Document:

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                                                                   Exhibit 10.57

                           FIRST AMENDED AND RESTATED
                    SUBORDINATION AND INTERCREDITOR AGREEMENT

         THIS FIRST AMENDED AND RESTATED SUBORDINATION AND INTERCREDITOR
AGREEMENT (this "AGREEMENT") is effective as of June ____, 2000 (the "EFFECTIVE
DATE") by and among Hybridon, Inc., a Delaware corporation ("BORROWER"), those
persons who from time to time hold the 8% senior notes (described herein) of the
Borrower due November 30, 2002 (collectively, the "SENIOR NOTEHOLDERS"), those
persons who have executed as lenders that certain Line of Credit and Security
Agreement (the "JUNE LOAN AGREEMENT"), dated as of June ____, 2000, between such
lenders and Borrower (collectively, the "SENIOR LENDERS", and together with the
Senior Noteholders, the "SENIOR SECURITY HOLDERS"), and Founders Financial Group
("FOUNDERS"), Delaware State Employees Retirement Fund, Declaration of Trust for
the Defined Benefit Plans of ICI American Holdings Inc., Declaration of Trust
for the Defined Benefit Plans of Zeneca Holdings Inc., The J.W. McConnell Family
Foundation and General Motors Employees Domestic Group Trust (said trusts,
foundation and fund being referred to collectively as the "PECKS PARTIES";
Founders and the Pecks Parties are collectively referred to as the "SUBORDINATE
LENDERS"). This Agreement amends and restates that certain Subordination and
Intercreditor Agreement, effective as of December 7, 1999, by and among the
Borrower, the Senior Noteholders and the Subordinate Lenders (the "ORIGINAL
AGREEMENT").

                                    RECITALS:

         A. Senior Security Holders have agreed to extend financial
accommodations to Borrower pursuant to the terms of the Senior Loan Documents
(defined below).

         B. Subordinate Lenders are also shareholders of Borrower and have
representatives on Borrower's Board of Directors.

         C. As of December 31, 1996, Borrower entered into a non-revolving term
loan with Silicon Valley Bank (the "BANK") which was evidenced, in part, by that
certain Loan and Security Agreement dated as of December 31, 1996 (the
"SUBORDINATE LOAN AGREEMENT").

         D. As security for the financial accommodations made pursuant to the
Subordinate Loan Agreement, Borrower granted to Bank a security interest in
certain assets of Borrower described more fully in the Subordinate Loan
Agreement and herein.

         E. Founders is the succeessor in interest to an investment portfolio
formerly held by Forum Capital Markets, LLC ("FORUM"). On or about November 20,
1998, Forum and the Pecks Parties purchased the interests of Bank in credit
facility evidenced and secured by the Subordinate Loan Agreement and the
Subordinate Loan Documents (defined herein).
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         F. When the Senior Noteholders made their advances to the Borrower,
they required that Borrower and Subordinate Lenders agree to subordinate certain
obligations of Borrower to Subordinate Lenders. To reflect that agreement,
Senior Noteholders, Forum and the Pecks Parties entered into the Original
Agreement.

         F. Borrower wishes to enter into an agreement with Boston Biosystems,
Inc. ("BBI"), to sell to BBI certain of Borrower's assets (the "TRANSFERRED
ASSETS") which are the subject of liens and security interests held by the
Senior Security Holders and the Subordinate Lenders upon terms and under
conditions set forth in an Asset Purchase Agreement between Borrower and BBI
(the "BBI TRANSACTION").

         G. To close the BBI Transaction, Borrower wishes to obtain from the
Senior Security Holders and the Subordinate Lenders a release of the Senior
Security Holders' and the Subordinate Lenders' entire respective right, title
and interest in and to their security interests in the Transferred Assets.

         H. As a condition to making their financial accommodations, Senior
Lenders have required, and the Borrower, Senior Noteholders and Subordinate
Lenders have agreed, that the obligations of Borrower to Subordinate Lenders be
further subordinated, that the Borrower's obligations to the Senior Lender's be
pari passu with its obligations to the Senior Noteholders and that other
processes be agreed to, as more fully set forth herein.

         NOW, THEREFORE, in consideration of the foregoing Recitals and the
mutual covenants and agreements set forth herein, and for other good and
valuable consideration, the mutuality, receipt and sufficiency of which hereby
are acknowledged, and intending to be legally bound, the parties hereto agree as
follows:

1.       DEFINITIONS.

Certain terms used herein and not otherwise defined (including capitalized terms
used in the foregoing Recitals) shall have the following meanings:

          An "ACCELERATION" shall mean the occurrence of any acceleration of the
principal and interest under any of the Borrower Obligations.

         "BORROWER'S PUBLIC FILINGS" shall mean the periodic filings on Forms
10-K, 10-Q and 8-K, as filed from time to time with the U.S. Securities and
Exchange Commission.

         "BORROWER OBLIGATIONS" means the Senior Obligations or the Subordinate
Obligations, as the context requires.

         "COMMITTEE EVENT" shall have the meaning set forth in Section 2.2(a).

         "DEFAULT" shall mean any Default or "default" under and as defined in
the Senior Loan Documents or the Subordinate Loan Documents, as the context
requires.

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         "EVENT OF DEFAULT" means any Senior Event of Default or Subordinate
Event of Default, as the context requires.

         "FOUNDERS REPRESENTATIVE" means Harold L. Purkey, or a successor chosen
by Founders.

         "LENDERS COMMITTEE" shall have the meaning set forth in Section 2.2(a).

         "PAYMENT IN FULL" or "PAID IN FULL" or any similar term(s) with respect
to any Borrower Obligation means (a) the indefeasible satisfaction and final
payment in full of such Borrower Obligation in cash or cash equivalents
reasonably acceptable to the payee and the termination of any obligation on the
part of the holder of such Borrower Obligation to make any loans or to afford
any financial accommodation to Borrower and the full and timely performance of
all other obligations to the holder of such Borrower Obligation or (b) in the
case of any Borrower Obligation consisting of contingent obligations (including
without limitation contingent obligations in respect of letters of credit or
other indemnifications under the Subordinate Loan Documents), the setting apart
of cash sufficient to discharge such portion of such Borrower Obligation in an
account for the exclusive benefit of the holders thereof, in which account such
holders shall be granted by Borrower a first priority perfected security
interest in a manner acceptable to such holders, which payment or perfected
security interest shall have been retained by the holders, in the case of each
of (a) and (b) above, for a period of time in excess of all applicable
preference or other similar periods under applicable bankruptcy, insolvency or
creditors' rights laws.

         "PECKS REPRESENTATIVE" means Arthur W. Berry or a successor chosen by
the holders of a majority of the interests held by the Pecks Parties.

         "REMEDY NOTIFICATION" means the written notification by Subordinate
Lenders to Senior Noteholders and/or Senior Lenders or by Senior Noteholders
and/or Senior Lenders to Subordinate Lenders of such party's desire to exercise
a Remedy following the occurrence of an Event of Default.

         "REMEDY" means any the following actions by either Senior Lenders or
Subordinate Lenders:

         (i) the exercise of any rights or remedies they may have under the
     Subordinate Loan Documents or otherwise (other than a declaration of an
     Acceleration);

         (ii) the commencement or joinder with any other creditors of Borrower
     in commencing any bankruptcy, reorganization, receivership or insolvency
     proceeding against Borrower; or

         (iii) the commencement of any action or proceeding against Borrower to
     enforce or collect any Borrower Obligation, to obtain possession of
     property of Borrower, to exercise control over property of Borrower or to
     create, perfect or enforce any lien against property of Borrower.

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         "SENIOR EVENT OF DEFAULT" means any Event of Default under and as
defined in the Senior Loan Documents.

         "SENIOR SECURITY HOLDERS' REPRESENTATIVE" means Youssef El-Zein (a
representative designated by Pillar Investments Ltd.) or a successor
representative chosen by the holders of a majority (measured by dollar amount)
of the Senior Obligations, outstanding from time to time.

         "SENIOR LOAN DOCUMENTS" means (i) the Borrower's 8% notes, due November
30, 2002, issued to Senior Noteholders, (ii) the Subscription Agreements between
Borrower and each Senior Noteholder, (iii) the Warrant Agreements between
Borrower and the Senior Noteholders, (iv) the Line of Credit and Security
Agreement, dated as of June ____, 2000, between the Senior Lenders and Borrower
(the "Line of Credit"), and (v) all other instruments, agreements and documents
which create, evidence or secure the Senior Obligations from time to time
(including but not limited to any promissory notes, security agreements, pledge
agreements, hypothecation agreements, mortgages, financing statements, and all
other agreements of any type whatsoever), delivered by Borrower to Senior
Lenders, as such may be amended, modified, supplemented, restated, replaced or
refinanced (in any such case with any Senior Lender) from time to time,
including all such extensions, renewals, refinancings or refundings thereof,
whether or not the principal amount is increased.

         "SENIOR OBLIGATIONS" means all obligations of the Borrower under the
Senior Loan Documents including but not limited to principal, interest, fees and
all other amounts owing to Senior Lenders under the Senior Loan Documents, from
time to time. Notwithstanding the foregoing, the Senior Obligations shall not
include any principal owed by the Borrower to the Senior Lenders in excess of
$10,000,000 except with the consent of the Senior Security Holders'
Representative and the Subordinate Lenders' Representatives.

         "SUBORDINATE DEBT" means all principal, interest, fees and other
amounts owing to Subordinate Lenders under the Subordinate Loan Documents from
time to time, whether in respect of principal, interest or otherwise.

         "SUBORDINATE EVENT OF DEFAULT" means any Event of Default under and as
defined in the Subordinate Loan Documents.

         "SUBORDINATE LENDERS' REPRESENTATIVES" shall mean the Pecks
Representative and the Founders Representative.

         "SUBORDINATE LOAN AGREEMENT" shall have the meaning set forth in the
Recitals.

         "SUBORDINATE LOAN DOCUMENTS" means Subordinate Loan Agreement and all
other instruments, agreements and documents which create, evidence or secure the
Subordinate Obligations from time to time.

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         "SUBORDINATE OBLIGATIONS" means all obligations of Borrower under the
Subordinate Loan Documents including but not limited to principal, interest,
fees and all other amounts owing to Subordinate Lenders under the Subordinate
Loan Documents, from time to time.

2.       SUBORDINATION AND INTERCREDITOR PROVISIONS.

         2.1.     Subordination.

         (a) Subordinate Lenders hereby consent to Borrower obtaining certain
financial accommodations from Senior Security Holders, all on a senior secured
basis.

         (b) Senior Security Holders hereby acknowledge that Subordinate Lenders
have been previously granted a security interest in certain of the assets of
Borrower. Subordinate Lenders hereby acknowledge and agree that they are willing
to and hereby do subordinate the Subordinate Obligations and the collateral
securing such obligations to the Senior Obligations.

         (c) Borrower and Subordinate Lenders each hereby represents and
warrants to Senior Security Holders that a true, accurate and complete copy of
all Subordinate Loan Documents has been either filed as an exhibit to Borrower's
Public Filings or otherwise provided to Senior Security Holders' Representative
or its counsel in writing, and that none of the Subordinate Loan Documents has
been amended or modified in any way from the versions so filed or provided.

         (d) Subordinate Lenders agree, for themselves and each future holder of
the Subordinate Obligations, that: (i) subject to the terms hereof, the
Subordinate Debt is and shall be expressly subordinate and junior in right of
payment to all Senior Obligations until the Senior Obligations have been Paid in
Full; (ii) Subordinate Lenders shall not accept additional security or further
collateral to support the payment or performance of the Subordinate Debt, unless
the Senior Security Holders are granted a lien or security interest in such
additional collateral, and such lien or security interest in favor of Senior
Security Holders is senior to the lien of the Subordinate Lenders; and (iii)
Senior Security Holders have advanced funds in reliance upon the subordination
of the Subordinate Debt and the collateral securing such debt to the Senior
Obligations.

         2.2.     Lenders Committee.

         (a) Senior Security Holders and Subordinate Lenders hereby agree to
constitute a "LENDERS COMMITTEE" immediately upon the first to occur of the
following: (i) the occurrence of an Acceleration, or (ii) the occurrence of a
Remedy Notification (a "COMMITTEE EVENT").

         (b) The Lenders Committee shall have three members which shall be
comprised of the Senior Security Holders' Representative and the two Subordinate
Lenders' Representatives. Any matter which, under the terms of this Agreement or
otherwise, requires a vote or action by the Lenders Committee, shall require the
affirmative votes of a majority of the members of the Lenders Committee.

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         (c) From and after its formation following a Committee Event, the
Lenders Committee shall be charged solely with liquidating any collateral held
by any of the Senior Security Holders or Subordinate Lenders by obtaining
possession of or exerting control over such collateral, and perfecting or
enforcing liens of the Senior Security Holders and the Subordinate Lenders
against such collateral. Borrower and the Lenders Committee shall disburse any
proceeds of such liquidation according to the priorities set by this Agreement.

         (d) From and after any Event of Default, neither Senior Security
Holders nor Subordinate Lenders may exercise a Remedy without first providing
not less that ten (10) days advance written notice to the other Lenders of its
desire to so exercise a Remedy (the "REMEDY NOTIFICATION"). Subsequent to the
delivery of the Remedy Notification and the resulting formation of the Lenders
Committee, then, until the date the Senior Obligations are Paid in Full,
Subordinate Lenders shall not exercise any Remedy without either (a) direction
or approval by the Lenders Committee or (b) express approval provided herein.
Similarly, at any time prior to the date the Subordinate Obligations are Paid in
Full, Senior Security Holders shall not exercise any Remedy, without either (a)
direction or approval by the Lenders Committee or (b) express approval provided
herein.

         (e) If any insolvency, bankruptcy, receivership, liquidation,
reorganization or other similar proceedings are commenced by or against Borrower
or its property, if any proceedings for involuntary liquidation, dissolution or
other winding up of Borrower whether or not involving insolvency or bankruptcy
are commenced by or against Borrower (collectively, any "REORGANIZATION
PROCEEDINGS"), then Senior Security Holders shall be entitled in any such
Reorganization Proceedings to receive Payment in Full of all Senior Obligations
before Subordinate Lenders are entitled in any the Reorganization Proceedings to
receive any payment on account of the Subordinate Obligations. In any
Reorganization Proceedings, any payment or distribution of any kind or
character, whether in cash or in property to which Subordinate Lenders would be
entitled on account of the Subordinate Obligations but for the provisions of
this Agreement, shall be delivered to Senior Security Holders to the extent
necessary to make Payment in Full of all Senior Obligations remaining unpaid,
after giving effect to any concurrent payment or distribution to or for Senior
Security Holders in respect thereof. Subject to the Payment-in-Full of all
Senior Obligations, the holders of Subordinate Obligations shall be subrogated
to the rights of the holders of the Senior Obligations (to the extent of
payments or distributions made to holders of Senior Obligations pursuant to the
foregoing sentence or Section 2.3(b)) to receive payments or distributions of
the assets of Borrower applicable to the Senior Obligations. No such payments or
distributions applicable to the Senior Obligations shall, as between Borrower
and its creditors, other than the holders of Borrower Obligations, be deemed to
be a payment by Borrower to or on account of the Subordinate Obligations; and
for the purposes of such subrogation, no payments or distributions to the
holders of Senior Obligations to which the holders of Subordinate Obligations
would be entitled except for the provisions of this section shall, as between
Borrower and its creditors, other than the holders of Borrower Obligations, be
deemed to be a payment by Borrower to or on account of the Senior Obligations.

         (f) Notwithstanding anything to the contrary contained herein,
Subordinate Lenders may, in any proceedings described in Section 2.2 (e), in the
name of Subordinate Lenders, file claims, proofs of claims and other instruments
of similar character necessary to enforce the

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obligations of Borrower in respect of the Subordinate Obligations.
Notwithstanding anything to the contrary contained herein, Senior Security
Holders may, in any proceedings described in Section 2.2 (e), in the name of
Senior Security Holders, file claims, proofs of claims and other instruments of
similar character necessary to enforce the obligations of Borrower in respect of
the Senior Obligations. Neither this Section 2.2(f) nor any other provision
hereof shall be construed to give Subordinate Lenders any right to vote any
Borrower Obligation held by Senior Security Holders, any related claim or any
portion of such claim, whether in connection with any resolution, arrangement,
plan or reorganization, compromise, settlement, election of trustees or
otherwise, all such votes, as to Senior Obligations to be made solely on the
direction of the Senior Security Holders. Neither this Section 2.2(f) nor any
other provision hereof shall be construed to give Senior Security Holders any
right to vote any Borrower Obligation held by Subordinate Lenders, any related
claim or any portion of such claim, whether in connection with any resolution,
arrangement, plan or reorganization, compromise, settlement, election of
trustees or otherwise, all such votes, as to Subordinate Obligations to be made
solely on the direction of the Subordinate Security Holders.

         2.3.     Payments of Borrower Obligations.

         (a) The following provisions shall govern Subordinate Lenders' right to
receive and Borrower's right and obligation to pay any amount due and owing
under the Subordinate Loan Documents:

                  (i) Provided that the Subordinate Lenders' Representatives
                  shall not have been notified that an Acceleration shall have
                  occurred and be continuing or would be created thereby under
                  the terms of any of the Senior Loan Documents, Subordinate
                  Lenders may receive and Borrower may pay interest only at the
                  interest rate set forth in the Subordinate Loan Documents as
                  of the Effective Date, when due and owing on an unaccelerated
                  basis and not at a rate applicable upon default.

                  (ii) Except as expressly permitted pursuant to Section
                  2.3(a)(i), Subordinate Lenders shall not be entitled to
                  receive or retain any direct or indirect payment (in cash,
                  cash-equivalents, property, by set-off or otherwise) of or on
                  account of any Subordinate Obligation at any time prior to
                  Payment in Full of the Senior Obligations; provided, however,
                  Borrower may deliver to Subordinate Lenders' Representatives,
                  at any time (including during the occurrence of an Event of
                  Default under any of the Senior Loan Documents and/or the
                  Subordinate Loan Documents), the proceeds from the sale of
                  Subordinate Lender's Collateral, which sale shall be made in a
                  manner directed or approved by the Lenders Committee. Except
                  as expressly permitted pursuant to Section 2.3(a)(i) and (ii),
                  at any time that any of the Senior Obligations is outstanding,
                  Borrower shall not make and Subordinate Lenders shall not
                  receive or accept any payment (in cash, cash-equivalents,
                  property, by set-off, "bid in" of debt in a disposition of
                  collateral or otherwise) of any kind or nature with respect to
                  the Subordinate Obligations.

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         (b) If Subordinate Lenders receive any payment with respect to the
Subordinate Obligations which Subordinate Lenders are not permitted to receive
and retain pursuant to this Agreement, then such payment shall be held in trust
for the benefit of, and shall be paid over promptly to Senior Security Holders,
for application to the payment of the Senior Obligations, in such order of
priority as Senior Security Holders' Representative shall determine. If
Subordinate Lenders pay over any payment or distribution as provided above, then
such payment or distribution shall be deemed to have been made by Borrower
directly to Senior Security Holders and not to Subordinate Lenders and no
Subordinate Obligation shall be discharged by reason of its receipt of any
payment or distribution which is so paid over to Senior Security Holders.

         (c) To the extent necessary for Senior Security Holders to realize the
benefits of the subordination of the Subordinate Obligations provided for
herein, Subordinate Lenders shall execute and deliver to Senior Security
Holders' Representative such instruments or documents (together with such
assignments or endorsements as Senior Security Holders shall deem necessary), as
are consistent with the terms of this Agreement and are reasonably requested by
Senior Security Holders' Representative.

         (d) In the event Subordinate Lenders at any time incur any obligation
to pay money to Borrower, Subordinate Lenders hereby irrevocably agree that they
shall pay such obligation in cash or cash equivalents in accordance with the
terms of the document or instrument governing such obligation without deduction
or set-off against the Subordinate Obligations.

         2.4. Borrower's Obligations Absolute. The provisions of this Agreement
are solely for the benefit of Borrower, Senior Security Holders and Subordinate
Lenders for the purpose of defining the relative rights of the parties thereto.
Nothing herein shall impair, as between Borrower and any other party hereto, the
obligations of Borrower, which are unconditional and absolute, to Senior
Security Holders and to Subordinate Lenders, respectively.

         2.5. Transfers. Any Senior Security Holder or any Subordinate Lender
may sell, assign or otherwise transfer, in whole or in part, any of the Borrower
Obligations or any interest therein to any other person or entity, but only on
the express condition that the transferee of the Borrower Obligations shall
expressly acknowledge to the other parties to this Agreement, in writing, that
it agrees to be bound by all of the terms hereof. Senior Security Holders and
Subordinate Lenders each hereby represents and warrants to the others that as of
the execution date hereof neither Senior Security Holders nor Subordinate
Lenders has transferred or entered into any agreement or understanding with a
proposed transferee that they will transfer any of the Borrower Obligations.

         2.6. Liens Subordinate. (a) Subordinate Lenders agree that any liens
upon Borrower's assets securing payment of the Subordinated Debt, now or
hereafter existing, are and shall be and remain inferior and subordinate to any
liens securing payment of the Senior Obligations regardless of whether such
encumbrances in favor of the Subordinated Lenders or Senior Security Holders
presently exist or are hereafter created or attach.

         (b) Senior Security Holders and Subordinate Lenders hereby agree that,
after the Lenders Committee is constituted, the Lenders Committee may file any
or all lien releases, UCC

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releases, and termination statements on behalf of the Senior Security Holders
and the Subordinate Lenders at any time Borrower, or any successor, assign or
agent of Borrower, proposes a sale of any asset that is approved by the Lenders
Committee. In furtherance thereof, the Senior Security Holders and the
Subordinate Lenders agree to execute, acknowledge and deliver any lien releases,
UCC-3 termination statements or such additional instruments or documents as may
be reasonably necessary to confirm the foregoing within three (3) business days
of the request therefor by Lenders Committee.

         2.7. Additional Representations and Warranties. Subordinate Lenders and
Borrower represent and warrant to Senior Security Holders that:

         (a) as of the date hereof, the total principal amount of the
Subordinate Obligations is $_______________ plus accrued but unpaid interest;

         (b) except as indicated in Borrower's Public Filings or disclosed in
writing to the Senior Security Holders' Representative and its counsel, which
writing is hereby made a part hereof, as of the date hereof, to the best of
their knowledge, after due enquiry, no default or Event of Default, or event
which with notice or passage of time or both would constitute an Event of
Default exists or has occurred under the Subordinate Loan Documents;

         (c) Subordinate Lenders are collectively the exclusive legal and
beneficial owner of all of the Subordinate Obligations;

         (d) except as indicated in Borrower's Public Filings or disclosed in
writing to the Senior Security Holders' Representative and its counsel, which
writing is hereby made a part of this Agreement, none of the Subordinate
Obligations is subject to any lien, security interest (other than Subordinate
Lender's Collateral), financing statements, subordination, assignment or other
claim; and

         (e) this Agreement constitutes the legal, valid and binding obligations
of Subordinate Lenders, enforceable in accordance with its terms.

         2.8. Legends. Subordinate Lenders agree that any instrument at any time
evidencing the Subordinate Obligations, or any portion thereof, shall be
permanently marked on its face with a legend conspicuously indicating that
payment thereof is subordinate in right of payment to the Senior Obligations and
subject to the terms and conditions of this Agreement, and after being so marked
certified copies thereof shall be delivered to Senior Security Holders. In the
event any legend or endorsement is omitted, Senior Security Holders or any of
their representatives, officers or employees are hereby irrevocably authorized
on behalf of Subordinate Lenders to make the same. No specific legend, further
assignment or endorsement or delivery of notes, guarantees or instruments shall
be necessary to subject any Subordinate Obligations to the subordination thereof
contained in this Agreement.

         2.9. Waiver of Covenant. Subordinate Lenders hereby waive any breaches
or defaults arising from Borrower's failure to maintain compliance with Section
6.9 of the Subordinate Loan Agreement, entitled "Minimum Liquidity", such waiver
to remain in effect so long as any amounts of Senior Obligations remain
outstanding,

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3.       AGREEMENT BY BORROWER.

         (a) Borrower hereby acknowledges and agrees to the foregoing terms and
provisions, and agrees that the provisions hereof will bind Borrower, together
with its successors and assigns.

         (b) Borrower acknowledges and agrees that: (i) in the event of a breach
by Borrower or Subordinate Lenders of any of the terms and provisions contained
in this Agreement, such a breach shall constitute an Event of Default, as
defined in and under the Senior Loan Documents; and (ii) it will execute and
deliver such additional documents and take such additional action as may be
necessary or desirable in the opinion of either Subordinate Lenders or Senior
Security Holders to effectuate the provisions and purposes of this Agreement.

4.       CONSENT AND RELEASE.

         (a) Subordinate Lenders and Senior Noteholders each hereby consent to
the execution of, and the parties' respective performance under, the June Loan
Agreement, including: (i) the characterization of the Senior Lenders, in
addition to the Senior Noteholders, as Senior Security Holders hereunder; (ii)
the grant to the Senior Lenders of a security interest in the Collateral (as
defined in the June Loan Agreement), which interest shall be subject to the
terms and conditions of this Agreement; (iii) the repayment of the amounts due
the Senior Lenders and the Senior Noteholders on a pari passu basis; and (iv)
the concomitant further subordination of the Subordinate Lenders' security
interest in certain of the assets of Borrower to the security interest of the
Senior Lenders (in addition to the Senior Noteholders).

         (b) Subject to the terms and conditions set forth in paragraphs (b) and
(c) below, upon the closing of the BBI Transaction, the Subordinated Lenders and
the Senior Security Holders each agree to forever release and surrender, in
accordance with Section 2.6(b) hereof, all right, title and interest in any
security interest such Subordinated Lender or Senior Security Holder may have in
the Transferred Assets (the "BBI SECURITY INTEREST"). Subordinate Lenders and
Senior Security Holders agree to execute and file a UCC-3 Partial Release, and
all other documents reasonably requested by Borrower, to effect as a matter of
public record the release contemplated by this

         (c) As consideration for the release and surrender of the BBI Security
Interest, concurrently with the closing of the BBI Transaction, Borrower shall
invest Five Million Dollars ($5,000,000) in a segregated, interest-bearing
instrument (the "MONEY MARKET INSTRUMENT") and shall deliver and pledge the
Money Market Instrument to the Subordinated Lenders and the Senior Security
Holders as collateral securing the payment of the Subordinated Obligations and
the Senior Obligations. The pledge of the Money Market Instrument shall be
pursuant to a written Pledge Agreement to be entered into by and between the
Borrower and the Senior Security Holder's Representative, as collateral agent
for the Senior Security Holders and the Subordinated Lenders. The Money Market
Instrument shall be deemed to be "Collateral" under the Subordinated Loan
Documents and the Senior Loan Documents, and shall be subject to and governed by
the terms and conditions of this Agreement, the Senior Loan Documents and the
Subordinate Loan Documents pertaining to Borrower's collateral. Borrower shall
be entitled to

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receive any and all interest or other income generated by the Money Market
Instrument for so long as no event of default on Borrower's part has occurred
under the Subordinated Loan Documents or the Senior Loan Documents.

         (d) To the extent that, and on each occasion that, the Senior Security
Holders convert all or a portion of the principal amount and interest of debt
held by them into capital stock of the Borrower pursuant to conversion rights
under the Senior Loan Documents, in the amount of One Million Dollars
($1,000,000) or more in the aggregate: (i) the pledge shall be released as to a
portion of the Money Market Instrument equal to the principal amount of debt so
converted; (ii) Borrower shall be entitled to reduce the amount of to use the
released funds as it sees fit; and (iii) the Subordinated Lenders and the Senior
Security Holders shall execute and deliver such instruments as may be necessary
to effectuate the reduction and release.

5.       MISCELLANEOUS.

         5.1. Notices. Any and all notices given in connection with this
Agreement shall be deemed adequately given only if in writing and addressed to
the party for whom such notices are intended at the address set forth below. All
notices shall be sent by personal delivery, Federal Express or other over-night
messenger service, first class registered or certified mail, postage prepaid,
return receipt requested or by other means at least as fast and reliable as
first class mail. A written notice shall be deemed to have been given to the
recipient party on the earlier of (a) the date it shall be delivered to the
address required by this Agreement; (b) the date delivery shall have been
refused at the address required by this Agreement; or (c) with respect to
notices sent by mail, the date as of which the postal service shall have
indicated such notice to be undeliverable at the address required by this
Agreement. Any and all notices referred to in this Agreement, or which either
party desires to give to the other, shall be addressed as follows:

<TABLE>
<S>                                                  <C>
         if to Borrower:                             Hybridon, Inc.
                                                     155 Fortune Blvd.
                                                     Milford, MA 01757
                                                     Attn.: President

         with a copy to:                             Holland & Knight
                                                     One Beacon Street
                                                     Boston, MA.
                                                     Attn.: James Pollock, Esq.

         if to Senior Security Holders:              Pillar Investments Ltd. Representative
                                                     28 Avenue de Messine
                                                     Paris, FRANCE 75008
                                                     Attn:    Youssef El-Zein

         with a copy to:                             Sachnoff & Weaver, Ltd.
                                                     30 South Wacker Drive
                                                     Suite 2900
                                                     Chicago, Illinois 60606
                                                     Attn:    Lance R. Rodgers, Esq.
</TABLE>

                                       11
<PAGE>   12
<TABLE>
<S>                                                  <C>
     if to Subordinate Lenders:                      Pecks Management
                                                     1 Rockefeller Plaza, Suite 900
                                                     New York, NY  10020
                                                     Attn: Arthur W. Berry
                                                         and
                                                     Founders Financial Group
                                                     53 Forest Avenue
                                                     Old Greenwich, CT  06870
                                                     Attn: Harold L. Purkey
</TABLE>

The above addresses may be changed by notice of such change, mailed as provided
herein, to the last address designated.

         5.2. No Fiduciary Duty. Nothing in this Agreement shall be construed to
create or impose upon any Senior Security Holders any fiduciary duty to any
Subordinate Lender, or any other implied obligation to act or refrain from
acting with respect to Borrower or the Senior Obligations or the collateral
security securing the Senior Obligations in any manner contrary to what any
Senior Security Holders may determine is in its own best interests. Similarly,
nothing in this Agreement shall be construed to create or impose upon any
Subordinate Lender any fiduciary duty to any Senior Security Holders, or any
other implied obligation to act or refrain from acting with respect to Borrower
or the Subordinate Obligations or the collateral security securing the
Subordinate Obligations in any manner contrary to what any Subordinate Lender
may determine is in its own best interests.

         5.3. Notice of Default. In addition to any other notices which may be
required hereunder, Subordinate Lenders shall give written notice to Senior
Security Holders' Representative, promptly after they become aware of the
occurrence of: (a) an Event of Default under the terms of the Subordinate Loan
Documents; (b) the cure of any such Event of Default; (c) the payment in full of
the Subordinate Debt; (d) any Acceleration of the Subordinate Debt; and (e) any
action or proceeding instituted against Borrower on account of any Event of
Default.

         5.4.     Successors; Continuing Effect.

         (a) This Agreement is being entered into for the benefit of, and shall
be binding upon, Borrower, each Senior Security Holders and each Subordinate
Lender and their respective successors and assigns, including each subsequent or
additional holder of Senior Obligations, or Subordinate Debt, and any
participant (whether now existing or hereafter arising) in the Senior
Obligations. The terms "Senior Security Holders" and "Subordinate Lenders" shall
include, respectively, any such subsequent or additional holder of or
participant in Senior Obligations or Subordinate Obligations whenever the
context permits. This Agreement shall inure to the benefit of and be enforceable
by any future holder or holders of the Borrower Obligations or any part of any
of the same; provided that, nothing contained in this Section 5.4 shall be
deemed to permit the transfer of the Subordinate Obligations in violation of the
provisions of Section 2.5.

                                       12
<PAGE>   13
         (b) Senior Security Holders reserve the right to grant participations
in, or otherwise sell, assign, transfer or negotiate all or any part of, or any
interest in, the Senior Obligations and the Collateral securing same. In
connection with any participation or other transfer or assignment, Senior
Security Holders (i) may disclose to such assignee, participant or other
transferee or assignee all documents and information which Senior Security
Holders now or hereafter may have relating to the Senior Obligations or the
Collateral, and (ii) shall disclose to such participant or other transferee or
assignee the existence and terms and conditions of this Agreement.

         5.5. Amendments. This Agreement may be amended only by a written
instrument executed by holders of a majorities in interest of each of the Senior
Obligations and the Subordinate Obligations and, if such amendment affects
Borrower, by Borrower.

         5.6. Term. This Agreement shall remain in full force and effect until
the Payment in Full of the Senior Obligations.

         5.7. Waivers. No waiver shall be deemed to be made by any party of any
of its rights hereunder unless the same shall be in writing and then only with
respect to the specific instance involved, and no such waiver shall impair or
offset the rights of the waiving party or the obligations of the party benefited
by such waiver in any other respect or at any other time.

         5.8. Governing Law. This Agreement, including the validity hereof and
the rights and obligations of the parties hereunder, shall be governed by and
construed and enforced in accordance with the laws of the Commonwealth of
Massachusetts.

         5.9. The Borrower May Not Impair Subordination. No right of Senior
Security Holders or Subordinate Lenders to enforce the subordination created
hereby shall be impaired by any act or failure to act by Borrower or by the
failure by Borrower to comply with this Agreement, regardless of any knowledge
which any Senior Security Holders or any Subordinate Lender may have or be
otherwise charged with.

         5.10. Specific Performance. The parties hereto acknowledge that legal
remedies may be inadequate and therefore Senior Security Holders and Subordinate
Lenders are hereby authorized to demand specific performance of the provisions
of this Agreement at any time when Borrower, Senior Security Holders or
Subordinate Lenders shall have failed to comply with any provision hereof. Each
party hereto hereby irrevocably waives any defense based on the adequacy of a
remedy at law that might be asserted as a bar to such remedy of specific
performance.

         5.11. Further Actions. After the execution of this Agreement each party
will execute and deliver all such documents and instruments and do all such
other acts and things as may be reasonably necessary to carry out the provisions
of this Agreement.

         5.12. Agreement to Control. If any provision in any document or
instrument relating to the Senior Obligations or the Subordinate Debt differs
with the terms of this Agreement

                                       13
<PAGE>   14
regarding the same or any similar matter, the provisions of this Agreement shall
control and each other provision shall be interpreted so as to give effect to
the provisions of this Agreement.

         5.13. Entire Agreement. This Agreement contains the entire agreement of
the parties with respect to the subject matter hereof and supersedes all prior
written and oral agreements, and all contemporaneous oral agreements, relating
to such matters.

         5.14. Severability. Any provision of this Agreement which is prohibited
or unenforceable in any jurisdiction shall, as to such jurisdiction, be
ineffective to the extent of such prohibition or unenforceability without
invalidating the remaining portions hereof or affecting the validity or
enforceability of such provision in any other jurisdiction.

         5.15. Facsimile. For purposes of negotiating and finalizing this
Agreement (including any subsequent amendments thereto), any signed document
transmitted by facsimile machine ("FAX") shall be treated in all manner and
respects as an original document. The signature of any party by Fax shall be
considered for these purposes as an original signature. Any such Fax document
shall be considered to have the same binding legal effect as an original
document, provided that an original of the faxed document was mailed by first
class U.S. Mail or personally delivered to the recipient, on the date of its
transmission with proof of the fax transmission. At the request of any party,
any Fax document subject to this Agreement shall be re-executed by both parties
in an original form. The undersigned parties hereby agree that neither shall
raise the use of the Fax or the fact that any signature or document was
transmitted or communicated through the use of a Fax as a defense to the
formation of this Agreement. This Agreement may be signed in one or more
counterparts, each of which shall be an original, but all of which together
shall constitute one agreement, binding on all of the parties hereto
notwithstanding that all of the parties hereto are not signatories to the same
counterpart. Each of the undersigned parties authorizes the assembly of one or
more original copies of this Agreement through the combination of the several
executed counterpart signature pages with one or more copies of this Agreement,
including the Schedules and Exhibits, if any, to this Agreement. Each such
compilation of this Agreement shall constitute one original of this Agreement.

         5.16.    Consent to Jurisdiction; Waiver of Jury Trial.

         (a) BORROWER, SUBORDINATE LENDERS AND SENIOR SECURITY HOLDERS EACH
HEREBY (i) TO THE EXTENT PERMITTED BY APPLICABLE LAW, IRREVOCABLY SUBMITS TO THE
JURISDICTION OF ANY STATE OR FEDERAL COURT LOCATED IN BOSTON, MASSACHUSETTS,
OVER ANY ACTION OR PROCEEDING TO ENFORCE OR DEFEND ANY MATTER ARISING FROM OR
RELATED TO THIS AGREEMENT; (ii) IRREVOCABLY WAIVES, TO THE FULLEST EXTENT
BORROWER, SUBORDINATE LENDERS AND SENIOR LENDERS MAY EFFECTIVELY DO SO, THE
DEFENSE OF AN INCONVENIENT FORUM TO THE MAINTENANCE OF ANY SUCH ACTION OR
PROCEEDING IN ANY SUCH COURT; (iii) AGREES THAT, TO THE EXTENT PERMITTED BY
APPLICABLE LAW, A FINAL JUDGMENT IN ANY SUCH ACTION OR PROCEEDING IN ANY SUCH
COURT SHALL BE CONCLUSIVE AND MAY BE ENFORCED IN ANY OTHER JURISDICTION BY SUIT
ON THE JUDGMENT OR IN ANY OTHER MANNER PROVIDED BY LAW; AND (iv) TO

                                       14
<PAGE>   15
THE EXTENT PERMITTED BY APPLICABLE LAW, AGREES NOT TO INSTITUTE ANY LEGAL ACTION
OR PROCEEDING AGAINST ANY PARTY HERETO OR ANY OF PARTY'S DIRECTORS, OFFICERS,
EMPLOYEES, AGENTS OR PROPERTY, CONCERNING ANY MATTER ARISING OUT OF OR RELATING
TO THIS AGREEMENT IN ANY COURT OTHER THAN ONE LOCATED IN BOSTON, MASSACHUSETTS.

         (b) NOTHING IN THIS SECTION SHALL AFFECT OR IMPAIR SENIOR SECURITY
HOLDERS' OR SUBORDINATE LENDERS' RIGHT TO SERVE LEGAL PROCESS ON BORROWER IN ANY
MANNER PERMITTED BY LAW OR SENIOR SECURITY HOLDERS' OR SUBORDINATE LENDERS'
RIGHT TO BRING ANY ACTION OR PROCEEDING AGAINST BORROWER OR BORROWER'S PROPERTY
IN THE COURTS OF ANY OTHER JURISDICTION.

         (c) BORROWER, SENIOR SECURITY HOLDERS AND SUBORDINATE LENDERS EACH
HEREBY KNOWINGLY, VOLUNTARILY AND INTENTIONALLY WAIVES THE RIGHT TO A TRIAL BY
JURY IN RESPECT OF ANY LITIGATION BASED HEREON, ARISING OUT OF, UNDER OR IN
CONNECTION WITH THIS AGREEMENT OR ANY OTHER LOAN DOCUMENT OR ANY COURSE OF
CONDUCT, COURSE OF DEALINGS, STATEMENTS (WHETHER VERBAL OR WRITTEN) OR ACTIONS
OF EITHER PARTY. EACH PARTY HERETO HEREBY EXPRESSLY ACKNOWLEDGES THIS WAIVER IS
A MATERIAL INDUCEMENT FOR SENIOR SECURITY HOLDERS TO ENTER INTO THIS AGREEMENT
AND TO MAKE THE LOANS EVIDENCED BY THE SENIOR LOAN DOCUMENTS.

                                       15
<PAGE>   16
IN WITNESS WHEREOF, the parties hereto have executed and delivered this
Subordination Agreement as of the day, month and year first above written.

                             HYBRIDON, INC.

                    By:      /s/ Robert G. Andersen
                             --------------------------------------------------
                    Name:      Robert G. Andersen
                    Title:     Vice-President and Chief Financial Officer

                             SENIOR LENDERS
                             By: Pillar Investments Ltd, Their Representative

                    By:      /s/ Youssef El Zein
                             --------------------------------------------------
                    Name:      Youssef El Zein

                             SENIOR NOTEHOLDERS
                             By: Pillar Investments Ltd, Their Representative

                    By:      /s/ Youssef El Zein
                             --------------------------------------------------
                    Name:      Youssef El Zein

                             FOUNDERS FINANCIAL GROUP

                    By:      /s/ Harold L. Purkey
                             --------------------------------------------------
                    Name:      Harold L. Purkey
                    Title:     Partner

                                       16
<PAGE>   17
                    DELAWARE STATE EMPLOYEES RETIREMENT
                    FUND DECLARATION OF TRUST FOR THE DEFINED
                    BENEFIT PLANS OF ICI AMERICAN HOLDINGS INC
                    DECLARATION OF TRUST FOR THE DEFINED
                    BENEFIT PLANS OF ZENECA HOLDINGS INC.
                    THE J.W. MCCONNELL FAMILY FOUNDATION
                    GENERAL MOTORS EMPLOYEES DOMESTIC
                    GROUP TRUST

                             By: PECKS MANAGEMENT PARTNERS, LTD.

                             By:     /s/ Arthur W. Berry
                                     ------------------------------------------
                             Name:   Arthur W. Berry
                             Title:  Principal

                                       17<PAGE>   1
                                                                   Exhibit 10.58

                                LICENSE AGREEMENT

         This Agreement, made as of this 20th day of September, 2000 is by and
between Boston Biosystems, Inc., a Delaware corporation (hereinafter,
"Licensee") and Hybridon, Inc., a Delaware corporation (hereinafter,
"Licensor").

                              W I T N E S S E T H:

         WHEREAS, Licensor and Licensee are entering into an Asset Purchase
Agreement dated as of the date hereof (the "Asset Purchase Agreement"), pursuant
to which Licensee is purchasing certain of Licensee's assets in connection with
the manufacture and sale of advanced chemistry compounds and pharmaceuticals
(the "Business"); and

         WHEREAS, Licensor has adopted and is using the trade names and
trademarks used in the operation of the Business as set forth on SCHEDULE A
attached hereto (hereinafter, the "Names & Marks") in connection with its
current operation of the Business; and

         WHEREAS, Licensor wishes to grant, and Licensee wishes to accept a
non-exclusive, royalty-free license providing for use by the Licensee of the
Names & Marks in connection with its operation of the Business for a period of
one (1) year commencing on the date hereof;

         NOW, THEREFORE, in consideration of the mutual covenants herein
contained, and for other good and valuable consideration, the receipt and
adequacy of which are acknowledged, the parties hereby agree as follows:

1.       LICENSE

         1.1 Licensor hereby grants to Licensee a non-exclusive, royalty-free,
worldwide license, for a term of one (1) year commencing on the date hereof, to
use the Names & Marks in connection with Licensee's operation of the Business,
primarily for the purpose of any packaging or marketing materials, for the
limited purposes of facilitating a smooth transition of the Business from the
Licensor to Licensee pursuant to the terms of the Asset Purchase Agreement,
subject to the terms and conditions contained herein.

         1.2 Licensee may (i) engage, employ or otherwise retain the services of
third parties to operate the Business using the Names &Marks, subject to the
quality control provision in Section 4 below, but may not transfer said license
rights to any other third party without the consent of Licensor, which consent
shall not be unreasonably withheld, or (ii) assign any or all of its rights and
interests in the Names and Marks hereunder to one or more of its Affiliates (as
defined in Rule 12b-2 of the regulations promulgated under the Securities
Exchange Act); PROVIDED, that in the event of (i) or (ii) the Licensee shall
nonetheless remain responsible for the performance of all of its obligations
hereunder.

<PAGE>   2
2.       TERMINATION

         2.1 This Agreement may be terminated by each of the parties hereto in
accordance with the following provisions:

         (i) Licensee shall have the right and option to terminate this
Agreement, for its convenience, by providing two (2) months written notice
thereof to Licensor.

         (ii) In the event of any material breach of this agreement by either
party hereto, the other party shall have the right, without limitation of any
other right it may have on account of such failure, to terminate this Agreement
by first giving the breaching party thirty (30) days written notice of its
intention to terminate, specifying the cause of default, and if the defaulting
party shall not remedy such failure during such thirty (30) day period, then the
other party may give further written notice to the defaulting party, terminating
the Agreement, in which event this Agreement shall be terminated on the date
specified in such further notice.

         2.2 Notwithstanding the above, this Agreement shall terminate
automatically without notice upon any of the following events:

         (i) An assignment for the benefit of creditors of Licensee.

         (ii) The appointment of a receiver or trustee to manage the affairs of
the Licensee unless removed within sixty (60) days.

         (iii) The involuntary or voluntary bankruptcy of the Licensee, unless
stayed within sixty (60) days.

3.       OBLIGATIONS OF LICENSOR.

         3.1 Licensor agrees to police the use of the Names & Marks, or
colorable imitations thereof, by others. It shall be in Licensor's sole
discretion, however, as to whether to bring, maintain or settle an infringement
action against a third party.

4.       QUALITY CONTROL.

         4.1 Licensee agrees that its operation of the Business while utilizing
the Names & Marks will comply with generally recognized industry standards with
respect to the manufacture and sale of advanced chemistry compounds and
pharmaceuticals.

         5. INDEMNIFICATION. To the extent a claim or action is brought against
the Licensor based on or related to Licensee's use of the Names and Marks or its
failure to observe or perform its obligations under this Agreement, Licensee
shall defend and hold the Licensor harmless from and against any and all claims,
liabilities, judgments, damages, costs and expenses, including reasonable
attorneys' fees, suffered by or awarded against the Licensor.

                                       -2-
<PAGE>   3
6.       MISCELLANEOUS.

         6.1 This Agreement contains the entire Agreement between the parties
regarding the subject matter hereof and supersedes all prior Agreements, whether
oral or written. No amendment to this Agreement may be made except by a writing
signed by both parties.

         6.2 No provision hereof may be waived unless in writing signed by both
parties affixing their signatures to this document. Waiver of any one provision
herein shall not be deemed to be a waiver of any other provision herein.

         6.3 This Agreement shall be governed in accordance with the laws of the
State of Delaware.

         6.4 Any notice, request, information or other document required to be
provided hereunder shall be in writing and delivered by first class mail,
postage prepaid, or by overnight delivery service as follows:

         If to Licensee:

                  Boston Biosystems, Inc.
                  75A Wiggins Avenue
                  Bedford, Massachusetts  01730
                  Attn: Michael Kallelis, Chief Operating Officer

                  with a copy to:

                  McDermott, Will & Emery
                  28 State Street
                  Boston, Massachusetts  02109
                  Attn:  Susan Cooke, Esq.

         If to Licensor:

                  Hybridon, Inc.
                  255 Fortune Boulevard
                  Milford, Massachusetts
                  Attn:  Robert Anderson

                  with a copy to:

                  Holland & Knight
                  One Beacon Street
                  Boston, Massachusetts
                  Attn:  James Pollock, Esq.

                                       -3-
<PAGE>   4
         6.5 It is the desire and intent of the parties hereto that the
provisions of this Agreement shall be enforced to the fullest extent permissible
under the laws and public policies applied in each jurisdiction in which
enforcement is sought. Accordingly, if any particular provision of this
Agreement shall be adjudicated to be invalid or unenforceable, such provision
shall be deemed amended to delete therefor the portion thus adjudicated to be
invalid or unenforceable and the Agreement shall otherwise remain in full force
and effect.

         6.6 In any action, suit or other proceeding instituted to enforce,
remedy, prevent or obtain relief from a breach or violation of this Agreement,
the substantially prevailing party shall recover all of such party's reasonable
attorneys' fees incurred therein, including any and all appeals or petitions
therefrom.

         6.7 Nothing contained herein shall be construed to create a joint
venture, partnership or agency between the parties and neither party may take
any action which binds the other or gives a color of authority than an act is on
behalf of the other party.

         6.8 This Agreement shall inure to the benefit of and shall be binding
upon the successors and assigns of any party, and each of them.

         6.9 The terms of this Agreement are the result of negotiation between
the parties. All parties to this Agreement therefore, agree that the normal rule
of construction to the effect that any ambiguities in an agreement are to be
resolved against the drafting party shall not be employed in the interpretation
of this Agreement.

         6.10 The signatories here below represent they are authorized to
execute this Agreement on behalf of their respective parties.

            [The remainder of this page is intentionally left blank.]

                                       -4-
<PAGE>   5

         IN WITNESS WHEREOF, the parties hereto have approved and executed this
Agreement effective as of the date first written above.

                             BOSTON BIOSYSTEMS, INC.

                             By: /s/ Gregory S. Kurey
                                  ----------------------------------------
                             Name:   Gregory S. Kurey
                             Title:  General Counsel

                             HYBRIDON, INC.

                             By: /s/ Robert G. Andersen
                                  ----------------------------------------
                             Name:   Robert G. Andersen
                             Title:  Chief Financial Officer

                             By: /s/ Sudhir Agrawal
                             Name:   Sudhir Agrawal
                             Title:  President and Chief Executive
                                         Officer

                                      -5-

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