** **

**UNITED STATES**

**SECURITIES AND EXCHANGE COMMISSION**

**Washington, DC 20549**

 

**FORM 10-Q/A**

 

**Amendment No. 2**

 

**(MARK ONE)**

 

**x**** ****QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934**

** **

**For the quarterly period ended March 31, 2016**

 

**or**

 

**o**** ****TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934**

 

**For the Transition Period from              to             **

 

**Commission File Number 000-50797**

** **

**Momenta Pharmaceuticals, Inc.**

(Exact name of registrant as specified in its charter)

 

| **Delaware**                                                       |   | **04-3561634**                         |
|--------------------------------------------------------------------|--------|----------------------------------------|
| (State or other   jurisdiction of   incorporation or organization) |   | (I.R.S. Employer   Identification No.) |

 

| **675   West Kendall Street, Cambridge, MA** |   | **02142**  |
|----------------------------------------------|--------|------------|
| (Address of principal   executive offices)   |   | (Zip Code) |

 

**(617) 491-9700**

(Registrant’s telephone number, including area code)

 

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 and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted 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 and post 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, or a smaller reporting company. See definitions of “large accelerated filer,” “accelerated filer,” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

 
| Large accelerated filer x                  |   | Accelerated filer o           |
|-------------------------------------------------|--------|------------------------------------|
|                                            |   |                               |
| Non-accelerated   filer o                  |   | Smaller reporting   company o |
| (Do not check if a   smaller reporting company) |   |                               |

 

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 January 27, 2017, there were 71,312,626 shares of the registrant’s common stock, par value $0.0001 per share, outstanding.

 

 

 

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** **

**EXPLANATORY NOTE**

 

Momenta Pharmaceuticals, Inc. (the “Company”) is filing this Amendment No. 2 (this “Amendment”) to its Quarterly Report on Form 10-Q for the quarterly period ended March 31, 2016 (the “Original Form 10-Q”), as amended by Amendment No. 1 to the Original Form 10-Q filed on September 1, 2016, as an exhibit-only filing in response to further comments received from the Securities and Exchange Commission regarding a request for confidential treatment of certain portions of Exhibit 10.2 to the Original Form 10-Q. This Amendment is being filed solely to re-file Exhibit 10.2 to remove the redaction of certain information. In addition, as required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, new certifications by our principal executive officer and principal financial officer are filed as exhibits to this Amendment.

 

This Amendment is limited in scope to the items identified above and should be read in conjunction with the Original Form 10-Q, as amended. This Amendment does not reflect events occurring after the filing of the Original Form 10-Q, as amended, and no revisions are being made to the Company’s financial statements pursuant to this Amendment. Other than the filing of the information identified above, this Amendment does not modify or update the disclosure in the Original Form 10-Q, as amended, in any way.

 

**Item 6.    EXHIBITS**

 
| ** **           |   | ** **                                                                                                                                     |   | ** **                  |   | **Incorporated by Reference to** |
|----------------------|--------|------------------------------------------------------------------------------------------------------------------------------------------------|--------|-----------------------------|--------|-------------------------------------------------|
| **Exhibit   Number** |   | **Description**                                                                                                                                |   | **Form or   Schedule** |   | **Exhibit   No.**                               |   | **Filing   Date   with SEC** |   | **SEC File   Number** |
| **10.1               |   | Non-Employee Director Compensation Summary.                                                                                                    |   |                        |   |                                            |   |   |   |   |
|                 |   |                                                                                                                                           |   |                        |   |                                            |   |   |   |   |
| *+10.2               |   | Collaboration Agreement, by and between Momenta   Pharmaceuticals, Inc. and Mylan Ireland Limited, executed as of   January 8, 2016. |   |                        |   |                                            |   |   |   |   |
|                 |   |                                                                                                                                           |   |                        |   |                                            |   |   |   |   |
| *31.1                |   | Certification of Chief Executive Officer pursuant to   Section 302 of the Sarbanes-Oxley Act of 2002.                                     |   |                        |   |                                            |   |   |   |   |
|                 |   |                                                                                                                                           |   |                        |   |                                            |   |   |   |   |
| *31.2                |   | Certification of Chief Financial Officer pursuant to   Section 302 of the Sarbanes-Oxley Act of 2002.                                     |   |                        |   |                                            |   |   |   |   |
|                 |   |                                                                                                                                           |   |                        |   |                                            |   |   |   |   |
| **32.1               |   | Certifications of Chief Executive Officer and Chief   Financial Officer pursuant to Section 906 of the Sarbanes-Oxley Act of   2002.      |   |                        |   |                                            |   |   |   |   |
|                 |   |                                                                                                                                           |   |                        |   |                                            |   |   |   |   |
| **101.INS            |   | XBRL Instance Document.                                                                                                                        |   |                        |   |                                            |   |   |   |   |
|                 |   |                                                                                                                                           |   |                        |   |                                            |   |   |   |   |
| **101.SCH            |   | XBRL Taxonomy Extension Schema Document.                                                                                                       |   |                        |   |                                            |   |   |   |   |
|                 |   |                                                                                                                                           |   |                        |   |                                            |   |   |   |   |
| **101.CAL            |   | XBRL Taxonomy Calculation Linkbase Document.                                                                                                   |   |                        |   |                                            |   |   |   |   |
|                 |   |                                                                                                                                           |   |                        |   |                                            |   |   |   |   |
| **101.LAB            |   | XBRL Taxonomy Label Linkbase Document.                                                                                                         |   |                        |   |                                            |   |   |   |   |
|                 |   |                                                                                                                                           |   |                        |   |                                            |   |   |   |   |
| **101.PRE            |   | XBRL Taxonomy Presentation Linkbase Document.                                                                                                  |   |                        |   |                                            |   |   |   |   |
|                 |   |                                                                                                                                           |   |                        |   |                                            |   |   |   |   |
| **101.DEF            |   | XBRL Taxonomy Extension Definition Linkbase   Document.                                                                                        |   |                        |   |                                            |   |   |   |   |

 

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| **101.REF |   | XBRL Taxonomy Reference Linkbase Document. |   |   |   |   |   |   |   |   |
|-----------|--------|--------------------------------------------|--------|--------|--------|--------|--------|--------|--------|--------|

 

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*                                    Filed herewith.

 

**                             Previously filed or furnished with, or incorporated by reference in, the Original Form 10-Q.

 

+                                    Confidential treatment has been requested as to certain portions, which portions have been omitted and filed separately with the Securities and Exchange Commission.

 

The following materials were filed with the Original Form 10-Q for the period ended March 31, 2016, formatted in XBRL (Extensible Business Reporting Language): (i) the Condensed Consolidated Balance Sheets at March 31, 2016 and December 31, 2015, (ii) the Condensed Consolidated Statements of Operations and Comprehensive Loss for the three months ended March 31, 2016 and 2015, (iii) the Condensed Consolidated Statements of Cash Flows for the three months ended March 31, 2016 and 2015, and (iv) Notes to Unaudited, Condensed Consolidated Financial Statements.

 

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**SIGNATURES**

 

Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

 
|                          | Momenta   Pharmaceuticals, Inc. |
|-------------------------------|--------------------------------------|
|                          |                                 |   |
| Date: February 3,   2017 | By:                                  | /s/ Craig A. Wheeler |
|                          |                                 | Craig A.   Wheeler, President and Chief Executive Officer |
|                          |                                 | (Principal Executive   Officer) |
|                          |                                 |   |
|                          |                                 |   |
| Date: February 3,   2017 | By:                                  | /s/ Scott M. Storer |
|                          |                                 | Scott M. Storer, Senior   Vice President and Chief Financial Officer |
|                          |                                 | (Principal Financial   and Accounting Officer) |

 

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