Docking, replicate molecular dynamics and MM-GBSA data for plant-derived constituents at ten bacterial targets, with crystallographic controls at FtsZ and DNA gyrase B

Derived data and analysis code for every figure and table in the related article, submitted to Computational Biology and Chemistry. The record covers two bacterial targets, each carrying a ligand whose pose is known crystallographically, and holds two archives. PaperA_docking_and_FtsZ.zip. AutoDock Vina scores and size-corrected values for 96 compounds against ten bacterial targets; per-target redocking validation; and for five complexes (four test ligands plus the co-crystallised inhibitor PC190723 on Staphylococcus aureus FtsZ, PDB 3VOB) the OpenMM System, starting coordinates, RMSD, RMSF, contact and hydrogen-bond occupancy, and MM-GBSA per-frame series. See DEPOSIT_README.txt inside the archive. This archive was called CTC_dataset_deposit.zip in versions 1 to 5; it was renamed in version 6 because that name recorded the journal to which the work was first submitted. No data file changed in the rename. PaperA_gyraseB_dataset.zip (added in version 5). The replicate half of the study: twelve independent 50 ns trajectories of the Escherichia coli DNA gyrase B ATPase domain, comprising three plant-derived constituents and an AMP-PNP nucleotide control with Mg2+, each run in three replicates that differ only in the random seed of the thermostat. For every run: ligand displacement measured against the pose the system was built in, RMSF, radius of gyration, residue contacts, hydrogen-bond occupancies and a per-run summary. MM-GBSA series are included for the nine constituent runs; the three control runs carry none, because GAFF atom typing fails on the AMP-PNP triphosphate and substituting a different ligand force field would have made the control incomparable with the rest. Also included are the four starting systems (solvated coordinates, OpenMM System XML and ligand SDF), the redocking validation, the ranking-sensitivity and control-core analyses, and the code that regenerates every value quoted in the article. See README.txt inside the archive. Production trajectories total 3.3 GB, which exceeds what can usefully be deposited here, and are available from the corresponding author on request. Version history. Version 2 (15 September 2026) corrected the ligand-set note, the zeroed MM-GBSA standard-error column, the unlabelled nine-target regression fields and working titles left in the shipped files. Version 3 (16 September 2026) added the ligand displacement measured against the docked pose (analysis/rmsd_vs_start.json), README commands that run against this archive's own layout and give the MM-GBSA stride for each complex, and make_analysis_master.py, which rebuilds analysis_master.csv from the archive. Version 4 (16 September 2026) is version 3 with one correction: in the five rmsd_vs_start.json files, ref_pose_file named the reference coordinate file by an absolute path on the machine that built the archive; it now names the file as this archive ships it (simulations/<complex>/complex_solv.pdb.gz). Version 5 (22 September 2026) added the gyrase B replicate dataset described above, retitled the record to cover both targets, and updated the related article from Computational and Theoretical Chemistry to Computational Biology and Chemistry; absolute build-machine paths were removed from the newly deposited code before archiving. Version 6 (25 September 2026) renamed the docking and FtsZ archive from CTC_dataset_deposit.zip to PaperA_docking_and_FtsZ.zip and updated DEPOSIT_README.txt inside it, which still named the article and journal of the earlier submission and carried a version history that stopped at version 2. That README is the only file whose bytes changed; every other file in the archive is byte-identical to version 4, and no docking or simulation result reported in an earlier version has changed. Zenodo files cannot be altered after publication, so each correction is a new version rather than an edit.