Molecular dynamics simulations of ligand binding to the MsepPR3/Orco receptor

This dataset contains the structural prediction–derived ligand position data and molecular dynamics (MD) simulation input files used in the study of ligand interactions with the MsepPR3/Orco receptor complex. The repository is organized into two compressed archives: AlphaFold3-derived ligand position data and MD simulation input data. 1. AlphaFold3 prediction–derived ligand position data The archive AF3_predict_results.zip contains the ligand coordinate datasets derived from AlphaFold3 predictions of the MsepPR3/Orco tetramer in complex with pheromone and aromatic ligands.These files do not contain the predicted structural models themselves, but instead include the ligand center-of-mass (COM) coordinates extracted from the predicted models, which were used to generate the ligand distribution density plots in the manuscript. Two subfolders correspond to predictions performed with different aromatic ligands: MsepPR3_Orco_Z&BA – predictions involving Z11-16:Ald and benzaldehyde (BA) MsepPR3_Orco_Z&MBA – predictions involving Z11-16:Ald and isoamyl alcohol (MBA) Within each subfolder, ligand coordinate data are provided for three binding scenarios: Single-ligand conditionThe receptor tetramer bound to one Z11-16:Ald molecule Dual-ligand conditionThe tetramer bound to one Z11-16:Ald and one BA/MBA molecule Multiple-ligand conditionThe tetramer bound to one Z11-16:Ald and ten BA/MBA molecules For each condition, the files contain the ligand center-of-mass (COM) coordinates extracted from all AlphaFold3-predicted models, which were used to construct the two-dimensional kernel density estimation (KDE) plots of ligand occupancy. These datasets correspond to: Figure 7 – Z11-16:Ald and BA systems Figure S5 – Z11-16:Ald and MBA systems 2. Molecular dynamics simulation inputs The archive MD_input_information.zip contains the input files used to perform the molecular dynamics simulations of ligand binding to the MsepPR3/Orco complex. Four simulation systems are provided: MsepPR3_Orco_onlyZ_pocket MsepPR3_Orco_Z&BA These correspond to the simulations shown in Figure 7. Additional simulations used to evaluate alternative ligand-binding starting positions are provided in: MsepPR3_Orco_onlyZ_TM2TM7 MsepPR3_Orco_onlyZ_TM5TM6 These correspond to Figure S6. Each simulation system contains three independent replicate runs: rep1/rep2/rep3/ Each replicate folder includes the following files: run.sh – shell script used to execute the MD simulation input.gro – initial structure generated using CHARMM-GUI md.mdp – MD simulation parameter file topol.top – system topology file toppar.zip – force-field and topology parameter files The simulations were performed using GROMACS, with system preparation conducted using CHARMM-GUI.