PHARMACOPEIA INC
8-K, 1998-06-19
COMMERCIAL PHYSICAL & BIOLOGICAL RESEARCH
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<PAGE>
 
                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C.  20549

                                    FORM 8-K

                                 CURRENT REPORT

     PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934


        Date of Report (Date of earliest event reported):  June 12, 1998

                               PHARMACOPEIA, INC.
              (Exact name of registrant as specified in its charter)

<TABLE>
<S>                            <C>                           <C>
        Delaware                       0-27188                            33-0557266
(State or other jurisdiction   (Commission File Number)       (IRS Employer Identification No.)
 of incorporation)
</TABLE>


101 College Road East, Princeton, New Jersey                 08540
(Address of principal executive offices)                    (Zip Code)
 
Registrant's telephone number, including area code:         (609) 452-3600


                                 Not Applicable
          (Former name or former address, if changed from last report)


                                       1
<PAGE>
 
Item 2.  Acquisition or Disposition of Assets
         ------------------------------------

     (a)  On June 12, 1998, Pharmacopeia, Inc. ("Pharmacopeia") completed its
acquisition of Molecular Simulations Incorporated ("MSI") by merging Micro
Acquisition Corporation, a wholly-owned subsidiary of Pharmacopeia ("Micro"),
with and into MSI, pursuant to the previously announced Agreement and Plan of
Merger and Reorganization dated as of February 4, 1998 by and among
Pharmacopeia, MSI and Micro (the "Merger Agreement").

     Upon the merger of Micro with and into MSI (the "Merger"), each outstanding
share of Common Stock, par value $.001 per share, of MSI ("MSI Common Stock"),
Class B Common Stock, par value $.001 per share, of MSI, and Series A
Convertible Preferred Stock, par value $.01 per share, of MSI (except for any
shares held by MSI or any subsidiary of MSI (or held by MSI as treasury stock)
and any such shares held by Pharmacopeia or any subsidiary of Pharmacopeia) was
converted into the right to receive 0.5292 of a share of Pharmacopeia Common
Stock, par value $.0001 per share ("Pharmacopeia Common Stock").  In addition,
upon the Merger, each outstanding option to purchase shares of MSI Common Stock
was converted into an option to purchase that number of shares of Pharmacopeia
Common Stock determined by multiplying the number of shares of MSI Common Stock
subject to such option immediately prior to the Merger by 0.5292 (rounded down
to the nearest whole share), at an exercise price equal to the exercise price of
such option prior to the Merger divided by 0.5292 (rounded up to the nearest
hundredth of a cent).

     The foregoing description of the Merger Agreement is qualified in its
entirety by reference to the Merger Agreement, together with the respective
exhibits thereto, listed as Exhibit 2 hereto, which was filed as Exhibit 2 to
Pharmacopeia's Current Report on Form 8-K filed with the Securities and Exchange
Commission on February 5, 1998, and is incorporated herein by reference.

     Fees, expenses and other costs related to the Merger are expected to be
funded by Pharmacopeia from a combination of available cash and cash
equivalents.

     A copy of the press release of Pharmacopeia announcing completion of the
Merger is filed as an exhibit hereto and is incorporated herein by reference.

     (b)  Assets constituting plant, equipment or other physical property
acquired by Pharmacopeia in the Merger were used by MSI in the design,
development, marketing and sale of software products that facilitate the
discovery and development of new products and processes in the pharmaceutical,
biotechnology, chemical and materials industries.  Pharmacopeia currently
intends to use these assets in the same manner in which they were used prior to
the Merger.


                                       2
<PAGE>
 
Item 7.  Financial Statements, Pro Forma Financial Information and Exhibits
         ------------------------------------------------------------------

     (a) Financial Statements of Business Acquired - The financial statements
required to be filed are incorporated herein by reference.

     (b)  Pro Forma Financial Information - The pro forma financial statements
required to be filed are filed as an exhibit hereto and are incorporated herein
by reference.

     (c)  Exhibits:


Exhibit Number      Description
- --------------      -------------
 
2                   Agreement and Plan of Merger and Reorganization, dated as of
                    February 4, 1998, by and among Pharmacopeia, MSI and Micro.
                    (1)

23                  Consent of Arthur Andersen LLP.

99.1                Text of Press Release, dated June 12, 1998, issued by
                    Pharmacopeia.
 
99.2                Certificate of Merger of Micro Acquisition Corporation and
                    Molecular Simulations Incorporated as filed with the
                    Secretary of State of the State of Delaware on June 12,
                    1998.


99.3                MSI Audited (i) Consolidated Balance Sheets as of December
                    31, 1996 and 1997; (ii) Consolidated Statements of Income
                    for the years ended December 31, 1995, 1996 and 1997; (iii)
                    Consolidated Statements of Stockholders' Equity for the
                    years ended December 31, 1995, 1996 and 1997; (iv)
                    Consolidated Statements of Cash Flows for the years ended
                    December 31, 1995, 1996 and 1997; and (v) related Notes to
                    Consolidated Financial Statements.(2)


                                       3
<PAGE>
 
99.4                Pharmacopeia Unaudited Pro Forma (i) Combined Condensed
                    Balance Sheet as of December 31, 1997; (ii) Combined
                    Condensed Statements of Operations for the years ended
                    December 31, 1995, 1996 and 1997; and (iii) related Notes to
                    Combined Condensed Financial Statements.

99.5                Pharmacopeia Unaudited Pro Forma (i) Combined Condensed
                    Balance Sheet as of March 31, 1998; (ii) Combined Condensed
                    Statements of Operations for the three months ended March
                    31, 1998 and 1997; and (iii) related Notes to Combined
                    Condensed Financial Statements.

____________________
(1)  Filed as an Exhibit to Pharmacopeia's Current Report on Form 8-K filed with
     the Securities and Exchange Commission on February 5, 1998, and
     incorporated herein by reference.

(2)  Incorporated by reference to Pharmacopeia's Registration Statement on Form
     S-4 (Registration No. 333-47475).


                                       4
<PAGE>
 
                                    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 hereunto duly authorized.


                                    PHARMACOPEIA, INC.


                                    By: /s/ Lewis J. Shuster
                                       _________________________
                                      Lewis J. Shuster, Executive Vice
                                      President, Corporate Development and Chief
                                      Financial Officer

                                      (Duly Authorized Officer and Chief
                                      Accounting Officer)

Date:  June 19, 1998


                                       5
<PAGE>
 
                                 EXHIBIT INDEX

Exhibit

- --------------------------------------------------------------------------------

2                   Agreement and Plan of Merger and Reorganization, dated as of
                    February 4, 1998 by and among Pharmacopeia, MSI and
                    Micro.(1)

23                  Consent of Arthur Andersen LLP.

99.1                Text of Press Release, dated June 12, 1998, issued by
                    Pharmacopeia.
 
99.2                Certificate of Merger of Micro Acquisition Corporation and
                    Molecular Simulations Incorporated as filed with the
                    Secretary of State of the State of Delaware on June 12,
                    1998.

99.3                MSI Audited (i) Consolidated Balance Sheets as of December 
                    31, 1996 and 1997; (ii) Consolidated Statements of Income
                    for the years ended December 31, 1995, 1996 and 1997; (iii)
                    Consolidated Statements of Stockholders' Equity for the
                    years ended December 31, 1995, 1996 and 1997; (iv)
                    Consolidated Statements of Cash Flows for the years ended
                    December 31, 1995, 1996 and 1997; and (v) related Notes to
                    Consolidated Financial Statements.(2)

99.4                Pharmacopeia Unaudited Pro Forma (i) Combined Condensed
                    Balance Sheet as of December 31, 1997; (ii) Combined
                    Condensed Statements of Operations for the years ended
                    December 31, 1995, 1996 and 1997; and (iii) related Notes to
                    Combined Condensed Financial Statements.

99.5                Pharmacopeia Unaudited Pro Forma (i) Combined Condensed
                    Balance Sheet as of March 31, 1998; (ii) Combined Condensed
                    Statements of Operations for the three months ended March
                    31, 1998 and 1997; and (iii) related Notes to Combined
                    Condensed Financial Statements.

____________________
(1)  Filed as an Exhibit to Pharmacopeia's Current Report on Form 8-K filed with
     the Securities and Exchange Commission on February 5, 1998, and
     incorporated herein by reference.

(2)  Incorporated by reference to Pharmacopeia's Registration Statement on Form
     S-4 (Registration No. 333-47475).



                                       6

<PAGE>
 
                                                                      Exhibit 23

                   CONSENT OF INDEPENDENT PUBLIC ACCOUNTANTS

As independent public accountants, we hereby consent to the incorporation by
reference in this Form 8-K of our report dated February 4, 1998 included in 
Pharmacopeia, Inc.'s Registration Statement on Form S-4 (File No. 333-47475). It
should be noted that we have not audited any financial statements of the company
subsequent to December 31, 1997 or performed any audit procedures subsequent to
the date of our report.

                                             /s/ Arthur Andersen LLP
                                             ARTHUR ANDERSEN LLP


June 18, 1998
San Diego, California


<PAGE>
 
                                                                    Exhibit 99.1

                   [On the letterhead of Pharmacopeia, Inc.]


FOR IMMEDIATE RELEASE
- ----------------------
 
CONTACTS:
- ---------
Sue Rodney                         David Hiatt
Manager, Investor Relations        Chief Financial Officer
Pharmacopeia, Inc.                 Molecular Simulations Inc.
(609) 452-3600                     (619) 597-9747
[email protected]              [email protected]
 

                     PHARMACOPEIA COMPLETES ACQUISITION OF
                          MOLECULAR SIMULATIONS INC.
                                        
Princeton, New Jersey, June 12, 1998  Pharmacopeia, Inc. (Nasdaq: PCOP) today
announced that it has completed its acquisition of Molecular Simulations Inc.
(MSI).  Stockholders of both companies have approved the acquisition and all
associated proposals.

Joseph A. Mollica, Chairman, President and CEO of Pharmacopeia says, "We are
excited to move forward with the multitude of opportunities this acquisition
brings to the combined company.  Our technology platform is significantly
enhanced by adding MSI's expertise in molecular modeling, simulation, and
informatics software.  Furthermore, the collection of products and services we
can now offer our customer base is broadened with the addition of an established
software sales and services business.  With more than 500 employees,
headquarters in Princeton, NJ and major regional operations in San Diego, CA,
Cambridge, England, and Tokyo, Japan, the `new' Pharmacopeia is poised to help
its customers improve chemical research and development productivity throughout
the world."

Pharmacopeia originally announced its intention to acquire MSI on February 4,
1998.  Pharmacopeia has acquired all of the outstanding stock of MSI for
approximately 7.1 million newly-issued shares of Pharmacopeia common stock.
Pharmacopeia will also convert the outstanding MSI options into Pharmacopeia
options, potentially resulting in the net issuance of an additional 1.4 million
new Pharmacopeia shares.  The transaction has been structured as a tax-free
stock-for-stock exchange and will be accounted for as a pooling of interests.
The name of the company will remain Pharmacopeia and the stock will continue to
trade on the Nasdaq National Market under the symbol "PCOP".

Pharmacopeia is a leader in drug discovery combining three platform
technologies: informatics, small molecule combinatorial chemistry, and high-
throughput screening.  Through its wholly-owned subsidiary, Molecular
Simulations Inc. (MSI), Pharmacopeia develops and commercializes molecular
modeling, simulation, and informatics software and services. Using ECLiPS/TM/,
its proprietary combinatorial chemistry technology, Pharmacopeia has generated
more than 3.9


                                       1
<PAGE>
 
million diverse, easily identifiable, small molecules. Pharmacopeia tests these
molecules using state-of-the-art high-throughput screening. These technologies
are integrated to support the following businesses: 1) selling predictive
modeling, information management, and structure-based design software to the
life and materials science marketplace, 2) licensing collections of compounds to
pharmaceutical companies for evaluation in multiple drug discovery programs, 3)
identifying and optimizing lead compounds for specific targets provided by
customers, and 4) licensing drug development candidates developed in
Pharmacopeia's internal drug discovery programs to pharmaceutical companies.

                                      ###

This press release is available on Pharmacopeia's Website at http://www.pcop.com

Except for the historical information contained herein, this statement may
contain projections or other forward-looking statements regarding future events
or the future financial performance of the Company.  We wish to caution you that
such statements are just predictions and that actual events or results may
differ materially.  We refer you to the documents that the Company files from
time to time with the Securities and Exchange Commission, specifically the
Company's last filed Annual Report on Form 10-K and subsequent Quarterly Reports
on Form 10-Q.  These documents contain and identify important factors that could
cause the actual results to differ materially from those contained in our
projections or forward-looking statements.


                                       2

<PAGE>

                                                                    Exhibit 99.2
 
                            CERTIFICATE OF MERGER OF
                         MICRO ACQUISITION CORPORATION
                                 WITH AND INTO
                       MOLECULAR SIMULATIONS INCORPORATED

          Molecular Simulations Incorporated ("MSI"), organized and existing
under the General Corporation Law of the State of  Delaware, does hereby certify
as follows:

          FIRST:    The name and state of incorporation of each of the
constituent corporations (the "Constituent Corporations") to the merger are:

          Name                                          State
          ----                                          -----

          Molecular Simulations Incorporated            Delaware

          Micro Acquisition Corporation                 Delaware

          SECOND:  An Agreement and Plan of Merger and Reorganization, dated as
of February 4, 1998 (the "Merger Agreement"), by and among Pharmacopeia, Inc.,
MSI and Micro Acquisition Corporation ("Merger Subsidiary"), providing for the
merger of Merger Subsidiary with and into MSI, has been approved, adopted,
certified, executed and acknowledged in accordance with the requirements of
Section 251(c) of the General Corporation Law of the State of Delaware.

          THIRD:  The name of the surviving corporation is Molecular Simulations
Incorporated (the "Surviving Corporation").

          FOURTH:  As a result of the Merger, the Restated Certificate of
Incorporation of MSI shall be amended in its entirety to read as set forth in
Exhibit A attached hereto and, as amended, shall be the Amended and Restated
Certificate of Incorporation of the Surviving Corporation.

          FIFTH:  The executed Merger Agreement is on file at the office of the
Surviving Corporation located at 9685 Scranton Road, San Diego, California
92121.

          SIXTH:  A copy of the Merger Agreement will be furnished by the
Surviving Corporation, on request and without cost, to any stockholder of either
of the Constituent Corporations.

          IN WITNESS WHEREOF, MSI has caused this Certificate of Merger to be
duly executed in its corporate name this 12th day of June, 1998.


                         MOLECULAR SIMULATIONS INCORPORATED

                         By:  /s/ David B. Hiatt
                            --------------------
                           Name:  David B. Hiatt
                           Title:  Chief Financial Officer


                                       1
<PAGE>

                                                                       Exhibit A
 
                              AMENDED AND RESTATED

                          CERTIFICATE OF INCORPORATION

                                       OF

                       MOLECULAR SIMULATIONS INCORPORATED

        1. Name. The name of the Corporation is Molecular Simulations
           ----
Incorporated.

        2. Registered Office and Agent. The address of the Corporation's
           ---------------------------
registered office in the State of Delaware is 1209 Orange Street, in the City of
Wilmington, County of New Castle. The name of the Corporation's registered agent
at such address is The Corporation Trust Company.

        3. Purpose. The purposes for which the Corporation is formed are to
           -------
engage in any lawful act or activity for which corporations may be organized
under the General Corporation Law of Delaware and to possess and exercise all of
the powers and privileges granted by such law and any other law of Delaware.

        4. Authorized Capital. The aggregate number of shares of stock which the
           ------------------
Corporation shall have authority to issue is One Thousand (1,000) shares, all of
which are of one class and are designated as Common Stock and each of which has
a par value of One Cent ($.01).

        5. Bylaws. The board of directors of the Corporation is authorized to
           ------
adopt, amend or repeal the bylaws of the Corporation, except as otherwise
specifically provided therein.

        6. Elections of Directors. Elections of directors need not be by written
           ----------------------
ballot unless the bylaws of the Corporation shall so provide.

        7. Right to Amend. The Corporation reserves the right to amend any
           --------------
provision contained in this Certificate as the same may from time to time be in
effect in the manner now or hereafter prescribed by law, and all rights
conferred on stockholders or others hereunder are subject to such reservation.

        8. Limitation on Liability. The directors of the Corporation shall be
            -----------------------           
entitled to the benefits of all limitations on the liability of directors
generally that are now or hereafter become available under the General
Corporation Law of Delaware. Without limiting the generality of the foregoing,
no director of the Corporation shall be liable to the Corporation or its
stockholders for monetary damages for breach of fiduciary duty as a director,
except for liability (i) for any breach of the director's duty of loyalty to the
Corporation or its stockholders, (ii) for acts or omissions not in good faith or
which involve intentional misconduct or a knowing violation of Law, (iii) under
Section 174 of the Delaware General Corporation Law, or (iv) for any transaction
from which the director derived an improper personal benefit. Any repeal or
modification of this Section 8 shall be prospective only, and shall not affect,
to the detriment of any director, any limitation on the personal liability of a
director of the Corporation existing at the time of such repeal or modification.


                                       2

<PAGE>

                                                                    Exhibit 99.4
 
          UNAUDITED PRO FORMA COMBINED CONDENSED FINANCIAL STATEMENTS
 
  The following unaudited pro forma combined condensed financial statements
give effect to the merger (the "Merger") of Pharmacopeia's wholly-owned
subsidiary, Micro Acquisition Corporation, with and into Molecular Simulations
Incorporated ("MSI") under the pooling of interests accounting basis. The pro
forma combined condensed financial statements are derived from and should be
read in conjunction with the respective historical financial statements and the
notes thereto of Pharmacopeia and MSI. The pro forma combined condensed balance
sheet combines Pharmacopeia's December 31, 1997 audited balance sheet with MSI's
December 31, 1997 audited balance sheet as if the Merger occurred as of December
31, 1997. The pro forma combined condensed statements of operations combine
Pharmacopeia's historical condensed statements of operations for the fiscal
years ended December 31, 1995, 1996 and 1997 with the corresponding MSI
historical condensed statements of operations for the fiscal years ended
December 31, 1995, 1996 and 1997, respectively, and assume that the Merger was
consummated on January 1, 1995. The unaudited pro forma combined financial
statements presented herein are not necessarily indicative of the combined
results of operations or the combined financial position that would have
resulted had the Merger been consummated at the beginning of the applicable
periods indicated, nor are they necessarily indicative of the results of
operations in future periods or the future financial position of the combined
entity.
 
                                       1
<PAGE>
 
           PHARMACOPEIA, INC. AND MOLECULAR SIMULATIONS INCORPORATED
 
              UNAUDITED PRO FORMA COMBINED CONDENSED BALANCE SHEET
 
                               DECEMBER 31, 1997
                                 (IN THOUSANDS)
 
<TABLE>
<CAPTION>
                                                       MERGER        PRO FORMA
                                                     PRO FORMA      PHARMACOPEIA
                            PHARMACOPEIA   MSI     ADJUSTMENTS(3)  AND MSI MERGER
                            ------------ --------  --------------  --------------
<S>                         <C>          <C>       <C>             <C>
          ASSETS
Current assets:
  Cash and cash
   equivalents............    $  9,590   $ 15,019     $               $ 24,609
  Marketable securities...      60,166                                  60,166
  Trade receivables, net
   of allowance for doubt-
   ful accounts of $466...                 19,424                       19,424
  Deferred tax asset......                  2,100      (2,100)(4)
  Prepaid expenses and
   other current assets...       1,890      2,781                        4,671
                              --------   --------     -------         --------
    Total current assets..      71,646     39,324      (2,100)         108,870
                              --------   --------     -------         --------
Non-current investments in
 marketable securities....      12,865                                  12,865
Property and equipment,
 net......................      10,874      2,267                       13,141
Software development
 costs, net of accumulated
 amortization of $5,813...                  3,437                        3,437
Investment in joint
 venture..................                  1,013                        1,013
Other assets..............         302        423                          725
                              --------   --------     -------         --------
                              $ 95,687   $ 46,464     $(2,100)        $140,051
                              ========   ========     =======         ========
     LIABILITIES AND
    STOCKHOLDERS EQUITY
Current liabilities:
  Accounts payable........    $  1,756   $  2,476                     $  4,232
  Accrued liabilities.....       2,726     15,568                       18,294
  Notes payable, current
   portion................         690        700                        1,390
  Deferred revenue,
   current portion........      16,091     13,254                       29,345
                              --------   --------     -------         --------
    Total current
     liabilities..........      21,263     31,998                       53,261
                              --------   --------     -------         --------
Notes payable, long-term
 portion..................         712        700                        1,412
Other long-term
 liabilities..............                    440                          440
Deferred revenue, long
 term.....................       3,275      1,067                        4,342
Commitments
Stockholders equity:
  Preferred stock.........                     22         (22)(1)
  Common stock............           1         11         (11)(1)            1
  Additional paid in
   capital................     104,909     39,498          33 (1)      144,440
  Accumulated deficit.....     (34,473)   (26,084)     (2,100)(4)      (62,657)
  Cumulative translation
   adjustment.............                 (1,188)                      (1,188)
                              --------   --------     -------         --------
    Total stockholders
     equity...............      70,437     12,259      (2,100)          80,596
                              --------   --------     -------         --------
                              $ 95,687   $ 46,464     $(2,100)        $140,051
                              ========   ========     =======         ========
</TABLE>
 
   See Notes to Unaudited Pro Forma Combined Condensed Financial Statements.
 
                                       2
<PAGE>
 
                               PHARMACOPEIA, INC.
 
         UNAUDITED PRO FORMA COMBINED CONDENSED STATEMENT OF OPERATIONS
 
                          YEAR ENDED DECEMBER 31, 1995
                     (IN THOUSANDS, EXCEPT PER SHARE DATA)
 
<TABLE>
<CAPTION>
                                                                  PRO FORMA
                                                                 PHARMACOPEIA
                                          HISTORICAL  HISTORICAL   AND MSI
                                         PHARMACOPEIA    MSI        MERGER
                                         ------------ ---------- ------------
<S>                                      <C>          <C>        <C>
Revenue:
  Contract.............................    $ 5,151     $           $  5,151
  Software license, service and
   hardware............................                  30,120      30,120
                                           -------     --------    --------
      Total revenue....................      5,151       30,120      35,271
Operating Expenses:
  Research and development
    Collaborative......................      5,563                    5,563
    Proprietary........................      5,468        7,603      13,071
  Software licenses and hardware.......                   6,609       6,609
  Sales, general and administrative....      3,781       15,386      19,167
  Acquisition related charges..........                  12,161      12,161
                                           -------     --------    --------
      Total operating expenses.........     14,812       41,759      56,571
                                           -------     --------    --------
Operating loss.........................     (9,661)     (11,639)    (21,300)
Interest and other income, net.........        705          319       1,024
                                           -------     --------    --------
Loss before provision for income
 taxes.................................     (8,956)     (11,320)    (20,276)
Provision for income taxes.............                     560         560
                                           -------     --------    --------
Net loss...............................    $(8,956)    $(11,880)   $(20,836)
                                           =======     ========    ========
Basic net loss per share...............    $ (2.77)    $  (2.28)   $  (3.48)(2)
                                           =======     ========    ========
Weighted average number of common stock
 outstanding--basic....................      3,231        5,206       5,986
</TABLE>
 
 
   See Notes to Unaudited Pro Forma Combined Condensed Financial Statements.
 
                                       3
<PAGE>
 
                               PHARMACOPEIA, INC.
 
         UNAUDITED PRO FORMA COMBINED CONDENSED STATEMENT OF OPERATIONS
 
                          YEAR ENDED DECEMBER 31, 1996
                     (IN THOUSANDS, EXCEPT PER SHARE DATA)
 
<TABLE>
<CAPTION>
                                                                     PRO FORMA
                                                        MERGER      PHARMACOPEIA
                             HISTORICAL  HISTORICAL   PRO FORMA       AND MSI
                            PHARMACOPEIA    MSI     ADJUSTMENTS(3)     MERGER
                            ------------ ---------- --------------  ------------
<S>                         <C>          <C>        <C>             <C>
Revenue:
  Contract................    $ 14,799    $            $              $14,799
  Software license,
   service and hardware...                 47,261                      47,261
                              --------    -------      -------        -------
      Total revenue.......      14,799     47,261                      62,060
Operating expenses:
  Research and development
    Collaborative.........      13,129                                 13,129
    Proprietary...........       8,111     12,834                      20,945
  Software license and
   hardware...............                  7,759                       7,759
  Sales, general and
   administrative.........       5,617     22,968                      28,585
                              --------    -------      -------        -------
      Total operating
       expenses...........      26,857     43,561                      70,418
                              --------    -------      -------        -------
Operating income (loss)...     (12,058)     3,700                      (8,358)
Interest and other income,
 net......................       3,675        368                       4,043
                              --------    -------      -------        -------
Income (loss) before
 provision for income
 taxes....................      (8,383)     4,068                      (4,315)
Provision for income
 taxes....................                  1,471        1,600 (4)      3,071
                              --------    -------      -------        -------
Net income (loss).........    $ (8,383)   $ 2,597      $(1,600)       $(7,386)
                              ========    =======      =======        =======
Basic net income (loss)
 per share................    $   (.77)   $   .27                     $  (.47)(2)
Diluted net income (loss)
 per share................    $   (.77)   $   .17                     $  (.47)(2)
Weighted average number of
 common stock,
 outstanding--basic.......      10,834      9,531                      15,878
Weighted average number of
 common stock, and common
 stock equivalents
 outstanding--diluted.....      10,834     15,160                      15,878
</TABLE>
 
 
   See Notes to Unaudited Pro Forma Combined Condensed Financial Statements.
 
                                       4
<PAGE>
 
                               PHARMACOPEIA, INC.
 
         UNAUDITED PRO FORMA COMBINED CONDENSED STATEMENT OF OPERATIONS
 
                          YEAR ENDED DECEMBER 31, 1997
                     (IN THOUSANDS, EXCEPT PER SHARE DATA)
 
<TABLE>
<CAPTION>
                                                                    PRO FORMA
                                                        MERGER     PHARMACOPEIA
                             HISTORICAL  HISTORICAL   PRO FORMA      AND MSI
                            PHARMACOPEIA    MSI     ADJUSTMENTS(3)    MERGER
                            ------------ ---------- -------------- ------------
<S>                         <C>          <C>        <C>            <C>
Revenue:
  Contract revenue........    $ 24,523    $             $            $24,523
  Software license,
   service and hardware...                 56,674                     56,674
                              --------    -------       -----        -------
      Total revenue.......      24,523     56,674                     81,197
Operating expenses:
  Research and development
    Collaborative.........      16,931                                16,931
    Proprietary...........      12,588     12,663                     25,251
  Software license and
   hardware...............                 10,232                     10,232
  Sales, general and
   administrative.........       5,848     25,959                     31,807
                              --------    -------       -----        -------
      Total operating
       expenses...........      35,367     48,854                     84,221
                              --------    -------       -----        -------
Operating income (loss)...     (10,844)     7,820                     (3,024)
Interest and other income,
 net......................       4,166        126                      4,292
                              --------    -------       -----        -------
Income (loss) before
 provision for income
 taxes....................      (6,678)     7,946                      1,268
Provision for income
 taxes....................                  2,496         500 (4)      2,996
                              --------    -------       -----        -------
Net income (loss).........    $ (6,678)   $ 5,450       $(500)       $(1,728)
                              ========    =======       =====        =======
Basic net income (loss)
 per share................    $   (.58)   $   .56                    $  (.10)(2)
Diluted net income per
 share....................    $   (.58)   $   .35                    $  (.10)(2)
Weighted average number of
 common stock
 outstanding--basic.......      11,454      9,709                     16,592
Weighted average number of
 common stock, and common
 stock equivalents
 outstanding--diluted.....      11,454     15,567                     16,592
</TABLE>
 
 
   See Notes to Unaudited Pro Forma Combined Condensed Financial Statements.
 
                                       5
<PAGE>
 
                     NOTES TO UNAUDITED PRO FORMA COMBINED
 
                        CONDENSED FINANCIAL STATEMENTS
 
(1) The Merger, which was completed on June 12, 1998, is being accounted for as
    a pooling of interests, and accordingly, the related pro forma adjustments
    herein reflect, where applicable, an Exchange Ratio of 0.5292 of a share of
    Pharmacopeia Common Stock for each outstanding share of MSI Common Stock,
    each outstanding share of MSI Class B Common Stock and each outstanding
    share of MSI Preferred Stock.

    As a result, information was adjusted for the Merger by the (i) addition of
    7,017,583 shares of Pharmacopeia Common Stock, (ii) elimination of
    9,791,633 shares of MSI Common Stock, elimination of 1,246,882 shares of
    MSI Class B Common Stock, and elimination of 2,222,223 shares of MSI
    Preferred Stock, and (iii) recording of approximately $33,000 as an
    increase to additional paid in capital at December 31, 1997.
 
(2) Pro forma loss per share data has been computed based on the combined
    historical net loss applicable to common stockholders of Pharmacopeia
    using the historical weighted average shares outstanding of Pharmacopeia
    Common Stock and the weighted average outstanding shares of MSI, adjusted
    to equivalent shares of Pharmacopeia Common Stock.
 
(3) The unaudited pro forma combined condensed financial statements do not
    include any material expenses related to the Merger, which are currently
    estimated to be $6,700,000 and are expected to be incurred in the second and
    third quarter of 1998.
 
(4) Reflects the reversal of a reduction to a valuation allowance for deferred
    tax assets during 1996 and 1997 of $1,600,000 and $500,000, respectively,
    which would not be expected to be realized given the combined tax position
    of the merged entity.
 
                                       6

<PAGE>
                                                                    Exhibit 99.5


                         UNAUDITED PRO FORMA COMBINED
                        CONDENSED FINANCIAL STATEMENTS

The following unaudited pro forma combined condensed financial statements give
effect to the merger (the "Merger") of Pharmacopeia's wholly-owned subsidiary,
Micro Acquisition Corporation, with and into Molecular Simulations Incorporated
("MSI") under the pooling of interests accounting basis. The pro forma combined
condensed financial statements are derived from and should be read in
conjunction with the respective historical financial statements and the notes
thereto of Pharmacopeia and MSI. The pro forma combined condensed balance sheet
combines Pharmacopeia's March 31, 1998 unaudited balance sheet with MSI's March
1998 unaudited balance sheet as if the Merger occurred as of March 31, 1998. The
pro forma combined condensed statements of operations combine Pharmacopeia's
historical condensed statements of operations for the unaudited three month
periods ended March 31, 1998 and 1997 with the corresponding MSI historical
condensed statements of operations for the unaudited three month periods ended
March 31, 1998 and 1997, respectively, and assume that the Merger was
consummated on January 1, 1997. The unaudited pro forma combined financial
statements presented herein are not necessarily indicative of the combined
results of operations or the combined financial position that would have
resulted had the Merger been consummated at the beginning of the applicable
periods indicated, nor are they necessarily indicative of the results of
operations in future periods or the future financial position of the combined
entity.
 
                                       1
<PAGE>
 
           PHARMACOPEIA, INC. AND MOLECULAR SIMULATIONS INCORPORATED
              UNAUDITED PRO FORMA COMBINED CONDENSED BALANCE SHEET
 
                                MARCH 31, 1998
                                (IN THOUSANDS)
 
<TABLE>
<CAPTION>
                                                       MERGER        PRO FORMA
                                                     PRO FORMA      PHARMACOPEIA
                            PHARMACOPEIA   MSI     ADJUSTMENTS(3)  AND MSI MERGER
                            ------------ --------  --------------  --------------
<S>                         <C>          <C>       <C>             <C>
          ASSETS
Current assets:
  Cash and cash
   equivalents............    $  3,492   $ 18,054     $               $ 21,546
  Marketable securities...      64,244                                  64,244
  Trade receivables, net
   of allowance for doubt-
   ful accounts of $396...                 11,158                       11,158
  Deferred tax asset......                  2,100      (2,100)(4)
  Prepaid expenses and
   other current assets...       2,458      3,223                        5,681
                              --------   --------     -------         --------
    Total current assets..      70,194     34,535      (2,100)         102,629
                              --------   --------     -------         --------
Non-current investments in
 marketable securities....       8,719                                   8,719
Property and equipment,
 net......................      10,528      2,637                       13,165
Software development
 costs, net of accumulated
 amortization of $6,141...                  3,483                        3,483
Other assets..............         329        795                        1,124
                              --------   --------     -------         --------
                              $ 89,770   $ 41,450     $(2,100)        $129,120
                              ========   ========     =======         ========
     LIABILITIES AND
    STOCKHOLDERS EQUITY
Current liabilities:
  Accounts payable........    $    993   $  1,739                     $  2,732
  Accrued liabilities.....       1,818     11,265                       13,083
  Notes payable, current
   portion................         680        700                        1,380
  Deferred revenue,
   current portion........      15,322     11,788                       27,110
                              --------   --------     -------         --------
    Total current
     liabilities..........      18,813     25,492                       44,305
                              --------   --------     -------         --------
Notes payable, long-term
 portion..................         558                                     558
Minority Interest.........         976                                     976
Other long-term
 liabilities..............                    363                          363
Deferred revenue, long
 term.....................       1,993        988                        2,981
Commitments
Stockholders equity:
  Preferred stock.........                     22         (22)(1)
  Common stock............           1         11         (11)(1)            1
  Additional paid in
   capital................     105,103     39,596          33 (1)      144,732
  Accumulated deficit.....     (36,698)   (24,643)     (2,100)(4)      (63,441)
  Cumulative translation
   adjustment.............                 (1,355)                      (1,355)
                              --------   --------     -------         --------
    Total stockholders
     equity...............      68,406     13,631      (2,100)          79,937
                              --------   --------     -------         --------
                              $ 89,770   $ 41,450     $(2,100)        $129,120
                              ========   ========     =======         ========
</TABLE>
 
   See Notes to Unaudited Pro Forma Combined Condensed Financial Statements.
 
                                       2
<PAGE>
 
                              PHARMACOPEIA, INC.
        UNAUDITED PRO FORMA COMBINED CONDENSED STATEMENT OF OPERATIONS
                         QUARTER ENDED MARCH 31, 1998
                     (In thousands, except per share data)
 
<TABLE>
<CAPTION>
                                                          MERGER        PRO FORMA
                                                        PRO FORMA      PHARMACOPEIA
                               PHARMACOPEIA   MSI     ADJUSTMENTS(3)  AND MSI MERGER
                               ------------ --------  --------------  --------------   
<S>                            <C>          <C>       <C>             <C>
Revenue:                  
  Contract                     $     6,432  $         $               $        6,432
  Software license, 
   and other                                  13,054                          13,054
  Hardware                                     1,066                           1,066
                               -----------  --------  --------------  --------------  
     Total Revenue                   6,432    14,120                          20,552
                          
Cost and expenses:                                                            
  Software, license 
   and other                                     769                             769
  Hardware                                       871                             871
  Research and development                                                    
    Collaborative                    4,420                                     4,420
    Proprietary                      3,724     3,033                           6,757
  Sales, general                                                      
   and administrative                1,587     7,054                           8,641
                               -----------  --------  --------------  --------------  
     Total cost and expenses         9,731    11,727                          21,458
                               -----------  --------  --------------  --------------  
Operating income/(loss)             (3,299)    2,393                            (906)
Interest and other income, net       1,073       (31)                          1,042 
                               -----------  --------  --------------  --------------  
Income/(loss) before provision                                                
 for income taxes                   (2,226)    2,362                             136
Provision for income taxes                       838             90(4)           928
                               -----------  --------  --------------  --------------  
Net income/(loss)              $    (2,226)    1,524  $         (90)  $         (792)
                               ===========  ========  ==============  ==============  
Basic net income/(loss) 
 per share                       $   (.19)  $    .15                     $   (.05)(2)
Diluted net income per share     $   (.19)  $    .10                     $   (.05)(2) 
Weighted average number of 
 common stock, outstanding      
 basic                             11,798      9,836                       17,003        
Weighted average number of 
 common stock, and common 
 stock equivalents 
 outstanding-diluted               11,798     16,039                       17,033
                          
                          
                              
</TABLE>
 
   See Notes to Unaudited Pro Forma Combined Condensed Financial Statements.
 
                                       3

<PAGE>
 
                              PHARMACOPEIA, INC.
        UNAUDITED PRO FORMA COMBINED CONDENSED STATEMENT OF OPERATIONS
                         QUARTER ENDED MARCH 31, 1997
                     (In thousands, except per share data)
 
<TABLE>
<CAPTION>
                                                          MERGER        PRO FORMA
                                                        PRO FORMA      PHARMACOPEIA
                               PHARMACOPEIA   MSI     ADJUSTMENTS(3)  AND MSI MERGER
                               ------------ --------  --------------  --------------   
<S>                            <C>          <C>       <C>             <C>
Revenue:                  
  Contract                     $     5,932  $         $               $        5,932
  Software license, 
   and other                                  11,304                          11,304
  Hardware                                     1,410                           1,410
                               -----------  --------  --------------  --------------  
     Total Revenue                   5,932    12,714                          18,646
                          
Cost and expenses:                                                            
  Software, license 
   and other                                     799                             799
  Hardware                                     1,238                           1,238
  Research and development                                                    
    Collaborative                    4,151                                     4,151
    Proprietary                      2,729     3,404                           6,133
  Sales, general                                                      
   and administrative                1,458     5,462                           6,920
                               -----------  --------  --------------  --------------  
     Total cost and expenses         8,338    10,903                          19,241
                               -----------  --------  --------------  --------------  
Operating income/(loss)             (2,406)    1,811                            (595)
Interest and other income, net         997       (80)                            917 
                               -----------  --------  --------------  --------------  
Income/(loss) before provision                                                
 for income taxes                   (1,409)    1,731                             322
Provision for income taxes                       544           109 (4)           653
                               -----------  --------  --------------  --------------  
Net income/(loss)              $    (1,409)    1,187  $       (109)   $         (331)
                               ===========  ========  ==============  ==============  
Basic net income/(loss) 
 per share                       $   (.13)  $    .12                     $   (.02)(2)
Diluted net income per share     $   (.13)  $    .08                     $   (.02)(2) 
Weighted average number of 
 common stock, outstanding      
 basic                             11,270      9,695                       16,400        
Weighted average number of 
 common stock, and common 
 stock equivalents 
 outstanding-diluted               11,270     15,461                       16,400
                          
                          
                              
</TABLE>
 
   See Notes to Unaudited Pro Forma Combined Condensed Financial Statements.
 
                                       4
<PAGE>
 
                     NOTES TO UNAUDITED PRO FORMA COMBINED
                        CONDENSED FINANCIAL STATEMENTS

(1)     The Merger, which was completed on June 12, 1998, is being accounted for
        as a pooling of interests, and accordingly, the related pro forma
        adjustments herein reflect, where applicable, an exchange ratio of
        0.5292 of a share of Pharmacopeia Common Stock for each outstanding
        share of MSI Common Stock, each outstanding share of MSI Class B Common
        Stock and each outstanding share of MSI Preferred Stock.

        As a result, information was adjusted for the Merger by the (i) addition
        of 7,069,365 shares of Pharmacopeia Common Stock, (ii) elimination of
        9,889,483 shares of MSI Common Stock, elimination of 1,246,882 shares of
        MSI Class B Common Stock, and elimination of 2,222,223 shares of MSI
        Preferred Stock, and (iii) recording of approximately $33,000 as an
        increase to additional paid in capital at March 31, 1998.

(2)     Pro forma loss per share data has been computed based on the combined
        historical net loss applicable to common stockholders of Pharmacopeia
        using the historical weighted average shares outstanding of Pharmacopeia
        Common Stock and the weighted average outstanding shares of MSI,
        adjusted to equivalent shares of Pharmacopeia Common Stock.

(3)     The unaudited pro forma combined condensed financial statements do not
        include any material expenses related to the Merger, which are currently
        estimated to be $6,700,000 and are expected to be incurred in the
        second and third quarter of 1998.

(4)     Reflects the reversal of a reduction to a valuation allowance for
        deferred tax assets during the three month periods ended March 31, 1998
        and 1997 of $90,000 and $109,000, respectively, which would not be
        expected to be realized given the combined tax position of the merger
        entity.


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