Table 4 Binding free energies (kcal/mol) of each complex calculated by the MM-GBSA method.

From: Identification of potential modulators for human GPD1 by docking-based virtual screening, molecular dynamics simulations, binding free energy calculations, and DeLA-drug analysis

Complexes

Energy (kcal/mol)

\({\Delta G}_{vdw}\)

\({\Delta G}_{ele}\)

\(\Delta {G}_{PB\_GB}\)

\(\Delta {G}_{SA}\)

\({\Delta G}_{gas}\)

\({\Delta G}_{solv}\)

total

Compound 4-GPD1

− 41.17

− 50.15

51.57

− 5.96

− 91.32

45.61

− 45.71

ZINC000049780570-GPD1

− 46.15

− 43.20

61.66

− 6.52

− 89.35

55.14

− 34.21

ZINC000058282139-GPD1

− 12.58

− 4.26

11.68

− 1.79

− 16.84

9.89

− 6.94

ZINC000077257642-GPD1

− 42.13

− 51.41

63.87

− 5.82

− 93.54

58.05

− 35.49

ZINC000225627518-GPD1

− 38.24

− 9.03

23.02

− 5.12

− 47.27

17.90

− 29.37

ZINC000585101368-GPD1

− 19.36

− 6.60

16.32

− 2.63

− 25.97

13.69

− 12.28

Compound 36-GPD1

− 22.54

− 146.27

161.67

− 3.80

− 168.81

157.86

− 10.94

Compound 87-GPD1

− 39.06

− 12.96

25.87

− 4.47

− 52.03

21.41

− 30.62

Compound 95-GPD1

− 40.67

− 1.55

16.45

− 5.28

− 42.22

11.17

− 31.05

Compound 785-GPD1

− 30.24

− 6.46

19.81

− 4.00

− 36.70

15.81

− 20.89

Compound 16-GPD1

− 40.77

− 22.21

33.20

− 5.55

− 62.98

27.64

− 35.34

  1. Total = \({\Delta G}_{gas}\)  + \({\Delta G}_{solv}\), \({\Delta G}_{gas}\) = \({\Delta G}_{vdw}\)  + \({\Delta G}_{elec}\), \({\Delta G}_{solv}\) = \(\Delta {G}_{PB\_GB}\)  + \(\Delta {G}_{SA}\).
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