Document:

EX-10.12

 Exhibit 10.12 

Schrödinger, Inc. 

Employment Agreement 
 This Employment
Agreement (“Agreement”) is dated April 15, 2013 and effective as of the Employment Commencement Date set forth in Section 1 below (“Effective Date”) by and between Schrödinger, Inc., a Delaware corporation
(“Company”), and Cony D’Cruz (“Employee”). 
 WHEREAS, the Company is currently in the business of (i) designing, developing,
distributing, selling, licensing, leasing and servicing computer software programs for use principally in the fields of quantum chemistry, computational chemistry, molecular mechanics/dynamics, protein structure prediction, computational ligand
docking, and other science and technology fields, and (ii) providing services and performing research involving the use of such software in connection with various biological, chemical, and materials science applications, and may engage in
other activities in the future (such current and future activities collectively, the “Company’s Business”); 
 WHEREAS, Employee is engaged
by the Company to perform certain services for Company and/or one or more subsidiaries of and/or other Affiliates (as hereinafter defined) of the Company (collectively, the Company, its subsidiaries, and its other Affiliates shall be referred to as
the “Schrödinger Companies”); 
 WHEREAS, in connection with such duties, Employee may have access to certain confidential information and
trade secrets of one or more Schrödinger Companies and/or, as the case may be, the D. E. Shaw Group (as hereinafter defined), and may in the course of Employee’s employment with the Company discover or conceive one or more inventions; and

 WHEREAS, the Company and Employee desire to define the rights and obligations between them with respect to the subject matter hereto. 

NOW THEREFORE, in consideration of the promises and covenants set forth below, the parties agree as follows: 

1. Employment. Employment commenced on April 15, 2013 (“Employment Commencement Date”) and may be terminated by either
party at any time, for any reason, upon 30 days’ notice (the “Notice Period”), which notice may be given either verbally or in writing. Notwithstanding the foregoing, the Company may elect to terminate employment immediately upon
notice, except that in this event, 30 days of the base salary set forth in Section 2 shall be paid in addition to the base salary earned up to the date of such termination. Neither the provision of notice nor pay in lieu of notice shall modify
the terms and conditions of any Company stock option plan. The Employee acknowledges and agrees that the Employee is an employee at will, and that just as the Employee is free to resign at any time, the Company has the right to terminate the
employment relationship at any time for any lawful reason. The Employee acknowledges and agrees that no representative of the Company may verbally change the at will employment relationship between the Employee and the Company. References to time
periods in this Agreement shall not be construed or interpreted as promising or guaranteeing employment for any specific duration or until any specific date. 

 2. Compensation. 

(a) Base Salary During the Compensation Period. As compensation for the Employee’s services during the period beginning
April 15, 2013 and ending on December 31, 2013 (the “Compensation Period”), the Company shall pay the Employee a base salary computed at an annual rate of $290,000 per year, prorated to correspond to that portion of the
Compensation Period during which the Employee is actually employed with the Company, such base salary to be paid twice per calendar month. If Employee is a commission-eligible member of the sales team, Employee shall be eligible to receive
commission under the Company’s standard sales commission plan, which may be modified by the Company at any time in the Company’s sole discretion. 

(b) Base Salary After the Compensation Period. As of the end of the Compensation Period, the Employee’s base salary may be
increased or decreased, or the manner in which the Employee is compensated may be changed, in the sole discretion of the Company. Any such change in compensation shall be deemed to modify only this Section 2 of this Agreement, and all other
provisions of this Agreement shall remain in effect following such change in compensation. In the absence of any such change, the Employee’s base salary shall remain the same as it was during the Compensation Period. 

(c) Standard Company Benefits. In addition to the compensation outlined elsewhere in this Section 2, the Company shall provide to
the Employee all of the benefits included in the Company’s standard benefit package, which currently include medical (hospitalization and major medical), dental, disability, life, and accidental death and dismemberment insurance. Most of the
cost of such benefits shall be borne by the Company. However, in the case of coverage for the Employee himself or for one or more of Employee’s beneficiaries, the Employee makes a pre-tax contribution to
the cost of the medical and dental insurance. Individual and dependent medical and dental insurance contribution amounts are determined on a set scale, based on the actual cost of the insurance. For additional levels of life insurance beyond the
Company’s basic benefit, the required contribution will be borne by the Employee by means of a voluntary salary reduction in the amount of the contribution implemented by Company at the request of the Employee. 

The standard benefit package also currently includes a flexible spending account plan, a transit reimbursement plan, and a 401(k) retirement plan, available
to all eligible employees. In electing to participate in one of these plans, Employee contributes pre-tax dollars that can be used in accordance with the applicable plan terms. The Employee agrees that the
composition, providers, and all other aspects of Company’s standard benefit package may be changed from time to time in the sole discretion of the Company. 

(d) Stock Plan. The Employee may be eligible to receive stock options under the Company’s standard stock plan, which may be
modified by the Company at any time, in the sole discretion of the Company. 
 (e) Exclusive Compensation. The compensation and
benefits described in this Section 2 shall be the exclusive compensation due to the Employee from the Company or any of its Affiliates during or on account of the services of the Employee. If directed by the Company, the Employee shall provide
the services described in this Agreement to one or more Affiliates of the Company without additional compensation. 

  
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 3. Duties. The Employee will devote Employee’s full time, skill, efforts, and
attention to the Company’s Business, and shall perform such duties at such locations and on behalf of such Schrödinger Companies as may be assigned by the officers or directors of the Company from time to time. The Employee agrees to abide
by all applicable laws and regulations in connection with the Employee’s employment. 
 4. Confidentiality. 

4.1 Definition. For the purposes of this agreement, “Confidential Information” shall mean any information, including but not
limited to: 
 (a) any inventions, trade secrets, discoveries, know-how, research, improvements,
concepts, ideas, and principles whether or not patentable or copyrightable (including without limitation processes, methods, formulas, techniques, devices, designs, software, computer processing systems and techniques, algorithms, flow charts,
specifications, computer graphics, data, apparatus, products, and molecular structures), relating to past, present, or contemplated future activities of one or more Schrödinger Companies; 

(b) price lists, customer lists, supplier lists, business plans, marketing plans, financial and payroll information, as well as any
information contained in documents marked “Confidential,” which relates to the business of one or more Schrödinger Companies and which Employee may prepare, use, or have access to during the term of the employment; 

(c) the fact that one or more Schrödinger Companies uses, has used, or has evaluated for potential use any inventions, discoveries, know-how, research, improvements, concepts, ideas, or principles whether or not patentable or copyrightable (including without limitation processes, methods, formulas, techniques, devices, designs, software,
computer processing systems and techniques, algorithms, flow charts, specifications, computer graphics, data, apparatus, products, and molecular structures), whether developed by such Schrödinger Companies or by any other party; 

(d) the results of any marketing, advertising, joint venture, business, financial, or other analysis conducted by (or on behalf of) one or
more Schrödinger Companies for the internal use of one or more Schrödinger Companies or for other non-public use (and not approved by Company for general dissemination to the public); 

(e) any information that would typically be included in Company’s income statements, including but not limited to the amount of
Company’s revenues, expenses, or net income; 
 (f) any plans for the business of one or more Schrödinger Companies (whether or
not such plans have been reduced to writing), financial information concerning such plans (including without limitation projected revenues, projected expenses, and projected net income), descriptions of such business and technical aspects of or
relating to the operation of such business, and products and services that one or more Schrödinger Companies is considering exploring, developing, and/or researching; 

  
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 (g) any other information gained in the course of the Employee’s employment with the
Company that could reasonably be expected to prove deleterious to any Schrödinger Company or to any entity within the D. E. Shaw Group if disclosed to third parties, including without limitation any information that could reasonably be expected
to aid a competitor of any Schrödinger Company or the D. E. Shaw Group in making inferences regarding the nature of the Schrödinger Companies’ or D. E. Shaw Group’s activities, where such inferences could reasonably be expected
to adversely affect the competitive position of any Schrödinger Company or the D. E. Shaw Group relative to that of such a competitor; 

(h) any other information gained in the course of or incident to the Employee’s employment that a Schrödinger Company has received
from a third party and is required to hold confidential; and 
 (i) any other information gained in the course of or incident to the
Employee’s employment that one or more Schrödinger Companies or the D. E. Shaw Group treats or designates as Confidential Information and that is not publicly available. 

“Confidential Information” shall not include information which Employee can show (x) is or becomes part of the public domain through no fault
of Employee; (y) is already known to Employee and has been identified in writing prior to the date of this Agreement; or (z) is subsequently received by Employee from a third party who has no obligation of confidentiality to one or more
Schrödinger Companies or the D. E. Shaw Group. 
 4.2 Acknowledgment of Proprietary Interest. Employee acknowledges that the
Confidential Information described above is proprietary to one or more Schrödinger Companies or, as the case may be, the D. E. Shaw Group and contains valuable trade secrets of one or more Schrödinger Companies or, as the case may be, the
D. E. Shaw Group. 
 4.3 Covenant Not to Disclose Confidential Information. During the term of Employee’s employment and at any
time thereafter, Employee agrees not to disclose or use, directly or indirectly, except in pursuit of the Employee’s duties to one or more Schrödinger Companies, any Confidential Information, unless Employee shall first secure written
consent of the Company to such disclosure or use, or unless Employee is compelled to do so by court order or applicable law and Employee provides prior written notice of such disclosure to the Company. Without limiting the foregoing, Employee agrees
not to publish, or cause or authorize to be published, any document containing Confidential Information or related to the Company’s Business, without the Company’s prior written approval (which may be granted or withheld in Company’s
sole discretion). 
 4.4 Acknowledgment of Reasonableness. The Company and Employee hereby acknowledge that (a) the
Company’s market for its products is unlimited geographically and the foregoing non-disclosure requirements shall apply to Employee on a worldwide basis, and (b) the geographical and durational
limitations imposed with respect to the Confidential Information are fair and reasonable, and are reasonably necessary to protect the Confidential 

  
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Information of the Company. In the event that any provision relating to the geographical, durational, or other restrictions on Employee are declared by a court of competent jurisdiction to exceed
the maximum time period, area, or other measure such court deems reasonable and enforceable, said time period, area, or other measure shall be deemed to become and thereafter be the maximum amount which such court deems reasonable and enforceable.

 4.5 Return of Materials at Termination. In the event of any termination of his employment, whether with or without cause and
regardless of the reason for such termination, Employee will promptly return to the Company all written materials, computer software programs, or other materials containing Confidential Information and all other materials or documents, including
without limitation mailing lists, rolodexes, computer print-outs, and computer disks and tapes, belonging to one or more Schrödinger Companies which contain information pertaining to the Company’s Business, methods, clients, potential
clients, customers, potential customers, funding providers, potential funding providers, or employees, unless the Company consents in writing to the Employee’s retention thereof. 

4.6 Remedies upon Breach. Employee recognizes that the disclosure or use of any Confidential Information would cause the Company
irreparable injury, which may not be adequately compensated by damages. Accordingly, in the event Employee breaches or threatens to breach any provision of this Agreement, the Company or, as the case may be, the D. E. Shaw Group, shall be entitled
to an injunction restraining Employee from disclosing or using, in whole or in part, any Confidential Information, or from rendering any services to any person, firm, corporation, or other entity to whom such Confidential Information, in whole or in
part, has been, is threatened to be, or would necessarily be disclosed or used by Employee. Nothing herein shall be construed as prohibiting the Company or, as the case may be, the D. E. Shaw Group, from pursuing any other remedies available to it
for such breach or threatened breach, including the recovery of damages from Employee or any third party. The right of the Company and/or the D. E. Shaw Group to seek equitable relief under this Agreement shall be in addition to (and not in
derogation of) the requirement imposed on each party hereto to arbitrate disputes as provided in Section 7.1 below. 
 4.7 Ownership
of Confidential Information. All Confidential Information and all right, title and interest in and to patents, patent rights, copyright rights, mask work rights, trade secret rights, and all other intellectual property and proprietary rights
anywhere in the world (collectively, “Rights”) in connection therewith shall be the sole property of the relevant Schrödinger Company, which, if other than Schrödinger, Inc., shall be a third-party beneficiary of this Agreement.
Employee hereby assigns to the Company any Rights Employee may have or acquire in such Confidential Information. 
 4.8 Confidential
Information of Others. The Employee agrees not to disclose to any Schrödinger Company any confidential or proprietary information belonging to any of the Employee’s previous employers, or belonging to any other party, without first
securing the written permission of such previous employers or other parties. In addition, Employee agrees that Employee will not bring with Employee any confidential or proprietary information belonging to any of Employee’s previous employers
or to any other person, that Employee will refrain from using while employed by the Company any such confidential or proprietary information, and that Employee will comply with the non-disclosure, non-compete, and other 

  
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provisions of Employee’s agreements with Employee’s prior employers and with other persons. The Employee agrees to indemnify each Schrödinger Company for any expense, claim, or
damages (including without limitation attorneys’ fees, costs of investigation, and costs of collection) suffered by such entity relating to a breach of the terms of this paragraph by the Employee. 

5. Inventions. 
 5.1 (a)
Proprietary Rights; Assignment. All right, title and interest, and all proprietary claims to all data and other information, inventions (whether or not patentable), works of authorship, processes or
know-how, designs, and/or ideas for formulae, including but not limited to methodology, computer programs, systems, materials and manuals that Employee, alone or with others, makes, creates, develops,
conceives, or reduces to practice (a) in the course of Employee’s employment with the Company, whether during regular working hours or other hours, or (b) during the period of Employee’s employment, whether or not in the course
of such employment, to the extent the same is related to the Company’s business or actual or demonstrably anticipated research or development or is made, created, developed, conceived, or first reduced to practice with the time, private or
proprietary information, or facilities of one or more Schrödinger Companies (collectively, the materials described in Subsections 5.1(a) and 5.1(b) heretofore shall be referred to as the “Developments”), including without limitation
all rights under applicable copyright, patent or trade secret laws, shall reside with Company (or such Schrödinger Company designated by Company) and, where applicable, shall be considered “works made for hire”; provided, however,
that such ownership may be subject to the rights, if any, of the United States government and agencies thereof arising from Federal grants to the Company. Employee hereby assigns to the Company (or such Schrödinger Company designated by the
Company) all right, title, and interest Employee has or may have in the Developments. Employee agrees that neither Employee nor Employee’s successors or assigns shall have any rights in the Developments. 

(b) Exclusions. As used herein, “Employee Pre-Existing Work” is defined as data,
information, inventions (whether or not patentable), works of authorship, processes, know-how, designs and/or ideas for formulae that meet both of the following criteria: (i) each such work was made,
created, developed, conceived or reduced to practice by Employee, alone or with others, prior to Employment Commencement Date and (ii) each such work is related to the Company’s business or actual or demonstrably anticipated research or
development. Company shall have no right, title and interest in the Employee Pre-Existing Work. Employee’s Pre-Existing Work is identified in Exhibit A attached
hereto. 
 [         ] By checking the immediately preceding box, Employee acknowledges that no Employee-Pre-Existing Work exists. 
 5.2 Disclosure; Attorney-in-Fact. Employee shall disclose promptly to the Company all Developments during the term of Employee’s employment with the Company. Any information required
to be disclosed under this Section 5.2 that has not yet been disclosed by the Employee to the Company at the time of the termination of the Employee’s employment with the Company, without regard to when or for what reason, if any, such
employment shall terminate, shall be disclosed to the Company in writing, or in such form and manner as the 

  
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Company may reasonably require, within 10 days of the termination of the Employee’s employment with the Company. Employee hereby irrevocably appoints the Company (or such Schrödinger
Company designated by the Company), and the Company’s duly authorized officers and agents, as Employee’s agent and attorney-in-fact to act for and on behalf of
Employee in filing all patent applications, applications for copyright protection and registration amendments, renewals, and all other appropriate documents in any way related to the Developments. Employee agrees to assist the Company (or such
Schrödinger Company designated by the Company) in any way such Schrödinger Company deems necessary or appropriate (at such Schrödinger Company’s expense) from time to time to apply for, obtain and enforce patents on, and to apply
for, obtain, and enforce copyright protection and registration of, the Developments in any and all countries. To that end, Employee shall (at the request of one or more Schrödinger Companies), without limitation, testify in any suit or other
proceeding involving any of the Developments, execute all documents which the relevant Schrödinger Company reasonably determines to be necessary or convenient for use in applying for and obtaining patents or copyright protection and
registration thereon and enforcing the same, and execute all necessary assignments thereof to the Company (or such Schrödinger Company designated by the Company). 

5.3 California Labor Code Section 2870(a). For the avoidance of doubt, Developments do not include any invention
covered by California Labor Code Section 2870(a). Section 2870(a) provides: 
 ANY PROVISION IN AN EMPLOYMENT AGREEMENT WHICH
PROVIDES THAT AN EMPLOYEE SHALL ASSIGN, OR OFFER TO ASSIGN, ANY OF HIS OR HER RIGHTS IN AN INVENTION TO HIS OR HER EMPLOYER SHALL NOT APPLY TO AN INVENTION THAT THE EMPLOYEE DEVELOPED ENTIRELY ON HIS OR HER OWN TIME WITHOUT USING THE EMPLOYER’S
EQUIPMENT, SUPPLIES, FACILITIES, OR TRADE SECRET INFORMATION EXCEPT FOR THOSE INVENTIONS THAT EITHER: 
  

	 	    a.	 RELATE AT THE TIME OF CONCEPTION OR REDUCTION TO PRACTICE OF THE INVENTION TO THE EMPLOYER’S BUSINESS, OR
ACTUAL OR DEMONSTRABLY ANTICIPATED RESEARCH OR DEVELOPMENT OF THE EMPLOYER; OR 

  

	 	    b.	 RESULT FROM ANY WORK PERFORMED BY THE EMPLOYEE FOR THE EMPLOYER. 

6. Non-Competition; Non-Solicitation. 

6.1 Covenant not to Compete During Term of Employment. During the term of his employment with the Company, the Employee will not,
directly or indirectly, without the written consent of the Company, and whether or not for compensation, either for his own account or as an employee, officer, agent, consultant, director, owner, partner, joint venturer, shareholder, investor, or in
any other capacity (except in the capacity of an employee or officer of the Company acting for the benefit of the Schrödinger Companies), knowingly engage in any activity or business which is the same nature as, or substantively similar to, the
Company’s Business or an activity or business which one or more Schrödinger Company is developing and of which the Employee has knowledge. 

  
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 6.2 Non-Solicitation of Customers, Vendors or
Business Partners. During the term of Employee’s employment and for a period of one (1) year thereafter, Employee shall not, directly or indirectly, solicit or encourage any customer, prospective customer, vendor, strategic partner or
business associate of a Schrödinger Company to cease doing business with a Schrödinger Company, reduce its relationship with a Schrödinger Company, or refrain from establishing or expanding a relationship with a Schrödinger
Company. For the purposes of this section, “prospective customer” shall mean any individual, business, firm or organization whom Employee or a Schrödinger Company has contacted during the term of the Employee’s employment or who
has been made known to Employee by a Schrödinger Company for the purpose of soliciting business. 
 6.3 Non-Solicitation of Employees. During the term of Employee’s employment and for a period one (1) year thereafter, Employee shall not directly or indirectly, without the prior written consent of the
Company, (a) solicit or induce any employee of a Schrödinger Company or the D. E. Shaw Group (or any consultant, sales agent, contract researcher, contract programmer, or other independent agent who is retained by a Schrödinger
Company or the D. E. Shaw Group) to cease his employment or retention by a Schrödinger Company or the D. E. Shaw Group, or (b) hire, retain, employ, or engage for any purpose any employee of a Schrödinger Company or the D. E. Shaw
Group. 
 6.4 Conflicts of Interest. During the term of Employee’s employment, Employee shall not engage in any activity or
business which impairs or hinders the Employee’s job duties and responsibilities for Company. Employee shall report to the Company any possible conflicts of interest on the basis of existing or planned activities of the Employee or members of
Employee’s immediate family. A conflict of interest shall be deemed to arise when the Employee or a member of Employee’s immediate family: (a) accepts any interest, services, products, commissions, share in profits or other payments,
gifts or remuneration from any organization which transacts or is seeking to transact business with one or more Schrödinger Companies or which competes with the Company’s Business, or (b) serves as director, partner, employee or
consultant, or becomes a shareholder of any organization doing business with or seeking to do business with or competitive with one or more Schrödinger Companies. 

7. General Provisions. 

7.1 Mandatory Arbitration. The Employee and the Company agree that any claim, controversy, or dispute between the Employee and the
Company (including without limitation Company’s Affiliates, officers, employees, representatives, or agents) arising out of or relating to this Agreement, the employment of the Employee, the cessation of employment of the Employee, or any
matter relating to the foregoing shall be submitted to and settled by arbitration before a single arbitrator in the forum of the American Arbitration Association (“AAA”) located in New York County in the State of New York and conducted in
accordance with the National Rules for the Resolution of Employment Disputes. In such arbitration, (a) the arbitrator shall agree to treat as confidential evidence and other information presented by the parties to the same

  
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extent as Confidential Information under this Agreement must be held confidential by the Employee, (b) the arbitrator shall have no authority to amend or modify any of the terms of this
Agreement, and (c) the arbitrator shall have ten business days from the closing statements or submission of post-hearing briefs by the parties to render his decision. Any arbitration award (regardless of the forum) shall be final and binding
upon the parties, and any court, state or federal, having jurisdiction may enter a judgment on the award. The foregoing requirement to arbitrate claims, controversies, and disputes applies to all claims or demands by the Employee, including without
limitation any rights or claims the Employee may have under the Age Discrimination in Employment Act of 1967 (which prohibits age discrimination in employment), Title VII of the Civil Rights Act of 1964 (which prohibits discrimination in employment
based on race, color, national origin, religion, sex, or pregnancy), the Equal Pay Act (which prohibits paying men and women unequal pay for equal work) or any other federal, state, or local laws or regulations pertaining to the Employee’s
employment or the termination of the Employee’s employment. All costs of said arbitration, including the arbitrator’s fees, if any, shall be borne equally by the parties, unless the arbitration decision and award provides otherwise. All
legal fees incurred by each party in connection with said arbitration shall be borne by the party who incurs them, unless applicable statutory authority exists providing for the award of attorneys’ fees to a prevailing party and the arbitration
decision and award provides for the award of such fees. 
 7.2 Choice of Law; Jurisdiction. This Agreement shall be governed by and
construed in accordance with the laws of the State of New York, without regard to conflicts-of-law principles. Each party submits to the jurisdiction of the courts,
state and federal, and arbitration forum (set forth in Section 7.1) located in the State of New York. 
 7.3 Compliance with U.S.
Export Controls and Sanctions laws. Employee acknowledges and understands that any software, technology or technical data of the Company is subject to U.S. export controls and sanctions laws, including the Export Administration Regulations
(“EAR”) enforced by the Department of Commerce, U.S. Sanctions Administered by the Department of Treasury’s Office of Foreign Assets Control (“OFAC”) and the International Traffic in Arms Regulations administered by the U.S.
Department of State. Employee hereby certifies that Employee will not disclose, export or transfer Company software, technology or technical data outside of the United States or to a foreign national within the United States or to a foreign
government without the required license(s) or authorization from the U.S. Departments of Commerce and/or State and/or OFAC. Employee further certifies that Employee will abide by and comply with all Company compliance procedures, requirements and
standards. 
 7.4 No Coercion or Duress. The Employee enters into this Agreement with full understanding of the nature and extent of
the restrictive covenants contained herein and acknowledges that because of the nature of the Company’s business, this Agreement would not be entered into without the restrictive covenants contained herein. The Employee acknowledges and agrees
that the Employee is entering into this Agreement voluntarily and of his own free will in order to obtain the benefits of employment, continued employment, and additional compensation by the Company. The Employee acknowledges and agrees that he has
not been coerced or suffered any duress in order to induce him to enter into this Agreement. 

  
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 7.5 Relationship of the Parties. The relationship between the Company and the
Employee hereunder is agreed to be solely that of employee and employer. Nothing contained herein and no modification of responsibility or compensation made hereafter shall be construed so as to constitute the parties as partners or joint venturers.

 7.6 Entire Agreement. This Agreement shall constitute the entire agreement between the Company and Employee relating to the subject
matter hereof, and supersedes all prior representations, promises or agreements, either oral or written, with regard to the subject matter hereof. No modification or amendments of this Agreement shall be of any effect unless signed in writing by the
President of the Company (or such other officer of the Company authorized by the President or Board of Directors of the Company) and Employee. The failure of the Company to terminate this Agreement for any breaches by Employee shall not affect the
Company’s right to terminate this Agreement for subsequent breaches of the same or other provisions thereof. 
 7.7 Severability; No
Waiver. The holding of any provision of this Agreement to be illegal, invalid, or unenforceable by a court of competent jurisdiction shall not affect any other provision of this Agreement, which shall remain in full force and effect. The failure
of the Company to enforce any of the provisions of this Agreement for any period of time shall not be construed as a waiver of such provisions or of the right of the Company to enforce each and every provision in the future. 

7.8 Amendments. No amendment or alteration of the terms of this Agreement shall be valid unless made in writing and signed by both of
the parties hereto. 
 7.9 Successors and Assigns; Assignment. Except as otherwise provided in this paragraph, this Agreement shall
inure to the benefit of and be binding upon the parties hereto and their respective heirs, representatives, successors, and assigns. Neither this Agreement nor any right or interest hereunder shall be assignable by the Employee, Employee’s
beneficiaries, or Employee’s legal representatives without Company’s prior written consent; provided, however, that nothing in this paragraph shall preclude the Employee from designating a beneficiary to receive any benefit payable
hereunder upon his death, or the executors, administrators, or other legal representatives of the Employee or his estate from assigning any rights hereunder to the person or persons entitled thereunto. This Agreement shall be assignable by Company
to (a) another Schrödinger Company, (b) any corporation, partnership, or other entity that may be organized by Company as a separate business unit in connection with the business activities of Company, or (c) any corporation,
partnership, or other entity resulting from the reorganization, merger, or consolidation of Company with any other corporation, partnership, or other entity, or any corporation, partnership, or other entity to or with which all or any portion of
Company’s business or assets may be sold, exchanged, or transferred. 
 7.10 No Attachment. Except as required by law, no right
to receive payments under this Agreement shall be subject to anticipation, commutation, alienation, sale, assignment, encumbrance, charge, pledge, or hypothecation, or to execution, attachment, levy, or similar process or assignment by operation of
law, and any attempt, voluntary or involuntary, to effect any such action shall be null, void, and of no effect. 

  
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 7.11 Headings. The section headings appearing in this Agreement are used for
convenience of reference only and shall not be considered a part of this Agreement or in any way modify, amend, or affect the meaning of any of its provisions. 

7.12 Construction. Whenever the context so requires, the use of the masculine gender shall be deemed to include the feminine and vice
versa, and the use of the singular shall be deemed to include the plural and vice versa. That this Agreement was drafted by the Company shall not be taken into account in interpreting or construing any provision of this Agreement. 

7.13 Certain Definitions. 

(a) For purposes of this Agreement, the term “Affiliate” shall mean any entity in which a party holds a 50% or greater equity
interest or any entity controlling, controlled by or under common control with such party, directly or indirectly by or through one or more intermediaries. 

(b) For purposes of this Agreement, the term “D. E. Shaw Group” shall include, individually and/or collectively: (i) D. E.
Shaw & Co., L.P., D. E. Shaw & Co., Inc., and D. E. Shaw & Co. II, Inc., and D. E. Shaw Development, L.L.C., or any Affiliate of any of the foregoing; (ii) any partnership, other entity or account that D. E.
Shaw & Co., L.P., D. E. Shaw & Co., Inc., D. E. Shaw & Co. II, Inc. or D. E. Shaw Development, L.L.C. owns, in whole or in part, or for which they act, directly or indirectly, as general partner, investment manager, or
management company, along with their respective subsidiaries; and (iii) any predecessor or successor entity to any partnership, entity, or account described in Subsection 7.12(b)(ii) above. The D. E. Shaw Group is a third-party beneficiary of
this Agreement. 
 IN WITNESS WHEREOF, each of the undersigned has caused this Agreement to be duly executed on its behalf as of the Effective Date. 

 

									
	Employee	 	        	  	Schrödinger, Inc.
					
	By:	 	 /s/ Cony D’Cruz
	 		  	By:	  	 /s/ Ramy Farid

		 	Cony D’Cruz 	 		  		  	 Ramy Farid
 President

	 Employee’s Address:
  

[**]
	 		  		  	

 EXHIBIT A 

  
 - 11 -EX-10.13

 Exhibit 10.13 

MANAGING DIRECTOR AGREEMENT 

(“Geschäftsführer-Anstellungsvertrag”) 

between 
 Schrödinger GmbH

 - hereafter the “Company” - 

and 
 Dr. Jörg Weiser

 - hereafter the “Managing Director” - 

§ 1 
 Duties and
Authority 
  

	(1)	 Dr. Jörg Weiser has been appointed Director of European Operations and Managing Director
(“Geschäftsführer”) of Schrödinger GmbH. He shall represent the Company alone or, as the case may be, together with one or more managing directors. The shareholder(s) of the Company (hereinafter, “shareholder
meeting”) reserves the right to appoint further managing directors and then confer a joint right to represent the Company upon the managing directors as well as to have such joint representation registered with the company register
(“Handelsregister”). 

  

	(2)	 The Managing Director shall manage the Company in accordance with the applicable law, this Agreement, the
Company’s Articles of Association and, insofar as any such regulations have been adopted, management regulations. Any changes to the applicable law, the Articles of Association and/or the management regulations become automatically binding and
relevant for the Managing Director’s duties when they become effective. 

 § 2 

Internal Limitations on Authority 
 The
Managing Director must obtain the consent of the shareholder meeting for the activities listed in Appendix § 2. 

 § 3 

Duration of Agreement 
  

	(1)	 This Managing Director’s Agreement shall stay in effect until terminated by either party by giving 30
days’ notice with the termination becoming effective at the end of the notice period. 

  

	(2)	 In order to be effective, the notice of termination must be in writing. 

 

	(3)	 This Agreement shall terminate, at the latest, at the end of the calendar month in which the Managing Director
reaches the age of 62 or at his death, whatever is earlier, as well as when the Managing Director becomes permanently physically or mentally unable to perform his obligations under this Agreement (“Invalidität im Sinne des deutschen
Angestellten-Versicherungsgesetzes”), by the end of the month, in which an expert opinion has certified such a case. The termination of the Agreement pursuant to this § 3(3) shall be effective immediately upon written notice by the
Company. 

  

	(4)	 Either party’s right to terminate this Agreement for cause hereby remains unaffected. The Company may
notably, but not exclusively, terminate this Agreement, if: 

  

	 	(a)	 the Managing Director breaches any of his obligations and duties under this Agreement; 

 

	 	(b)	 the Managing Director breaches any of his obligations under the Employee Confidentiality Agreement attached as
Appendix § 8; 

  

	 	(c)	 the Managing Director is convicted of any crime involving moral turpitude, or the Managing Director enters a
plea of guilty or “no contest” with respect to the foregoing; 

  

	 	(d)	 the Managing Director acts in a manner which, in the reasonable determination of the shareholder meeting, is
likely to affect adversely the reputation or public image of the Company; 

  

	 	(e)	 the Managing Director commits an act involving fraud, misappropriation of funds, dishonesty, disloyalty, breach
of fiduciary duty or other gross misconduct against the Company; or 

  

	 	(f)	 the Managing Director fails to follow the instructions of the shareholder meeting. 

  
 2 

	(5)	 The shareholder meeting shall be entitled to release the Managing Director from his duties for the period
between the date on which notice to terminate was given and the effective date of termination upon further payment of his salary by the Company and taking into account possible holiday entitlements. The Managing Director shall voluntarily disclose
and accept to be deducted from his continuous salary payments any remuneration for work he is entitled to from any party other than the Company or an affiliate of Schrödinger, Inc. for the period between notification of the termination of this
Agreement and the effective date of such termination. 

  

	(6)	 The appointment of the Managing Director can be revoked at any time upon the passing of a shareholder
resolution, but without prejudice to the Managing Director’s rights for compensation resulting from this Agreement. The revocation shall be deemed to be a notice of termination of the Agreement effective on the next permissible date.

 § 4 

Working Hours/Place of Work 
  

	(1)	 The Managing Director undertakes to devote his full time, skill, efforts, attention and working capacity to the
interests and to the business of the Company and, if required, to work in excess of the Company’s normal working hours. 

  

	(2)	 The Managing Director shall perform his obligations under this agreement at the Company’s statutory seat
as well as at any other location out of which the Company performs its business activities. 

 § 5 

Additional Activities 
  

	(1)	 The Managing Director agrees not to perform services for any other company during the continuance of this
Agreement. The carrying out of other gainful employment is not permitted without the prior express and written approval of the shareholder meeting. The same shall apply with regard to the acceptance of any position as member of a Supervisory Board
and similar activities. Notwithstanding the foregoing, the Managing Director shall be permitted to serve on the Scientific Advisory Board of anterio consult & research GmbH. The Managing Director may publish and lecture as member of the
Scientific 

  
 3 

 
Advisory Board of anterio consult & research GmbH; provided, however, that (a) the Managing Director shall comply with the terms and conditions of the Employee Confidentiality
Agreement attached hereto as Appendix § 8, and (b) such publishing or lecturing shall require the prior express and written approval of the shareholder meeting if the subject matter concerns the Company or any of
Company’s affiliates. 
  

	(2)	 The Managing Director requires the prior written approval of the shareholder meeting before giving any speech,
publishing any written material, or in any other way making a public statement insofar as the same affect the Company’s interests. 

  

	(3)	 The Managing Director shall inform the shareholder meeting immediately if he accepts a position in a public or
private organization. 

 § 6 

Financial Statements/Reports 
  

	(1)	 The Managing Director is in charge of establishing the Company’s annual financial statements according to
the applicable statutory provisions as set out in the German Commercial Code (“Handelsgesetzbuch”). He shall present these annual financial statements to the shareholders immediately, in no event, however, later than on January 31 of
the following year. 

  

	(2)	 The Managing Director shall provide to the shareholder meeting any written reports of the Company’s
financial situation and other reports as the shareholder meeting may from time to time require or as the Managing Director is aware to be customary within the Company’s affiliates. In particular, but without limitation, such reports shall
contain the following: stock, sales, profits and losses, personnel expenses, claims, assets, liabilities, and cash flow. The financial reports shall be submitted at the latest on the fifteenth day of the immediately following month unless any other
practice has been established or turns out to have been established in this respect. 

  
 4 

	(3)	 The Managing Director shall be responsible for the supervision of the Company’s financial situation as
well as of supervising any possible insolvency of the Company. If the Managing Director becomes aware of a possible insolvency of the Company, he undertakes to notify and consult immediately with the shareholder meeting and, if he deems appropriate,
to convoke a formal meeting of the shareholders. This § 6(3) shall not be deemed to grant the Managing Director authority to convoke a formal meeting of the shareholders other than as required under applicable law for purposes of supervising
any possible insolvency of the Company. 

 § 7 

Inspection of the Books 
 The Managing
Director shall permit the shareholder meeting or their representatives access to the books of the Company at any time. 
 § 8

 Confidentiality; Non-compete; Inventions/Intellectual Property Rights 

The Managing Director has entered into an Employee Confidentiality Agreement, attached hereto as Appendix § 8. 

§ 9 
 Remuneration

  

	(1)	 The Managing Director shall receive a gross salary of EUR 89,600.00 per annum, payable in twelve equal
installments, one at the end of each calendar month. 

  

	(2)	 The above-mentioned total remuneration includes compensation for all overtime work and public holidays,

  

	(3)	 The Managing Director shall be eligible to receive commission under the Company’s standard sales
commission plan, which may be modified by the Company at any time in Company’s sole discretion. For the period October 1, 2002 to December 31, 2002, the Managing Director shall receive commission calculated as follows:

  

	 	(a)	 The Managing Director shall receive a commission (“New Sales Commission”) on new sales (“New
Sales”) generated by Managing Director in the “European Territory” (as defined in Appendix § 9(3)(a)), according to a target sales amount (“Target Amount”) for certain products. For the period
October 1, 2002 to December 31, 2002, the Target Amount shall be US$672,000. The Managing 

  
 5 

 
Director shall receive New Sales Commission of (a) for New Sales up to the first 80% of the Target Amount, 7%; (b) for New Sales greater than 80% but not greater than 100% of the Target
Amount, 9%; and (c) for New Sales greater than 100% of the Target Amount, 12%. Notwithstanding the foregoing, the Managing Director shall not receive commission for any revenue on which commissions are payable by Schrödinger, Inc.
(“Schrodinger”) to anterio consult & research GmbH (“anterio”) pursuant to the Letter Agreement dated July 1, 2001 (as amended, the “Schrödinger-anterio Agreement”) between Schrodinger and anterio
regarding “European Sales.” For the sole purpose of determining which commission rate (7%, 9%, or 12%) is applicable for the calculation of commissions to be paid to the Managing Director for New Sales generated by the Managing Director in
the European Territory between October 1, 2002 and December 31, 2002, the Company will attribute to Managing Director any New Sales generated by anterio during calendar year 2002 and credited to anterio under the Schrödinger-anterio
Agreement. 
  

	(b)	 The Managing Director shall receive a commission (“Maintenance and Recurring Revenues Commission”) of
3% on maintenance and recurring revenues (“Maintenance and Recurring Revenues”) generated by Managing Director in the European Territory. 

  

	(c)	 The Managing Director shall receive a commission (“Services Commission”) of 3% on services revenue
(“Services Revenue”) generated by the Managing Director in the European Territory, provided that Services Commission shall be payable solely for Services Revenue up to US$300,000. 

 

	(d)	 If the sum of all revenues generated by anterio and all revenues generated by the Managing Director during
calendar year 2002 exceeds US$950,000 (where “all revenues” includes New Sales, Maintenance and Recurring Revenues, and Services Revenues), the Managing Director shall be entitled to receive a
year-end bonus of US$5,000. 

  
 6 

	(4)	 The Managing Director, in addition, is entitled to 20,000 (twenty thousand) option rights for common stock
under the “Schrödinger Stock Incentive Plan,” vesting 25% on each of the first 4 anniversaries of the date of this Agreement, granted at an exercise price of fair market value as of the grant date. 

 

	(5)	 The Company shall pay the cost of premiums for life insurance coverage up to a maximum, of (a) for death,
a one-time aggregate payment of EURO3890.70 to the Managing Director’s beneficiary or beneficiaries, (b) for occupational invalidity, EURO1459/month, and (c) a
one-time payment of EUR126,548 upon Managing Director reaching the age of 60 years plus one day. 

  

	(6)	 The Company shall pay the cost, up to a maximum of EUR1000 per year, of preparation of Managing Director’s
income tax filings. 

 § 10 

Remuneration in Case of Illness 
 In case
of a temporary incapacity to work caused by illness or other reasons which axe beyond the control of the Managing Director, the Managing Director shall continue to receive remuneration pursuant to § 11 (1) for the duration of his incapacity for
a continuous period of three months. 
 § 11 

Holidays 
 The Managing Director shall have
an annual holiday entitlement of 30 working days, excluding weekends. The Managing Director shall agree upon the precise time of his holidays with the shareholder meeting. 

§ 12 
 Expenses

 The reimbursement of expenses shall be made according to the relevant Company regulations. 

§ 13 
 Final
Provisions 
  

	(1)	 Amendments or modifications to this Agreement are not valid unless made in writing. There are no oral
agreements supplementing this contract. 

  
 7 

	(2)	 Should any provision of this Agreement be or become invalid in whole or in part, the validity of the remaining
provisions of this Agreement shall not be affected hereby, provided that the remaining provisions do not contravene the principles of good faith. Should any provisions of this Agreement prove invalid, the parties shall be bound to agree to replace
the invalid provision by means of interpretation or of amendment of this Agreement by a provision pursuing the same or as close as possible an economic and legal purpose as the invalid provision. 

 

	(3)	 This Agreement shall be governed by, interpreted, and enforced in accordance with the laws of the Federal
Republic of Germany (without giving effect to conflict of law principles). The non-exclusive place of performance under this Agreement shall be the Company’s statutory seat. 

 

											
	Place: Köln	 		 	Date: 1. October 2002	  	
				
	Company	 		 	Managing Director	  	
				
	By: Schrödinger, Inc., Its Sole Shareholder	 		 		  	
				
	 /s/ Jennifer Mayer
	 		 	 /s/ Jörg Weiser
	  	
	Jennifer Mayer	 		 	Dr. Jörg Weiser	  	
	Vice President, Strategic Growth	 		 		  	

  
 8 

 Appendix § 2 to the Managing Director Agreement 

The Managing Director requires the consent of the shareholder meeting, in the form of a prior written, approval, for any decisions, acts, and/or declarations
in a widest sense that the shareholder meeting may reasonably consider to fall outside the scope of the Company’s ordinary business, including but not limited to: 
  

	1.	 the sale of the Company in whole or in part, any substantial change of the Company’s business, as well as
any change to the Company’s fundamental standard contracts and/or terms and conditions; 

  

	2.	 the entering and/or amending of enterprise contracts (“Unternehmensvertäge”), notably but
without limitation, contracts with any customer, profit and loss agreements, tax integration contracts as well as settlements of disputes with tax authorities, and other such contracts which entail restrictions of substantial business functions;

  

	3.	 the acquisition and disposal of equity in other enterprises, as well as the issuance of any equity to third
parties; 

  

	4.	 the commencement of building construction, acquisition of land, or other fixed assets if the cost of such
measures exceed EUR10,000 in each instance or series of related instances; 

  

	5.	 the promising or granting of any pension entitlements; 

 

	6.	 the entering and/or extension and/or amendment to any rental or lease contracts with obligations of more than
EUR10,000 yearly or with a term of more than 1 year; 

  

	7.	 prepayment to suppliers and any other creditors in an amount exceeding EUR 10,000 in each instance;

  

	8.	 any granting of credit except for ordinary trade credits to customers on the basis of the Company’s
standard terms and conditions or any other ordinary terms of payment; 

  

	9.	 the taking of any loans or granting or allowing to exist any security interest, lien, claim, or encumbrance on
assets of the Company; 

  
 9 

	10.	 the assumption of any guarantees and/or joint liabilities; 

 

	11.	 the appointment of authorized signatories (“Prokurist”); 

 

	12.	 the entering into, modification, and/or termination of any employment contracts; 

 

	13.	 the granting of profit shares, stock options, or similar payments to an employee; 

 

	14.	 the entering into any license agreements with regard to the products of the Company or the Company’s
affiliates; 

  

	15.	 the choosing, retaining, and/or dismissing of the Company’s attorneys, accountants, auditors, financial
advisors, and/or other advisors; 

  

	16.	 the initiating or settling of any litigation when the amount in controversy exceeds EUR 500 in the individual
case; 

  

	17.	 Payments (other than those enumerated elsewhere in this Appendix § 2) of more than
EUR 500 with the exception of payments to the parent company; 

  

	18.	 Activities outside of the ordinary activities of the Company consistent with past practice;

  

	19.	 Incurring any liability or other obligation (other than those enumerated elsewhere in this Appendix
§ 2) by or on behalf of the Company or any affiliate in excess of EUR10,000 in any one instance or series of related instances; 

  

	20.	 Entering into any agreement or other arrangement by or on behalf of the Company with the Managing Director, any
family member of the Managing Director or any of their respective affiliates; 

  

	21.	 Adoption of the Company’s budget or business plan; and/or 

 

	22.	 Making of any regulatory filings. 

  
 10 

 Appendix § 8 to the Managing Director Agreement 

Employee Confidentiality Agreement 

  
 11 

 Appendix § 9(3)(a) to the Managing Director Agreement 

“European Territory” shall mean commercial and government accounts in Albania, Andorra, Austria, Belarus, Belgium,
Bosnia-Herzegovina, Bulgaria, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Hungary, Iceland, Ireland, Latvia, Liechtenstein, Lithuania, Luxembourg, Macedonia, Malta,
Moldova, Monaco, Netherlands, Norway, Poland, Portugal, Romania, Russia, Serbia/Montenegro, Slovakia, Slovenia, Spain, Sweden, Switzerland, Ukraine, United Kingdom, and India. 

  
 12

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