Dataset Open Access

Solvated protein fragments

Unke, Oliver Thorsten; Meuwly, Markus

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  <identifier identifierType="DOI">10.5281/zenodo.2605372</identifier>
      <creatorName>Unke, Oliver Thorsten</creatorName>
      <givenName>Oliver Thorsten</givenName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0001-7503-406X</nameIdentifier>
      <affiliation>University of Basel</affiliation>
      <creatorName>Meuwly, Markus</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0001-7930-8806</nameIdentifier>
      <affiliation>University of Basel</affiliation>
    <title>Solvated protein fragments</title>
    <subject>condensed phase</subject>
    <subject>quantum chemistry</subject>
    <subject>density functional theory</subject>
    <date dateType="Issued">2019-03-25</date>
  <resourceType resourceTypeGeneral="Dataset"/>
    <alternateIdentifier alternateIdentifierType="url"></alternateIdentifier>
    <relatedIdentifier relatedIdentifierType="arXiv" relationType="IsDocumentedBy">arXiv:1902.08408</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.2605371</relatedIdentifier>
    <rights rightsURI="">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
    <description descriptionType="Abstract">&lt;p&gt;The solvated protein fragments dataset probes many-body intermolecular interactions between&amp;nbsp;&lt;br&gt;
&amp;quot;protein fragments&amp;quot; and water molecules, which are important for the description of many&amp;nbsp;&lt;br&gt;
biologically relevant condensed phase systems. It contains structures for all possible&amp;nbsp;&lt;br&gt;
&amp;quot;amons&amp;quot; [1] (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms&amp;nbsp;&lt;br&gt;
(C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural&lt;br&gt;
amino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur&amp;nbsp;&lt;br&gt;
in different charge states due to (de-)protonation (i.e. carboxylic acids that can be&amp;nbsp;&lt;br&gt;
negatively charged or amines that can be positively charged), all possible structures with&amp;nbsp;&lt;br&gt;
up to a total charge of +-2e are included. In total, the dataset provides reference energies,&amp;nbsp;&lt;br&gt;
forces, and dipole moments for 2731180 structures calculated at the revPBE-D3(BJ)/def2-TZVP&amp;nbsp;&lt;br&gt;
level of theory [2-5] using the ORCA 4.0.1 code [6,7].&amp;nbsp;&lt;/p&gt;

&lt;p&gt;For more details, see;/p&gt;

&lt;p&gt;[1] Huang, B. and von Lilienfeld, O. A. arXiv:1707.04146 (2017).&lt;br&gt;
[2] Grimme, S.; Antony, J.; Ehrlich, S. and Krieg, H. J. Chem. Phys. 132, 154104 (2010).&lt;br&gt;
[3] Grimme, S.; Ehrlich, S. and Goerigk, L. J. Comput. Chem. 32, 1456-1465 (2011).&lt;br&gt;
[4] Weigend, F. and Ahlrichs, R. Phys. Chem. Chem. Phys. 7, 3297-3305 (2005).&lt;br&gt;
[5] Zhang, Y. and Yang, W. Phys. Rev. Lett. 80, 890 (1998).&lt;br&gt;
[6] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2, 73-78 (2012).&lt;br&gt;
[7] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1327 (2018).&lt;/p&gt;</description>
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