5. Collaboration and License Agreements

The fololowing tables provide amounts by year and by line item included in the Company’s consolidated statements of comprehensive (loss) income attributable to transactions arising from its collaborative arrangements, as defined in the Financial Accounting Standards Board’s Accounting Standards Codification Topic 808, Collaborative Arrangements. The Company does not have any insignificant collaborative arrangements.

	For the Three Months Ended September 30, 2015 (in thousands)
	2003 Sandoz Collaboration		2006 Sandoz Collaboration		Baxalta Agreement		Total Collaborations
Collaboration revenues:
Product revenue	$	—	$	8,666	$	—	$	8,666


Research and development revenue:
Regulatory and commercial milestones	—		—		—		—
Amortization of upfront payments	—		—		2,442		2,442
Research and development services (FTEs) and external costs	69		742		1,876		2,687

Total research and development revenue	$	69	$	742	$	4,318	$	5,129


Total collaboration revenues	$	69	$	9,408	$	4,318	$	13,795


Operating expenses:
Research and development expense (1)	$	—	$	274	$	251	$	525
General and administrative expense (1)	$	104	$	38	$	166	$	308

Total operating expenses	$	104	$	312	$	417	$	833

	For the Three Months Ended September 30, 2014 (in thousands)
	2003 Sandoz Collaboration		2006 Sandoz Collaboration		Baxalta Agreement		Total Collaborations
Collaboration revenues:
Product revenue	$	4,714	$	—	$	—	$	4,714


Research and development revenue:
Amortization of upfront payments	—		121		767		888
Research and development services (FTEs) and external costs	195		944		2,595		3,734

Total research and development revenue	$	195	$	1,065	$	3,362	$	4,622


Total collaboration revenues	$	4,909	$	1,065	$	3,362	$	9,336


Operating expenses:
Research and development expense (1)	$	50	$	444	$	3,639	$	4,133
General and administrative expense (1)	$	15	$	84	$	242	$	341

Total operating expenses	$	65	$	528	$	3,881	$	4,474

	For the Nine Months Ended September 30, 2015 (in thousands)
	2003 Sandoz Collaboration		2006 Sandoz Collaboration		Baxalta Agreement		Total Collaborations
Collaboration revenues:
Product revenue	$	2,843	$	27,850	$	—	$	30,693


Research and development revenue:
Regulatory and commercial milestones	—		20,000		—		20,000
Amortization of upfront payments	—		—		6,572		6,572
Research and development services (FTEs) and external costs	450		2,220		7,323		9,993

Total research and development revenue	$	450	$	22,220	$	13,895	$	36,565


Total collaboration revenues	$	3,293	$	50,070	$	13,895	$	67,258


Operating expenses:
Research and development expense (1)	$	208	$	703	$	1,376	$	2,287
General and administrative expense (1)	$	326	$	149	$	798	$	1,273

Total operating expenses	$	534	$	852	$	2,174	$	3,560

	For the Nine Months Ended September 30, 2014 (in thousands)
	2003 Sandoz Collaboration		2006 Sandoz Collaboration		Baxalta Agreement		Total Collaborations
Collaboration revenues:
Product revenue	$	15,216	$	—	$	—	$	15,216


Research and development revenue:
Amortization of upfront payments	—		480		2,309		2,789
Research and development services (FTEs) and external costs	796		1,738		10,532		13,066

Total research and development revenue	$	796	$	2,218	$	12,841	$	15,855


Total collaboration revenues	$	16,012	$	2,218	$	12,841	$	31,071


Operating expenses:
Research and development expense (1)	$	134	$	973	$	11,868	$	12,975
General and administrative expense (1)	$	110	$	315	$	399	$	824

Total operating expenses	$	244	$	1,288	$	12,267	$	13,799

(1)

The amounts represent external expenditures, including amortization of an intangible asset, and exclude salaries and benefits, share-based compensation, facilities, depreciation and laboratory supplies, as these costs are not directly charged to programs.

2003 Sandoz Collaboration

In 2003, the Company entered into a collaboration and license agreement, or the 2003 Sandoz Collaboration, with Sandoz AG (formerly Sandoz N.V. and Biochemie West Indies, N.V.) and Sandoz Inc. (formerly Geneva Pharmaceuticals, Inc.) to jointly develop, manufacture and commercialize Enoxaparin Sodium Injection, a generic version of Lovenox®, in the United States. Sandoz N.V. later assigned its rights in the 2003 Sandoz Collaboration to Sandoz AG, an affiliate of Novartis Pharma AG. The Company refers to Sandoz AG and Sandoz Inc. together as Sandoz.

Under the terms of the 2003 Sandoz Collaboration, the Company and Sandoz agreed to exclusively work with each other to develop and commercialize Enoxaparin Sodium Injection for any and all medical indications within the United States. In addition, the Company granted Sandoz an exclusive license under its intellectual property rights to develop and commercialize injectable enoxaparin for all medical indications outside the United States. The Company identified two significant deliverables in this arrangement consisting of: (i) the license and (ii) development and related services. The Company determined that the license did not meet the criteria for separation as it did not have stand-alone value apart from the development services, which are proprietary to the Company. Therefore, the Company determined that a single unit of accounting exists with respect to the 2003 Sandoz Collaboration.

The Company is paid at cost for external costs incurred for commercial and related activities and is paid for full time equivalents, or FTEs, performing commercial and related services.

Sandoz began selling Enoxaparin Sodium Injection in July 2010. Under the original payment terms of the 2003 Sandoz Collaboration, Sandoz was obligated to pay the Company either a contractually-defined profit-share or royalty on net sales depending on the kind and number of other marketed generic versions of Lovenox. The Company received 45% of profits from July 2010 through September 2011, a royalty on net sales from October 2011 through December 2011 and a share of profits in January 2012. From February 2012 to March 2015, the Company received a 10% royalty on net sales (12% on net sales above a certain threshold). In June 2015, the Company and Sandoz amended the 2003 Sandoz Collaboration, effective April 1, 2015, to provide that Sandoz would pay the Company 50% of contractually-defined profits on sales. For the three months ended September 30, 2015, Sandoz recorded a loss on its third quarter sales of Enoxaparin Sodium Injection. See “Product revenue” in the tables above for product revenue earned by the Company in the nine months ended September 30, 2015 and the three and nine months ended September 30, 2014 on Sandoz’s sales of Enoxaparin Sodium Injection.

The Company is no longer eligible to receive milestones under the 2003 Sandoz Collaboration because the remaining milestones were contingent upon there being no third-party competitors marketing a substitutable generic version of a Lovenox-Equivalent Product.

The collaboration is governed by a joint steering committee and a joint project team, each consisting of an equal number of Sandoz and Company representatives. Most decisions must be made unanimously, with Sandoz collectively having one vote and the Company having one vote. Sandoz has the sole authority to determine the price at which it sells Enoxaparin Sodium Injection.

Any product liability costs and certain other expenses arising from patent litigation may also reduce the amount of profit-share, royalty and milestone payments paid to the Company by Sandoz, but only by up to 50% of these amounts due to the Company from Sandoz each quarter.

A portion of Enoxaparin Sodium Injection development expenses and certain legal expenses, which in the aggregate have exceeded a specified amount, are offset against profit-sharing amounts, royalties and milestone payments. The Company’s contractual share of these development and other expenses is subject to an annual claw-back adjustment at the end of each product year, with the product year beginning on July 1 and ending on June 30. The annual adjustment can only reduce the Company’s profits, royalties and milestones by up to 50% in a given calendar quarter and any excess amount due will be carried forward into future quarters and reduce any profits in those future periods until it is paid in full. Annual adjustments, including amounts carried forward into future periods, are recorded as a reduction in product revenue. The annual adjustment was approximately $1.9 million for the product year ending June 30, 2015 and in the second quarter the Company paid $0.1 million of the total annual adjustment through a reduction of its second quarter product revenue. The amount of the annual adjustment that will be carried forward into future periods and repaid by offsetting Momenta’s future Enoxaparin product revenue was approximately $1.8 million as of September 30, 2015.

The Company recognizes research and development revenue from FTE services and research and development revenue from external development costs upon completion of the performance requirements (i.e., as the services are performed and the reimbursable costs are incurred). Revenue from external development costs is recorded on a gross basis as the Company contracts directly with, manages the work of and is responsible for payments to third-party vendors for such development and related services. See “Research and development revenue” in the tables above for research and development revenue earned by the Company under the 2003 Sandoz Collaboration.

2006 Sandoz Collaboration

In 2006 and 2007, the Company entered into a series of agreements, including a Stock Purchase Agreement and an Investor Rights Agreement, with Novartis Pharma AG, and a collaboration and license agreement, as amended, or the Second Sandoz Collaboration Agreement, with Sandoz AG. Together, this series of agreements is referred to as the 2006 Sandoz Collaboration. Under the Second Sandoz Collaboration Agreement, the Company and Sandoz AG agreed to exclusively collaborate on the development and commercialization of Glatopa and M356 (40 mg), among other products. Further, under the Second Sandoz Collaboration Agreement, the Company and Sandoz AG expanded the geographic markets for Enoxaparin Sodium Injection covered by the 2003 Sandoz Collaboration to include the European Union. Under the Stock Purchase Agreement, the Company sold 4,708,679 shares of common stock to Novartis Pharma AG at a per share price of $15.93 (the closing price of the Company’s common stock on the NASDAQ Global Market was $13.05 on the date of the Stock Purchase Agreement) for an aggregate purchase price of $75.0 million, resulting in a paid premium of $13.6 million, which was recognized as revenue on a straight-line basis over the estimated development period. See “Amortization of upfront payments” in the tables above for research and development revenue earned by the Company relating to this paid premium. The equity premium was fully earned and amortized to revenue in 2014.

Under the Second Sandoz Collaboration Agreement, costs, including development costs and the costs of clinical studies, are borne by the Company and Sandoz AG in varying proportions depending on the type of expense and the related product. For Glatopa and M356 (40 mg), the Company is generally responsible for all of the development costs in the United States. For Glatopa and M356 (40 mg) outside of the United States and for Enoxaparin Sodium Injection in the European Union, the Company shares development costs in proportion to its profit sharing interest. The Company is reimbursed at a contractual FTE rate for any full-time equivalent employee expenses as well as any external costs incurred in the development of products to the extent development costs are born by Sandoz AG. All commercialization responsibilities are borne by Sandoz AG worldwide as they are incurred for all products. The Company and Sandoz AG will share profits in varying proportions, depending on the product.

Sandoz commenced sales of Glatopa in the United States on June 18, 2015. Under the Second Sandoz Collaboration Agreement, the Company earns 50% of contractually-defined profits on Sandoz’s worldwide net sales of Glatopa. Upon approval of the ANDA and commercialization, the Company then will earn 50% of contractually-defined profits on Sandoz’s worldwide net sales of M356 (40 mg). Profits on net sales of Glatopa and M356 (40 mg) are calculated by deducting from net sales the costs of goods sold and an allowance for selling, general and administrative costs, which is a contractual percentage of net sales. Sandoz AG is responsible for funding all of the legal expenses incurred under the Second Sandoz Collaboration Agreement; however a portion of certain legal expenses, including any patent infringement damages, can be offset against the profit-sharing amounts in proportion to the Company’s 50% profit sharing interest.

For the three months ended September 30, 2015, the Company recorded $8.7 million in product revenues from Sandoz’s profits earned on sales of Glatopa. For the nine months ended September 30, 2015, the Company recorded $27.9 million in product revenues from Sandoz’s sales of Glatopa, reflecting $36.9 million in profits net of a deduction of $9.0 million for reimbursement to Sandoz of the Company’s 50% share of pre-launch Glatopa-related legal expenses. These expenses consist primarily of the costs incurred by Sandoz in connection with the patent infringement suit brought in 2008 by Teva Pharmaceuticals Industries Ltd. and related parties. See Note 9 “Commitments and Contingencies” for information on the suit. In the nine months ended September 30, 2015, the Company earned a $10.0 million regulatory milestone payment upon Glatopa receiving sole FDA approval and an additional $10.0 million milestone payment upon the first commercial sale. The Company is eligible to receive up to $143.0 million in additional milestone payments upon the achievement of certain commercial and sales-based milestones for Glatopa in the United States and Enoxaparin Sodium Injection in the European Union. The Glatopa milestone payments include up to $120.0 million in additional milestone payments upon the achievement of certain U.S. commercial and sales-based milestones for Glatopa. If Enoxaparin Sodium Injection is commercialized in the European Union, the Company is eligible to receive up to $23.0 million in sales-based and commercial milestones. None of these payments, once received, is refundable and there are no general rights of return in the arrangement. Sandoz AG has agreed to indemnify the Company for various claims, and a certain portion of such costs may be offset against certain future payments received by the Company.

The term of the Second Sandoz Collaboration Agreement extends throughout the development and commercialization of the products until the last sale of the products, unless earlier terminated by either party pursuant to the provisions of the Second Sandoz Collaboration Agreement. The Second Sandoz Collaboration Agreement may be terminated if either party breaches the Second Sandoz Collaboration Agreement or files for bankruptcy. In addition, either the Company or Sandoz AG may terminate the Second Sandoz Collaboration Agreement as it relates to the remaining products, on a product-by-product basis, if clinical trials are required.

The Company recognizes research and development revenue from FTE services and research and development revenue from external development costs upon completion of the performance requirements (i.e., as the services are performed and the reimbursable costs are incurred). Revenue from external development costs is recorded on a gross basis as the Company contracts directly with, manages the work of and is responsible for payments to third-party vendors for such development and related services, except with respect to any amounts due Sandoz for shared development costs, which are recorded on a net basis. See “Research and development services and external costs” in the tables above for research and development revenue earned by the Company from FTE services and external development costs under the 2006 Sandoz Collaboration.

Baxalta Agreement

In December 2011, the Company entered into a global collaboration and license agreement with Baxter International Inc., Baxter Healthcare Corporation and Baxter Healthcare SA (collectively, “Baxter”) to develop and commercialize biosimilars. The agreement became effective in February 2012. Effective as of July 1, 2015, Baxter completed its restructuring into two independent companies. In connection with the restructuring, in April 2015, Baxter assigned all of its rights and obligations under the collaboration agreement relating to M923 (the “Baxter Agreement”) to Baxalta U.S. Inc., Baxalta GmbH and Baxalta Incorporated (collectively, “Baxalta”). In light of the assignment, all references to “Baxter” and the “Baxter Agreement” have been replaced with references to “Baxalta” and the “Baxalta Agreement,” respectively.

Under the Baxalta Agreement, the Company and Baxalta agreed to collaborate, on a world-wide basis, on the development and commercialization of two biosimilars, M923, a biosimilar of HUMIRA® (adalimumab), and M834, a biosimilar of ORENCIA® (abatacept). In addition, Baxalta had the right to select four additional originator biologics to target for biosimilar development under the collaboration. In July 2012, Baxalta selected an additional product: M511, a biosimilar of AVASTIN® (bevacizumab). In December 2013, Baxalta terminated its option to license M511 under the Baxalta Agreement following an internal portfolio review. In February 2015, Baxalta’s right to select additional programs expired without being exercised. Also in February 2015, Baxalta terminated in part the Baxalta Agreement as it relates specifically to M834. The Company retains all worldwide development and commercialization rights for M834. The Baxalta Agreement remains in effect and unchanged with respect to M923.

Under the Baxalta Agreement, each party has granted the other an exclusive license under its intellectual property rights to develop and commercialize M923 for all therapeutic indications. The Company has agreed to provide development and related services on a commercially reasonable basis through the filing of an Investigational New Drug application, or IND, or equivalent application in the European Union for M923. Development and related services include high-resolution analytics, characterization, and product and process development. Baxalta is responsible for clinical development, manufacturing and commercialization activities and will exclusively distribute and market M923. The Company has the right to participate in a joint steering committee, consisting of an equal number of members from the Company and Baxalta, to oversee and manage the development and commercialization of M923 under the collaboration. Costs, including development costs, payments to third parties for intellectual property licenses, and expenses for legal proceedings, including the patent exchange process pursuant to the Biologics Price Competition and Innovation Act of 2009, will be borne by the parties in varying proportions, depending on the type of expense and the stage of development. The Company will generally be responsible for research and process development costs prior to filing an IND or equivalent application in the European Union, and the cost of in-human clinical trials, manufacturing in accordance with current good manufacturing practices and commercialization will be borne by Baxalta.

Baxalta has a right of first negotiation with respect to collaborating with the Company on the development of any biosimilar product candidate that could compete with M923 based on the same mechanism of action. This right is effective until December 2017, subject to certain restrictions as outlined in the Baxalta Agreement.

Under the terms of the Baxalta Agreement, the Company received an initial cash payment of $33.0 million, a $7.0 million license payment for achieving pre-defined “minimum development criteria” for M834, and $12.0 million in technical and development milestone payments in connection with the UK Medicines and Healthcare Products Regulatory Agency’s acceptance of Baxalta’s clinical trial application to initiate a pharmacokinetic clinical trial for M923. The Company is eligible to receive from Baxalta, in aggregate, up to $50.0 million in regulatory milestone payments for M923, on a sliding scale, where, based on the product’s regulatory application, there is a significant reduction in the scope of the clinical trial program required for regulatory approval.

In addition, if M923 is successfully developed and launched, Baxalta will be required to pay to the Company royalties on net sales of licensed products worldwide, with a base royalty rate in the high single digits with the potential for significant tiered increases based on the number of competitors, the interchangeability of the product, and the sales tier for the product. The maximum royalty with all potential increases would be slightly more than double the base royalty.

The term of the collaboration shall continue throughout the development and commercialization of M923 on a country-by-country basis until there is no remaining payment obligation with respect to the product in the relevant territory, unless earlier terminated by either party pursuant to the terms of the Baxalta Agreement.

The Baxalta Agreement may be terminated by:

either party for breach by or bankruptcy of the other party;

Baxalta for its convenience; or

the Company in the event Baxalta does not exercise commercially reasonable efforts to commercialize M923 in the United States or other specified countries, provided that the Company also has certain rights to directly commercialize M923, as opposed to terminating the Baxalta Agreement, in event of such a breach by Baxalta.

At the inception of the Baxalta Agreement, the Company identified seven deliverables under the arrangement in accordance with FASB’s ASU No. 2009-13: Multiple-Deliverable Revenue Arrangements (Topic 615). The deliverables were determined to include (i) the development and product licenses to the two initial biosimilars (M923 and M834) and the four additional biosimilars, (ii) the research and development services related to the two initial biosimilars and the four additional biosimilars and (iii) the Company’s participation in a joint steering committee. Baxalta’s termination of its option to license M511 in December 2013, Baxalta’s termination of M834 and the lapsing of Baxalta’s right to select additional products in February 2015 reduced the number of deliverables from seven to two and decreased the total consideration from $61.0 million to $40.0 million. The Company determined that the change in total consideration received and total deliverables under the arrangement represented a change in estimate and, as a result, the Company reallocated the revised total consideration of $40.0 million to the remaining deliverables under the agreement using the original best estimate of selling price. The remaining deliverables are the combined unit of account for the M923 license and the related research and development services and the Company’s participation on the joint steering committee. Of the $40.0 million, $39.6 million was allocated to the M923 product license together with the related research and development services and $0.4 million was allocated to the joint steering committee unit of accounting. The Company recognized the resulting change in revenue as a result of the decrease in deliverables and expected consideration on a prospective basis beginning in the first quarter of 2015. The Company records this revenue on a straight-line basis over the applicable performance period, which begins upon delivery of the development and product license and ends upon FDA approval of the product. The Company currently estimates that the performance period for M923 and for the joint steering committee is approximately six years. Refer to the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2014 for more information on the identification of deliverables and the allocation of arrangement consideration under the Baxalta Agreement. As of September 30, 2015, $24.4 million of revenue was deferred under this agreement, of which $9.8 million was included in current liabilities and $14.6 million was included in non-current liabilities in the consolidated balance sheet.

The Company recognizes research and development revenue from FTE services and research and development revenue from external development costs upon completion of the performance requirements (i.e., as the services are performed and the reimbursable costs are incurred). Revenue from external development costs is recorded on a gross basis as the Company contracts directly with, manages the work of and is responsible for payments to third-party vendors for such development and related services. Beginning in the second quarter of 2013, the Company commenced billing to Baxalta external development costs for reimbursable activities related to M923. Beginning in the second half of 2013, the Company commenced billing to Baxalta FTE fees related to M923. See tables above for research and development revenue earned by the Company under the Baxalta Agreement.

The Company has concluded that the M923 technical development milestones and the IND milestones pursuant to the Baxalta Agreement are substantive. The Company evaluated factors such as the scientific and regulatory risks that must be overcome to achieve these milestones, the level of effort and investment required and whether the milestone consideration is reasonable relative to all deliverables and payment terms in the arrangement in making this assessment. Revenues from the non-refundable, technical development and IND milestones were recognized upon successful accomplishment of the milestones as research and development revenue.

The regulatory milestones, along with any associated royalty or profit sharing payments, will be considered contingent fees that will be recorded as earned in future periods.