Table 4.
Energy calculations on 3D models of Chimera 1A and Chimera 2 before and after molecular dynamics (MD) runs
| Free energy of Unfolding (FoldX Stability) | ||||
|---|---|---|---|---|
| Chimera 1A before MD runs | Chimera 2 before MD runs | Chimera 1A after 2 ns MD runs | Chimera 2 after 2 ns MD runs | |
| Total energy (kcal/mol) | 759.20 | 920.57 | 710.074 | 296.381 |
| Backbone Hbond | −862.97 | −873.78 | −752.668 | −811.358 |
| Sidechain Hbond | −243.51 | −259.01 | −273.993 | −445.516 |
| Van der Waals | −1691.34 | −1710.85 | −1560.22 | −1520.93 |
| Electrostatics | −56.90 | −58.59 | −83.3617 | −66.8915 |
| Solvation polar | 2357.03 | 2394.64 | 2170.46 | 2015.5 |
| Solvation hydrophobic | −2159.72 | −2186.73 | −1996.63 | −1977.47 |
| Van der Waals clashes | 274.48 | 485.84 | 129.53 | 45.4159 |
| Entropy side chain | 818.76 | 828.27 | 809.921 | 853.432 |
| Entropy main chain | 2317.25 | 2258.53 | 2237.97 | 2205.79 |
| cis_bond | 17.21 | 19.10 | 18.2409 | 16.9042 |
| Torsional clash | 49.11 | 82.16 | 71.7265 | 43.0954 |
| Backbone clash | 404.81 | 496.37 | 363.938 | 345.245 |
| Helix dipole | −0.88 | −2.84 | −2.59994 | −6.1477 |
| Disulfide | −60.50 | −59.23 | −58.1953 | −57.014 |
| Electrostatic kon | −3.87 | −2.07 | −3.86614 | −3.01727 |
| Energy ionization | 5.06 | 5.13 | 3.74828 | 4.58387 |
| Interaction energies (FoldX AnalyseComplex) | ||||
|---|---|---|---|---|
| Chimera 1A before MD runs | Chimera 2 before MD runs | Chimera 1A after 2 ns MD runs | Chimera 2 after 2 ns MD runs | |
| Group 1 | S (receptor) | S (receptor) | S (receptor) | S (receptor) |
| Group 2 | B (closest antibody chain) | Z (closest antibody chain) | B (closest antibody chain) | Z (closest antibody chain) |
| Intraclashes Group 1 | 34.57 | 93.00 | 22.05 | 8.14 |
| Intraclashes Group 2 | 42.32 | 60.05 | 56.12 | 24.45 |
| Interaction energy (kcal/mol) | 82.95 | 134.88 | −3.96 | −9.11 |