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