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. 2018 Nov 20;19(Suppl 14):419. doi: 10.1186/s12859-018-2387-8

Table 1.

The Gibbs free binding energy (∆Gbinding), RMSD value and two-dimensional (2D) molecular structure of the ten best ligands, including two standard ligands, from docking simulation

No ZINC Code
(Molecule Name)		 ∆Gbinding (RMSD)
Rigid Docking Induced-fit Docking
1 ZINC14262121
(Calbistrin C)		 − 7.1685 kcal/mol
(3.4650)		 −7.9228 kcal/mol
(2.3913)
2 ZINC56874155
(α-Lipomycin)		 −7.0181 kcal/mol
(2.5151)		 − 7.8387 kcal/mol
(1.7895)
3 ZINC85596639
((R)-4-(ethylamino)-5-(2-hydroxy-5-((2S,4S,6S)-4-hydroxy-6-(4-hydroxy-3-methoxyphenethyl)tetrahydro-2H-pyran-2-yl)-3-methoxyphenoxy)pentanoic acid)		 −6.5605 kcal/mol
(2.2021)		 − 7.4919 kcal/mol
(2.0385)
4 ZINC504747685 / ZINC218110007
(3-[(2Z)-6-hydroxy-3-oxo-2-(pyridin-3-ylmethylidene)-1-benzofuran-7-yl]-3-[3-methoxy-4-[(1-methylimidazol-2-yl)methoxy]phenyl]propanoic acid)		 −7.1475 kcal/mol
(1.5076)		 −7.4020 kcal/mol
(1.8379)
5 ZINC85628951
(3-(((S)-1-amino-1,2,3,4-tetrahydroisoquinolin-5-yl)methyl)-5-((5-((5R,7S)-5,7-dihydroxy-3-oxodecyl)-2-hydroxyphenoxy)methyl)pyrrolo[3,4-b]pyrrol-5-ium)		 −7.2411 kcal/mol
(1.8548)		 − 7.2843 kcal/mol
(1.7994)
6 ZINC85570811
(2,3-dihydroamentoflavone 7,4′-dimethyl ether)		 − 6.1927 kcal/mol
(2.4844)		 −7.2385 kcal/mol
(1.8455)
7 ZINC5431307
(Lappaol C)		 − 6.5308 kcal/mol
(2.4881)		 − 7.2291 kcal/mol
(2.0008)
8 ZINC24986227
(5-(2-(4-(3-chlorophenyl)piperazin-1-yl)ethoxy)-2-(5-methyl-4-phenyl-1H-pyrazol-3-yl)phenol)		 − 6.3802 kcal/mol
(2.0664)		 − 7.1857 kcal/mol
(2.1222)
9 ZINC85569343
((7aS,10S,11R,11aS)-2,6,10-trihydroxy-3-(4-hydroxy-3-(3-hydroxybenzyl)-5-isobutylphenyl)-11-(hydroxymethyl)-7a,10,11,11a-tetrahydro-1H,7H-pyrano[2,3-c]xanthen-1-one)		 − 6.5689 kcal/mol
(1.7370)		 −7.1604 kcal/mol
(1.7080)
10 ZINC85837484
(Rhusflavone)		 − 6.8751 kcal/mol
(1.4505)		 − 7.1453 kcal/mol
(1.6734)
S1 ZINC3873122
(Licochalcone A)		 −5.0048 kcal/mol
(2.3374)
S2 ZINC3947479
(18β-Glycyrrhetinic Acid)		 −5.0058 kcal/mol
(3.8390)