Molecular Dynamics Trajectory of MDM2(25-109)–candidates Complex: 5/100 ns CHARMM36m Simulation

README — MDM2(25-109):peptide CHARMM36m simulations Supporting data for the SPAFESTWDILK / MDM2 manuscript (Sherman Tree Nutraceuticals, in preparation). 5NS.rar — 5 ns CHARMM36m triage (17 systems) Coarse stability filter applied to AF3 hits and reference systems.Candidates with stable backbone RMSD in the equilibrated window were promoted to 100 ns production. Plant-derived candidates (pharmacophore F-x(1-3)-W): SPAFESTWDILK Zingiber officinale (ginger) [LEAD] FESTWDILK Zingiber officinale (ginger) HAFPELWNIEK Zingiber officinale (ginger) DDFLNSWK Camellia sinensis (green tea) EFSDLWDNK Vanilla planifolia (vanilla) DNEFLQDWSK Artemisia SDLTSFMEEWR Artemisia FQSWEDLSK Cordyceps QNSFVDLWK Grifola frondosa (maitake) ISTAFLNDWDLAK Grifola frondosa (maitake) EHFETLWSSVK plant proteome candidate Hard negatives (non-canonical W-position or F-W spacing, scrambled): EWSLDQSKF Cordyceps (scrambled) FSNLDKWDE Vanilla (scrambled) WSADITKFESPL Zingiber officinale (scrambled) FWELDSTLKLPNEQS scrambled Reference negative controls: AAAAAAAAAAAAAAAAA poly-Ala 17-mer (no aromatics, no pharmacophore) SQETFSDLAKLLPEN p53(15-29) W23A mutant (Trp anchor abolished) 100NS.rar — SPAFESTWDILK production simulation (100 ns) Full-length molecular dynamics of the SPAFESTWDILK:MDM2(25-109) complexunder CHARMM36m force field. No dissociation observed throughout the simulation. Run parameters and full setup are documented in the included GROMACS .mdp files. CONTENTS PER ARCHIVE Initial structure (.pdb), topology (.top/.itp), MDP files (run parameters), trajectory (.xtc), run input (.tpr), final structure (.gro), and analysis outputs (.xvg: RMSD, RMSF, contacts, hbonds, gyrate, SASA, DSSP). All simulation parameters (timestep, thermostat, barostat, cutoffs, water model, ion concentration, equilibration protocol) are specified in the .mdp files within each archive. SOFTWARE GROMACS / CHARMM36m force field. Run on Google Colab GPU. RELATED OUTPUTS (not in this deposit) Three reference positive controls (PMI, 12/1, p53(15-29) wild-type) were simulated in the same campaign and are referenced in the manuscript. Co-folding predictions (AF3, Protenix, Chai-1), additional MD runs (AMBER99SB-ILDN, CHARMM27), EvoEF2 binding energies, MM-PBSA analyses, and the AF3 expanded benchmark with 29 hard negatives are publicly accessible via the Neurosnap platform; full job links are provided in the manuscript Data Availability section. License: CC BY 4.0