Table 2.
The free energy of binding components of the c-Jun–c-Jun complex with/without capping using the ff98SB/TIP3P and ff02.r1/POL3 force field and water potential combinations (kcal/mol). One of the peptides in the complex is labeled as c-Jun1 and the other one c-Jun2
| E ele | E vdw | E int | G gbsa | G mmgbsa | TS | G bind-gb | |
|---|---|---|---|---|---|---|---|
| POL3 | |||||||
| c-Jun1 | −1326.5/−1197.8 | −68.6/−68.2 | 803.5/785.3 | −586.3/−797.9 | −1177.9/−1278.6 | 475.8/467.8 | −1653.6/−1746.4 |
| c-Jun2 | −1342.7/−1185.4 | −69.8/−68.4 | 805.5/787.1 | −567.8/−807.4 | −1174.8/−1274.1 | 473.3/468.5 | −1648.1/1742.6 |
| Cplx | −2620.9/−2225.6 | −230.0/−229.2 | 1609.0/1572.4 | −1168.8/−1721.9 | −2410.7/−2604.2 | 901.6/888.6 | −3312.3/−3492.8 |
| Delta | 48.3/157.6 | −91.6/−92.5 | 0.0/0.0 | −14.7/−116.6 | −58.1/−51.5 | −47.5/−47.8 | −10.6/−3.7 |
| TIP3P | |||||||
| c-Jun1 | −1251.8/−1042.8 | −78.0/−72.3 | 817.1/782.8 | −521.0/−739.4 | −1033.8/−1071.7 | 473.0/473.4 | −1506.7/−1545.1 |
| c-Jun2 | −1299.5/−1180.4 | −77.7/−69.3 | 819.4/788.6 | −480.6/−643.5 | −1038.4/−1104.6 | 470.3/468.9 | −1508.7/−1573.5 |
| Cplx | −2503.5/−2143.9 | −231.4/−224.7 | 1636.5/1571.4 | −1026.1/−1429.7 | −2124.5/−2226.9 | 897.8/894.1 | −3022.3/−3121.0 |
| Delta | 47.8/79.2 | −75.7/−83.1 | 0.0/0.0 | −24.5/−46.7 | −52.3/−50.6 | −45.4/−48.2 | −6.9/−2.4 |