Dataset: 800 QM/MM minimum energy pathway conformations for the acylation reactions of Toho-1/ampicillin and Toho-1/cefalexin

This dataset consists of 800 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the acylation reactions between a Class A beta-lactamases (Toho-1) and two beta-lactam antibiotic molecules (ampicillin and cefalexin). These files are: toho_amp.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Ampicillin (200 pathways); toho_amp.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Ampicillin (200 pathways); toho_cex.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Cefalexin (200 pathways); toho_cex.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Cefalexin (200 pathways); energies.zip: the replica energies at B3LYP-D3/6-31+G**/C36 level; chelpgs.zip: the ChElPG charges of all reactant replicas at B3LYP-D3/6-31+G**/C36 level; farrys.zip: the featurzied NumPy arrays for model training; peephole.zip: an example file for how the optimized MEPs look like. The R1-AE pathways are the acylation uses Glu166 as the general base; the R2-AE pathways uses Lys73 and Glu166 as the concerted base. All QM/MM pathways are optimized at the DFTB3/3OB-f/CHARMM36 level of theory.本数据集包含800份CHARMM psf/cor格式的坐标文件，对应A类β-内酰胺酶（Toho-1）与两种β-内酰胺类抗生素——氨苄西林和头孢氨苄之间酰化反应的量子力学/分子力学（QM/MM）最低能量路径。相关文件详情如下： toho_amp.r1-ae.zip：Toho-1与氨苄西林的R1-AE酰化路径（共200条）； toho_amp.r2-ae.zip：Toho-1与氨苄西林的R2-AE酰化路径（共200条）； toho_cex.r1-ae.zip：Toho-1与头孢氨苄的R1-AE酰化路径（共200条）； toho_cex.r2-ae.zip：Toho-1与头孢氨苄的R2-AE酰化路径（共200条）； energies.zip：包含B3LYP-D3/6-31+G**/C36理论水平下的复性能量数据； chelpgs.zip：包含B3LYP-D3/6-31+G**/C36理论水平下所有反应物复本的ChElPG电荷； farrys.zip：用于模型训练的特征化NumPy数组； peephole.zip：用于展示优化后最低能量路径形态的示例文件。 其中，R1-AE路径为以Glu166作为通用碱的酰化反应路径；R2-AE路径为以Lys73与Glu166作为协同碱的酰化反应路径。所有QM/MM路径均在DFTB3/3OB-f/CHARMM36理论水平下完成优化。