Molecular Dynamics Simulation and MM/PBSA Binding Free Energy Analysis of Compound 2 and Reference Ligand in Complex with NAMPT
Year: 2026
Type: article
Abstract: This dataset contains the complete Molecular Dynamics (MD) simulation trajectories and Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) binding free energy calculation results for the NAMPT protein target. Molecular Dynamics simulations were performed using GROMACS in three independent replicates, each with a simulation duration of 100 ns. Two molecular systems were investigated: NAMPT complexed with the proposed Compound 2 and NAMPT complexed with its respective reference drug/ligand. The dataset provides the raw simulation data and energy calculation results to support the evaluation of protein–ligand complex stability and binding energetics. This dataset is organized into two main directories: Compound_2/: Simulation and MM/PBSA calculation data for the NAMPT–Compound 2 complex. Reference/: Simulation and MM/PBSA calculation data for the NAMPT–reference ligand complex. Each system contains the following components: 1. Molecular Dynamics Simulation Data (Trajectory/) md_[1-3].xtc: Raw, unprocessed MD trajectory files containing atomic coordinates for the three independent simulation replicates. MD_rep[1-3].tpr: GROMACS portable binary run input files containing the system topology and simulation parameters. md_[1-3].gro: Final coordinate files of the simulated systems. md_[1-3].log: GROMACS log files documenting the simulation progression. topol.top: Master topology file describing the protein–ligand complex. 2. MM/PBSA Binding Free Energy Calculations (MMPBSA/) FINAL_RESULTS_MMPBSA_rep[1-3].dat: Total binding free energy calculation results for each independent replicate. FINAL_DECOMP_MMPBSA_rep[1-3].dat: Per-residue energy decomposition results, providing information on the energetic contributions of individual protein residues to ligand binding. Notes on Data Processing and Reproducibility The raw .xtc trajectory files retain Periodic Boundary Conditions (PBC). Standard GROMACS post-processing procedures, such as gmx trjconv, are required for trajectory centering and fitting before visualization and subsequent structural analysis. MM/PBSA calculations were performed using the gmx_MMPBSA tool with the sander Poisson–Boltzmann (PB) backend. The dataset includes the original simulation input and output files required to support further trajectory processing and inspection of the reported binding free energy calculations.
Language: English
Subfield: Drug Discovery
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7225421126