Molecular docking raw datasets for Neisseria gonorrhoeae carbonic anhydrase binding-site screening: post-docking score tables and ligand–site complex structures (1KOQ orthosteric; 3KS3 orthosteric and allosteric_1)

This Figshare deposit provides the complete raw molecular docking outputs generated in the docking phase of the study, including (i) post-docking score tables and derived post-processing summaries and (ii) structure files for ligand poses and receptor–ligand complexes for the top-ranked ligand–site combinations across three screened binding sites: 1KOQ orthosteric, 3KS3 orthosteric, and 3KS3 allosteric_1.The deposit is organised into two internal sections to preserve provenance and enable reproducibility. The post-docking tables capture Vina docking energies (ΔGdock) and inferred binding constants (Ki) across sites, together with downstream interaction counts and short MD/NMA-derived metrics where applicable. The structure section contains pose PDBs and assembled receptor–ligand complex PDBs supporting visual inspection, interaction profiling (e.g., LigPlot/LigPlus), and downstream stability analysis.ContentsSection A1: Post-docking analysis tables (scores + derived metrics)Dataset 1A_10%combined_scores_all_sites_final.csv: combined docking results table across the screened sites, including: site, receptor_id, site_label, ligand_id, ligand_path, pose/log paths, Vina ΔGdock (kcal/mol), Ki (M, µM), and execution status (return_code/stdout).Dataset 1B_10percent_postdocking_final_summary.csv: expanded post-docking summary table containing the docking metrics above plus: rank per site, interaction counts (H-bonds, hydrophobic, π–π, cation–π, ionic, π–anion, van der Waals), MD sanity-check stability metrics for 3KS3 pockets (mean/max Cα RMSD; final potential energy), normal-mode eigenvalues (eig1–eig3), and Ki class labels.Section A2: Ligand-site structural outputs (poses + receptor–ligand complexes + MD/NMA artefacts)This section provides the structure-level artefacts supporting docking interpretation and downstream analyses.(i) Docked ligand poses (PDB)Pose files named in the pattern: LIGAND__RECEPTOR__SITE_pose.pdb, ..._pose_simple.pdb, and ..._pose_nma.pdb,where SITE ∈ {orthosteric, allosteric_1} depending on the receptor.(ii) Assembled receptor–ligand complex structures (PDB)Complex files named in the pattern: RECEPTOR_receptor__LIGAND__RECEPTOR__SITE_pose__complex.pdb (and corresponding ..._pose_simple__complex.pdb). These are pre-built complex structures intended for direct visualisation and interaction profiling.(iii) Post-docking analysis artefacts (CSV/TXT/DCD)10percent_postdocking_final_summary.csv (replicated/paired summary for the structure set)interaction_summary_topN_mdana.csv (interaction profile summaries consistent with ST3 fields: interaction-type counts)md_site_summary.csv (site-level MD summary)3KS3__orthosteric_md_log.txt, 3KS3__allosteric_1_md_log.txt (MD logs)3KS3__orthosteric.dcd, 3KS3__allosteric_1.dcd (short MD trajectories for 3KS3 pockets)nma_summary_topK.csv (normal mode analysis summary consistent with ST4 eigenvalue reporting)