Supporting data for publication: The Activation of Glycyl Radical Enzymes – Multiscale Modelling Insights into Catalysis and Radical Control in Pyruvate Formate-Lyase Activating Enzyme

Supporting data for the publication "The Control Mechanisms of Activation and Glycyl Radical Formation in Glycyl Radical Enzymes as Catalysed by the Pyruvate Formate-Lyase Activating Enzyme" by Marko Hanzevacki, Anna K. Croft, and Christof M. Jäger including: <br> - Directory PARAMETERS contains subdirectories with force field parameters, initial toplogy and coordinate files for MD simulations for each system: Gly-Peptide-PFL-AE, Gly-radical-Peptide-PFL-AE, S-Ala-Peptide-PFL-AE, R-Ala-Peptide-PFL-AE, Ala-radical-Peptide-PFL-AE, Gly-PFL and Gly-radical-PFL. - Directory DOCKING contains subfolders 1, 2 and 3 with force field parameters, topology and coordinates for best three docking complexes between Gly-C-terminus and PFL-AE. - Additional DOCKING structures for C-terminus docking added (C-TERMINUS-OPEN/CLOSED-DOCKING)<br> - Directory RSE contains Gaussian QM output files used to calculate the RSEs.<br> - Directory ONIOM contains subdirectories with Gaussian ONIOM outputs and pdb files used to calculate the H-abstraction profiles for each system: Gly-Peptide (6 structures), Ala-Peptide (6 structures), Gly-C-terminus (10 structures) and Ala-C-terminus (1 structure).<br>

本数据集为Marko Hanzevacki、Anna K. Croft与Christof M. Jäger发表的论文《丙酮酸甲酸裂合酶激活酶催化的甘氨酰自由基酶中激活过程与甘氨酰自由基形成的调控机制》的配套支撑数据，具体内容如下：
- PARAMETERS目录包含各分子动力学（Molecular Dynamics, MD）模拟体系的力场参数、初始拓扑文件与坐标文件对应的子目录，涉及体系包括：Gly-Peptide-PFL-AE、Gly-radical-Peptide-PFL-AE、S-Ala-Peptide-PFL-AE、R-Ala-Peptide-PFL-AE、Ala-radical-Peptide-PFL-AE、Gly-PFL以及Gly-radical-PFL。
- DOCKING目录包含子文件夹1、2、3，存放甘氨酸C端（Gly-C-terminus）与丙酮酸甲酸裂合酶激活酶（Pyruvate Formate-Lyase Activating Enzyme, PFL-AE）之间最优的三个对接复合物的力场参数、拓扑文件与坐标文件。
- 新增了针对C端对接的额外对接结构（C-TERMINUS-OPEN/CLOSED-DOCKING）。
- RSE目录存放用于计算相对稳定能（Relative Stabilization Energy, RSE）的Gaussian量子力学（Quantum Mechanics, QM）输出文件。
- ONIOM目录包含各体系氢提取反应势能剖面计算所用的Gaussian ONIOM输出文件与PDB（Protein Data Bank）文件，涉及体系及对应结构数量如下：Gly-Peptide（6个结构）、Ala-Peptide（6个结构）、Gly-C-terminus（10个结构）以及Ala-C-terminus（1个结构）。