TABLE 1.

Summary of all simulations performed.

Simulation index	PDB	Protein system	Length
Summary of simulations
MD1 (1, 2)	6W9C	CoV2 PLpro	1 μs, 500 ns
MD2 (1, 2)	6WRH	CoV2 PLpro	1 μs, 500 ns
MD3 (1, 2)	4OW0	CoV1 PLpro	1 μs, 500 ns
MD4 (1, 2)	4RNA	MERS-CoV PLpro	1 μs, 500 ns
MD5a (1–3)	6W9C	CoV2 PL pro complexed w/3k (pose A)	1 μs, 500 ns, 200 ns
MD5b (1–3)	6W9C	CoV2 PL pro complexed w/3k (pose B)	3 × 200 ns
MD5c (1–3)	6W9C	CoV2 PL pro complexed w/3k (pose C)	3 × 200 ns
MD5d (1–3)	6W9C	CoV2 PL pro complexed w/3k (pose D)	3 × 200 ns
MD6 (1–3)	4OW0	CoV1 PLpro complexed w/3k	1 μs, 500 ns, 200 ns
MD7a (1–3)	6W9C	CoV2 PLpro complexed w/6MP (in putative site)	3 × 200 ns
MD7b (1–3)	6W9C	CoV2 PLpro complexed w/6MP (in active site)	3 × 200 ns

All ligand-free proteins were simulated twice under identical conditions except for the initial random number seed, first for 1 μs, followed by a 500 ns secondary run to confirm consistency in the observed dynamics. Similarly, all ligand-bound proteins were simulated three times for at least 200 ns. Where necessary, secondary and tertiary runs are referred to by a dash and number after the main designation, e.g., MD1-2 means the second run of simulation MD1. These trajectories are available on our group webpage: http://chemcha-gpu0.ucr.edu/software/ and the COVID -19 Molecular Structure and Therapeutics Hub: https://covid.molssi.org/.