Supplementary tables and figures for molecular docking, molecular-dynamics refinement, MM-GBSA analysis, and dual-target pIC50 modelling of phytoligands against NgCA and hCA II

Abstract This deposit contains supplementary tables and figures supporting the structure-based and predictive-modelling component of a thesis on phytoligands from medicinal plants used for venereal-disease management. The files include docking subset descriptors, combined docking-score outputs, MD stability and contact analyses, MM-GBSA binding-energy summaries, NgCA/hCA II pIC50 model-validation outputs, full-library activity predictions, and ranked ligand-prioritisation summaries. The accompanying figures visualise ligand stability, binding-site interactions, energetic profiles, model diagnostics, and selectivity-oriented screening outcomes. The deposit supports transparency, reproducibility, and traceability of the computational prioritisation workflow. Methodological description The supplementary tables and figures were generated from a cheminformatics workflow involving representative phytochemical-subset selection, molecular docking, molecular-dynamics refinement, MM-GBSA-based binding-energy estimation, and dual-target pIC50 prediction. The ligand subset was screened against Neisseria gonorrhoeae carbonic anhydrase and human carbonic anhydrase II models using docking-derived scores and post-docking ranking procedures. Selected ligand–NgCA complexes were subsequently evaluated by molecular-dynamics simulations, with trajectory-derived metrics used to assess ligand retention, protein stability, Zn²⁺-site proximity, persistent residue contacts, and binding-energy estimates. Target-specific pIC50 prediction models were developed for NgCA and hCA II using docking and physicochemical descriptors. The final outputs include model-validation metrics, training-set predictions, full-library predicted activities, applicability-domain annotations, predicted NgCA-over-hCA II preference, estimated IC50 conversions, and top-ranked ligand summaries. The PDF figures provide graphical representations of the MD and pIC50 modelling outputs, while the Excel files provide the underlying tabulated results used for reporting and interpretation in the thesis. Files included 1. Supplementary tables archive File Description ST5.1_forST2.xlsx Physicochemical suitability and drug-likeness profile of the representative phytochemical subset advanced for docking. It also includes subset representativeness summaries, docking-ready ligand files, and ligand entries excluded during molecular standardisation/PDBQT preparation. ST5.2_forST7.xlsx Combined docking scores and ranked top 50 ligands for orthosteric sites of 1KOQ and 3KS3, including AutoDock Vina scores and inferred inhibition constant estimates. ST5.3_forST8.xlsx Replicate-resolved MD stability, ligand-retention, Zn²⁺-site proximity/deviation, and MM-GBSA-derived binding-energy metrics for selected phytoligand-NgCA and benchmark control-NgCA complexes. ST5.4_forST10.xlsx Trajectory-derived ligand-residue interaction profiles and representative-replicate MM-GBSA binding-energy estimates for selected NgCA-ligand complexes during the 10–20 ns production-analysis window. ST5.5_forST9.xlsx MD/topology contact-index mapping and synopsis of persistent residue-atom contact architecture across NgCA complexes. ST5.6_forST11.xlsx Integrated MD-informed prioritisation matrix for shortlisted phytoligands and benchmark controls against NgCA. ST5.7_forST12.xlsx Expanded validation metrics, tuning parameters, and model-selection metadata for target-specific pIC50 models. ST5.8_forST13.xlsx Training-set observed and final-model predicted pIC50 values, residuals, leverage values, standardised residuals, and applicability-domain assignments for NgCA and hCA II models. ST5.9_forST14.xlsx Full-library predicted target-specific pIC50 values, predicted NgCA-over-hCA II preference, IC50 conversions, and applicability-domain annotations for the ligand screening set. ST5.10_forST15.xlsx Top-ranked ligand summaries based on predicted NgCA pIC50, predicted hCA II pIC50, and predicted NgCA-over-hCA II preference. 2. Supplementary figures archive File Description SF5.1.pdf Aggregate ligand RMSD-in-pocket profiles across NgCA complexes during the 10–20 ns evaluation window. SF5.2.pdf MD-refined 3D visualisation of ligand binding within the catalytic Zn²⁺-containing active-site region for selected phytoligand–NgCA complexes. SF5.3.pdf Residue-atom contact-persistence landscape of ligand-bound NgCA complexes during 20 ns molecular-dynamics refinement. SF5.4.pdf Aggregate MM-GBSA-derived binding-energy estimates across phytoligand-NgCA and control-NgCA complexes. SF5.5.pdf Exploratory response and predictor structure of the dual-target pIC50 training set. SF5.6.pdf NgCA model-class comparison and diagnostic support plots for exploratory pIC50 modelling. SF5.7.pdf hCA II model-class comparison and diagnostic support plots for exploratory pIC50 modelling. SF5.8.pdf Ranked prediction summaries and selectivity-oriented screening views for the phytochemical library.