Solvated protein fragments

The solvated protein fragments dataset probes many-body intermolecular interactions between <br> "protein fragments" and water molecules, which are important for the description of many <br> biologically relevant condensed phase systems. It contains structures for all possible <br> "amons" [1] (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms <br> (C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural<br> amino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur <br> in different charge states due to (de-)protonation (i.e. carboxylic acids that can be <br> negatively charged or amines that can be positively charged), all possible structures with <br> up to a total charge of +-2e are included. In total, the dataset provides reference energies, <br> forces, and dipole moments for 2731180 structures calculated at the revPBE-D3(BJ)/def2-TZVP <br> 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).<br> [2] Grimme, S.; Antony, J.; Ehrlich, S. and Krieg, H. J. Chem. Phys. 132, 154104 (2010).<br> [3] Grimme, S.; Ehrlich, S. and Goerigk, L. J. Comput. Chem. 32, 1456-1465 (2011).<br> [4] Weigend, F. and Ahlrichs, R. Phys. Chem. Chem. Phys. 7, 3297-3305 (2005).<br> [5] Zhang, Y. and Yang, W. Phys. Rev. Lett. 80, 890 (1998).<br> [6] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2, 73-78 (2012).<br> [7] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1327 (2018).溶剂化蛋白质片段数据集（solvated protein fragments dataset）旨在探究蛋白质片段与水分子之间的多体分子间相互作用，这类相互作用对于描述诸多具有生物学意义的凝聚相体系至关重要。 该数据集涵盖了所有可通过20种天然氨基酸（通过肽键或二硫键连接构成的蛋白质）的化学图谱得到的amon[1]（氢饱和共价键合片段）的结构，这类amon最多包含8个重原子（碳C、氮N、氧O、硫S）。 对于可因质子化/去质子化作用呈现不同电荷状态的氨基酸（即可带负电的羧酸基团与可带正电的氨基基团），数据集收录了所有总电荷介于±2e之间的可能结构。 本数据集总计为2731180个结构提供了参考能量、原子受力与偶极矩数据，所有数据均通过ORCA 4.0.1量化软件[6,7]，在revPBE-D3(BJ)/def2-TZVP理论级别[2-5]下计算得到。 更多详细信息可参考：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).