Markiewicz Michal, Szczelina Robert, Pasenkiewicz-Gierula Marta
Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland.
Division of Computational Mathematics, Faculty of Mathematics and Computer Science, Jagiellonian University, Krakow, Poland.
Data Brief. 2021 Oct 14;39:107483. doi: 10.1016/j.dib.2021.107483. eCollection 2021 Dec.
This data article contains partial charges generated for cholesterol, C7-hydroxycholesterol and C7-hydroperoxycholesterol and torsional parameters for hydroperoxy of C7-hydroperoxycholesterol for molecular dynamics simulations in the OPLSAA force field [1] using the package Gromacs [2]. The hydroperoxy group remained unparameterized in the OPLSAA force field and the parameters obtained have the potential for re-use in similar simulations. The atom-centred point charges on each sterol molecule were derived using the restrained electrostatic potential (RESP) approach [3]. The parameters for the C7-O-O-H and C8-C7-O-O torsion angles were derived by fitting the parameters of the torsional term (Ryckaert-Bellemans function) of the OPLSAA potential energy function to the quantum mechanical rotational energy profile calculated at CCSD(T)/cc-pVQZ level of theory. This article presents data used in the research article "Chirality affects cholesterol-oxysterol association in water, a computational study" [4].
本数据文章包含为胆固醇、7-羟基胆固醇和7-氢过氧胆固醇生成的部分电荷，以及7-氢过氧胆固醇中氢过氧基的扭转参数，用于在OPLSAA力场[1]中使用Gromacs软件包[2]进行分子动力学模拟。在OPLSAA力场中，氢过氧基尚未参数化，所获得的参数有可能在类似模拟中重复使用。每个甾醇分子上以原子为中心的点电荷是使用受限静电势（RESP）方法[3]推导出来的。C7-O-O-H和C8-C7-O-O扭转角的参数是通过将OPLSAA势能函数的扭转项（Ryckaert-Bellemans函数）的参数拟合到在CCSD(T)/cc-pVQZ理论水平计算的量子力学旋转能轮廓而推导出来的。本文展示了研究论文《手性影响水中胆固醇-氧化甾醇的缔合，一项计算研究》[4]中使用的数据。
