Dataset for Multiscale modelling and simulations of the tetrameric metallo–β–lactamase L1 with indole-2-carboxylate inhibitors

Files associated with performed simulations, including starting structures, parameters, simulation input files, and short videos of simulation trajectories. Simulation files include: Initial coordinates of the ligands for geometry optimization and RESP calculations in GAUSSIAN Parameter and starting files for QM/MM calculations of protein–ligand complexes. Input files for hybrid Monte Carlo Simulations Parameter, coordinate and input files for MD simulations in GROMACS Parameter, coordinate and input files for MD simulations in DESMOND Additionally, short videos are included of simulations showing the close-to-open conformation and the open-to-close conformation.本数据集包含已完成模拟的关联文件，涵盖初始结构、参数文件、模拟输入文件以及模拟轨迹短视频。 模拟文件具体包含以下内容： 用于GAUSSIAN软件中几何优化与约束静电势（RESP）计算的配体初始坐标文件 蛋白质-配体复合物量子力学/分子力学（QM/MM）计算所需的参数与初始文件 混合蒙特卡洛模拟的输入文件 GROMACS软件中分子动力学（MD）模拟所需的参数、坐标与输入文件 DESMOND软件中分子动力学（MD）模拟所需的参数、坐标与输入文件 此外，数据集还收录了展示配体闭合-张开构象与张开-闭合构象转变过程的模拟短视频。