Exhibit 10.4

EXECUTION COPY

PROPRIETARY SOFTWARE LICENSE AGREEMENT

This PROPRIETARY SOFTWARE LICENSE AGREEMENT (this “ Agreement ”) is dated as of October 10, 2008, between Misys Open Source Solutions LLC, a Delaware limited liability company, having a principal place of business at 103 Foulk Road, Suite 202, Wilmington, Delaware 19803 (“ Licensor ”) and Misys Healthcare Systems, LLC, a North Carolina limited liability company, having its principal place of business at 8529 Six Forks Road, Raleigh, North Carolina 27615 (“ Licensee ”). Licensor and Licensee are referred to herein collectively as “ Parties ” and each individually as a “ Party ”.

W I T N E S S E T H :

WHEREAS, Licensee is an Affiliate of Licensor, and both Licensor and Licensee are wholly-owned indirect subsidiaries of Misys plc, a public limited company organized under the laws of England, having a principal place of business at One Kingdom Street, London W26BL, United Kingdom (“ Misys ”);

WHEREAS, at the Closing (as defined in the Agreement and Plan of Merger, dated as of March 17, 2008, by and among Misys, Licensee, Allscripts Healthcare Solutions Inc., a Delaware corporation, having its principal place of business at 222 Merchandise Mart, Suite 2024, Chicago, IL 60654 (“ Allscripts ”) and Patriot Merger Company, LLC, a North Carolina limited liability company (the “ Merger Agreement ”)), Misys will ( i ) cause Licensee to merge with a wholly-owned subsidiary of Allscripts, with Licensee as the surviving company and ( ii ) acquire, directly or indirectly, 54.5% of the equity interests in Allscripts on a fully-diluted basis (as determined pursuant to the Merger Agreement);

WHEREAS, Section 5.2(e) of the Merger Agreement provides that no later than the Closing Date (as defined in the Merger Agreement), Licensee shall transfer assets related to the products known as the Misys Connect products to Misys or its designee, and that Misys or its designee will, in consideration of such transfer, enter into arrangements to provide Licensee with continued access to such assets;

WHEREAS, Misys has selected Licensor as its designee for purposes of Section 5.2(e) of the Merger Agreement;

WHEREAS, pursuant to a Software Assignment Agreement of even date herewith, Licensee transferred, assigned and delivered to Licensor all of Licensee’s right, title and interest in, to and under the software commonly referred to as Misys Connect and all intellectual property developed and owned by Licensee and used solely in connection with Misys Connect, including software, copyrights, patents, trade secrets and non-software items relating thereto (the “ Misys Connect Software ”);

WHEREAS, the Misys Connect Software is comprised of both proprietary and open-source components, certain open-source components of which are being

licensed to Licensee by Licensor pursuant to the Apache License V2.0 (the “ Open Source Software License Agreement ”), and the proprietary components of which and non-software items relating thereto are being licensed to Licensee by Licensor pursuant to this Agreement; and

WHEREAS, subject to the terms and conditions contained herein, Licensee desires to use, and Licensor is willing to license Licensee to use, the Licensed Works (as defined below) on the terms and conditions set forth herein.

NOW THEREFORE, for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows:

ARTICLE I

DEFINITIONS

1.1. “ Affiliate ” means, with respect to any Person, another Person that, at the time of determination, directly or indirectly, through one or more intermediaries, controls, is controlled by, or is under common control with, the first Person, whether by contract, possession (directly or indirectly) of power to direct or cause the direction of the management or policies of such entity or the ownership (directly or indirectly) of securities or other interests in such Person.

1.2. “ Affiliate Sublicensee ” has the meaning set forth in Section 2.2.

1.3. “ Agreement ” has the meaning set forth in the preamble.

1.4. “ Allscripts ” has the meaning set forth in the second WHEREAS clause.

1.5. “ Confidential Information ” means all written or oral information disclosed by either Party to the other relating to the business of either Party that has been identified as confidential or that by the nature of the circumstances surrounding disclosure ought to be treated as confidential. Without limiting the foregoing, Confidential Information shall include, but not be limited to, information regarding either Party (or information of an Affiliate or third party which the disclosing party is required to maintain as confidential) that pertains to the financial condition of such Party (or Affiliate or third Person), other financial information, business plans and processes, trade secrets, proprietary technical information, know-how, inventions, techniques, software (including, but not limited to, the Proprietary Misys Connect Software and Improvements, Maintenance Releases and Upgrades), documentation (including, but not limited to, the Proprietary Misys Connect Software Documentation), personnel records, sales data and contractual arrangements between such Party or an Affiliate and a third Person. Notwithstanding the definition set forth herein, Confidential Information shall not include information that: ( i ) is publicly available or in the public domain at the time disclosed; ( ii ) is or becomes publicly available or enters the public domain through no fault of the recipient; ( iii ) is rightfully communicated to the recipient by Persons not bound by confidentiality obligations with respect thereto; ( iv ) is already in the recipient’s

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possession free of any confidentiality obligations with respect thereto at the time of disclosure; ( v ) is independently developed by the recipient; ( vi ) is approved for release or disclosure by the disclosing Party without restriction; ( vii ) is disclosed in response to an order of a court or other governmental body, provided that the Party making the disclosure pursuant to the order shall first have given notice to the other Party and made a reasonable effort to obtain a protective order; ( viii ) is otherwise required by law or regulation to be disclosed; ( ix ) is commingled with other third Person information for statistical purposes; or ( x ) is disclosed to establish a Party’s rights under this Agreement, including to make such court filings as may be required to do so.

1.6. “ End User License Agreement ” has the meaning set forth in Section 2.3.

1.7. “ Existing Customers ” has the meaning set forth in Section 2.4.

1.8. “ Field of Use ” means healthcare information technology products and services.

1.9. “ Improvements ” has the meaning set forth in Section 3.1(a).

1.10. “ Licensed Software ” means the object code form of Licensed Works and written documentation related thereto that is licensed by Licensee or its Affiliate Sublicensees to their respective customers.

1.11. “ Licensed Works ” means the Proprietary Misys Connect Software and the Proprietary Misys Connect Software Documentation.

1.12. “ Licensee ” has the meaning set forth in the preamble.

1.13. “ Licensee Improvements ” has the meaning set forth in Section 9.3(c).

1.14. “ Licensor ” has the meaning set forth in the preamble.

1.15. “ Maintenance Releases ” means releases of the Proprietary Misys Connect Software or part thereof in source code and object code versions designed to correct errors and otherwise cause the Proprietary Misys Connect Software to substantially conform to the operational features detailed in the Proprietary Misys Connect Software Documentation.

1.16. “ Merger Agreement ” has the meaning set forth in the second WHEREAS clause.

1.17. “ Misys ” has the meaning set forth in the first WHEREAS clause.

1.18. “ Misys Connect Software ” has the meaning set forth in the fifth WHEREAS clause.

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1.19. “ Open Source Software License Agreement ” has the meaning set forth in the sixth WHEREAS clause.

1.20. “ Open-Sourced Works ” has the meaning set forth in Section 2.8.

1.21. “ Parties ” and “ Party ” each have the meaning set forth in the preamble.

1.22. “ Person ” means an individual, corporation, partnership, joint venture, association, trust, limited liability company, Governmental Entity (as such term is defined in the Merger Agreement), unincorporated organization or other entity.

1.23. “ Proprietary Misys Connect Software ” means the proprietary components of the Misys Connect Software set forth on Exhibit A attached hereto and made a part hereof, in both source code and object code forms, in such forms and media as they shall exist from time to time.

1.24. “ Proprietary Misys Connect Software Documentation ” means all non-software items identified on Exhibit A hereto.

1.25. “ Shared Services Agreement ” means that certain Shared Services Agreement to be executed following the Closing Date (as defined in the Merger Agreement) between Misys and Allscripts.

1.26. “ Territory ” means worldwide.

1.27. “ Upgrades ” means software in source code and object code versions that accomplishes performance, structural or functional improvements or changes, or adds features to, whether by modification, adaptation, replacement, supplement or revision, or that is a derivative work of, the Proprietary Misys Connect Software.

1.28. “ Virus ” means malicious code, whether or not capable of replication or attachment to disks or other files, that is capable of performing an illicit activity or replicating itself on a computer or network of computers and thereby of damaging other computer programs or data located on such computer or network or otherwise causing a defect in the operation of such computer or network, including by causing any computer data, memory, or related hardware to become, without specific user instructions, erased, altered or unusable. The term “Virus” includes, but is not limited to, viruses, Trojan horses, time bombs, worms or similar malicious software, programs or files.

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ARTICLE II

LICENSE

2.1. Grant of License . Subject to the terms and conditions contained herein, Licensor hereb