DOI: 10.6084/m9.figshare.30921515
title: <b>Molecular docking raw datasets for </b><b><i>Neisseria gonorrhoeae</i></b><b> carbonic anhydrase binding-site screening: post-docking score tables and ligand–site complex structures (1KOQ orthosteric; 3KS3 orthosteric and allosteric_1)</b>

description: This Figshare deposit provides the complete <b>raw molecular docking outputs</b> generated in the docking phase of the study, including (i) <b>post-docking score tables</b> and derived post-processing summaries and (ii) <b>structure files for ligand poses and receptor–ligand complexes</b> for the top-ranked ligand–site combinations across three screened binding sites: <b>1KOQ orthosteric</b>, <b>3KS3 orthosteric</b>, and <b>3KS3 allosteric_1</b>.The deposit is organised into two internal sections to preserve provenance and enable reproducibility. The post-docking tables capture Vina docking energies (ΔG<sub>dock</sub>) and inferred binding constants (K<sub>i</sub>) 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.<br><br><b>Contents</b><b>Section A1: Post-docking analysis tables (scores + derived metrics)</b><b>Dataset 1A_10%combined_scores_all_sites_final.csv: c</b>ombined docking results table across the screened sites, including:<i> </i><i>site, receptor_id, site_label, ligand_id, ligand_path, pose/log paths, Vina ΔG</i><sub><em>dock</em></sub><i> (kcal/mol), K</i><sub><em>i</em></sub><i> </i><sub><em>(M, µM)</em></sub><i>, and execution status (return_code/stdout).</i><b>Dataset 1B_10percent_postdocking_final_summary.csv: e</b>xpanded post-docking summary table containing the docking metrics above plus: <i>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 (eig</i><sub><em>1</em></sub><i>–eig</i><sub><em>3</em></sub><i>), and Ki class labels.</i><b>Section A2: Ligand-site structural outputs (poses + receptor–ligand complexes + MD/NMA artefacts)</b>This section provides the structure-level artefacts supporting docking interpretation and downstream analyses.<b>(i) Docked ligand poses (PDB)</b>Pose files named in the pattern:<code> </code><code>LIGAND__RECEPTOR__SITE_pose.pdb</code>, <code>..._pose_simple.pdb</code>, and <code>..._pose_nma.pdb,</code>where <i>SITE ∈ {orthosteric, allosteric_1}</i> depending on the receptor.<b>(ii) Assembled receptor–ligand complex structures (PDB)</b>Complex files named in the pattern:<code> </code><code>RECEPTOR_receptor__LIGAND__RECEPTOR__SITE_pose__complex.pdb</code> (and corresponding <code>..._pose_simple__complex.pdb</code>). These are pre-built complex structures intended for direct visualisation and interaction profiling.<b>(iii) Post-docking analysis artefacts (CSV/TXT/DCD)</b><code>10percent_postdocking_final_summary.csv</code> (replicated/paired summary for the structure set)<code>interaction_summary_topN_mdana.csv</code> (interaction profile summaries consistent with ST3 fields: interaction-type counts)<code>md_site_summary.csv</code> (site-level MD summary)<code>3KS3__orthosteric_md_log.txt</code>, <code>3KS3__allosteric_1_md_log.txt</code> (MD logs)<code>3KS3__orthosteric.dcd</code>, <code>3KS3__allosteric_1.dcd</code> (short MD trajectories for 3KS3 pockets)<code>nma_summary_topK.csv</code> (normal mode analysis summary consistent with ST4 eigenvalue reporting)<br>