Supporting data: The Control Mechanisms of Activation and Glycyl Radical For-mation in Glycyl Radical Enzymes as Catalysed by the 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.<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及Christof M. Jäger发表的论文《丙酮酸甲酸裂解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调控机制》的配套支撑数据，具体包含以下内容：<br>- PARAMETERS目录：存储各分子动力学（Molecular Dynamics, MD）模拟体系对应的力场参数、初始拓扑文件与坐标文件的子目录，涉及体系包括：甘氨酰肽（Gly-Peptide）-PFL-AE、甘氨酰自由基（Gly-radical）-肽-PFL-AE、S-丙氨酰肽（S-Ala-Peptide）-PFL-AE、R-丙氨酰肽（R-Ala-Peptide）-PFL-AE、丙氨酰自由基（Ala-radical）-肽-PFL-AE、甘氨酰肽-PFL（Gly-PFL）与甘氨酰自由基（Gly-radical）-PFL。<br>- DOCKING目录：包含子文件夹1、2、3，内存储甘氨酸C端肽（Gly-C-terminus）与PFL-AE之间的三套最优对接复合物的力场参数、拓扑文件与坐标文件。<br>- RSE目录：存储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。<br>- ONIOM目录：包含各体系氢原子攫取（H-abstraction）反应能谱计算所用的Gaussian ONIOM输出文件与pdb格式文件，涉及体系包括：甘氨酰肽（Gly-Peptide，6个结构）、丙氨酰肽（Ala-Peptide，6个结构）、甘氨酸C端肽（Gly-C-terminus，10个结构）及丙氨酸C端肽（Ala-C-terminus，1个结构）。