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. Author manuscript; available in PMC: 2023 Nov 7.
Published in final edited form as: J Chem Inf Model. 2020 Dec 16;60(12):5832–5852. doi: 10.1021/acs.jcim.0c01010

Table 1.

Model Systems Simulated

Protein/ System Notes
S (Spike) Protein Receptor Binding Domain (RBD) / “Apo” (PDB: 6W41) S Protein RBD / Complexed with ACE2 (PDB: 6W41) MPro / monomer, CHARMM-GUI default protonation (PDB: 6Y2E)
MPro / dimer, CHARMM-GUI default protonation (PDB: 6Y2E) MPro / dimer, ‘charged’ protonation variant (PDB: 6WQF) MPro monomer/ HIE41 protonation variant (PDB: 6WQF)
MPro dimer / HIE protonation variant (PDB: 6WQF) MPro monomer / HID41 protonation variant (PDB: 6WQF) MPro dimer / HID41 protonation variant (PDB: 6WQF)
NSP15 (endoribonuclease) / hexamer (PDB: 6VWW) NSP15 (Endoribonuclease) / monomer (PDB: 6VWW) NSP10:NSP16 Complex (Methyltransferase) (PDB: 6W4H)
NSP10 / monomer (PDB: 6W4H) NSP16 / monomer (PDB: 6W4H) N (nucleocapsid) N-terminus phosphoprotein / monomer (PDB: 6M3M)
N (nucleocapsid) N-terminus phosphoprotein / tetramer (PDB: 6M3M) N (nucleocapsid) N-terminus phosphoprotein / tetramer complexed with Zn (PDB: 6YVO) N (nucleocapsid) N-terminus phosphoprotein / monomer alternate crystal structure (PDB: 6YVO)
NSP9 / monomer (PDB: 6W4B) NSP9 / dimer (PDB: 6W4B) NSP3 ADP ribose phosphatase / asymmetric unit (PDB: 6W02)
PLPro / monomer ‘charged’ protonation variant (PDB: 6W9C) PLPro / monomer ‘neutral’ variant (PDB: 6WRH) NSP3 ADP ribose phosphatase (PDB: 6W02)