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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, DC 20549
________________________________________
FORM 10-Q
________________________________________
(Mark One)
xQUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the quarterly period ended September 30, 2023
OR
oTRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the transition period from          to
Commission File Number: 001-39206
________________________________________
Schrodinger, Inc.
(Exact Name of Registrant as Specified in its Charter)
________________________________________
Delaware95-4284541
(State or other jurisdiction of
incorporation or organization)
(I.R.S. Employer
Identification No.)
1540 Broadway, 24th Floor
New York, NY
10036
(Address of principal executive offices)(Zip Code)
Registrant’s telephone number, including area code: (212) 295-5800
________________________________________
Securities registered pursuant to Section 12(b) of the Act:
Title of each classTrading
Symbol(s)
Name of each exchange on which registered
Common stock, par value $0.01 per shareSDGR
The Nasdaq Stock Market LLC
Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes x No o
Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes x No o
Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.
Large accelerated filer
x
Accelerated filero
Non-accelerated fileroSmaller reporting companyo
Emerging growth companyo
If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. o
Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes o No x
As of October 25, 2023, the registrant had 62,868,572 shares of common stock, $0.01 par value per share, and 9,164,193 shares of limited common stock, $0.01 par value per share, outstanding.



Table of Contents
Page
Condensed Consolidated Statements of Comprehensive (Loss) Income for the three and nine months ended September 30, 2023 and 2022 (Unaudited)


CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS
This Quarterly Report on Form 10-Q, or this Quarterly Report, contains forward-looking statements within the meaning of the U.S. Private Securities Litigation Reform Act and Section 21E of the Securities Exchange Act of 1934, as amended, that involve substantial risks and uncertainties. All statements, other than statements of historical fact, contained in this Quarterly Report, including statements regarding our strategy, future operations, future financial position, future revenue, projected costs, prospects, plans and objectives of management, are forward-looking statements. The words “aim,” “anticipate,” “believe,” “contemplate,” “continue,” “could,” “estimate,” “expect,” “goal,” “intend,” “may,” “might,” “plan,” “potential,” “predict,” “project,” “should,” “target,” “will,” “would” or the negative of these words or other similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words.
The forward-looking statements in this Quarterly Report include, among other things, statements about:
the potential advantages of our physics-based computational platform;
our strategic plans to accelerate the growth of our software business;
our research and development efforts for our proprietary drug discovery programs and our computational platform;
the initiation, timing, progress, and results of drug discovery programs, preclinical studies and clinical trials of ours and those of our collaborators;
our plans to submit investigational new drug applications to the U.S. Food and Drug Administration for our proprietary drug discovery programs;
our plans to discover and develop product candidates and to maximize their commercial potential by advancing such product candidates ourselves or in collaboration with others;
our plans to leverage the synergies between our businesses;
the timing of, the ability to submit applications for, and the ability to obtain and maintain regulatory approvals for any product candidates we or one of our collaborators may develop;
our drug discovery collaborations and our estimates or expectations regarding any milestone or other payments we may receive from such collaborations, including pursuant to our collaboration with Bristol-Myers Squibb Company;
our expectations regarding our ability to fund our operating expenses and capital expenditure requirements with our cash, cash equivalents, and marketable securities;
the potential advantages of our drug discovery programs;
the rate and degree of market acceptance of our software solutions;
the potential impact of public health epidemics or pandemics, including the COVID-19 pandemic;
the potential impact of general economic conditions, including inflation and interest rates;
the rate and degree of market acceptance and clinical utility of our products;
our estimates regarding the potential market opportunity for our software solutions and any product candidate we or any of our collaborators may develop;
our marketing capabilities and strategy;
our intellectual property position;
our ability to identify technologies with significant commercial potential that are consistent with our commercial objectives;
our expectations related to the use of our cash, cash equivalents, and marketable securities;
our expectations related to the key drivers of our performance;
the impact of government laws and regulations;
our competitive position and expectations regarding developments and projections relating to our competitors and any competing products, technologies, or therapies that are or become available;
2

our ability to maintain and establish collaborations or obtain additional funding; and
our reliance on key personnel and our ability to identify, recruit, and retain skilled personnel.
We may not actually achieve the plans, intentions, or expectations disclosed in our forward-looking statements, and you should not place undue reliance on our forward-looking statements. Actual results or events could differ materially from the plans, intentions, and expectations disclosed in the forward-looking statements we make. We have included important factors in the cautionary statements included in this Quarterly Report, particularly in “Risk Factor Summary” below and Part II, Item 1A. “Risk Factors”, that we believe could cause actual results or events to differ materially from the forward-looking statements that we make. Moreover, we operate in a competitive and rapidly changing environment. New risks and uncertainties emerge from time to time, and it is not possible for us to predict all risks and uncertainties that could have an impact on the forward-looking statements contained in this Quarterly Report. Our forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, collaborations, joint ventures, or investments we may make or enter into.
You should read this Quarterly Report and the documents that we file with the Securities and Exchange Commission, or the SEC, with the understanding that our actual future results may be materially different from what we expect. The forward-looking statements contained in this Quarterly Report are made as of the date of this Quarterly Report, and we do not assume any obligation to update any forward-looking statements, whether as a result of new information, future events or otherwise, except as required by applicable law.
In addition, statements that “we believe” and similar statements reflect our beliefs and opinions on the relevant subject. These statements are based upon information available to us as of the date of this Quarterly Report, and while we believe such information forms a reasonable basis for such statements, such information may be limited or incomplete. Our statements should not be read to indicate that we have conducted an exhaustive inquiry into, or review of, all potentially available relevant information. These statements are inherently uncertain and investors are cautioned not to unduly rely upon these statements.
Unless the context otherwise requires, we use the terms “company,” “we,” “us,” and “our” in this Quarterly Report to refer to Schrödinger, Inc. and its consolidated subsidiaries.
3

RISK FACTOR SUMMARY
Our business is subject to a number of risks of which you should be aware before making an investment decision. Below we summarize what we believe are the principal risk factors but these risks are not the only ones we face, and you should carefully review and consider the full discussion of our risk factors in the section titled “Risk Factors”, together with the other information in this Quarterly Report.
We have a history of significant operating losses, and we expect to incur losses over the next several years.
If we are unable to increase sales of our software, increase revenue from our drug discovery collaborations, or if we and our current and future collaborators are unable to successfully develop and commercialize drug products, our revenues may be insufficient for us to achieve or maintain profitability.
Our quarterly and annual results may fluctuate significantly, which could adversely impact the value of our common stock.
If our existing customers do not renew their licenses, do not buy additional solutions from us, or renew at lower prices, our business and operating results will suffer.
A significant portion of our revenues are generated by sales to life sciences industry customers, and factors that adversely affect this industry could adversely affect our software sales.
The markets in which we participate are highly competitive, and if we do not compete effectively, our business and operating results could be adversely affected.
We may never realize a return on our investment of resources and cash in our drug discovery collaborations.
Although we believe that our computational platform has the potential to identify more promising molecules than traditional methods and to accelerate drug discovery, our focus on using our platform technology to discover and design molecules with therapeutic potential may not result in the discovery and development of commercially viable products for us or our collaborators.
We may not be successful in our efforts to identify, discover or develop product candidates and may fail to capitalize on programs, collaborations, or product candidates that may present a greater commercial opportunity or for which there is a greater likelihood of success.
As a company, we have very limited experience in clinical development and have not yet demonstrated our ability to complete any clinical trials.
Conducting successful clinical trials requires the enrollment of a sufficient number of patients, and suitable patients may be difficult to identify and recruit.
We rely on, and plan to continue to rely on, third parties to conduct our clinical trials, and those third parties may not perform satisfactorily, including failing to meet deadlines for the completion of such trials, which may prevent or delay our ability to seek or obtain marketing approval for or commercialize our product candidates or otherwise harm our business.
The outcome of preclinical studies and early clinical trials may not be predictive of the success of later clinical trials, and the results of our clinical trials may not satisfy the requirements of the FDA or other comparable foreign regulatory authorities.
If we fail to comply with our obligations under our existing license agreements with Columbia University, under any of our other intellectual property licenses, or under any future intellectual property licenses, or otherwise experience disruptions to our business relationships with our current or any future licensors, we could lose intellectual property rights that are important to our business.
If we are unable to obtain, maintain, enforce, and protect patent protection for our technology and product candidates or if the scope of the patent protection obtained is not sufficiently broad, our competitors could develop and commercialize technology and products similar or identical to ours, and our ability to successfully develop and commercialize our technology and product candidates may be adversely affected.
4

Our internal information technology systems, or those of our third-party vendors, contractors, or consultants, may fail or suffer security breaches, loss or leakage of data, and other disruptions, which could result in a material disruption of our services, compromise sensitive information related to our business, or prevent us from accessing critical information, potentially exposing us to liability or otherwise adversely affecting our business.
Our future success depends on our ability to retain key executives and to attract, retain, and motivate qualified personnel.
We are pursuing multiple business strategies and expect to expand our development and regulatory capabilities, and as a result, we may encounter difficulties in managing our multiple business units and our growth, which could disrupt our operations.
Our executive officers, directors, and principal stockholders, if they choose to act together, have the ability to influence all matters submitted to stockholders for approval.
Our actual operating results may differ significantly from our guidance.
We identified a material weakness in our internal control over our financial reporting. If we are unable to remediate this material weakness, we may not be able to accurately or timely report our financial condition or results of operations, and we may conclude that our internal control over financial reporting is not effective, which could adversely impact our investors’ confidence and our stock price.
5

PART I—FINANCIAL INFORMATION
Item 1. Financial Statements.
SCHRÖDINGER, INC. AND SUBSIDIARIES
Condensed Consolidated Balance Sheets (Unaudited)
(in thousands, except for share and per share amounts)
AssetsSeptember 30, 2023December 31, 2022
Current assets:
Cash and cash equivalents$249,378 $90,474 
Restricted cash6,230 5,243 
Marketable securities246,905 360,613 
Accounts receivable, net of allowance for doubtful accounts of $150 and $125
19,884 55,953 
Unbilled and other receivables, net for allowance for unbilled receivables of $100 and $100
12,253 13,137 
Prepaid expenses13,111 8,569 
Total current assets547,761 533,989 
Property and equipment, net22,498 14,244 
Equity investments91,863 25,683 
Goodwill4,791 4,791 
Intangible assets, net 587 
Right of use assets - operating leases119,822 105,982 
Other assets7,413 3,311 
Total assets$794,148 $688,587 
Liabilities and Stockholders' Equity:
Current liabilities:
Accounts payable$10,318 $9,470 
Income taxes payable1,084 355 
Accrued payroll, taxes, and benefits25,508 24,882 
Deferred revenue43,313 57,931 
Lease liabilities - operating leases16,279 11,006 
Other accrued liabilities8,536 5,166 
Total current liabilities105,038 108,810 
Deferred revenue, long-term12,102 25,598 
Lease liabilities - operating leases, long-term112,720 105,485 
Other liabilities, long-term707 800 
Total liabilities230,567 240,693 
Commitments and contingencies (Note 5)
Stockholders' equity:
Preferred stock, $0.01 par value. Authorized 10,000,000 shares; zero shares issued and outstanding at September 30, 2023 and December 31, 2022, respectively
  
Common stock, $0.01 par value. Authorized 500,000,000 shares; 62,823,295 and 62,163,739 shares issued and outstanding at September 30, 2023 and December 31, 2022, respectively
628 622 
Limited common stock, $0.01 par value. Authorized 100,000,000 shares; 9,164,193 shares issued and outstanding at September 30, 2023 and December 31, 2022, respectively
92 92 
Additional paid-in capital871,100 828,700 
Accumulated deficit(307,748)(379,138)
Accumulated other comprehensive loss(491)(2,382)
Total stockholders' equity563,581 447,894 
Total liabilities and stockholders' equity$794,148 $688,587 
See accompanying notes to unaudited condensed consolidated financial statements.
6

SCHRÖDINGER, INC. AND SUBSIDIARIES
Condensed Consolidated Statements of Operations (Unaudited)
(in thousands, except for share and per share amounts)
Three Months Ended September 30,Nine Months Ended September 30,
2023202220232022
Revenues:
Software products and services$28,904 $24,667 $90,469 $87,759 
Drug discovery13,665 12,313 52,071 36,353 
Total revenues42,569 36,980 142,540 124,112 
Cost of revenues:
Software products and services7,034 6,866 20,844 21,478 
Drug discovery11,896 12,913 38,554 40,316 
Total cost of revenues18,930 19,779 59,398 61,794 
Gross profit23,639 17,201 83,142 62,318 
Operating expenses:
Research and development46,833 32,885 130,279 91,830 
Sales and marketing9,109 7,161 27,276 21,260 
General and administrative23,890 23,318 73,414 67,507 
Total operating expenses79,832 63,364 230,969 180,597 
Loss from operations(56,193)(46,163)(147,827)(118,279)
Other (expense) income
(Loss) gain on equity investments (3)147,322 11,825 
Change in fair value(14,522)5,273 61,869 (16,591)
Other income5,804 1,234 13,067 1,265 
Total other (expense) income(8,718)6,504 222,258 (3,501)
(Loss) income before income taxes(64,911)(39,659)74,431 (121,780)
Income tax (benefit) expense(2,887)194 3,041 199 
Net (loss) income$(62,024)$(39,853)$71,390 $(121,979)
Net (loss) income per share of common and limited common stockholders, basic:$(0.86)$(0.56)$1.00 $(1.71)
Weighted average shares used to compute net (loss) income per share of common and limited common stockholders, basic:71,924,45171,207,99271,679,76571,140,682
Net (loss) income per share of common and limited common stockholders, diluted:$(0.86)$(0.56)$0.95 $(1.71)
Weighted average shares used to compute net (loss) income per share of common and limited common stockholders, diluted:71,924,45171,207,99274,966,79171,140,682
See accompanying notes to unaudited condensed consolidated financial statements.
7

SCHRÖDINGER, INC. AND SUBSIDIARIES
Condensed Consolidated Statements of Comprehensive (Loss) Income (Unaudited)
(in thousands)
Three Months Ended September 30,Nine Months Ended September 30,
2023202220232022
Net (loss) income$(62,024)$(39,853)$71,390 $(121,979)
Changes in market value of investments, net of tax:
Unrealized gain (loss) on marketable securities192 (283)1,891 (3,035)
Comprehensive (loss) income$(61,832)$(40,136)$73,281 $(125,014)
See accompanying notes to unaudited condensed consolidated financial statements.
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SCHRÖDINGER, INC. AND SUBSIDIARIES
Condensed Consolidated Statements of Stockholders’ Equity (Unaudited)
(in thousands, except for share amounts)
Common stockLimited common
stock
Additional
paid-in
capital
Accumulated
deficit
Accumulated other comprehensive (loss) gainTotal stockholders’
equity
SharesAmountSharesAmount
Balance at December 31, 202262,163,739 $622 9,164,193 $92 $828,700 $(379,138)$(2,382)$447,894 
Change in unrealized gain on marketable securities— — — — — — 1,483 1,483 
Issuances of common stock upon stock option exercises186,201 1 — — 866 — — 867 
Issuance of common stock upon vesting of restricted stock units12,075 — — — — — — — 
Stock-based compensation— — — — 10,880 — — 10,880 
Net income— — — — — 129,136 — 129,136 
Balance at March 31, 202362,362,015 623 9,164,193 92 840,446 (250,002)(899)590,260 
Change in unrealized gain on marketable securities216 216 
Issuances of common stock upon stock option exercises340,2294 — 4,694 — — 4,698 
Stock-based compensation— — 11,773 — — 11,773 
Net income— — — 4,278 4,278 
Balance at June 30, 202362,702,244 627 9,164,193 92 856,913 (245,724)(683)611,225 
Change in unrealized gain on marketable securities— — — — — — 192 192 
Issuances of common stock upon stock option exercise119,885 1 — — 1,533 — — 1,534 
Issuance of common stock upon vesting of restricted stock units1,166 — — — — — — — 
Stock-based compensation— — — — 12,654 — — 12,654 
Net loss— — — — — (62,024)— (62,024)
Balance at September 30, 202362,823,295 $628 9,164,193 $92 $871,100 $(307,748)$(491)$563,581 
       
Balance at December 31, 202161,834,515 $618 9,164,193 $92 $786,964 $(229,952)$(651)$557,071 
Change in unrealized loss on marketable securities— — — — — — (2,006)(2,006)
Issuances of common stock upon stock option exercises137,885 2 — — 906 — — 908 
Stock-based compensation— — — — 9,134 — — 9,134 
Net loss— — — — — (34,440)— (34,440)
Balance at March 31, 202261,972,400 620 9,164,193 92 797,004 (264,392)(2,657)530,667 
Change in unrealized loss on marketable securities— — — — — — (746)(746)
Issuances of common stock upon stock option exercises54,661 — — — 396 — — 396 
Stock-based compensation— — — — 10,427 — — 10,427 
Net loss— — — — — (47,686)— (47,686)
Balance at June 30, 202262,027,061 620 9,164,193 92 807,827 (312,078)(3,403)493,058 
Change in unrealized loss on marketable securities— — — — — — (283)(283)
Issuances of common stock upon stock option exercise40,707 — — — 324 — — 324 
Stock-based compensation— — — — 9,864 — — 9,864 
Net loss— — — — — (39,853)— (39,853)
Balance at September 30, 202262,067,768 $620 9,164,193 $92 $818,015 $(351,931)$(3,686)$463,110 
See accompanying notes to unaudited condensed consolidated financial statements.
9

SCHRÖDINGER, INC. AND SUBSIDIARIES
Condensed Consolidated Statements of Cash Flows (Unaudited)
(in thousands)
Nine Months Ended September 30,
20232022
Cash flows from operating activities:
Net income (loss) $71,390 $(121,979)
Adjustments to reconcile net income (loss) to net cash used in operating activities:
Gain on equity investments(147,322)(11,825)
Fair value adjustments(61,869)16,591 
Depreciation and amortization4,198 3,202 
Stock-based compensation35,307 29,425 
Noncash investment (accretion) amortization(4,962)2,102 
Loss on disposal of property and equipment140 14 
Decrease (increase) in assets, net of acquisition:
Accounts receivable, net36,069 8,673 
Unbilled and other receivables884 (3,272)
Reduction in the carrying amount of right of use assets - operating leases5,722 4,812 
Prepaid expenses and other assets(13,048)(6,837)
Increase (decrease) in liabilities, net of acquisition:
Accounts payable742 1,959 
Income taxes payable729 638 
Accrued payroll, taxes, and benefits626 499 
Deferred revenue(28,114)(19,535)
Lease liabilities - operating leases(2,577)920 
Other accrued liabilities2,607 (128)
Net cash used in operating activities(99,478)(94,741)
Cash flows from investing activities:
Purchases of property and equipment(10,924)(6,668)
Purchases of equity investments(4,125)(600)
Distribution from equity investment147,136 11,825 
Acquisition, net of acquired cash (6,427)
Purchases of marketable securities(224,513)(203,375)
Proceeds from maturity of marketable securities345,074 283,711 
Net cash provided by investing activities252,648 78,466 
Cash flows from financing activities:
Issuances of common stock upon stock option exercises7,099 1,628 
Principal payments on finance leases(5) 
Payment of offering costs(373) 
Net cash provided by financing activities6,721 1,628 
Net increase (decrease) in cash and cash equivalents and restricted cash159,891 (14,647)
Cash and cash equivalents and restricted cash, beginning of period95,717 123,267 
Cash and cash equivalents and restricted cash, end of period$255,608 $108,620 
Supplemental disclosure of cash flow and noncash information
Cash paid for income taxes$2,194 $462 
Supplemental disclosure of non-cash investing and financing activities
Purchases of property and equipment in accounts payable274 198 
Purchases of property and equipment in accrued liabilities685 109 
Acquisition of right of use assets - operating leases, contingency resolution514 1,513 
Acquisition of right of use assets - operating leases in exchange for lease liabilities - operating leases15,085 14,767 
Acquisition of right of use assets in exchange for lease liabilities - finance leases279  
See accompanying notes to unaudited condensed consolidated financial statements.
10

SCHRÖDINGER, INC. AND SUBSIDIARIES
Notes to Condensed Consolidated Financial Statements (Unaudited)
For the three and nine months ended September 30, 2023 and 2022
(in thousands, except for share and per share amounts and note 3(c))
(1)    Description of Business
Schrödinger, Inc. (the “Company”) has developed a differentiated, physics-based computational platform that enables discovery of high-quality, novel molecules for drug development and materials applications more rapidly and at a lower cost, compared to traditional methods. The Company's software platform is licensed by biopharmaceutical and industrial companies, academic institutions, and government laboratories around the world. The Company also applies its computational platform to a broad pipeline of drug discovery and development programs in collaboration with biopharmaceutical companies. In addition, the Company uses its platform to advance a pipeline of partnered and wholly-owned drug discovery programs, which the Company refers to as its proprietary drug discovery programs.
(2)    Significant Accounting Policies
(a)    Basis of Presentation and Use of Estimates
The accompanying unaudited condensed consolidated financial statements and the related interim disclosures have been prepared in accordance with U.S. generally accepted accounting principles (“U.S. GAAP”) and pursuant to the rules and regulations of the Securities and Exchange Commission (“SEC”) for the interim financial information. These unaudited condensed consolidated financial statements include all adjustments necessary, consisting of only normal recurring adjustments, to fairly state the financial position and the results of the Company’s operations and cash flows for interim periods in accordance with U.S. GAAP. Certain information and footnote disclosures normally included in financial statements prepared in accordance with U.S. GAAP have been condensed or omitted as permitted by the SEC’s rules and regulations for interim reporting. Interim period results are not necessarily indicative of results of operations or cash flows for a full year or any subsequent interim period. The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2022, which was filed with the SEC on February 28, 2023.
The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent assets and liabilities at the date of the consolidated financial statements, and the reported amounts of revenues and expenses during the reporting period. Significant estimates include the assumptions used in the allocation of revenue and estimates regarding the progress of completing performance obligations under collaboration agreements. Actual results could differ from those estimates, and such differences may be material to the unaudited condensed consolidated financial statements.
(b)    Principles of Consolidation
The Company’s unaudited condensed consolidated financial statements include the accounts of Schrödinger, Inc., its wholly owned subsidiaries, and its variable interest entity. All intercompany balances and transactions have been eliminated in consolidation. The functional currency for foreign entities is the United States dollar. The Company accounts for investments over which it has significant influence, but not a controlling financial interest, using the equity method.
(c)    Restricted Cash
Restricted cash consists of letters of credit held with the Company’s financial institution related to facility leases and is classified as current in the Company’s balance sheets based on the maturity of the underlying letters of credit. Additionally, funds received from certain grants are restricted as to their use and are therefore classified as restricted cash.
(d)    Concentrations
Financial instruments that potentially subject the Company to concentrations of credit risk consist primarily of trade receivables and contract assets, which represent contracted unbilled receivables.
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The Company does not require customers to provide collateral to support accounts receivable. If deemed necessary, credit reviews of significant new customers may be performed prior to extending credit. The determination of a customer’s ability to pay requires judgment, and failure to collect from a customer can adversely affect revenue, cash flows, and results of operations.
As of September 30, 2023, three customers accounted for more than 10% of total accounts receivable. As of December 31, 2022, one customer accounted for 26% of total accounts receivable. As of September 30, 2023, two customers accounted for 32% and 23% of total contract assets, respectively. As of December 31, 2022, two customers accounted for 23% and 17% of total contract assets, respectively. For the three months ended September 30, 2023, one customer accounted for 28% of total revenue. For the nine months ended September 30, 2023, one customer accounted for 29% of total revenue. For the three months ended September 30, 2022, one customer accounted for 28% of total revenue. For the nine months ended September 30, 2022, one customer accounted for 17% of total revenue.
(e)    Income Taxes
The Company records deferred tax assets and liabilities for the expected future tax consequences of temporary differences between the financial statement carrying amounts and the tax basis of the assets and liabilities. Deferred tax assets are reduced by a valuation allowance when it is estimated to become more likely than not that a portion of the deferred tax assets will not be realized. Accordingly, the Company currently maintains a full valuation allowance against existing net deferred tax assets.
The Company recognizes the effect of income tax positions only if such positions are deemed “more likely than not” capable of being sustained. Interest and penalties accrued on unrecognized tax benefits are included within income tax expense in the unaudited condensed consolidated financial statements.
(f)    Equity Investments
In the normal course of business, the Company has entered, and may continue to enter, into collaboration agreements with companies to perform drug design services for such companies in exchange for equity ownership stakes in such companies. If it is determined that the Company has control over the investee, the investee is consolidated in the financial statements. If the investee is consolidated with the Company and less than 100% of the equity is owned by the Company, the Company will present non-controlling interest to represent the portion of the investee owned by other investors. If it is determined that the Company does not have control over the investee, the Company evaluates the investment for the ability to exercise significant influence.
Equity investments over which the Company has significant influence may be accounted for under equity method accounting in accordance with Accounting Standards Codification ("ASC") Topic 323, Equity Method and Joint Ventures. If it is determined that the Company does not have significant influence over the investee, and there is no readily determinable fair value for the investment, the equity investment may be accounted for at cost less impairment, in accordance with ASC Topic 321, Equity Securities.
For further information regarding the Company’s equity investments, see Note 4, Fair Value Measurements and Note 10, Equity Investments.
(g)    Net (Loss) Income per Share Attributable to Common and Limited Common Stockholders
The outstanding equity of the Company consists of common stock and limited common stock. Under the Company’s certificate of incorporation, the rights of the holders of common stock and limited common stock are identical, except with respect to voting and conversion. Holders of limited common stock are precluded from voting such shares in any election of directors or on the removal of directors. Limited common stock may be converted into common stock at any time at the option of the stockholder.
Undistributed earnings allocated to the participating securities are subtracted from net income in determining net income (loss) attributable to common and limited common stockholders. Basic net income (loss) per share is computed by dividing net income (loss) attributable to common and limited common stockholders by the weighted-average number of shares of common and limited common stock outstanding during the period.
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For the calculation of diluted net income, net income attributable to common and limited common stockholders for basic net income is adjusted by the effect of dilutive securities, including awards under the Company’s equity compensation plans. Diluted net income per share attributable to common and limited common stockholders is computed by dividing the resulting net income attributable to common and limited common stockholders by the weighted-average number of fully diluted shares of common and limited common stock outstanding.
(3)    Revenue Recognition
Revenue is recognized upon transfer of control of promised products or services to customers in an amount that reflects the consideration to which the Company expects to be entitled in exchange for promised goods or services. The Company’s performance obligations are satisfied either over time or at a point in time, which can result in different revenue recognition patterns.
The following table illustrates the timing of the Company’s revenue recognition patterns:
Three Months Ended September 30,Nine Months Ended September 30,
2023202220232022
Software products and services – point in time37.0 %34.1 %36.8 %41.9 %
Software products and services – over time30.9 32.6 26.6 28.8 
Drug Discovery – point in time 2.7 19.1 9.4 
Drug Discovery – over time32.1 30.6 17.5 19.9 
(a)Software Products and Services
The Company enters into contracts that can include various combinations of licenses, products and services, some of which are distinct and are accounted for as separate performance obligations. For contracts with multiple performance obligations, the Company allocates the transaction price of the contract to each performance obligation on a relative standalone selling price (“SSP”) basis. Revenue is recognized net of any sale and value-added taxes collected from customers and subsequently remitted to governmental authorities.
The Company’s software business derives revenue from five sources: (i) on-premise software license fees, (ii) hosted software subscription fees, (iii) software maintenance fees, (iv) professional services fees, and (v) contributions.
On-premise software. The Company’s on-premise software license arrangements grant customers the right to use its software on their own in-house servers or their own cloud instances for a specified term, typically for one year. The Company recognizes revenue for on-premise software license fees upfront, either upon delivery of the license or the effective date of the agreement, whichever is later. In instances where the timing of delivery differs from the timing of invoicing, the Company considers whether a significant financing component exists. The Company has elected the practical expedient to not assess for significant financing where the term is less than one year. The Company’s updates and upgrades are not integral to maintaining the utility of the software licenses. Payments typically are received upfront or annually.
Hosted software. Hosted software revenue consists primarily of fees to provide the Company’s customers with hosted licenses, which allows these customers to access the Company’s cloud-based software solution on their own hardware without taking control of licenses. Hosted software revenue is recognized ratably over the term of the arrangement.
Software maintenance. Software maintenance includes technical support, updates, and upgrades related to our on-premise software licenses. Software maintenance revenue is considered to be a separate performance obligation and is recognized ratably over the term of the arrangement.
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Professional services. Professional services include training, technical setup, installation or assisting customers with modeling and structural biology services, where the Company uses its software to perform tasks such as virtual screening and homology modeling on behalf of the Company’s customers. These services are generally not related to the core functionality of the Company’s software and are recognized as revenue when resources are consumed. The Company has historically estimated project status with relative accuracy, although a number of internal and external factors can affect such estimates, including labor rates, utilization and efficiency variances. Payments for services are due in advance or upon consumption of resources.
Software contribution revenue. Software contribution revenue consists of funds received under a non-reciprocal agreement with Gates Ventures, LLC. The agreement is an unconditional non-exchange contribution without restrictions. Revenue was recognized upon execution of the agreement, on the first and second anniversary of the agreement, and upon extension of the agreement when invoiced in accordance with ASC Topic 958, Not-for-Profit Entities as the agreement was not an exchange transaction.
The agreement with Gates Ventures, LLC initially covered the period from June 23, 2020 through June 22, 2023 for total consideration of up to $3,000. The Company recognized revenue of $1,000 upon entry into the agreement and $1,000 upon each of the first and second anniversary of the agreement. During the three months ended September 30, 2023, the agreement was extended through August 13, 2026 and provides for total additional consideration of up to $6,000. The Company recognized revenue of $1,800 upon extension of the agreement. As of September 30, 2023, the Company had no deferred revenue balance related to this agreement. As of September 30, 2023, the Company had $1,800 of accounts receivable related to this agreement.
The following table presents the revenue recognized from the sources of software products and services revenue:
Three Months Ended September 30,Nine Months Ended September 30,
2023202220232022
On-premise software$13,806 $12,579 $50,564 $50,860 
Hosted software5,463 3,914 14,366 10,765 
Software maintenance5,752 5,063 17,378 14,741 
Professional services2,083 3,111 6,361 10,393 
Revenue from contracts with customers27,104 24,667 88,669 86,759 
Software contribution1,800  1,800 1,000 
Total software revenue$28,904 $24,667 $90,469 $87,759 
(b)Drug Discovery
Drug discovery services. Revenue from drug discovery and collaboration services contracts is recognized either over time or at a point in time, typically by using costs incurred, hours expended to measure progress, or based on the achievement of milestones. Payments for services are generally due upfront at the start of a contract, upon achieving milestones stated in a contract, or upon consumption of resources. Services may at times include variable consideration, and the Company has estimated the amount of consideration that is variable using the most likely amount method. The Company evaluates milestones on a case-by-case basis, including whether there are factors outside the Company’s control that could result in a significant reversal of revenue, and the likelihood and magnitude of a potential reversal. If achievement of a milestone is not considered probable, the Company constrains (reduces) variable consideration to exclude the milestone payment until it is probable to be achieved. Upon removal of the constraint on variable consideration, revenue may be recognized at a point in time by applying the allocation guidance of ASC Topic 606, Revenue from Contracts with Customers ("Topic 606").
As of September 30, 2023, there were no milestones not yet achieved that were determined to be probable of achievement, and no corresponding drug discovery milestone revenue was recognized for the nine months ended September 30, 2023. As of September 30, 2022, milestones not yet achieved that were determined to be probable of achievement totaled $2,000, of which $2,000 was recognized as drug discovery milestone revenue for the nine months ended September 30, 2022.
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Drug discovery contribution revenue. Drug discovery contribution revenue consists of funds received under an agreement with the Bill and Melinda Gates Foundation on a cost reimbursement basis, to perform services aimed at accelerating drug discovery in women’s health. The initial agreement began in November 2021 and expired in September 2023. In September 2023, the Company entered into a new agreement with the Bill and Melinda Gates Foundation to perform services aimed at accelerating drug discovery in women's health that expires in March 2025. Revenue is recognized as conditions are met in accordance with ASC Topic 958, Not-for-Profit Entities. As of September 30, 2023 and December 31, 2022, the Company had deferred revenue balances related to these agreements of $2,098 and $1,718, respectively.
The following table presents the revenue recognized from the sources of drug discovery revenue:
Three Months Ended September 30,Nine Months Ended September 30,
2023202220232022
Drug discovery services revenue from contracts with customers$12,730 $11,717 $49,765 $34,976 
Drug discovery contribution935 596 2,306 1,377 
Total drug discovery revenue$13,665 $12,313 $52,071 $36,353 
(c)Collaboration and License Agreement
On November 22, 2020, the Company entered into an exclusive, worldwide collaboration and license agreement with Bristol-Myers Squibb Company (“BMS”), pursuant to which the Company and BMS have agreed to collaborate in the discovery, research and preclinical development of new small molecule compounds for disease indications in oncology, neurology, and immunology therapeutics areas. Under the agreement, the Company was initially responsible, at its own cost and expense, for the discovery of small molecule compounds directed to five specified biological targets pursuant to a mutually agreed research plan for each such target. The initial targets included HIF-2 alpha and SOS1/KRAS, which were two of the Company’s wholly-owned programs. In November 2021, the Company and BMS mutually agreed to replace the HIF-2 alpha target with another precision oncology target. Following the replacement election, all rights to the HIF-2 alpha target program reverted to the Company. In September 2022, BMS elected not to proceed with further development of another target and all rights to this program reverted to the Company, which increased revenue recognition in the third quarter of 2022 due to the accelerated completion of the Company's obligations related to the program. In December 2022, the Company and BMS entered into an amendment to the agreement to include an additional target in neurology on terms similar to the original agreement. Once a development candidate meeting specified criteria for a target under the agreement has been identified by the Company, BMS will be solely responsible for the further development, manufacturing and commercialization of such development candidate at its own cost and expense. In September 2023, BMS elected not to proceed with further development of two related oncology programs and all rights to these programs reverted to the Company, which increased revenue recognition in the third quarter of 2023 due to the accelerated completion of the Company's obligations related to those programs.
Under the terms of the agreement, as amended, BMS paid the Company an initial upfront fee payment of $55.0 million in November 2020 and an additional upfront payment in December 2022. The Company also is eligible to receive up to $1.5 billion in total milestone payments across the remaining potential targets subject to the collaboration, consisting of: a) up to $585.0 million in milestone payments per oncology target, consisting of $360.0 million in the aggregate for the achievement of certain specified research, development, and regulatory milestones and $225.0 million in the aggregate for the achievement of certain specified commercial milestones; and b) up to $489.0 million in milestone payments per neurology and immunology target, consisting of $264.0 million in the aggregate for the achievement of certain specified research, development, and regulatory milestones and $225.0 million in the aggregate for the achievement of certain specified commercial milestones. As of September 30, 2023, the Company had recognized $25.0 million in revenue related to milestones under this agreement.
The Company is also entitled to a tiered percentage royalty on annual net sales ranging from mid-single digits to low-double digits, subject to certain specified reductions. Royalties are payable by BMS on a licensed product-by-licensed product and country-by-country basis until the later of the expiration of the last valid claim covering the licensed product in such country, expiration of all applicable regulatory exclusivities in such country for such licensed product and the tenth anniversary of the first commercial sale of such licensed product in such country.
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The Company assessed the collaboration and license agreement in accordance with Topic 606, and concluded that BMS is a customer based on the agreement structure. At inception, the Company identified one performance obligation for each of the five programs initially covered under the agreement, which includes research activities for each program and a license grant for the underlying intellectual property. The Company determined that the license grant for intellectual property is not separable from the research activities, as the research activities are expected to significantly modify or enhance the license grant over the period of service, and therefore are not distinct in the context of the contract.
The Company determined that the transaction price at the onset of the agreement is $55.0 million. Additional consideration to be paid to the Company upon the achievement of future milestone payments were excluded from the transaction price as they represent milestone payments that are not considered probable as of the inception date such that there is not a significant risk of revenue reversal.
The Company has allocated the transaction price of $55.0 million to each performance obligation based on the SSP of each performance obligation at inception, which was determined based on each performance obligation’s estimated SSP. The Company determined the estimated SSP at contract inception of the research activities based on internal estimates of the costs to perform the services, inclusive of a reasonable profit margin. Significant inputs used to determine the total costs to perform the research activities included the length of time required, the internal hours expected to be incurred on the services and the number and costs of various studies that will be performed to complete the research plan.
Revenue associated with the research activities is recognized on a proportional performance basis over the period of service for research activities, using input-based measurements of total costs of research incurred to estimate the proportion performed. Progress towards completion is remeasured at the end of each reporting period.
During the three and nine months ended September 30, 2023, the Company recognized $11.2 million and $40.0 million of revenue, respectively, associated with the agreement based on the research activities performed and milestones achieved. During the three and nine months ended September 30, 2022, the Company recognized $9.9 million and $19.3 million, respectively, associated with the agreement based on the research activities performed. As of September 30, 2023 and December 31, 2022, there was $10.5 million and $25.5 million, respectively, of deferred revenue related to the agreement, which was classified as either current or non-current in the condensed consolidated balance sheet based on the period the services are expected to be performed. As of September 30, 2023, the Company had no outstanding receivables for this collaboration. As of December 31, 2022, the Company had $8.0 million of outstanding receivables for this collaboration.
(d)Significant Judgments
Significant judgments and estimates are required under Topic 606. Due to the complexity of certain contracts, the actual revenue recognition treatment required under Topic 606 for the Company’s arrangements may be dependent on contract-specific terms and may vary in some instances.
The Company’s contracts with customers often include promises to transfer multiple software products and services, including training, professional services, technical support services, and rights to unspecified updates. Determining whether licenses and services are distinct performance obligations that should be accounted for separately, or are not distinct and therefore should be accounted for together, requires significant judgment. In some arrangements, such as most of the Company’s term-based software license arrangements, the Company has concluded that the licenses and associated services are distinct from each other. In other arrangements, including collaboration services arrangements, the licenses and certain services may not be distinct from each other. The Company’s time-based software arrangements may include multiple software licenses and a right to updates or upgrades to the licensed software products, and technical support. The Company has concluded that such promised goods and services are separate distinct performance obligations.
The Company is required to estimate the total consideration expected to be received from contracts with customers, including any variable consideration. For collaborative arrangements, under which the Company is eligible to receive variable consideration in the form of milestones payments, judgment is required to evaluate whether the milestones are considered probable of being achieved. If it is probable that a significant revenue reversal would not occur, the constraint is removed and value of the associated milestone is included in the estimated transaction price using the most likely amount method based on contractual requirements and historical experience. Once the estimated transaction price is established, amounts are allocated to the performance obligations that have been identified. The transaction price is allocated to each separate performance obligation on a relative SSP basis consistent with the allocation objectives of Topic 606.
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Judgment is required to determine the SSP for each distinct performance obligation. The Company rarely licenses or sells products on a standalone basis, so the Company is required to estimate the range of SSPs for each performance obligation. In instances where the SSP is not directly observable because the Company does not sell the license, product, or service separately, the Company determines the SSP using information that includes historical discounting practices, market conditions, cost-plus analysis, and other observable inputs. The Company typically has more than one SSP for individual performance obligations due to the stratification of those items by classes of customers and circumstances. In these instances, the Company may use information such as the size and geographic region of the customer in determining the SSP. Professional service revenue is recognized as costs and hours are incurred, and judgment is required in estimating both the project status and the costs incurred or hours expended.
If a group of agreements are so closely related to each other that they are, in effect, part of a single arrangement, such agreements are deemed to be one arrangement for revenue recognition purposes. The Company exercises significant judgment to evaluate the relevant facts and circumstances in determining whether the separate agreements should be accounted for separately or as, in substance, a single arrangement. The Company’s judgments about whether a group of contracts comprises a single arrangement can affect the allocation of consideration to the distinct performance obligations, which could have an effect on results of operations for the periods involved.
Judgment is required to determine the total costs to perform research activities, which include the length of time required, the internal hours expected to be incurred on the services, and the number and costs of various studies that may be performed by third-parties to complete the research plan.
Generally, the Company has not experienced significant returns or refunds to customers.
The Company’s estimates related to revenue recognition may require significant judgment and a change in these estimates could have an effect on the Company’s results of operations during the periods involved.
(e)Contract Balances
The timing of revenue recognition may differ from the timing of invoicing to customers and these timing differences result in receivables, contract assets, or contract liabilities (deferred revenue) on the condensed consolidated balance sheets. The Company records a contract asset when revenue is recognized prior to invoicing. A deferred revenue liability is recorded when revenue is expected to be recognized subsequent to invoicing. For the Company’s time-based software agreements, customers are generally invoiced at the beginning of the arrangement for the entire term, though when the term spans multiple years the customers may be invoiced on an annual basis. For certain drug discovery agreements where the milestones are deemed probable in a period prior to when the milestone is achieved, the Company records a contract asset for the full value of the milestone.
Contract assets are included in unbilled and other receivables within the condensed consolidated balance sheets and are transferred to receivables when the Company invoices the customer.
Contract balances were as follows:
As of
September 30,
2023
As of
December 31,
2022
Contract assets$13,161 $11,378 
Deferred revenue, short-term:
Software products and services29,583 37,085 
Drug discovery13,730 20,846 
Deferred revenue, long-term:
Software products and services2,590 2,526 
Drug discovery9,512 23,072 
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For the three and nine months ended September 30, 2023 and 2022, the Company recognized $25,439, $55,807, $22,621, and $51,816 of revenue, respectively, that was included in deferred revenue at the end of the respective preceding periods. All other deferred revenue activity is due to the timing of invoices in relation to the timing of revenue, as described above. The Company expects to recognize as revenue approximately 78% of its September 30, 2023 deferred revenue balance in the next 12 months and the remainder thereafter. Additionally, contracted but unsatisfied performance obligations that had not yet been billed to the customer or included in deferred revenue were $18,672 as of September 30, 2023.
Payment terms and conditions vary by contract type, although terms typically require payment within 30 to 60 days. In instances where the timing of revenue recognition differs from that of invoicing, the Company has determined that its contracts generally do not include a significant financing component. The primary purpose of invoicing terms is to provide customers with simplified and predictable ways of purchasing the Company’s products and services, not to facilitate financing arrangements.
(f)Deferred Sales Commissions
The Company has applied the practical expedient for sales commission expense, as any material compensation paid to sales representatives to obtain a contract relates to a period of one year or less. The Company has not capitalized any costs related to sales commissions.
(4)    Fair Value Measurements
Various inputs are used in determining the fair value of the Company’s financial assets and liabilities. These inputs are summarized into the following three broad categories:
Level 1 – quoted prices in active markets for identical securities
Level 2 – other significant observable inputs, including quoted prices for similar securities, interest rates, credit risk, etc.
Level 3 – significant unobservable inputs, including the Company’s own assumptions in determining fair value
The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities. Marketable securities, which consist primarily of corporate and U.S. government agency bonds, are classified as available for sale and fair value did not differ significantly from carrying value as of September 30, 2023 and December 31, 2022. The following table presents information about the Company’s assets measured at fair value as of September 30, 2023:
Level 1Level 2Level 3Total
Assets:
Cash and cash equivalents and restricted cash$255,608 $ $ $255,608 
Marketable securities 246,905  246,905 
Equity investments87,793  2,370 90,163 
Total$343,401 $246,905 $2,370 $592,676 
The following table presents information about the Company’s assets measured at fair value as of December 31, 2022:
Level 1Level 2Level 3Total
Assets:
Cash and cash equivalents and restricted cash$95,717 $ $ $95,717 
Marketable securities 360,613  360,613 
Equity investments22,335  1,629 23,964 
Total$118,052 $360,613 $1,629 $480,294 
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The following table sets forth changes in fair value of the Company’s Level 3 investments:
Amount
As of December 31, 2021$1,887 
Cash contributions600 
Unrealized loss(858)
As of December 31, 20221,629 
Realized gain147,322 
Cash distributions(111,328)
Transfer to Level 1(1,629)
As of March 31, 202335,994 
Cash distributions(35,789)
As of June 30, 2023205 
Unrealized gain2,165 
As of September 30, 2023$2,370 
The fair value of the Company’s investment in Nimbus Therapeutics, LLC (“Nimbus”), classified as Level 3 in the fair value hierarchy, was recorded as an equity method investment under ASC Topic 323, Investments - Equity Method and Joint Ventures, using the hypothetical liquidated book value method (“HLBV method”) through June 30, 2023, as further described in Note 10, Equity Investments. Significant unobservable inputs used to determine Nimbus’ fair value under the HLBV method were the entity's annual financial statements and the Company’s liquidation preference. During the three months ended March 31, 2023, the Company recorded a gain of $147,322 on account of its equity position in Nimbus following the closing of Takeda's acquisition of Nimbus Lakshmi, Inc., a wholly-owned subsidiary of Nimbus, and its tyrosine kinase 2 inhibitor, NDI-034858. On February 13, 2023, the Company reported receipt of a $111,328 cash distribution from Nimbus related to the sale. On April 6, 2023, the Company reported receipt of a $35,789 cash distribution from Nimbus related to the sale. The realized gain on Level 3 investment as of June 30, 2023 relates to an additional expected cash receipt of $205 from Nimbus. Following the dilution of the Company's investment in Nimbus during the three months ended September 30, 2023, the fair value of the Company's investment is recorded under ASC Topic 321 ("Topic 321"), Investments - Equity Securities as a non-marketable equity security as the Company no longer exercises significant influence over Nimbus. This change in accounting method resulted in an unrealized gain of $2,165.
During the three months ended March 31, 2023, the Company recorded a transfer from a Level 3 investment to a Level 1 investment due to the completion of Structure Therapeutics Inc.'s, ("Structure Therapeutics"), initial public offering ("IPO"). The Company's investment in Structure Therapeutics was previously recorded using the HLBV method. Following the completion of Structure Therapeutics' IPO, the Company's investment in Structure Therapeutics is recorded under Topic 321 because there is an observable price of the investment. During the year ended December 31, 2022 there were no transfers between Level 1, Level 2 and Level 3 investments.
Unrealized gains and losses arising from changes in fair value of the Company’s equity investments are classified within change in fair value in the condensed consolidated statements of operations. Realized gains arising from distributions receivable from the Company's equity investments are classified within gain on equity investments in the condensed consolidated statements of operations.
For further information regarding the Company’s equity investments, see Note 10, Equity Investments.
(5)    Commitments and Contingencies
(a)    Leases
The Company has multiple operating leases for office space and a finance lease for equipment that expire at various dates through 2037. The Company has elected the package of practical expedients under the transition guidance of ASC Topic 842, Leases, to exclude short-term leases from the balance sheet and to combine lease and non-lease components. The Company classifies finance lease right of use assets under property and equipment, net and finance short-term and long-term lease liabilities under other accrued liabilities and other liabilities, long-term, respectively.
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Upon inception of a lease, the Company determines if an arrangement is a lease, if it is classified as an operating or finance lease, if it includes options to extend or terminate the lease, and if it is reasonably certain that the Company will exercise the options. Lease cost, representing lease payments over the term of the lease and any capitalizable direct costs less any incentives received, is recognized on a straight-line basis over the lease term as lease expense.
In determining the present value of lease payments, the Company uses its incremental borrowing rate based on the information available at the lease commencement date if the rate implicit in the lease is not readily determinable. Upon execution of a new lease, the Company performs an analysis to determine its incremental borrowing rate using its current borrowing rate, adjusted for various factors including level of collateralization and lease term. As of September 30, 2023, the remaining weighted average lease term for operating and finance leases was 12 years.
During the nine months ended September 30, 2023, operating lease right of use assets increased by $15,085 due to the accounting commencement of new leases and by $4,388 due to contingency resolutions associated with office leases. During the nine months ended September 30, 2023, operating lease liabilities increased by $15,085 due to the accounting commencement of new leases. During the nine months ended September 30, 2023, finance lease right of use assets and lease liabilities each increased by $279 due to the accounting commencement of an equipment lease for our Framingham, Massachusetts lab.
Variable and short-term lease costs for the Company's operating and finance leases were immaterial for the nine months ended September 30, 2023. Additional details of the Company’s operating and finance leases are presented in the following table:
Three Months Ended September 30,Nine Months Ended September 30,
2023202220232022
Lease costs$4,393 $3,151 $12,318 $8,441 
Cash paid for leases3,229 992 8,789 2,293 
Maturities of operating and finance lease liabilities as of September 30, 2023 under noncancelable periods were as follows:
Year ending December 31:
Remainder of 2023$3,710 
202417,476 
202517,535 
202617,222 
202716,054 
Thereafter127,005 
Total future minimum lease payments199,002 
Less: imputed interest(69,722)
Present value of future minimum lease payments129,280 
Less: current portion of lease payments16,353 
Lease liabilities, long-term$112,927 
(b)    Legal Matters
From time to time, the Company may become involved in routine litigation arising in the ordinary course of business. While the results of such litigation cannot be predicted with certainty, management believes that the final outcome of such matters is not likely to have a material adverse effect on the Company’s financial position or results of operations or cash flows.
(c)    Contingencies
The Company is currently under audit with a royalty partner. As of September 30, 2023, the Company believes a contingency is probable, but not material.
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(6)    Income Taxes
The Company estimates an annual effective income tax rate based on projected results for the year and applies this rate to income before taxes to calculate income tax expense. Any refinements made due to subsequent information that affects the estimated annual effective income tax rate are reflected as adjustments in the current period.
For the three months ended September 30, 2023, the Company’s income tax benefit was $2,887. For the nine months ended September 30, 2023, the Company’s income tax expense was $3,041. For the three and nine months ended September 30, 2022, the Company's income tax expense was $194 and $199, respectively. For the three and nine months ended September 30, 2023, the difference between the effective rate and the statutory rate was primarily attributed to the application of research and development credits and the change in the valuation allowance against net deferred tax assets.
The Company recognizes the effect of income tax positions only if those positions are “more likely than not” capable of being sustained. As of September 30, 2023, the Company had $2,658 of unrecognized tax benefits. Interest and penalties accrued on unrecognized tax benefits are recorded as tax expense within the unaudited condensed consolidated financial statements. The Company does not expect a significant increase or decrease to the total amounts of unrecognized tax benefits within the next twelve months.
The Company and its subsidiaries file U.S. federal income tax returns and various state, local and foreign income tax returns. At September 30, 2023, the Company’s statutes of limitations are open for all federal and state tax returns filed after the years ended December 31, 2018 and 2017, respectively. Net operating loss (“NOL”) and credit carryforwards from all years are subject to examination and adjustments for the three years following the year in which the carryforwards are utilized. The Company is not currently under Internal Revenue Service or state examination.
Pursuant to Internal Revenue Code Sections 382 and 383, the utilization of NOLs and other tax attributes may be substantially limited due to cumulative changes in ownership greater than 50% that may have occurred or could occur during applicable testing periods. The Company has performed an analysis through December 31, 2022 and determined that such an ownership change occurred on March 31, 2021. There was no material impact to the financial statements due to this ownership change.
(7)    Stockholders’ Equity
(a)    Common Stock
As of September 30, 2023, the Company had authorized 500,000,000 shares of common stock with a par value of $0.01 per share. Holders of common stock are entitled to one vote per share, to receive dividends, if and when declared by the board of directors, and upon liquidation or dissolution, to receive a portion of the assets available for distributions to stockholders, subject to preferential amounts owed to holders of the Company’s preferred stock, if any.
Common stockholders have no preemptive or other subscription rights and there are no redemption or sinking fund provisions with respect to such shares. The rights, preferences and privileges of holders of the common stock are subject to and may be adversely affected by the right of the holders of shares of any series of preferred stock that the Company may designate and issue in the future.
(b)    Limited Common Stock
As of September 30, 2023, the Company had authorized 100,000,000 shares of limited common stock with a par value of $0.01 per share. Holders of limited common stock are entitled to one vote per share, however, the holders of limited common stock shall not be entitled to vote such shares in any election of directors or on the removal of directors. Holders of limited common stock are entitled to receive dividends, if and when declared by the board of directors, and upon liquidation or dissolution, to receive a portion of the assets available for distributions to stockholders, subject to preferential amounts owed to holders of the Company’s preferred stock, if any. Holders of the Company’s limited common stock have the right to convert each share of limited common stock into one share of the Company’s common stock.
Limited common stockholders have no preemptive or other subscription rights and there are no redemption or sinking fund provisions with respect to such shares. The rights, preferences and privileges of holders of the limited common stock are subject to and may be adversely affected by the right of the holders of shares of any series of preferred stock that the Company may designate and issue in the future.
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(c)    Preferred Stock
As of September 30, 2023, the Company had authorized 10,000,000 shares of undesignated preferred stock with a par value of $0.01 per share. The Company’s board of directors has the discretion to determine the rights, preferences, privileges, and restrictions, including voting rights, dividend rights, conversion rights, redemption privileges, and liquidation preferences, of each series of preferred stock.
(8)    Stock-Based Compensation
Stock Incentive Plans
As of September 30, 2023, the Company’s stock incentive plans included the 2010 Stock Plan (the “2010 Plan”), the 2020 Equity Incentive Plan (the “2020 Plan”), the 2021 Inducement Equity Incentive Plan, as amended (the “2021 Plan”), and the 2022 Equity Incentive Plan (the “2022 Plan”) (together, the “Plans”).
The 2022 Plan provides for the award of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units, other stock-based awards, and cash-based awards to employees, directors, consultants or advisors. Shares of common stock subject to outstanding awards granted under the 2020 Plan and the 2010 Plan that expire, terminate, or are otherwise surrendered, cancelled, forfeited, or repurchased by the Company are available for issuance under the 2022 Plan.
The 2021 Plan provides for the award of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units, and other stock-based awards to persons who were not previously an employee or director of the Company or who are commencing employment with the Company following a bona fide period of non-employment, in either case, as an inducement material to such person’s entry into employment with the Company and in accordance with the requirements of the Nasdaq Stock Market Rule 5635(c)(4). Neither consultants nor advisors are eligible to participate in the 2021 Plan.
The 2020 Plan provided for the award of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units, and other stock-based awards to employees, directors, consultants or advisors. As of June 15, 2022, the effective date of the 2022 Plan, no further awards will be made under the 2020 Plan. Any options or awards outstanding under the 2020 Plan remain outstanding and effective.
The 2010 Plan provided for the granting of incentive stock options and nonstatutory stock options to employees, directors, consultants or advisors. As of the effective date of the 2020 Plan, no further awards will be made under the 2010 Plan. Any options or awards outstanding under the 2010 Plan remain outstanding and effective.
As of September 30, 2023 and December 31, 2022, there were 3,430,664 and 5,470,240 shares available for grant under the Plans, respectively. The following table presents classification of stock-based compensation expense within the unaudited condensed consolidated statements of operations:
Three Months Ended September 30,Nine Months Ended September 30,
2023202220232022
Cost of sales$1,234 $1,360 $3,922 $4,175 
Research and development4,101 3,026 11,422 8,585 
Sales and marketing914 728 2,705 1,951 
General and administrative6,405 4,750 17,258 14,714 
Total stock-based compensation$12,654 $9,864 $35,307 $29,425 
Restricted Stock Units
Each restricted stock unit (“RSU”) represents the right to receive one share of the Company’s common stock upon vesting. The fair value of RSUs granted by the Company was calculated based upon the Company’s closing stock price on the date of the grant, and the stock-based compensation expense is recognized over the vesting period. RSUs generally vest over four years with 25% of the grants vesting at the end of the first year and the remaining vesting annually over the following three years.
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There were 33,285, 748,265, zero, and 48,700 RSUs granted during the three and nine months ended September 30, 2023 and 2022, respectively. The weighted average grant date fair value for each RSU granted during the three and nine months ended September 30, 2023 and 2022 was $41.08, $26.07, zero, and $27.76, respectively.
As of September 30, 2023, there was $16,663 of unrecognized compensation cost related to RSUs granted under the Plans, which is expected to be recognized over a weighted average period of 3.14 years. During the three and nine months ended September 30, 2023 1,166 and 13,241 RSUs vested, respectively. The fair value of RSUs vested during the three and nine months ended September 30, 2023 was $62 and $355, respectively. No RSUs vested during the three and nine months ended September 30, 2022.
Performance-Based Restricted Stock Units
In February 2023, the Company awarded performance-based restricted stock units ("PRSUs") under the 2022 Plan. Each PRSU represents a contingent right to receive one share of common stock upon the achievement of specified performance goals. The fair value of PRSUs granted by the Company was calculated based upon the Company's closing stock price on the date of the grant, and the stock-based compensation expense is recognized when the grant date is determined and performance conditions are probable of achievement. At the point where performance conditions are considered probable of achievement, the Company records stock-based compensation expense with a cumulative catch-up expense in the period first recognized and on a straight-line basis over the remaining period for which the performance criteria are expected to be completed.
In March 2023, the Company awarded to certain executive officers PRSUs for a maximum of 62,693 shares (based on 150% achievement of the applicable performance conditions outlined in the awards), with a target award of 41,795 PRSUs (based on 100% achievement of the applicable performance conditions), and a threshold award of 20,898 PRSUs (based on 50% achievement of the applicable performance conditions). All PRSUs were considered granted under ASC 718, Compensation—Stock Compensation ("Topic 718"). The PRSUs granted in March 2023 are scheduled to vest, if at all, upon the certification by the Company's compensation committee of the achievement of the applicable performance conditions following the filing of the Company's Annual Report on Form 10-K for the fiscal year ending December 31, 2025.
In August 2022, the Company awarded 90,000 PRSUs to an executive officer of which 30,150 PRSUs were considered granted under Topic 718 at the time the PRSUs were awarded. In March 2023, of the 90,000 PRSUs awarded in August 2022, an additional 45,000 PRSUs were considered granted under Topic 718. Of the 45,000 PRSUs that were considered granted in March 2023, 18,000 PRSUs are scheduled to vest, if at all, upon the certification by the Company's compensation committee of the achievement of the applicable performance conditions following the filing of the Company's Annual Report on Form 10-K for the fiscal year ending December 31, 2023 and 27,000 PRSUs are scheduled to vest, if at all, upon the certification by the Company's compensation committee of the achievement of the applicable performance conditions following the filing of the Company's Annual Report on Form 10-K for the fiscal year ending December 31, 2025.
The weighted average grant date fair value for each PRSU granted during the three and nine months ended September 30, 2023 and 2022 was zero, $22.48, $28.55, and $28.55, respectively. No PRSUs vested during the three and nine months ended September 30, 2023 and 2022.
Stock Options
Stock options must be granted at an exercise price not less than 100% of the fair market value per share at the grant date. The board of directors or compensation committee determines the exercise price of the Company’s stock options based on the closing price of the common stock as reported on the Nasdaq Global Select Market on the date of the grant. The maximum contractual term of options granted under the Plans is typically 10 years, options generally vest over four years with 25% of the shares underlying the option vesting at the end of the first year and the remaining vesting monthly over the following three years. In February 2023, the Company granted the chief executive officer a premium priced option to purchase 65,525 shares of common stock with an exercise price equal to 110% of the closing price of the Company's common stock on the date of grant.
During the three and nine months ended September 30, 2023 and 2022, 119,885, 646,315, 40,707, and 233,253 options under the Plans were exercised for total proceeds of $1,534, $7,099, $324, and $1,628, respectively.
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The fair value of each option award is determined on the date of grant using the Black Scholes Merton option-pricing model. The calculation of fair value includes several assumptions that require management’s judgment. The expected terms of options granted to employees during 2023 and 2022 were calculated using an average of historical exercises. Estimated volatility for the nine months ended September 30, 2023 and 2022 incorporates a calculated volatility derived from the historical closing prices of shares of common stock of similar entities whose share prices were publicly available for the expected term of the option. The risk-free interest rate is based on the U.S. Treasury constant maturities in effect at the time of grant for the expected term of the option. The Company accounts for forfeitures as they occur; as such, the Company does not estimate forfeitures at the time of grant.
Following are the weighted average valuation assumptions used for option awards during the periods presented:
Nine Months Ended September 30,
20232022
Valuation assumptions
Expected dividend yield % %
Expected volatility67 %56 %
Expected term (years)4.984.77
Risk-free interest rate3.80 %2.02 %
The weighted average grant date fair value per share of options granted during the three and nine months ended September 30, 2023 and 2022 was $24.75, $15.99, $15.52, and $13.74, respectively. The intrinsic value of options exercised during the three and nine months ended September 30, 2023 and 2022 was $2,835, $14,140, $859, and $5,145, respectively.
As of September 30, 2023, there was $74,044 of unrecognized compensation cost related to unvested stock options granted under the Plans, which is expected to be recognized over a weighted average period of 2.25 years. The fair value of shares vested during the three and nine months ended September 30, 2023 and 2022 was $9,991, $37,858, $7,016, and $36,720, respectively.
(9)    Net (Loss) Income per Share Attributable to Common and Limited Common Stockholders
The following table presents the calculation of basic and diluted net (loss) income per share attributable to common and limited common stockholders for the periods presented (in thousands, except for share and per share data):
Three Months Ended September 30,Nine Months Ended September 30,
2023202220232022
Numerator:
Net (loss) income attributable to Schrödinger common and limited common stockholders$(62,024)$(39,853)$71,390 $(121,979)
Denominator:
Weighted average shares used to compute net (loss) income per share of common and limited common stockholders, basic:71,924,45171,207,99271,679,76571,140,682
Effect of the exercise of common stock options and vested RSUs on weighted average common and limited common shares  3,287,026  
Weighted average shares used to compute net (loss) income per share of common and limited common stockholders, diluted:71,924,451 71,207,992 74,966,791 71,140,682 
Net (loss) income per share of common and limited common stockholders, basic:$(0.86)$(0.56)$1.00 $(1.71)
Net (loss) income per share of common and limited common stockholders, diluted:$(0.86)$(0.56)$0.95 $(1.71)
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For the nine months ended September 30, 2023, in order to calculate diluted net income per share, the weighted average shares used to compute net income is adjusted by the effect of dilutive securities, including awards under the Plans. Diluted net income per share is computed by dividing the resulting net income by the weighted average number of fully diluted common and limited shares outstanding.
Since the Company was in a loss position for the three months ended September 30, 2023 and the three and nine months ended September 30, 2022, basic net loss per share is the same as diluted net loss per share as the inclusion of all potential common shares and limited common shares outstanding would have been anti-dilutive. Potentially dilutive securities that were not included in the diluted per share calculations because they would be anti-dilutive were as follows:
Three Months Ended September 30,Nine Months Ended September 30,
2023202220232022
Shares subject to outstanding common stock options and RSUs12,243,35210,932,6126,192,74710,932,612
(10)    Equity Investments
(a)    Nimbus
The Company provides collaboration services for Nimbus under the terms of a master services agreement executed on May 18, 2010, as amended. Collaboration agreements are separate from the transaction that resulted in equity ownership and related fees are paid in cash to the Company. Nimbus was previously recorded as an equity method investment under the HLBV method, as the entity is a limited liability company and the Company was determined to have significant influence due to the Company's collaboration with Nimbus on a number of drug discovery targets, as well as the Company's level of ownership in Nimbus. During the three months ended September 30, 2023, the Company's equity ownership in Nimbus was diluted to the point that the Company no longer has significant influence over the entity. As the Company no longer has significant influence over Nimbus, after June 30, 2023, the equity investment in Nimbus is valued as a non-marketable equity security.
The carrying value of the Nimbus investment was $2,370 and zero as of September 30, 2023 and December 31, 2022, respectively. The Company has no obligation to fund Nimbus losses in excess of its initial investment. For the three months ended September 30, 2023, the Company reported a gain of $2,165 on the Nimbus investment, which reflected the change in accounting method from an equity method investment under the HLBV method to a non-marketable equity security measured at fair value. For the nine months ended September 30, 2023, the Company reported a realized gain of $147,322 on the Nimbus investment, which reflected the total cash distribution the Company was eligible to receive from Nimbus on account of Takeda's acquisition of Nimbus Lakshmi, Inc., a wholly-owned subsidiary of Nimbus, and its tyrosine kinase 2 inhibitor NDI-034858, as well as an unrealized gain of $2,165 due to the change in accounting method. For the three and nine months ended September 30, 2022, the Company reported no gains or losses on the Nimbus investment.
(b)    Morphic
The Company accounts for its investment in Morphic Holding, Inc. (“Morphic”) at fair value based on the share price of Morphic’s common stock at the measurement date.
For the three and nine months ended September 30, 2023, the Company reported a loss of $28,740 and $3,206 on the Morphic investment, respectively. For the three and nine months ended September 30, 2022, the Company reported a gain of $5,511 and a loss of $15,931 on the Morphic investment, respectively. As of September 30, 2023 and December 31, 2022, the carrying value of the Company’s investment in Morphic was $19,129 and $22,335, respectively.
(c)    Ajax
In May 2021, the Company purchased 631,377 shares of Series B preferred stock of Ajax Therapeutics, Inc. (“Ajax”) for $1,700 in cash. The Company has concluded that its equity investment in Ajax should be valued as a non-marketable equity security as the Company does not exercise significant influence over Ajax. As of each of September 30, 2023 and December 31, 2022, the carrying value of the Company’s investment in Ajax was $1,700.
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(d)    Structure Therapeutics
In July 2021, the Company purchased 494,035 shares of Series B preferred stock of Structure Therapeutics for $2,000 in cash. In April 2022, the Company purchased an additional 148,210 shares of Series B preferred stock for $600 in cash. On February 7, 2023, Structure Therapeutics completed its IPO. Immediately upon the closing of Structure Therapeutic's IPO, all of the outstanding Series B preferred stock automatically converted into ordinary shares on a one-for-one basis. As of September 30, 2023, the Company owned 3,260,495 ordinary shares of Structure Therapeutics. The Company purchased 275,000 American Depository Shares ("ADS") at $15 per ADS in the IPO. Each ADS represents three ordinary shares.
Upon completion of Structure Therapeutic's IPO, the Company changed the valuation methodology used to value the Structure Therapeutics investment from an equity method investment under the HLBV method to an equity investment reported at fair value. As there is a readily available market price for Structure Therapeutics' ADSs, the Company values its investment based on the closing price of Structure Therapeutic's ADSs as of the reporting date.
The carrying value of Structure Therapeutics was $68,664 and $1,629 as of September 30, 2023 and December 31, 2022, respectively. For the three and nine months ended September 30, 2023, the Company recorded a mark-to-market gain of $12,052 and $62,910, respectively, on the Structure Therapeutics investment. For the three and nine months ended September 30, 2022, the Company reported a loss of $237 and $659, respectively, on the Structure Therapeutics investment under the HLBV method.
(11)    Related Party Transactions
(a)    Board Member
For the three and nine months ended September 30, 2023 and 2022, the Company paid consulting fees of $105, $315, $105, and $305, respectively, to a member of its board of directors.
(b)    Bill and Melinda Gates Foundation
The Bill & Melinda Gates Foundation, an entity under common control with Bill and Melinda Gates Foundation Trust, a stockholder of the Company, issued a grant under which it agreed to pay the Company directly for certain licenses and services provided to a specified group of third-party organizations. Revenue recognized for services provided by the Company under this grant were $63, $183, $122, and $337 for the three and nine months ended September 30, 2023 and 2022, respectively. As of September 30, 2023 and December 31, 2022, the Company had net receivables of zero and $20, respectively, due from the Bill & Melinda Gates Foundation.
For the three and nine months ended September 30, 2023 and 2022, the Company recognized $935, $2,306, $595, and $1,376, respectively, in drug discovery contribution revenue related to funds received under agreements with the Bill & Melinda Gates Foundation, aimed at accelerating drug discovery in women’s health. As of September 30, 2023 and December 31, 2022, the Company had no receivables due under these agreements from the Bill & Melinda Gates Foundation. As of September 30, 2023 and December 31, 2022, restricted cash on hand related to the arrangement was $2,729 and $1,742, respectively.
Gates Ventures, LLC is an entity under the control of William H. Gates III, who may be deemed to be the beneficial owner of more than 5% of the Company’s voting securities. The Company received $1,000 in contribution revenue in connection with its entry into an agreement with Gates Ventures, LLC annually from June 2020 to June 2022. In August 2023, the Company renewed the agreement with Gates Ventures, LLC and recognized $1,800 in contribution revenue. As of September 30, 2023 and December 31, 2022, the Company had $1,800 and zero net receivables due from Gates Ventures, LLC, respectively.
(c)    Structure Therapeutics
During the year ended December 31, 2021, the Company entered into multiple software agreements with Structure Therapeutics and its subsidiaries for approximately $650. For the three and nine months ended September 30, 2023 and 2022, the Company recognized revenue of $62, $221, $73, and $223, respectively, related to these software agreements. As of September 30, 2023 and December 31, 2022, the Company had no net receivables due from Structure Therapeutics.
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(12)    Segment Reporting
The Company has determined that its chief executive officer (“CEO”) is its chief operating decision maker (“CODM”). The Company’s CEO evaluates the financial performance of the Company based on two reportable segments: Software and Drug Discovery. The Software segment is focused on licensing the Company’s software to transform molecular discovery. The Drug Discovery segment is focused on building a portfolio of preclinical and clinical drug programs, internally and through collaborations.
The CODM reviews segment performance and allocates resources based upon segment revenue and segment gross profit of the Software and Drug Discovery reportable segments. Segment gross profit is derived by deducting operational expenditures, with the exception of research and development, sales and marketing, and general and administrative activities from U.S. GAAP revenue. Operational expenditures are expenditures made that are directly attributable to the reportable segment. These expenditures are allocated to the segments based on headcount. The reportable segment expenditures include compensation, supplies, and services from contract research organizations.
Certain cost items are not allocated to the Company’s reportable segments. These cost items primarily consist of compensation and general operational expenses associated with the Company’s research and development, sales and marketing, and general and administrative. These costs are incurred by both segments and due to the integrated nature of the Company’s Software and Drug Discovery segments, any allocation methodology would be arbitrary and provide no meaningful analysis.
Segment revenue is primarily earned in the United States and there are no intersegment revenues. Additionally, the Company reports assets on a consolidated basis and does not allocate assets to its reportable segments for purposes of assessing segment performance or allocating resources.
Presented below is financial information with respect to the Company’s reportable segments for the periods presented:
Three Months Ended September 30,Nine Months Ended September 30,
2023202220232022
Segment revenues:
Software$28,904 $24,667 $90,469 $87,759 
Drug discovery13,665 12,313 52,071 36,353 
Total segment revenues$42,569 $36,980 $142,540 $124,112 
Segment gross profit:    
Software$21,870 $17,801 $69,625 $66,281 
Drug discovery1,769 (600)13,517 (3,963)
Total segment gross profit23,639 17,201 83,142 62,318 
Unallocated:    
Research and development(46,833)(32,885)(130,279)(91,830)
Sales and marketing(9,109)(7,161)(27,276)(21,260)
General and administrative(23,890)(23,318)(73,414)(67,507)
(Loss) gain on equity investments (3)147,322 11,825 
Change in fair value(14,522)5,273 61,869 (16,591)