Mechanism of the dibutyl 4-nitrophenyl phosphate hydrolysis by Pd-PTE phosphotriesterase revealed by QM/MM MD simulations

1. Topology psf file of the model system comprosing Pd-PTE phosphotriesterase and dibutyl 4-nitrophenyl phosphate solvated in the rectangular water box and neutralized. PDB files obtained from QM/MM MD rajectories of correspondig regions: ES – enzyme-substrate complex; TS1 and TS2 – transition states; INT – intermediate; EP – enzyme product.

2. A complete set of classical MD, QM/MM and QM/MM MD files.

Notation:

Substrates: S10 - substrate (1), S01 - substrate (2), S11 - substrate (3), S08 - substrate (4).

Stationary points: ES – reactants (enzyme-substrate complex), TS1 and TS2 – transition states of the first and second steps, respectively, INT – reaction intermediate, EP – enzyme-product complex.

Files:

par_* - parameter files.

*.psf - topology files.

md.conf - example config file for classical MD run.

Pd-PTE_ES_S10.pdb, Pd-PTE_ES_S01.pdb, Pd-PTE_ES_S11.pdb, Pd-PTE_ES_S08.pdb - structures selected from classical molecular dynamics trajectories for further calculations QM/MM calculations.

qmmm_md.conf - example config file for QM/MM MD run.

run_terachem.py - script for terachem operation, contains a description of the quantum part.

QMpart_S* - file containing the quantum part (beta 1 - atoms in the quantum part, occupancy 1 - atoms on the border of QM and MM regions).

*_INT_QMMM_MD_pbe0.dcd -  QM/MM MD trajectories of the INT states.

opt.chm - example config for optimization in chemshell.

ES_mult*.molden, INT_mult*.molden, EP_mult*.molden - optimized stationary points with different multiplicities.

US.7z – files containing reaction coordinate values at each QM/MM MD step and corresponding parameters of biasing potential, k and x0.

PES.7z - stationary points on potential energy surface for S10.

mechanism.7z - representative frames from QM/MM MD with the addition of a biasing potential in the stationary point regions on the Gibbs energy profiles for substrate (1) containing system.