Table I.

Model Systems Simulated

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