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. 2023 Mar 13;14:1112816. doi: 10.3389/fimmu.2023.1112816

Table 5.

Docking analysis of vaccine-receptors complexes.

Server Parameter MPXV-2-TLR2 MPXV-2-TLR4 MPXV-2-HLA-A*02:01 MPXV-2-HLA-DRB1*01:01 MPXV-5-TLR2 MPXV-5-TLR4 MPXV-5-HLA-A*02:01 MPXV-5-HLA-DRB1*01:01
ClusPro 2.0 Center -953.1 -1088 -998.6 -1092.7 -1203.8 -1166.8 -875.8 -1224.5
Lowest Energy -1110.3 -1473.3 -1033.6 -1330.8 -1203.8 -1261.8 -1037.5 -1224.5
HADDOCK 2.4 HADDOCK score -171.0 +/- 0.9 -242.1 +/- 3.7 -378.0 +/- 3.4 -676.9 +/- 2.4 -275.6 +/- 3.2 -306.2 +/- 1.6 -423.8 +/- 7.2 -675.7 +/- 1.7
Cluster size 20 20 20 20 20 20 20 20
RMSD from the overall lowest-energy structure 0.6 +/- 0.4 0.6 +/- 0.3 0.6 +/- 0.3 0.6 +/- 0.3 0.6 +/- 0.4 0.6 +/- 0.3 0.6 +/- 0.3 0.6 +/- 0.3
Van der Waals energy -84.8 +/- 2.3 -115.0 +/- 2.6 -176.2 +/- 2.2 -304.9 +/- 6.4 -122.2 +/- 1.4 -138.5 +/- 1.8 -186.7 +/- 3.0 -316.1 +/- 2.4
Electrostatic energy -108.1 +/- 6.0 -297.5 +/- 22.0 -589.8 +/- 25.1 -1254.2 +/- 23.7 -364.6 +/- 11.1 -323.4 +/- 35.9 -703.2 +/- 17.4 -1154.4 +/- 21.3
Desolvation energy -64.6 +/- 3.3 -67.6 +/- 2.2 -83.7 +/- 2.0 -121.1 +/- 1.4 -80.4 +/- 1.4 -103.0 +/- 5.7 -96.5 +/- 6.8 -128.8 +/- 4.2
Restraints violation energy 0.0 +/- 0.0 0.0 +/- 0.0 0.0 +/- 0.0 0.0 +/- 0.0 0.0 +/- 0.0 0.0 +/- 0.0 0.0 +/- 0.0 0.0 +/- 0.0
Buried Surface Area 2557.1 +/- 16.1 3619.9 +/- 65.0 5011.4 +/- 65.8 7923.8 +/- 34.6 3871.2 +/- 70.5 4361.5 +/- 75.1 5447.7 +/- 98.5 8418.8 +/- 83.3
Z-Score 0 0 0 0 0 0 0 0
PRODIG ΔG (kcal/mol) -9.4 -19.1 -11.9 -11.6 -16.1 -16.5 -12.9 -12.3
Kd (M) at 25.0 °C 1.30E-07 1.00E-14 1.80E-09 2.90E-09 1.70E-12 7.70E-13 3.50E-10 8.80E-10
PDBsum Number of hydrogen bonds 6 11 12 16 12 18 12 12
Number of salt Bridges 0 2 1 6 3 3 3 5

ΔG, binding energy; Kd, dissociation constant.