Table 2. Binding Energies (kcal/mol) and Intermolecular Bonds of the Selected Ligands with the Active Sites of the Cell Wall Proteins.
| ligands | receptors | dock score (kcal/mol) | XP G-score (kcal/mol) | MM-GBSA (ΔGbind) | no. of the H-bonds and the participating residuesa | other bonds and the participating residues |
|---|---|---|---|---|---|---|
| DB145 | FemA | –6.601 | –6.601 | –45.822 | 4(Glu36, Try38, Pro1512) | |
| FemB | –7.743 | –7.743 | –54.455 | 6(Arg34, Tyr70, Thr152, Ser1532, Asn228) | ||
| MraY | –6.192 | –6.192 | –59.339 | 1(Asn102) | ||
| MurA | –4.635 | –4.635 | –46.493 | 4(Asp1262, Thr1442) | ||
| MurB | –13.483 | –13.483 | –69.224 | 6(Val199, Gly81, Ser822, Asn83, Arg225) | ||
| MurC | –8.756 | –8.756 | –59.742 | 5(Hid263, Tyr260, Asn267, Lys296, Arg318) | ||
| MurE | –8.639 | –8.639 | –66.193 | 9(Thr46, Ala150, Asn151, Thr1522, Arg187, Glu382, Arg383, Lys470) | ||
| MurF | –10.531 | –10.531 | –69.345 | 5(Ile31, Ala3372, Thr340, Leu366) | ||
| DB150 | FemA | –7.23 | –7.23 | –72.039 | 3(Lys33, Tyr38, Leu153) | pi–pi stacking (1: Tyr69) |
| FemB | –5.042 | –5.042 | –49.513 | 4(Arg34, Asp37, Pro63, Thr152) | pi–pi stacking (1: Thr225) | |
| pi–cation (1: Lys221) | ||||||
| MurA | –5.00 | –5.00 | –53.468 | 6(Asn882, Glu912, Thr1452,) | ||
| MurC | –7.673 | –7.673 | –71.686 | 6(Thr113, Ser114, Asn267, Gly294, Glu319, Tyr260) | pi–pi stacking (1: Tyr260) | |
| MurE | –7.735 | –7.735 | –59.663 | 6(Thr111, His205, Glu382, Arg383, Tyr462, Hip468) | pi–pi stacking (4: His205, His353, Hip4682) | |
| pi–cation (2: Arg383, Lys470) | ||||||
| MurG | –6.199 | –6.199 | –56.023 | 4(Ser263, Glu268, Asp289, Gln290) | pi–cation (1: Arg166) | |
| DB200 | MurB | –8.667 | –9.9 | –60.864 | 3(Ser82, Ser 143, Gly153) | pi–cation (1: Arg225) |
| MurC | –6.801 | –7.145 | –56.103 | 3(Asn267, Gln259, Lys296) | pi–pi stacking (1: Tyr260) | |
| MurF | –8.72 | –9.064 | –74.392 | 5(Asn492, Asn140, Ser338, Thr340) | ||
| MraY | –6.783 | –7.127 | –63.071 | 1(Asn166) | ||
| PBP | –3.729 | –4.073 | –30.305 | 1(Tyr446) | pi–pi stacking (1: His583) | |
| DB211 | FemA | –9.867 | –10.761 | –57.477 | 6(Pro1512, Gln1543, Try328) | pi–cation (2: Phe149, Phe224) |
| MurA | –5.89 | –6.544 | –47.405 | 6(Cys118, Asp1262, Glu1412, Thr144) | salt bridge (2: Asp126, Glu141) | |
| MurD | –7.775 | –8.429 | –56.924 | 9(Asn114, Lys116, Asn1394, Glu158, Asp1832) | salt bridge (2: Glu158, Asp183) | |
| MurE | –10.641 | –11.535 | –57.132 | 5(His181, Asp2072, Tyr351, Glu460) | pi–cation (1: His353), Salt bridge (1: Asp207) | |
| MurF | –10.17 | –11.064 | –71.140 | 4(Ile31, Asn140, Asn1432) | salt bridge (1: Asp32) | |
| PBP | –7.481 | –9.335 | –42.626 | 6(Glu460, Thr5823, Asp586, Ser643) | salt bridge (3: Glu4472, Asp586) | |
| DB269 | FemA | –12.073 | –12.101 | –46.549 | 5 (Lys33, Glu36, Asp221, Arg228, Val252) | pi–pi stacking (1: Try71) |
| MurG | –10.958 | –10.986 | –62.08 | 5(His14, Gly198, Lys200, Ser263, Gln290) | pi–cation (1: Arg260) | |
| PBP | –6.069 | –6.098 | –30.822 | 6(Glu447, Gln457, Glu4602, Lys581, Glu585) | pi–pi stacking (1: His583) | |
| DB278 | MurA | –3.376 | –4.608 | –45.7204 | 3(Arg94, Arg123, Tyr97) | |
| MurB | –10.805 | –12.037 | –63.9688 | 4(Asn80, Tyr77, Val199, Leu197) | ||
| MurC | –6.359 | –6.702 | –56.9374 | 2(Hid110, Gln259) | ||
| MurG | –5.885 | –6.228 | –52.169 | 3(Ser2632, Glu268) | ||
| PBP | –3.233 | –3.576 | –29.7808 | 3(Tyr4462, Glu447) | ||
| DB307 | FemB | –4.585 | –4.597 | –43.807 | 3(Asn30, Asp37, Tyr70) | pi–cation (1: Arg34) |
| MurA | –1.17 | –1.182 | –46.3829 | 1(Asp126) | ||
| PBP | –4.252 | –4.265 | –34.6695 | 2(Tyr4462) | ||
| DB335 | FemA | –3.319 | –3.372 | –52.10 | 2(Lys33, Asp150) | |
| MurA | –1.771 | –1.825 | –46.4847 | 1(Glyl17) | ||
| MurF | –7.772 | –7.826 | –66.334 | 1(Asn49) | ||
| MurG | –5.114 | –5.167 | –52.6321 | 2(Ser196, Ser263) | ||
| DB350 | FemA | –2.396 | –2.835 | –59.167 | 1(Lys33) | pi–pi stacking (1: Phe224) |
| FemB | –3.056 | –3.882 | –58.176 | 2(Asp224, Asn228) | salt bridge (1: Asp37) | |
| MurA | –1.758 | –2.197 | –48.7741 | 1(Cys118) | salt bridge (3: Asp126, Glu1412) | |
| MurC | –3.58 | –4.406 | –56.0035 | pi–cation (1: Try260) | ||
| MurD | –4.626 | –5.066 | –56.2331 | 3(Asn1393) | ||
| MurE | –3.471 | –3.911 | –56.9907 | 1(Thr28) | salt bridge (1: Asp29) | |
| MurG | –1.879 | –2.705 | –54.3209 | 2(Thr164, Asn264) |
a
Amino acid residues with superscripts represent the number of hydrogen atoms participating in the interaction. Amino acids residues with numbers represent the total residues involved in the interaction.