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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