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. 2021 Apr 29;275:106608. doi: 10.1016/j.bpc.2021.106608

Table 1.

Lowest binding energy (BE: kcal/mol), number of poses, and Mpro residues involved in H-bonds with each compound for the selected clusters obtained by AutoDock4.2.6 program [31].

Compound Cluster BE Poses Residues involved in H-bonds IFIE
1 2 −5.18 141 Glu166 −41.4
3 −5.13 77 Gln189 −67.0
5 −4.82 33 Thr24, Thr26 −66.3
2 1 −4.65 52 Thr24, Thr26, Asn142, His163 −55.0
2 −4.58 131 Thr26, Leu141,Gly143, Ser144, His164 −64.6
3 −4.56 42 Leu141, Gly143, Ser144, Cys145, Glu166 −94.6
3 2 −3.95 31 Thr25, Thr26, Thr45, Ser144 −86.8
7 −3.87 60 Thr26, Leu141, Gly143, Ser144, Glu166 −83.3
10 −3.61 37 Thr24, Thr26, Leu141, Asn142, Gly143 −58.7
4 1 −6.64 193 No H-bonds −72.9
2 −6.46 25 No H-bonds −73.1
4 −5.74 18 Glu166 −83.9
5 1 −3.49 85 Glu166 −25.9
2 −3.46 94 Leu141, Gly143, Ser144 −50.5
3 −3.38 77 Glu166, Gln189 −19.5
6 1 −3.12 62 Leu141, Gly143, His163, Glu166 −112.0
2 −2.81 41 Asn142, Glu166 −95.0
3 −2.76 69 Thr24, Thr26, Cys44, Thr45, Ser46 −57.4
7 1 −4.25 181 No H-bonds −35.7
2 −4.17 50 No H-bonds −37.1
3 −3.99 25 No H-bonds −30.6
8 2 −4.39 28 Glu166, His172 −105.1
3 −4.11 22 Glu166 −94.7
10 −3.83 57 Thr26, Phe140, Gly143, Glu166 −66.5
9 1 −4.95 28 Thr26, Gln189 −108.2
3 −4.78 24 His41, Asn142, His164, Glu166, Gln189 −92.3
6 −4.02 30 Gly143, Glu166, Gln189 −136.5
10 2 −4.58 67 Asn142, His164, Glu166, Gln189 −106.1
9 −3.85 25 Thr26, Gly143, Gln189 −77.3
14 −3.67 24 Thr26, Gly143, His164 −75.1
11 1 −4.33 36 His164, Glu166 −97.0
2 −4.28 40 Asn142, His164, Glu166, Gln189 −63.7
5 −3.81 40 Thr26, Gly143, Gln189 −72.5
12 1 −5.41 37 Gly143, Glu166, Gln189, Thr190 −111.0
2 −5.11 42 Asn142, Glu166 −119.0
3 −4.87 29 Asn142, Gly143, Glu166, Gln189 −107.1

The created 256 poses were clustered based on their structural similarity, and each cluster was ranked in the order of BE between Mpro and each compound from Moringa oleifera. We selected three clusters with the largest number of poses, and the total inter fragment interaction energy (IFIE: kcal/mol) between each compound and all Mpro residues was evaluated using the FMO method. These values are listed in the last column.