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Published March 25, 2019 | Version v1
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Solvated protein fragments

  • 1. University of Basel


The solvated protein fragments dataset probes many-body intermolecular interactions between 
"protein fragments" and water molecules, which are important for the description of many 
biologically relevant condensed phase systems. It contains structures for all possible 
"amons" [1] (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms 
(C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural
amino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur 
in different charge states due to (de-)protonation (i.e. carboxylic acids that can be 
negatively charged or amines that can be positively charged), all possible structures with 
up to a total charge of +-2e are included. In total, the dataset provides reference energies, 
forces, and dipole moments for 2731180 structures calculated at the revPBE-D3(BJ)/def2-TZVP 
level of theory [2-5] using the ORCA 4.0.1 code [6,7]. 

For more details, see

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



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Is documented by
arXiv:1902.08408 (arXiv)