Table 1.

Summary of simulation. $N_{\mathrm{atoms}}$ is the number of atoms in a simulation system, $t_{\mathrm{each}}$ is the total simulation time of each run, and $N_{\mathrm{runs}}$ is the number of runs. All simulations were performed at $310\mathrm{K}$.

Target	State	No	Ref	PDB ID	$N_{\text{atoms}}$	$N_{\text{runs}}$	$t_{\text{each}},\mu s$
SASRS-CoV 3CLpro	Dimeric	1	[9]	1UK3a	87,554	5	1.0
		2	[9]	1UJ1b	79,123	5	1.0
	Monomeric	3	[9]	1UK3Ac	68,521	5	1.0
		4	[9]	1UK3Bd	70,073	5	1.0
SASRS-CoV-2 3CLpro	Dimeric	5	N/A	HMe	78,938	5	1.0
		6	[18]	6LU7f	79,466	10	1.0
	Monomeric	7	[18]	6LU7f	62,290	5	1.0
	Dimericg	8	[19]	6WQF	77,617	5	1.0
	Monomericg	9	[19]	6WQF	62,200	5	1.0

^aThis structure was determined at pH 7.6.⁹ MD simulations were performed for this in our previous study [20].

^bThis structure was determined at pH 6.0.⁹

^cProtomer A of 1UK3

^dProtomer B of 1UK3

^eA homology model (HM) derived from 1UJ1. This model was built by SWISS-MODEL [21],[22]. The query sequence is shown in Table S1 in the supporting information.

^fThe ligand was removed from 6LU7, and thus the systems from 6LU7 were an apo form.

^gThe dyad was ionized (i.e., H41⁺…C145⁻).