Sampled ΔH/Δλ and ΔH data from ABFE calculations of 10 ligands bound to Cyclophilin D

Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands bound to Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike the other Cyclophilin D<br> dataset provided in this work, simulations for these ABFE calculations were carried out using hydrogen mass repartitioning (HMR). The MCL-1, HSP90, and PWWP1 also used HMR. All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).<br>补充信息：《评估绝对结合自由能在片段优化流程中的应用》 本数据集包含10个结合于亲环蛋白D（Cyclophilin D）的绝对结合自由能（Absolute Binding Free Energy, ABFE）原始自由能采样数据，对应多组重复实验（以`run`编号标记）。该批配体最初由Grädler等人于文献中详述（https://doi.org/10.1016/j.bmcl.2019.126717）。 与本研究中提供的其他亲环蛋白D数据集不同，本次ABFE计算所用的分子动力学模拟采用了氢质量再分区（Hydrogen Mass Repartitioning, HMR）技术。MCL-1、HSP90及PWWP1数据集同样采用了HMR技术。 所有采样数据均以GROMACS 2021生成的`.xvg`格式文件提供（https://doi.org/10.5281/zenodo.5849961）。该`.xvg`文件命名格式为`dhdl.N.xvg`，其中N代表采集自由能数值所对应的λ状态。该`.xvg`文件同时包含ΔH/Δλ与ΔH两类数值，详细信息请参阅各文件的文件头。 配体与蛋白-配体复合物的部分去耦合采样数据存放在`complex`文件夹中，该类数据包含三个步骤：取向约束添加步骤（位于`restraints-xvg`子文件夹）、电荷湮灭步骤（位于`coul-xvg`子文件夹）以及范德华（Van der Waals）去耦合步骤（位于`vdw-xvg`子文件夹）。 配体与溶剂的部分去耦合采样数据存放在`ligand`文件夹中，该类数据包含两个步骤：电荷湮灭步骤（位于各独立的`coul-xvg`子文件夹）以及范德华去耦合步骤（位于各独立的`vdw-xvg`子文件夹）。