Table 1.

Estimated docking scores (in kcal/mol) and binding features for rutin and the top nine potent analogs against SARS-CoV-2 M^pro.

No.	PubChem code	2D-Chemical Structure	Docking Score (kcal/mol)	Cluster Populationa	Binding Featuresb
1	Rutin (PubChem-528-080-5)		−7.2	43	ASP187 (1.90 Å), HIS164 (2.25 Å), GLU166 (2.05 Å), GLN192 (2.86 Å), THR190 (2.19, 1.92 Å)
2	PubChem-137-399-195		−10.9	38	GLN189 (2.22 Å), GLU166 (1.92, 1.90, 2.99 Å), GLY143 (1.95, 2.88 Å), LEU141 (2.57 Å), SER144 (1.83 Å)
3	PubChem-129-716-607		−10.7	37	THR26 (2.07 Å), GLU166 (2.06 Å), HIS164 (2.03 Å), TYR54 (2.33 Å), ASP187 (2.32 Å), THR190 (2.20, 2.02 Å)
4	PubChem-893-333-51		−9.9	47	THR190 (1.92 Å), ASP187 (1.90 Å), GLU166 (2.02, 1.85, 1.78 Å), HIS164 (2.28 Å), HIS41 (2.40 Å), LEU141 (1.83 Å), SER144 (1.96 Å), GLY143 (2.37 Å), CYS145 (2.59, 2.61 Å)
5	PubChem-123-170-316		−9.9	27	THR190 (1.85 Å), GLU166 (1.94 Å), HIS164 (2.45 Å), ASP187 (1.93 Å)
6	PubChem-142-513-769		−9.8	29	GLY143 (1.62 Å), ASN142 (2.33 Å), PHE140 (2.09 Å), HIS163 (2.08 Å), HIS164 (2.74 Å), GLU166 (2.13, 2.16, 2.96 Å), PRO168 (2.05 Å)
7	PubChem-101-020-740		−9.7	35	THR190 (1.98, 2.08 Å), GLN189 (1.99 Å), GLU166 (1.93 Å), ASP187 (2.78 Å), HIS164 (2.92 Å), HIS163 (2.09 Å), SER144 (2.12 Å), LEU141 (2.21 Å), LEU141 (1.98, 2.21 Å)
8	PubChem-142-513-754		−9.7	37	LEU141 (2.79 Å), HIS163 (1.65 Å), GLU166 (2.48, 2.16 Å), ASP187 (2.00 Å), THR190 (2.18, 2.26 Å)
9	PubChem-885-071-27		−9.5	42	THR26 (2.07 Å), ASN142 (2.06 Å), PHE140 (2.8 Å), HIS163 (1.99 Å), GLU166 (2.07 Å), MET165 (2.4, 2.72 Å), GLN192 (2.73 Å), THR190 (2.21, 1.73 Å), PRO168 (2.20, 1.89 Å)
10	PubChem-101-133-681	1	−9.2	34	GLY143 (2.08 Å), GLU166 (1.70, 2.20, 1.86 Å), THR190 (2.22, 2.54 Å)

^aNumber of conformations in the largest cluster.

^bOnly hydrogen bonds (in Å) were listed.