MD simulations data of G6PDi-1 inhibitor for G6PD

This dataset contains MD simulation data for glucose-6-phosphate dehydrogenase (G6PD) in complex with the inhibitor G6PDi-1, docked at six distinct binding sites identified from docking calculations. For each docked complex (dockFile_1 to dockFile_6), four independent MD replicas were simulated for approximately 5 μs each using the GROMACS 2024.2 simulation package with the Amber19SB force field for the protein and the TIP3P water model. The total production simulation time across all systems is approximately 120 μs. Due to storage limitations, trajectories contain only protein and ligand coordinates, saved every 100 ps. The dataset is organised by docked complex: dockFile_1 dockFile_2 dockFile_3 dockFile_4 dockFile_5 dockFile_6 Each docked complex folder contains:1. starting docked structure2. topol.top – topology file3. four replica directories: rep-1 rep-2 rep-3 rep-4 Each replica directory contains:1. md.tpr – simulation input file2. md_ProLIG.tpr – processed run input file containing only protein and ligand3. traj_ProLIG_noPBC_FitProBB_dt100ps.xtc The dataset contains the folder monomer_concat_traj.tar.gz. This folder contains post-500 ns equilibrated trajectories concatenated and derived from four independent replica simulations of 1 μs each. The protein system was simulated using the Amber19SB force field. The folder contains one tpr/topology file and the concatenated trajectory saved every 100 ps. The dataset contains the folder active_tetramer.tar.gz. This folder contains three independent MD replicas of the active tetrameric state of G6PD, based on PDB ID 7SNI, simulated for 100 ns each. The protein system was simulated using the CHARMM36 force field. The folder contains one tpr file and three protein only trajectories saved every 100 ps.