NDM-1 Aryl Bisphosphonate Inhibitor Discovery: Structure-Based Virtual Screening, Molecular Dynamics, and Bonded-Zinc Validation Datasets

This dataset supports the study entitled “Structure-based virtual screening and molecular dynamics identify an aryl bisphosphonate as a candidate inhibitor of New Delhi metallo-β-lactamase 1” (Yeşil & Yeşil, 2026). It provides all data and scripts necessary to reproduce the computational workflow and figures reported in the manuscript. The dataset comprises a structure-based virtual screening pipeline targeting NDM-1 (PDB ID: 5ZGE) applied to 20,546 ADMET-filtered compounds derived from DrugBank v5.1 and COCONUT v2.0, GAFF2/AM1-BCC parameterisation files for the candidate inhibitor DB04204, and molecular dynamics simulations including three independent 1 μs trajectories generated using Li/Merz 12–6 non-bonded zinc parameters with the AMBER ff19SB force field and TIP3P water model, as well as three independent 500 ns trajectories generated using the CADM bonded-zinc approach (gen_seed = 200, 137, 271) to assess parameterisation robustness. The dataset further includes re-docking validation against taniborbactam (PDB ID: 6RMF) and L-captopril (PDB ID: 4EXS), together with all analysis scripts and per-figure CSV files used to generate the reported results. Trajectories are provided as solvent-stripped GROMACS .xtc files (50 ps stride) to reduce storage requirements, with full system reconstruction enabled via the accompanying topology and coordinate files. All simulations and analyses were performed using GROMACS 2024.5, AmberTools 23, RDKit 2024.03, gnina 1.3, and MDAnalysis 2.10. The dataset is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.