(File-01) Free enzymes molecular dynamics: input parameters and topologies for aPGA, ecPGA and paPvdQ enzymes general input files for MD simulations in AMBER output restart files from minimization, equilibration and production runs output files from minimization, equilibration and production runs raw data for analysis and visualization: protein backbone RMSD evolution binding cavity dynamics analysis principal component analysis of catalytic machinery (with states' representatives in PDF format) (File-02) Ligand-enzyme complexes molecular dynamics: input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules general input files for MD simulations in AMBER output restart files from minimization, equilibration and production runs output files from minimization, equilibration and production runs raw data for analysis and visualization: protein backbone RMSD evolution near-attack-conformation (NAC) stabilization HSLs RMSD evolution MM/PBSA binding energy estimation HSLs heavy atoms RMSF (File-03) Michaelis complex ensemble generation molecular dynamics: input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules general input files for MD simulations in AMBER output restart files from ensemble generation production runs output files from ensemble generation production runs (Files-04-06) Ligand-enzyme QM/MM steered molecular dynamics: input parameters for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules ensemble of input restart files generated in stage 3 general input files for QM/MM steered MD simulations in AMBER output restart files from QM/MM MD equilibration simulations and QM/MM steered MD simulations output files and output work from QM/MM steered MD simulations (File-07) Ligand-enzyme QM/MM steered molecular dynamics data for analysis and visualization: reaction states ensembles (in PDB format) extracted from QM/MM steered MD simulations with crucial distances measured evolution of the reaction coordinate elements in the first and second step of acylation representative states of the reaction stages for visualization (in PDB format) different dynamics of the residues gating access to acyl-binding cavity at TS1 different dynamics of the residues gating overall access to active site at TS2a different system-dependent bending of the HSLs at TS1 and TS2a

This work was supported by the National Science Centre, Poland (Grant Numbers 2017/25/B/NZ1/01307 and 2021/41/N/NZ2/01365) and by the Institutional Research project RVO61388971 from the Institute of Microbiology of the CAS. B.S. is a recipient of a scholarship provided by POWER project POWR.03.02.00-00-I022/16. The computations were performed at the Poznan Supercomputing and Networking Center.