Molecular dynamics data for compound and Mycobacterium tuberculosis shikimic acid kinase targets

This repository contains data on the molecular dynamics (MD) of Mycobacterium tuberculosis shikimic acid kinase (MtSK) and (2-[(5Z)-5-(1-benzyl-5-bromo-2oxoindol-3-ylidene)-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]acetic acid). MtSK crystal structure was obtained from the Protein Data Bank (PDB ID: 2IYQ). The simulation system was created using Solution Builder on a CHARMM-GUI server with the compound conformation output from GOLD. The system was solvated using the TIP3P water model, and the necessary ions were added to balance the charges. The energies were minimized in up to 5,000 steps using the steepest descent method. Equilibration was performed for 100 ps under the standard NVT and NPT conditions. The temperature and pressure were adjusted to 310 K and 1 bar, respectively. The final MD simulation was performed for 100 ns with a 2 fs time step of under the NPT conditions. Gromacs 2021.4 was used for the simulations. Various analyses, ranging from energy calculations to Sasa analysis, were performed on the obtained trajectories.

本数据集存储了结核分枝杆菌莽草酸激酶（MtSK）与(2-[(5Z)-5-(1-苄基-5-溴-2-氧代吲哚-3-亚基)-4-氧代-2-硫代亚基-1,3-噻唑烷-3-基]乙酸)的分子动力学（MD）模拟数据。MtSK的晶体结构获取自蛋白质数据银行（Protein Data Bank，PDB），其PDB编号为2IYQ。模拟系统通过CHARMM-GUI服务器的溶液构建器（Solution Builder）构建，配体构象由GOLD软件生成。采用TIP3P水模型对体系进行溶剂化处理，并添加必要离子以平衡体系电荷。使用最速下降法进行能量最小化，最大迭代步数达5000步。在标准NVT和NPT系综条件下开展时长100皮秒的平衡模拟，模拟温度与压力分别设置为310开尔文与1巴。最终的分子动力学模拟在NPT系综条件下以2飞秒的时间步长运行100纳秒，本次模拟采用Gromacs 2021.4软件完成。针对获取的模拟轨迹，开展了涵盖能量计算、溶剂可及表面积（Solvent Accessible Surface Area, SASA）分析在内的各类分析工作。