PDB files used in the system preparation, AMBER topologies and coordinates and force field parameters for non-standard residues: The Influence of Chemical Change on Protein Dynamics: A Case Study with Pyruvate Formate-Lyase

We provide AMBER topology (parm7) and coordinate files (pdb and rst7) for PFL systems before and after the first half-reaction together with library and frcmod files (lib and frcmod) for non-standard residues (bonded and non-bonded force field parameters).

mPFL - monomeric PFL system before the first half-reaction (radical on C418)
dPFL - dimeric PFL system before the first half-reaction (radical on C418)
mAcPFLI - monomeric PFL system after the first half-reaction (radical on formyl)
dAcPFLI - dimeric PFL system after the first-half reaction (radical on formyl)
mAcPFLII - monomeric PFL system after the first half-reaction (radical on C419)
dAcPFLII - dimeric PFL system after the first half-reaction (radical on C419)
PYR - pyruvate
FOR - CO₂^- radical
FOH - formate
CYR - cysteinyl radical
CYA - S-acetyl-cysteine

Electrostatic potentials were derived from the IEF-PCM B3LYP/cc-pVTZ//HF/6-31G(d,p) calculationsm while the atomic partial charges were developed using RESP procedure.