Notice, divided by USD 1,000, and (B) the Number of Options as of the date Dealer designates such Early Termination Date and, as of such date, the Number of Options shall be
reduced by the number of Repayment Options. Any payment hereunder with respect to such termination (the “Repayment Unwind Payment”) shall be calculated pursuant to Section 6 of the Agreement as if (1) an Early Termination
Date had been designated in respect of a Transaction having terms identical to the Transaction and a Number of Options equal to the number of Repayment Options, (2) Counterparty were the sole Affected Party with respect to such Additional
Termination Event and (3) the terminated portion of the Transaction were the sole Affected Transaction. Counterparty 

  
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acknowledges its responsibilities under applicable securities laws, and in particular Section 9 and Section 10(b) of the Exchange Act and the rules and regulations thereunder, in
respect of any action taken by Counterparty in respect of a Repayment Event, including, without limitation, the delivery of a Repayment Notice. “Repayment Event” means the occurrence of (i) any repurchase by Counterparty or any
of its subsidiaries of Convertible Securities (whether in connection with or as a result of a “fundamental change”, howsoever defined, or for any other reason), (ii) any Convertible Securities are delivered to Counterparty or any of
its subsidiaries in exchange for delivery of any property or assets of such party (howsoever described), (iii) the repayment of any principal of any of the Convertible Securities prior to the final maturity date of the Convertible Securities
(for any reason other than as a result of an acceleration of the Convertible Securities that results in an Additional Termination Event pursuant to the preceding Section 8(a)(i)), or (iv) any Convertible Securities are exchanged by or for
the benefit of the holders thereof for any other securities of Counterparty or any of its subsidiaries (or any other property, or any combination thereof) pursuant to any exchange offer or similar transaction. For the avoidance of doubt, any
conversion of Convertible Securities pursuant to the terms of the Indenture shall not constitute a Repayment Event. 
 (b) Alternative
Calculations and Payment on Early Termination and on Certain Extraordinary Events. If Dealer shall owe Counterparty any amount pursuant to “Consequences of Merger Events” above or Sections 12.6, 12.7 or 12.9 of the Equity Definitions
or pursuant to Section 6(d)(ii) of the Agreement (a “Payment Obligation”), Counterparty shall have the right, in its sole discretion, to require Dealer to satisfy any such Payment Obligation by the Share Termination Alternative
(as defined below) by giving irrevocable telephonic notice to Dealer, confirmed in writing within one Scheduled Trading Day, no later than 9:30 A.M. New York City time on the relevant merger date, Announcement Date, Early Termination Date or date of
cancellation or termination in respect of another Extraordinary Event, as applicable (“Notice of Share Termination”); provided that if Counterparty does not elect to require Dealer to satisfy its Payment Obligation by the
Share Termination Alternative, Dealer shall have the right, in its sole discretion, to elect to satisfy its Payment Obligation by the Share Termination Alternative, notwithstanding Counterparty’s failure to elect or election to the contrary;
and provided further that Counterparty shall not have the right to so elect (but, for the avoidance of doubt, Dealer shall have the right to so elect) in the event (i) of an Insolvency, a Nationalization or a Merger Event, in each case,
in which the consideration or proceeds to be paid to holders of Shares consists solely of cash, (ii) of an Event of Default in which Counterparty is the Defaulting Party or a Termination Event in which Counterparty is the Affected Party or an
Extraordinary Event, which Event of Default, Termination Event or Extraordinary Event resulted from an event or events within Counterparty’s control or (iii) that Counterparty fails to remake the representation set forth in
Section 7(a)(i) as of the date of such election. Upon such Notice of Share Termination, the following provisions shall apply on the Scheduled Trading Day immediately following the relevant merger date, Announcement Date, Early Termination Date
or date of cancellation or termination in respect of another Extraordinary Event, as applicable: 
  

			
	Share Termination Alternative:	  	If applicable, means that Dealer shall deliver to Counterparty the Share Termination Delivery Property on the date on which the Payment Obligation would otherwise be due pursuant to “Consequences of Merger Events” above,
Section 12.7 or 12.9 of the Equity Definitions or Section 6(d)(ii) of the Agreement, as applicable, or such later date or dates as the Calculation Agent may reasonably determine (the “Share Termination Payment Date”), in
satisfaction of the Payment Obligation.
		
	Share Termination Delivery Property:	  	A number of Share Termination Delivery Units, as calculated by the Calculation Agent, equal to the Payment Obligation divided by the Share Termination Unit Price. The Calculation Agent shall adjust the Share Termination Delivery
Property by replacing any fractional portion of the aggregate amount of a security therein with an amount of cash equal to the value of such fractional security based on the values used to calculate the Share Termination Unit Price.
		
	Share Termination Unit Price:	  	The value of property contained in one Share Termination Delivery Unit on the date such Share Termination Delivery Units are to be delivered as Share Termination Delivery Property, as determined by the Calculation Agent in its
discretion by commercially reasonable means and notified by the Calculation Agent to Dealer.
		
	Share Termination Delivery Unit:	  	In the case of a Termination Event, Event of Default, Delisting or Additional Disruption Event, one Share or, in the case of an Insolvency, Nationalization or


  
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		  	Merger Event, one Share or a unit consisting of the number or amount of each type of property received by a holder of one Share (without consideration of any requirement to pay cash or other consideration in lieu of fractional
amounts of any securities) in such Insolvency, Nationalization or Merger Event, as applicable. If such Insolvency, Nationalization or Merger Event involves a choice of consideration to be received by holders, such holder shall be deemed to have
elected to receive the maximum possible amount of cash.
		
	Failure to Deliver:	  	Applicable
		
	Other applicable provisions:	  	If Share Termination Alternative is applicable, the provisions of Sections 1.27, 9.8, 9.9 and 9.11 (except that the Representation and Agreement contained in Section 9.11 of the Equity Definitions shall be modified by excluding any
representations therein relating to restrictions, obligations, limitations or requirements under applicable securities laws arising as a result of the fact that Counterparty is the issuer of the Shares or any portion of the Share Termination
Delivery Units) of the Equity Definitions will be applicable as if “Physical Settlement” applied to the Transaction, except that all references to “Shares” shall be read as references to “Share Termination Delivery
Units.”

 (c) Disposition of Hedge Shares. Counterparty hereby agrees that if, in the good faith reasonable
judgment of Dealer, based on advice of counsel, any Shares (the “Hedge Shares”) acquired by Dealer or any of its affiliates (Dealer and its affiliates collectively for purposes of this Section 8(c) only,
“Dealer”) for the purpose of hedging its obligations pursuant to the Transaction cannot be sold in the public market by Dealer without registration under the Securities Act, Counterparty shall, at its election: (i) in order to
allow Dealer to sell the Hedge Shares in a registered offering, make available to Dealer an effective registration statement under the Securities Act to cover the resale of such Hedge Shares and (A) enter into an agreement substantially similar
to underwriting agreements customary for registered secondary offerings of a substantially similar size by similar companies, in form and substance reasonably satisfactory to Dealer, substantially in the form of an underwriting agreement for a
registered offering, (B) provide accountant’s “comfort” letters in customary form for registered offerings of equity securities, (C) provide disclosure opinions of nationally recognized outside counsel to Counterparty
reasonably acceptable to Dealer, (D) provide other customary opinions, certificates and closing documents customary in form for registered offerings of equity securities and (E) afford Dealer a reasonable opportunity to conduct a “due
diligence” investigation with respect to Counterparty customary in scope for underwritten offerings of equity securities; provided, however, that if Dealer, in its sole reasonable discretion, is not satisfied with access to due diligence
materials, the results of its due diligence investigation, or the procedures and documentation for the registered offering referred to above, then clause (ii) or clause (iii) of this Section 8(c) shall apply at the election of
Counterparty; (ii) in order to allow Dealer to sell the Hedge Shares in a private placement, enter into a private placement agreement substantially similar to private placement purchase agreements customary for private placements of equity
securities of a substantially similar size by similar companies, in form and substance reasonably satisfactory to Dealer, including customary representations, covenants, blue sky and other governmental filings and/or registrations, indemnities to
Dealer, due diligence rights (for Dealer or any designated buyer of the Hedge Shares from Dealer), opinions and certificates and such other documentation as is customary for private placements agreements, all reasonably acceptable to Dealer (in
which case, the Calculation Agent shall make any adjustments to the terms of the Transaction that are necessary, in its reasonable judgment, to compensate Dealer for any discount from the public market price of the Shares incurred on the sale of
Hedge Shares in a private placement); or (iii) purchase the Hedge Shares from Dealer at the VWAP Price on such Exchange Business Days, and in the amounts, requested by Dealer. “VWAP Price” means, on any Exchange Business Day,
the per Share volume-weighted average price as displayed under the heading “Bloomberg VWAP” on Bloomberg Screen LGND <Equity> VAP (or any successor thereto) in respect of the period from 9:30 a.m. to 4:00 p.m. (New York City time) on
such Exchange Business Day (or if such volume-weighted average price is unavailable or is manifestly incorrect, the market value of one Share on such Exchange Business Day, as determined by the Calculation Agent using a volume-weighted method). 

(d) Amendment to Equity Definitions. The following amendment shall be made to the Equity Definitions: 

Section 12.6(a)(ii) of the Equity Definitions is hereby amended by (1) deleting from the fourth line thereof the word
“or” after the word “official” and inserting a comma therefor, and (2) deleting the semi-colon at the end of subsection (B) thereof and inserting the following words therefor “or (C) at Dealer’s option,
the occurrence of any of the events specified in Section 5(a)(vii) (1) through (9) of the ISDA 2002 Master Agreement with respect to that Issuer.” 

  
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 (e) Repurchase and Conversion Rate Adjustment Notices. Counterparty shall, at least one
Scheduled Trading Day prior to effecting any repurchase of Shares or consummating or otherwise executing or engaging in any transaction or event (a “Conversion Rate Adjustment Event”) that would lead to an increase in the Conversion
Rate (as such term is defined in the Indenture), give Dealer a written notice of such repurchase or Conversion Rate Adjustment Event (a “Repurchase Notice”) if, following such repurchase or Conversion Rate Adjustment Event, the
Notice Percentage as determined on the date of such Repurchase Notice is greater by 0.5% than the Notice Percentage included in the immediately preceding Repurchase Notice (or, in the case of the first such Repurchase Notice, greater by 0.5% than
the Notice Percentage as of the date hereof), and, if such repurchase or Conversion Rate Adjustment Event, or the intention to effect the same, would constitute material non-public information with respect to Counterparty or the Shares, Counterparty
shall make public disclosure thereof at or prior to delivery of such Repurchase Notice. The “Notice Percentage” as of any day is the fraction, expressed as a percentage, the numerator of which is the Number of Shares plus the number
of Shares underlying any other call options sold by Dealer to Counterparty and the denominator of which is the number of Shares outstanding on such day. In the event that Counterparty fails to provide Dealer with a Repurchase Notice on the day and
in the manner specified in this Section 8(e) then Counterparty agrees to indemnify and hold harmless Dealer, its affiliates and their respective directors, officers, employees, agents and controlling persons (Dealer and each such person being
an “Indemnified Party”) from and against any and all losses, claims, damages and liabilities (or actions in respect thereof), joint or several, to which such Indemnified Party may become subject under applicable securities laws,
including without limitation, Section 16 of the Exchange Act, relating to or arising out of such failure. If for any reason the foregoing indemnification is unavailable to any Indemnified Party or insufficient to hold harmless any Indemnified
Party, then Counterparty shall contribute, to the maximum extent permitted by law, to the amount paid or payable by the Indemnified Party as a result of such loss, claim, damage or liability. In addition, Counterparty will reimburse any Indemnified
Party for all reasonable expenses (including reasonable counsel fees and expenses) as they are incurred (after notice to Counterparty) in connection with the investigation of, preparation for or defense or settlement of any pending or threatened
claim or any action, suit or proceeding arising therefrom, whether or not such Indemnified Party is a party thereto and whether or not such claim, action, suit or proceeding is initiated or brought by or on behalf of Counterparty. This indemnity
shall survive the completion of the Transaction contemplated by this Confirmation and any assignment and delegation of the Transaction made pursuant to this Confirmation or the Agreement shall inure to the benefit of any permitted assignee of
Dealer. 
 (f) Transfer and Assignment. Either party may transfer any of its rights or obligations under the Transaction with the
prior written consent of the non-transferring party, such consent not to be unreasonably withheld or delayed. For the avoidance of doubt, Dealer may condition its consent on any of the following, without limitation: (i) the receipt by Dealer of
opinions and documents reasonably satisfactory to Dealer in connection with such assignment, (ii) such assignment being effected on terms reasonably satisfactory to Dealer with respect to any legal and regulatory requirements relevant to
Dealer, (iii) Counterparty continuing to be obligated to provide notices hereunder relating to the Convertible Securities and continuing to be obligated with respect to “Disposition of Hedge Shares” and “Repurchase and Conversion
Rate Adjustment Notices” above, (iv) payment by Counterparty of all reasonable costs and expenses, including reasonable counsel fees, incurred by Dealer in connection with such assignment, (v) Dealer not being obliged, as a result of
such assignment, to pay the assignee on any payment date, an amount greater than Dealer would have been required to pay in the absence of such assignment, (vi) no Event of Default, Potential Event of Default or Termination Event existing or
occurring as a result of such assignment and (vii) Counterparty causing the transferee to make such Payee Tax Representations and to provide such tax documentation as may be reasonably requested by Dealer to permit Dealer to determine that the
results described in clauses (v) and (vi) will not occur upon or after such transfer. In addition, Dealer may transfer or assign without any consent of Counterparty its rights and obligations hereunder and under the Agreement, in whole or
in part, to any affiliate of Dealer that is (or whose guarantor is) of credit quality equivalent to Dealer, in each case, only if (x) an Event of Default, Potential Event of Default or Termination Event will not occur as a result of such
transfer or assignment, (y) as a result of such transfer or assignment, Counterparty will not be required to pay the transferee on any payment date an amount under Section 2(d)(i)(4) of the Agreement, all applicable, greater than the
amount that Counterparty would have been required to pay to Dealer in the absence of such transfer or assignment and (z) such transfer or assignment would not result in a deemed exchange by Counterparty of the transferred or assigned portion of
the Transaction for a modified transaction that differs materially in kind or extent for U.S. federal income tax purposes. At any time at which any Excess Ownership Position exists, if Dealer, in its discretion, is unable to effect a transfer or
assignment to a third party in accordance with the requirements set forth above after using its commercially reasonable efforts on pricing terms and within a time period reasonably acceptable to Dealer


  
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such that an Excess Ownership Position no longer exists, Dealer may designate any Scheduled Trading Day as an Early Termination Date with respect to a portion (the “Terminated
Portion”) of the Transaction, such that such Excess Ownership Position no longer exists. In the event that Dealer so designates an Early Termination Date with respect to a portion of the Transaction, a payment or delivery shall be made
pursuant to Section 6 of the Agreement and Section 8(b) of this Confirmation as if (i) an Early Termination Date had been designated in respect of a Transaction having terms identical to the Terminated Portion of the Transaction,
(ii) Counterparty shall be the sole Affected Party with respect to such partial termination and (iii) such portion of the Transaction shall be the only Terminated Transaction. “Excess Ownership Position” means any of the
following: (i) the Equity Percentage exceeds 8.0% or (ii) Dealer, Dealer Group (as defined below) or any person whose ownership position would be aggregated with that of Dealer or Dealer Group (Dealer, Dealer Group or any such person, a
“Dealer Person”) under any federal, state or local (including non-U.S.) laws, regulations, regulatory orders or organizational documents or contracts of Counterparty that are, in each case, applicable to ownership of Shares
(“Applicable Laws”), owns, beneficially owns, constructively owns, controls, holds the power to vote or otherwise meets a relevant definition of ownership in excess of a number of Shares equal to (x) the number of Shares that
would give rise to reporting or registration obligations or other requirements (including obtaining prior approval by a local, state, federal or non-U.S. regulator) of a Dealer Person, or could result in an adverse effect on a Dealer Person, under
Applicable Laws, as determined by Dealer in its reasonable discretion, and with respect to which such requirements have not been met or the relevant approval has not been received or that would give rise to any consequences under the constitutive
documents of Counterparty or any contract or agreement to which Counterparty is a party (in each case, excluding any filings of Form 13F, Schedule 13D or Schedule 13G under the Exchange Act), in each case minus (y) 1% of the number of
Shares outstanding on the date of determination. The “Equity Percentage” as of any day is the fraction, expressed as a percentage, (A) the numerator of which is the number of Shares that Dealer and any of its affiliates or any
other person subject to aggregation with Dealer, for purposes of the “beneficial ownership” test under Section 13 of the Exchange Act, or any “group” (within the meaning of Section 13) of which Dealer is or may be
deemed to be a part (Dealer and any such affiliates, persons and groups, collectively, “Dealer Group”), beneficially owns (within the meaning of Section 13 of the Exchange Act), without duplication, on such day (or, to the
extent that, as a result of a change in law, regulation or interpretation after the date hereof, the equivalent calculation under Section 16 of the Exchange Act and the rules and regulations thereunder results in a higher number, such number)
and (B) the denominator of which is the number of Shares outstanding on such day. 
 (g) Staggered Settlement. If upon advice of
counsel with respect to applicable legal and regulatory requirements, including any requirements relating to Dealer’s hedging activities hereunder, Dealer reasonably determines that it would not be advisable to deliver, or to acquire Shares to
deliver, any or all of the Shares to be delivered by Dealer on the relevant “Nominal Settlement Date”, Dealer may, by notice to Counterparty on or prior to any Settlement Date (a “Nominal Settlement Date”), elect to
deliver the Shares on two or more dates (each, a “Staggered Settlement Date”) or at two or more times on the Nominal Settlement Date as follows: 

(i) in such notice, Dealer will specify to Counterparty the related Staggered Settlement Dates (each of which will be on or
prior to such Nominal Settlement Date, but not prior to the beginning of the related “Observation Period”, as defined in the Indenture) or delivery times and how it will allocate the Shares it is required to deliver under
“Delivery Obligation” (above) among the Staggered Settlement Dates or delivery times; and 
 (ii) the aggregate
number of Shares that Dealer will deliver to Counterparty hereunder on all such Staggered Settlement Dates and delivery times will equal the number of Shares that Dealer would otherwise be required to deliver on such Nominal Settlement Date. 

(h) Right to Extend. The Calculation Agent, acting commercially reasonably, may postpone or add, in whole or in part, any Exercise Date
or Settlement Date or any other date of valuation or delivery by Dealer, with respect to some or all of the relevant Options (in which event the Calculation Agent shall make appropriate adjustments to the Delivery Obligation), if Dealer determines,
in its reasonable discretion, based on advice of counsel in the case of the immediately following clause (ii), that such extension is reasonably necessary or appropriate (i) to preserve Dealer’s commercially reasonable hedging or hedge
unwind activity hereunder in light of existing liquidity conditions in the cash market, the stock loan market or any other relevant market or (ii) to enable Dealer to effect purchases of Shares in connection with its commercially reasonable
hedging, hedge unwind or settlement activity hereunder in a manner that would, if Dealer were Counterparty or an affiliated purchaser of Counterparty, be in compliance with applicable legal, regulatory or self-regulatory requirements, or with
related policies and procedures applicable to Dealer (whether or not such requirements, policies or procedures are imposed by law or have been voluntarily adopted by Dealer in good faith in relation to such requirements). 

  
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 (i) Adjustments. For the avoidance of doubt, whenever the Calculation Agent is called upon
to make an adjustment pursuant to the terms of this Confirmation or the Definitions to take into account the effect of an event, the Calculation Agent shall make such adjustment by reference to the effect of such event on the Hedging Party, assuming
that the Hedging Party maintains a commercially reasonable hedge position. 
 (j) Disclosure. Effective from the date of commencement
of discussions concerning the Transaction, Counterparty and each of its employees, representatives, or other agents may disclose to any and all persons, without limitation of any kind, the tax treatment and tax structure of the Transaction and all
materials of any kind (including opinions or other tax analyses) that are provided to Counterparty relating to such tax treatment and tax structure. 

(k) Designation by Dealer. Notwithstanding any other provision in this Confirmation to the contrary requiring or allowing Dealer to
purchase, sell, receive or deliver any Shares or other securities to or from Counterparty, Dealer may designate any of its affiliates to purchase, sell, receive or deliver such Shares or other securities and otherwise to perform Dealer’s
obligations in respect of the Transaction and any such designee may assume such obligations. Dealer shall be discharged of its obligations to Counterparty to the extent of any such performance. 

(l) No Netting and Set-off. Each party waives any and all rights it may have to set off obligations arising under the Agreement and the
Transaction against other obligations between the parties, whether arising under any other agreement, applicable law or otherwise. 
 (m)
Equity Rights. Dealer acknowledges and agrees that this Confirmation is not intended to convey to it rights with respect to the Transaction that are senior to the claims of common stockholders in the event of Counterparty’s bankruptcy.
For the avoidance of doubt, the parties agree that the preceding sentence shall not apply at any time other than during Counterparty’s bankruptcy to any claim arising as a result of a breach by Counterparty of any of its obligations under this
Confirmation or the Agreement. For the avoidance of doubt, the parties acknowledge that this Confirmation is not secured by any collateral that would otherwise secure the obligations of Counterparty herein under or pursuant to any other agreement.

 (n) Early Unwind. In the event the sale by Counterparty of the Base Convertible Securities is not consummated with the Initial
Purchasers pursuant to the Purchase Agreement for any reason by 9:00 A.M. (New York City time) on the third (fourth, if the pricing occurs after 4:30 P.M. (New York City time) on any given day) business day after the Trade Date (or such later date
as agreed upon by the parties, which in no event shall be later than ten business days after such third or fourth business day) (such third or fourth business day or such later date being the “Early Unwind Date”), the Transaction
shall automatically terminate (the “Early Unwind”), on the Early Unwind Date and the Transaction and all of the respective rights and obligations of Dealer and Counterparty thereunder shall be cancelled and terminated. Following
such termination and cancellation, each party shall be released and discharged by the other party from and agrees not to make any claim against the other party with respect to any obligations or liabilities of either party arising out of and to be
performed in connection with the Transaction either prior to or after the Early Unwind Date. Dealer and Counterparty represent and acknowledge to the other that upon an Early Unwind, all obligations with respect to the Transaction shall be deemed
fully and finally discharged. 
 (o) Wall Street Transparency and Accountability Act of 2010. The parties hereby agree that none of
(v) Section 739 of the Wall Street Transparency and Accountability Act of 2010 (“WSTAA”), (w) any similar legal certainty provision in any legislation enacted, or rule or regulation promulgated, on or after the Trade
Date, (x) the enactment of WSTAA or any regulation under the WSTAA, (y) any requirement under WSTAA nor (z) an amendment made by WSTAA, shall limit or otherwise impair either party’s rights to terminate, renegotiate, modify,
amend or supplement this Confirmation or the Agreement, as applicable, arising from a termination event, force majeure, illegality, increased costs, regulatory change or similar event under this Confirmation, the Equity Definitions incorporated
herein, or the Agreement (including, but not limited to, rights arising from Change in Law, Hedging Disruption, an Excess Ownership Position or Illegality (as defined in the Agreement)). 

(p) Tax Matters 

(i) Withholding Tax imposed on payments to non-US counterparties under the United States Foreign Account Tax Compliance
Act. “Tax” and “Indemnifiable Tax”, each as defined in Section 14 of the Agreement, shall not include any U.S. federal withholding tax imposed or collected pursuant to Sections 1471 through 1474 of the U.S. Internal
Revenue Code of 1986, as amended (the “Code”), any current or future regulations or official interpretations thereof, any agreement entered into pursuant to Section 1471(b) of the Code, or any fiscal or regulatory legislation,
rules or practices adopted pursuant to any intergovernmental 

  
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agreement entered into in connection with the implementation of such Sections of the Code (a “FATCA Withholding Tax”). For the avoidance of doubt, a FATCA Withholding Tax is a
Tax the deduction or withholding of which is required by applicable law for the purposes of Section 2(d) of the Agreement. 

(ii) HIRE Act. “Tax” and “Indemnifiable Tax”, each as defined in Section 14 of the
Agreement, shall not include any tax imposed on payments treated as dividends from sources within the United States under Section 871(m) of the Code or any regulations issued thereunder. 

(iii) Tax documentation. Counterparty shall provide to Dealer a valid U.S. Internal Revenue Service Form W-9, or any
successor thereto, (i) on or before the date of execution of this Confirmation and (ii) promptly upon learning that any such tax form previously provided by Counterparty has become obsolete or incorrect. Additionally, Counterparty
shall, promptly upon request by Dealer, provide such other tax forms and documents as are reasonably requested by Dealer. Dealer shall provide Counterparty, as applicable, (x) a valid U.S. Internal Revenue Service Form W-9 or W-8ECI or
(y) (A) a valid Internal Revenue Service Form W-8IMY along with a withholding statement and (B) attached a valid Internal Revenue Service Form W-9 or Internal Revenue Service Form W-8ECI, or, in each case, any successor thereto,
(i) on or before the date of execution of this Confirmation and (ii) promptly upon learning that any such tax form previously provided by Dealer has become obsolete or incorrect. Additionally, Dealer shall, promptly upon request by
Counterparty, provide such other tax forms and documents as are reasonably requested by Counterparty. 
 (iv) Tax
Representations. Counterparty is a corporation for U.S. federal income tax purposes and is organized under the laws of the State of Delaware. Counterparty is a “U.S. person” (as that term is used in section 1.1441-4(a)(3)(ii) of United
States Treasury Regulations) for U.S. federal income tax purposes and an exempt recipient under Treasury Regulation Section 1.6049-4(c)(1)(ii). 

(q) Reserved. 
 (r) Reserved.

 (s) Reserved. 
 (t)
Reserved. 
 (u) Waiver of Trial by Jury. EACH OF COUNTERPARTY AND DEALER HEREBY IRREVOCABLY WAIVES (ON ITS OWN BEHALF AND, TO THE
EXTENT PERMITTED BY APPLICABLE LAW, ON BEHALF OF ITS STOCKHOLDERS) ALL RIGHT TO TRIAL BY JURY IN ANY ACTION, PROCEEDING OR COUNTERCLAIM (WHETHER BASED ON CONTRACT, TORT OR OTHERWISE) ARISING OUT OF OR RELATING TO THE TRANSACTION OR THE ACTIONS OF
DEALER OR ITS AFFILIATES IN THE NEGOTIATION, PERFORMANCE OR ENFORCEMENT HEREOF. 
 (v) Governing Law; Jurisdiction.
THIS CONFIRMATION AND ANY CLAIM, CONTROVERSY OR DISPUTE ARISING UNDER OR RELATED TO THIS CONFIRMATION SHALL BE GOVERNED BY THE LAWS OF THE STATE OF NEW YORK. THE PARTIES HERETO IRREVOCABLY SUBMIT TO THE EXCLUSIVE JURISDICTION OF THE COURTS OF THE
STATE OF NEW YORK AND THE UNITED STATES COURT FOR THE SOUTHERN DISTRICT OF NEW YORK IN CONNECTION WITH ALL MATTERS RELATING HERETO AND WAIVE ANY OBJECTION TO THE LAYING OF VENUE IN, AND ANY CLAIM OF INCONVENIENT FORUM WITH RESPECT TO, THESE
COURTS. 
 [Signature Page Follows] 

  
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 Counterparty hereby agrees (a) to check this Confirmation carefully and immediately upon
receipt so that errors or discrepancies can be promptly identified and rectified and (b) to confirm that the foregoing (in the exact form provided by Dealer) correctly sets forth the terms of the agreement between Dealer and Counterparty with
respect to the Transaction, by manually signing this Confirmation or this page hereof as evidence of agreement to such terms and providing the other information requested herein and immediately returning an executed copy to Dealer. 

 

			
	Yours faithfully,
	
	BANK OF AMERICA, N.A.
		
	By:	 	 /s/ Christopher A. Hutmaker

		 	Name: Christopher A. Hutmaker
		 	Title: Managing Director


  

			
	Agreed and Accepted By:
	
	LIGAND PHARMACEUTICALS INCORPORATED
		
	By:	 	 /s/ Nishan de Silva

	Name:	 	Nishan de Silva
	Title:	 	Vice President, Finance and Strategy, and Chief Financial Officer


  
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