Dataset Open Access

Solvated protein fragments

Unke, Oliver Thorsten; Meuwly, Markus


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        <foaf:name>Meuwly, Markus</foaf:name>
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    <dct:title>Solvated protein fragments</dct:title>
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    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2019</dct:issued>
    <dcat:keyword>proteins</dcat:keyword>
    <dcat:keyword>amons</dcat:keyword>
    <dcat:keyword>condensed phase</dcat:keyword>
    <dcat:keyword>quantum chemistry</dcat:keyword>
    <dcat:keyword>density functional theory</dcat:keyword>
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    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2019-03-25</dct:issued>
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    <dct:description>&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 https://arxiv.org/abs/1902.08408.&lt;/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;</dct:description>
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