Table 1.

Binding affinities and interactions of top ten ligands against the cysteine proteases

Target	Cpd	Binding affinity (kcal/mol)	Hydrogen bonds	Other interactions
PLpro	1	− 10.8	His342, Lys711, Arg712	Lys711, Asp339, Arg558, Ile310, Ile580, Ala579, Leu742
	2	− 10.7	None	His342, Leu557, Ala579, Leu742
	3	− 10.7	Lys711, Arg712	Ile310, Ala338, His342, Leu557, Ala579, Ile580, Val635, Lys694, Arg712
	4	− 10.6	Thr583, Arg586, Tyr634	Asp339, Arg558, Ala579, Ile580, Met630, Leu742
	5	− 10.4	Val659	Leu557, Arg558, Met560, Ala579, Ile580, Leu742
	6	− 10.3	Asp226	None
	7	− 10.2	Lys711, Arg712	None
	8	− 10.2	Asp339, Arg586, Tyr634	Val304, Ala338, Asp339, Arg558, Ala579, Lys711, Leu742
	9	− 10.2	Gly337, Asp339, Arg345, Arg558, Arg712	Ile310
	10	− 10.1	Asp339, Arg345, Tyr634	Leu557, Ile580, Met630, Val635, Lys711, Leu741
3CLpro	1	− 8.6	Cys44, Val186, Arg188, Glu166	Thr25, His41, Asn142, Cys145, Met165
	11	− 8.6	Cys145, Glu166	Thr25, His41
	12	− 8.5	Thr24, Ser46, Thr190, Gln192	Thr25, His41
	13	− 8.5	Thr26, His41	Met49, Pro168
	4	− 8.5	Arg188, Gln189	None
	8	− 8.4	Thr26, Gln189, Thr190	Leu27, Met49, Glu166, Met165, Pro168
	14	− 8.4	Phe140, Gly143, Arg188, Gln189	His41
	15	− 8.1	Asn119, Val186	None
	16	− 7.9	Gly143, Cys145, Glu166, Gln189	His41, Gln189
	17	− 7.9	His41, Asn119	His41, Gly143, His163
	3	− 7.9	His41	Leu27, His41