Solvated protein fragments

• Main Authors: Unke, Oliver Thorsten, Meuwly, Markus
• Format: Dataset
• Language: unknown
• Published: Zenodo 2019
• Subjects: proteins; amons; condensed phase; quantum chemistry; density functional theory; DFT; Orca
• Online Access: https://dx.doi.org/10.5281/zenodo.2605372; https://zenodo.org/record/2605372

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 https://arxiv.org/abs/1902.08408. [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).