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Table 3 Compounds with a maximum dcTMD free energy of over 10 kJ/mol, together with all other calculated scores, and interactions inherited from the component fragments

From: Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease

Index

dcTMD maximum free energy / kJ/mol

Parent (and other component) fragments

Distance of dcTMD maximum from binding site / nm

MMGBSA / kcal/mol

SuCOS

TransFS

Interactions, with occupancy and derived fragment

1

22.41

x0387 (x0434)

0.45

\(-\)17.74

0.56

0.94

Cys44BO HB 91.5% (x0387)

Met165 HI 88.5% (x0434)

Gln189 HI 94.5% (x0434)

His41 pi stacking 6.5% (x0387)

2

18.4

x0387 (x0434)

0.34

\(-\)25.51

0.54

0.95

Met165 HI 94% (x0434)

His41 pi stacking 44% (x0387)

Gln189 HI 88% (x0434)

3

16.45

x0991 (x0946)

0.24

\(-\)29.93

0.64

0.96

 

4

15.25

x0397

0.24

\(-\)31.97

0.65

0

Gly143BN HB 100% (x0397)

Cys145BN HB 83.5% (x0397)

Thr25 HI 10.5% (x0397)

5

14.57

x0397

0.18

\(-\)30.74

0.61

0

Gly143BN HB 85.5% (x0397)

Cys145BN HB 89.5% (x0397)

Thr25 HI 62.5% (x0397)

6

13.89

x0434

0.38

\(-\)25.42

0.49

0.65

Glu166BN HB 84.5% (x0434)

Met165 HI 64% (x0434)

Gln189 HI 19% (x0434)

7

13.61

x0678

0.73

\(-\)26.4

0.53

0.94

His163SC HB 14% (x0678)

Met165 HI 50% (x0678)

Glu166 HI 90% (x0678)

8

11.96

x0305

0.52

\(-\)25.07

0.54

0.94

Met165 HI 87.5% (x0305)

Gln189SC HB 13% (x0305)

9

10.95

x0434

0.43

\(-\)22.71

0.52

0.68

Gln189 HI 50.5% (x0434)

Met165 HI 10.5% (x0434)

Glu166BN HB 3.5% (x0434)

10

10.57

x0434 (x0387)

0.29

\(-\)34.78

0.52

0.77

Glu166BN HB 77.5% (x0434)

Met165 HI 61.5% (x0434)

His163SC HB: 44% (x0434)

  1. The chemical structures of the compounds are depicted in Additional file 1: Fig. S2. BO backbone oxygen, BN backbone nitrogen, SC side chain, HB hydrogen bond, HI hydrophobic interaction