Development of novel antibiotics agains R67 DHFR

Supporting data for "Computational development of inhibitors of plasmid-borne bacterial dihydrofolate reductase", published in "Antibiotics". https://doi.org/10.3390/antibiotics11060779 QM_inputs.zip - Firefly 8.0 input files for geometry optimizations (xxx.txt) , single-point energies in the gas phase (xxx_SP.txt) and single-point energies in solution (xxx_SP_pcm.txt). QM_outputs.zip - Firefly 8.0 output files for the geometry optimizations (xxx.out) , single-point energies in the gas phase (xxx_SP.out) and single-point energies in solution (xxx_SP_pcm.out) S_aureus_DHFR_ligand_32_snapshots.zip - PDB snapshots of three different runs of the complex between S. aureus DHFR (PDB:3FRE) and ligand 32. To convert file names to position in the trajectory (in nanoseconds) , please divide the snapshot number by 4 (e.g. 3fre_32k_2nd_run_00100.pdb corresponds to the snapshot at 100/4=25 ns along the trajectory in the second simulation) human_DHFR_and_R67_DHFR_snapshots.zip - PDB snapshots of three different runs of the complex between human DHFR or R67 and ligands 31 , 32, deprotonated 1 (1k), protonated 1, (1l), protonated dihydrofolate (1g) and deprotonated dihydrofolate (1f). To convert file names to position in the trajectory (in nanoseconds) , please divide the snapshot number by 8 (e.g. hDHFR_32k_2nd_runr_00100.pdb corresponds to the snapshot at 100/8=12.5 ns along the trajectory in the second simulation of the complex of human DHFR bound to ligand 32) MD_inputs_and_scripts.zip - YASARA scenes and macros to perform the moleuclar dynamics simulations and analyze the MD trajectories本数据集为发表于《Antibiotics》期刊、DOI为https://doi.org/10.3390/antibiotics11060779的论文《质粒源性细菌二氢叶酸还原酶抑制剂的计算开发》的配套支撑数据。 QM_inputs.zip：包含用于几何优化的Firefly 8.0输入文件（xxx.txt）、气相单点能计算输入文件（xxx_SP.txt）以及采用极化连续介质模型（Polarizable Continuum Model, PCM）的溶液相单点能计算输入文件（xxx_SP_pcm.txt）。 QM_outputs.zip：包含对应几何优化的Firefly 8.0输出文件（xxx.out）、气相单点能计算输出文件（xxx_SP.out）以及采用极化连续介质模型的溶液相单点能计算输出文件（xxx_SP_pcm.out）。 S_aureus_DHFR_ligand_32_snapshots.zip：包含金黄色葡萄球菌二氢叶酸还原酶（dihydrofolate reductase, DHFR，PDB编号3FRE）与配体32形成的复合物的三次独立分子动力学模拟轨迹快照（PDB格式）。若需将快照编号转换为轨迹时间（单位：纳秒），请将快照编号除以4（例如：3fre_32k_2nd_run_00100.pdb对应第二次模拟中轨迹时间为100/4=25 ns的快照）。 human_DHFR_and_R67_DHFR_snapshots.zip：包含人源二氢叶酸还原酶（dihydrofolate reductase, DHFR）或R67型二氢叶酸还原酶分别与配体31、配体32、去质子化形式1（1k）、质子化形式1（1l）、质子化二氢叶酸（1g）以及去质子化二氢叶酸（1f）形成的复合物的三次独立分子动力学模拟轨迹快照（PDB格式）。若需将快照编号转换为轨迹时间（单位：纳秒），请将快照编号除以8（例如：hDHFR_32k_2nd_runr_00100.pdb对应人源二氢叶酸还原酶与配体32结合复合物的第二次模拟中，轨迹时间为100/8=12.5 ns的快照）。 MD_inputs_and_scripts.zip：包含用于执行分子动力学模拟及分析分子动力学轨迹的YASARA场景文件与宏脚本。