ATLAS VENTURE FUND II L P
SC 13G/A, 1999-02-12
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                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                  SCHEDULE 13G

                    UNDER THE SECURITIES EXCHANGE ACT OF 1934
                               (AMENDMENT NO.     1      )*
                                              ----------

                                              
                                    ILOG S.A.
- --------------------------------------------------------------------------------
                                (Name of Issuer)


                          AMERICAN DEPOSITORY RECEIPTS
- --------------------------------------------------------------------------------
                         (Title of Class of Securities)

                                   0004523601
                      ------------------------------------
                                 (CUSIP Number)


- --------------------------------------------------------------------------------
             (Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule
is filed:

[ ] Rule 13d-1(b)
[ ] Rule 13d-1(c)
[X] Rule 13d-1(d)

*The remainder of this cover page shall be filled out for a reporting person's
initial filing on this form with respect to the subject class of securities, and
for any subsequent amendment containing information which would alter the
disclosures provided in a prior cover page.

The information required in the remainder of this cover page shall not be deemed
to be "filed" for the purpose of Section 18 of the Securities Exchange Act of
1934 ("Act") or otherwise subject to the liabilities of that section of the Act
but shall be subject to all other provisions of the Act (however, see the
Notes).


                               Page 1 of 17 Pages


<PAGE>   2


- --------------------------                            --------------------------
 CUSIP NO.  0004523601                 13G             Page   2  of  17  Pages
- --------------------------                            --------------------------


- --------------------------------------------------------------------------------
1     NAME OF REPORTING PERSON
      S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

      Atlas Venture Fund II, L.P.
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* 
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      Delaware Limited Partnership
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  0 shares
           SHARES             --------------------------------------------------
        BENEFICIALLY            6    SHARED VOTING POWER
          OWNED BY
            EACH                     1,065,491 shares
         REPORTING            --------------------------------------------------
           PERSON               7    SOLE DISPOSITIVE POWER
            WITH:
                                     0 shares
                              --------------------------------------------------
                                8    SHARED DISPOSITIVE POWER

                                     1,065,491 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      1,065,491 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      7.8%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON* 

      PN
- --------------------------------------------------------------------------------


                               Page 2 of 17 Pages


<PAGE>   3


- --------------------------                            --------------------------
 CUSIP NO.  0004523601                 13G             Page   3  of  17 Pages
- --------------------------                            --------------------------


- --------------------------------------------------------------------------------
1     NAME OF REPORTING PERSON
      S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSONS 

      Atlas Venture Associates II, L.P.
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      Delaware Limited Partnership
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

           NUMBER OF                 0 shares
            SHARES            --------------------------------------------------
         BENEFICIALLY           6    SHARED VOTING POWER
           OWNED BY
             EACH                    1,065,491 shares
          REPORTING           --------------------------------------------------
            PERSON              7    SOLE DISPOSITIVE POWER
             WITH:
                                     0 shares
                              --------------------------------------------------
                                8    SHARED DISPOSITIVE POWER

                                     1,065,491 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      1,065,491 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      7.8%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON*

      PN
- --------------------------------------------------------------------------------


                               Page 3 of 17 Pages


<PAGE>   4


- --------------------------                            --------------------------
 CUSIP NO.  0004523601                13G             Page   4   of   17  Pages
- --------------------------                            --------------------------



- --------------------------------------------------------------------------------
1     NAMES OF REPORTING PERSON
      S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

      Atlas Venture Europe Fund B.V. 
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      The Netherlands
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  0 shares
           SHARES             --------------------------------------------------
        BENEFICIALLY            6    SHARED VOTING POWER
          OWNED BY
            EACH                     1,065,491 shares
         REPORTING            --------------------------------------------------
           PERSON               7    SOLE DISPOSITIVE POWER
            WITH:
                                     0 shares
                              --------------------------------------------------
                                8    SHARED DISPOSITIVE POWER

                                     1,065,491 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      1,065,491 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*  [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      7.8%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON*

      CO
- --------------------------------------------------------------------------------


                               Page 4 of 17 Pages


<PAGE>   5


- --------------------------                            --------------------------
 CUSIP NO.  0004523601                13G             Page   5   of   17 Pages
- --------------------------                            --------------------------



- --------------------------------------------------------------------------------
1     NAMES OF REPORTING PERSON
      S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

      Atlas InvesteringsGroep N.V.
- --------------------------------------------------------------------------------
2     CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                        (a) [ ]
                                                                        (b) [ ]
- --------------------------------------------------------------------------------
3     SEC USE ONLY

- --------------------------------------------------------------------------------
4     CITIZENSHIP OR PLACE OF ORGANIZATION

      The Netherlands
- --------------------------------------------------------------------------------
                                5    SOLE VOTING POWER

          NUMBER OF                  0 shares
           SHARES             --------------------------------------------------
        BENEFICIALLY            6    SHARED VOTING POWER
          OWNED BY
            EACH                     1,065,491 shares
         REPORTING            --------------------------------------------------
           PERSON               7    SOLE DISPOSITIVE POWER
            WITH:
                                     0 shares
                              --------------------------------------------------
                                8    SHARED DISPOSITIVE POWER

                                     1,065,491 shares
- --------------------------------------------------------------------------------
9     AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

      1,065,491 shares
- --------------------------------------------------------------------------------
10    CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*  [ ]

- --------------------------------------------------------------------------------
11    PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

      7.8%
- --------------------------------------------------------------------------------
12    TYPE OF REPORTING PERSON*

      CO
- --------------------------------------------------------------------------------


                               Page 5 of 17 Pages


<PAGE>   6


                                  SCHEDULE 13G

Item 1(a).  NAME OF ISSUER:  ILOG S.A.

Item 1(b).  ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES:
            9, rue de Verdun, 94253 Gentilly, France.

Item 2(a).  NAMES OF PERSONS FILING:  Atlas Venture Fund II, L.P., Atlas 
            Venture Associates II, L.P., Atlas Venture Europe Fund B.V. and
            Atlas InvesteringsGroep N.V.

            Atlas Venture Associates II, L.P. is the sole general partner of
            Atlas Venture Fund II, L.P. Atlas InvesteringsGroep N.V. is the sole
            shareholder of Atlas Venture Europe Fund B.V.

Item 2(b).  ADDRESS OF PRINCIPAL BUSINESS OFFICE OR, IF NONE, RESIDENCE: The
            address of the principal business office of Atlas Venture Fund II,
            L.P. and Atlas Venture Associates II, L.P. is Atlas Venture, 222
            Berkeley Street, Boston, Massachusetts 02116. The address of the
            principal business office of Atlas Venture Europe Fund B.V. and
            Atlas InvesteringsGroep N.V. is Atlas InvesteringsGroep N.V.,
            Naarderpoort 1, 1411 MA Naarden, The Netherlands.

Item 2(c).  CITIZENSHIP: Atlas Venture Fund II, L.P. and Atlas Venture
            Associates II, L.P. are each a limited partnership organized under
            the laws of the State of Delaware. Atlas Venture Europe Fund B.V.
            and Atlas InvesteringsGroep N.V. are each a corporation organized
            under the laws of The Netherlands.

Item 2(d).  TITLE OF CLASS OF SECURITIES:  American Depositary Receipts

Item 2(e).  CUSIP NUMBER:  0004523601

Item 3.     IF THIS STATEMENT IS FILED PURSUANT TO RULES 13d-1(b), OR 13D-2(b) 
            or (c), CHECK WHETHER THE PERSON FILING IS A:
            
            Not Applicable.

Item 4.     OWNERSHIP.

            (a)   Amount Beneficially Owned:

            Each of Atlas Venture Fund II, L.P., Atlas Venture Associates II,
            L.P., Atlas Venture Europe Fund B.V. and Atlas InvesteringsGroep
            N.V. (individually an "Entity" and collectively the "Entities") may
            be deemed to own beneficially 1,065,491 shares of Common Stock as of
            December 31, 1998 (the "Beneficial Shares").

            As of December 31, 1998, Atlas Venture Fund II, L.P. is the record
            owner of 344,380 shares of Common Stock and Atlas Venture Europe
            Fund B.V. is the record owner of 488,944 shares of Common Stock. In
            addition, an affiliate of


                               Page 6 of 17 Pages


<PAGE>   7


                  the Entities shares dispositive and voting control with
                  certain third parties as to 232,167 shares held by Parquest
                  Venture Partnership. By virtue of the affiliate relationships
                  among the Entities, each Entity may be deemed to own
                  beneficially all of the Beneficial Shares. Hence, each Entity
                  may be deemed to own beneficially 1,065,491 shares of Common
                  Stock.

            (b)   Percent of Class:

                  Atlas Venture Fund II, L.P.                           7.8%
                  Atlas Venture Associates II, L.P.                     7.8%
                  Atlas Venture Europe Fund B.V.                        7.8%
                  Atlas InvesteringsGroep N.V.                          7.8%

            The foregoing percentages are calculated based on the 13,740,677
            shares of Common Stock reported to be outstanding in an Annual
            Report on Form 20-F for ILOG S.A. for the year ended June 30, 1998.

            (c)   Number of shares as to which such person has:

                  (i)   sole power to vote or to direct the vote:

                        0 shares for each reporting person

                  (ii)  shared power to vote or to direct the vote:

                        Atlas Venture Fund II, L.P.          1,065,491 shares
                        Atlas Venture Associates II, L.P.    1,065,491 shares
                        Atlas Venture Europe Fund B.V.       1,065,491 shares
                        Atlas InvesteringsGroep N.V.         1,065,491 shares

                  (iii) sole power to dispose or to direct the disposition of:

                        0 shares for each reporting person

                  (iv)  shared power to dispose or to direct the disposition of:

                        Atlas Venture Fund II, L.P.          1,065,491 shares
                        Atlas Venture Associates II, L.P.    1,065,491 shares
                        Atlas Venture Europe Fund B.V.       1,065,491 shares
                        Atlas InvesteringsGroep N.V.         1,065,491 shares

            Each of the reporting persons expressly disclaims beneficial
            ownership of any shares of Common Stock of ILOG S.A., except in the
            case of (i) Atlas Venture Fund II, L.P. for the 344,380 shares which
            it holds of record and (ii) Atlas Venture Europe Fund B.V. for the
            488,944 shares which it holds of record.

Item  5.    OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS.

            Not Applicable.


                               Page 7 of 17 Pages


<PAGE>   8


Item  6.    OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER PERSON.

            Not Applicable.

Item  7.    IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH ACQUIRED
            THE SECURITY BEING REPORTED ON BY THE PARENT HOLDING COMPANY.

            Not Applicable.

Item  8.    IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF THE GROUP.

            Not Applicable. The reporting persons expressly disclaim membership
            in a "group" as defined in Rule 13d-1(b)(1)(ii)(J).

Item  9.    NOTICE OF DISSOLUTION OF GROUP.

            Not Applicable.

Item 10.    CERTIFICATIONS.

            Not Applicable. This statement on Schedule 13G is not filed pursuant
            to Rule 13d-1(b) or Rule 13d-1(c).


                               Page 8 of 17 Pages

<PAGE>   9


                                   SIGNATURES

     After reasonable inquiry and to the best of our knowledge and belief, we
certify that the information set forth in this statement is true, complete and
correct. We also hereby agree to file this statement jointly pursuant to the
Agreement listed on EXHIBIT 1 hereto.

Dated:  February 10, 1999


ATLAS VENTURE FUND II, L.P.                 ATLAS INVESTERINGSGROEP N.V.


By: Atlas Venture Associates II, L.P.

                                            By:        *        
                                                --------------------------------
                                                Michiel de Haan,
                                                Managing Director
 
By:                *            
   ------------------------------------
    Christopher J. Spray,
    General Partner                         ATLAS VENTURE EUROPE FUND B.V.


ATLAS VENTURE ASSOCIATES II, L.P.           By: Atlas InvesteringsGroep N.V.


By:                *                        By:           *                   
    -----------------------------------         --------------------------------
    Christopher J. Spray,                       Michiel de Haan,
    General Partner                             Managing Director




*     The undersigned attorney-in-fact, by signing her name below, does hereby
      sign this statement on behalf of the above indicated filers pursuant to
      Powers of Attorney filed hereto as EXHIBIT 2.

     /s/ Jeanne Larkin Henry                                 
     ----------------------------------
     Jeanne Larkin Henry
     Attorney-in-fact


                               Page 9 of 17 Pages



<PAGE>   1


                                                                     EXHIBIT 1

                                    AGREEMENT

     Pursuant to Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, the
undersigned hereby agree that only one statement containing the information
required by Schedule 13G need be filed with respect to the ownership by each of
the undersigned of shares of Common Stock of ILOG S.A.

     This agreement may be executed in any number of counterparts, each of which
shall be deemed an original.

     EXECUTED this 10th day of February, 1999.


ATLAS VENTURE FUND II, L.P.                 ATLAS INVESTERINGSGROEP N.V.


By: Atlas Venture Associates II, L.P.
                                            By:                * 
                                                --------------------------------
                                               Michiel de Haan,
                                               Managing Director

By:              *          
    ----------------------------------
    Christopher J. Spray,
    General Partner                         ATLAS VENTURE EUROPE FUND B.V.


ATLAS VENTURE ASSOCIATES II, L.P.           By: Atlas InvesteringsGroep N.V.
                                                --------------------------------


By:              *                          By:                 *            
    ----------------------------------          -------------------------------
    Christopher J. Spray,                       Michiel de Haan,
    General Partner                             Managing Director



*     The undersigned attorney-in-fact, by signing her name below, does hereby
      sign this statement on behalf of the above indicated filers pursuant to
      Powers of Attorney filed hereto as EXHIBIT 2.

     /s/ Jeanne Larkin Henry                                 
     ---------------------------------
     Jeanne Larkin Henry
     Attorney-in-fact



                              Page 10 of 17 Pages



<PAGE>   1


                                                                     EXHIBIT 2

                                POWER OF ATTORNEY

     KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears
below hereby constitutes and appoints each and any of Christopher J. Spray and
Jeanne Larkin Henry his true and lawful attorney-in-fact and agent, with full
power of substitution and resubstitution, for him and in his name, place and
stead, in any and all capacities (until revoked in writing) to sign any and all
instruments, certificates and documents required to be executed on behalf of
himself individually or on behalf of each or any of Atlas Venture Fund, L.P.,
Atlas Venture Associates, L.P., Atlas Venture Partners III, B.V., Atlas Venture
Fund II, L.P., Atlas Venture Associates II, L.P., Atlas Venture Europe Fund
B.V., Atlas InvesteringsGroep N.V., and Atlas Venture Beheer II B.V. pursuant to
sections 13 and 16 of the Securities Exchange Act of 1934, as amended (the
"Exchange Act"), and any and all regulations promulgated thereunder, and to file
the same, with all exhibits thereto, and any other documents in connection
therewith, with the Securities and Exchange Commission, and with any other
entity when and if such is mandated by the Exchange Act or by the By-laws of the
National Association of Securities Dealers, granting unto said attorney-in-fact
and agent full power and authority to do and perform each and every act and
thing requisite and necessary fully to all intents and purposes as he might or
could do in person thereby ratifying and confirming all that said
attorney-in-fact and agent, or his substitute or substitutes, may lawfully do or
cause to be done by virtue hereof.



                  [REMAINDER OF PAGE LEFT BLANK INTENTIONALLY]

                      [SIGNATURE PAGE FOLLOWS IMMEDIATELY]



                              Page 11 of 17 Pages


<PAGE>   2


     IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.

                                            /s/ Christopher J. Spray 
                                            ------------------------------------
                                            Christopher J. Spray


Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

     On this 31st day of January, 1997, before me personally came Christopher J.
Spray, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.

[Notary Seal]                               /s/ Elizabeth  A. LeBlanc 
                                            ------------------------------------
                                            Notary Public

                                            My commission expires: July 3, 1998



                               Page 12 of 17 Pages

<PAGE>   3


     IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.

                                            /s/ Barry Fidelman                
                                            ------------------------------------
                                            Barry Fidelman

Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

     On this 31st day of January, 1997, before me personally came Barry
Fidelman, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.

[Notary Seal]                               /s/ Elizabeth  A. Leblanc 
                                            ------------------------------------
                                            Notary Public

                                            My commission expires: July 3, 1998



                               Page 13 of 17 Pages
<PAGE>   4


     IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.

                                            /s/ Michiel De Haan             
                                            ------------------------------------
                                            Michiel de Haan

Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

     On this 31st day of January, 1997, before me personally came Michiel de
Haan, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.

[Notary Seal]                               /s/ Elizabeth  A. LeBlanc 
                                            ------------------------------------
                                            Notary Public

                                            My commission expires: July 3, 1998



                              Page 14 of 17 Pages


<PAGE>   5


    IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.

                                            /s/ Allan R. Ferguson 
                                            ------------------------------------
                                            Allan R. Ferguson

Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

     On this 31st day of January, 1997, before me personally came Allan R.
Ferguson, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.

[Notary Seal]                               /s/ Elizabeth  A. LeBlanc 
                                            ------------------------------------
                                            Notary Public

                                            My commission expires: July 3, 1998


                              Page 16 of 17 Pages


<PAGE>   6


IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st day of
January, 1997.

                                            /s/ Jean-Francois Formela
                                            ------------------------------------
                                            Jean-Francois Formela

Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

     On this 31st day of January, 1997, before me personally came Jean-Francois
Formela, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.

[Notary Seal]                               /s/ Elizabeth  A. LeBlanc 
                                            ------------------------------------
                                            Notary Public

                                            My commission expires: July 3, 1998



                               Page 17 of 17 Pages



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