Table 1.

Residues of SARS-CoV-2 M^pro interacting with the three ligands before and during the simulation run.

		Types of interactions and residues of main protease involved
		Pre-MD interactions		Interactions during MD simulations
Ligand bound	Docking score (Kcal/mol)	H-bonds	Hydrophobic interactions and pi-pi stacking	H-bonds	Hydrophobic interactions and pi-pi stacking
N3 inhibitor	−5.68	Glu166, Thr190	His41, Cys44, Met49, Pro52, Tyr54, Phe140, Leu141, Asn142, His164, Met165, Leu167, Pro168, Thr169, Gly170, His172, Asp187, Arg188, Gln189, Ala191, Gln192	Asn142, Glu166, Arg188, Gln189, Thr190, Gln192	His41, Ser46, Met49, Lys138, Ser139, Phe140, Asn142, Gly143, Ser144, Cys145, His163, His163, His164, Met165, Glu166, Leu167, Pro168, Thr169, Gly170, His172, Val186, Arg188, Gln189, Thr190, Ala191, Gln192
Wi-N	−4.42	Cys145	Thr24, Thr25, Thr26, Leu27, His41, Met49, Tyr54, Asn142, Gly143, His164, Met165, Glu166, Arg188, Asp188, Gln189	Thr26, His41, Cys44, Asn119, Asn142, Gly143, Gln189, Thr190, Gln192	Gln19, Thr24, Thr25, Thr26, His41, Cys44, Thr45, Ser46, Glu47, Met49, Pro52, Tyr54, Asn119, Asn142, Gly143, Ser144, Cys145, His164, Met165, Glu166, Leu167, Pro168, Gly170, Asp187, Arg188, Gln189, Thr190, Gln192
CAPE	−4.79	Asn142, Glu166	Leu27, Cys44, Met49, Pro52, Tyr54, Phe140, Leu141, Ser144, Cys145, His163, His164, Met165, Glu166, His172, Asp187, Arg188, Gln189	Thr25, Cys44, Ser46, Phe140, Asn142, Cys145, Glu166, His172, Gln189, Thr190, Ala191, Gln192	Thr24, Thr25, Thr26, Pro39, His41, Cys44, Thr45, Ser46, Glu47, Met49, Leu50, Asn51, Cys85, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His164, Met165, Glu166, Leu167, Pro168, His172, Phe181, Val186, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192, Ala193, Ala194