Table 1.
The Binding Energy Calculation of Human CDK8-CycC Complex by MM/PBSA and MM/GBSA Methods.
| Methods | Energy Component |
CDK8-CycC Complex (kcal/mol) |
CDK8 (kcal/mol) |
CycC (kcal/mol) |
Difference (Complex – CDK8 – CycC) (kcal/mol) |
|---|---|---|---|---|---|
| GENERALIZED BORN |
VDWAALS | −4989.5033 ± 29.1219 | −2548.0729 ± 22.9616 | −2259.4853 ± 19.3454 | −181.9451 ± 6.9641 |
| EEL | −42816.1127 ± 138.5376 | −23548.6335 ± 106.0965 | −18986.0963 ± 74.4193 | −281.3829 ± 35.8417 | |
| EGB | −7494.7055 ± 106.5943 | −4487.4092 ± 87.8479 | −3391.7071 ± 55.1357 | 384.4108 ± 35.2996 | |
| ESURF | 216.1872 ± 2.1345 | 138.0664 ± 1.8321 | 104.4015 ± 1.1693 | −26.2807 ± 0.5023 | |
| G gas | −47805.6160 ± 141.5653 | −26096.7064 ± 108.5528 | −21245.5816 ± 76.8926 | −463.3280 ± 36.5120 | |
| G solv | −7278.5183 ± 106.6157 | −4349.3428 ± 87.8670 | −3287.3056 ± 55.1481 | 358.1301 ± 35.3032 | |
| TOTAL | −55084.1343 ± 78.4694 | −30446.0492 ± 52.0191 | −24532.8872 ± 50.4504 | −105.1979 ± 7.7940 | |
| POISSON BOLTZMANN |
VDWAALS | −4989.5033 ± 29.1219 | −2548.0729 ± 22.9616 | −2259.4853 ± 19.3454 | −181.9451 ± 6.9641 |
| EEL | −42816.1127 ± 138.5376 | −23548.6335 ± 106.0965 | −18986.0963 ± 74.4193 | −281.3829 ± 35.8417 | |
| EPB | −7358.6092 ± 107.4503 | −4397.9726 ± 86.7258 | −3339.6900 ± 54.8069 | 379.0534 ± 37.7017 | |
| ECAVITY | 160.2009 ± 1.6427 | 102.2377 ± 1.4619 | 76.9701 ± 0.9047 | −19.0068 ± 0.3807 | |
| G gas | −47805.6160 ± 141.5653 | −26096.7064 ± 108.5528 | −21245.5816 ± 76.8926 | −463.3280 ± 36.5120 | |
| G solv | −7198.4083 ± 107.4629 | −4295.7350 ± 86.7381 | −3262.7199 ± 54.8144 | 360.0466 ± 37.7036 | |
| TOTAL | −55004.0243 ± 81.6833 | −30392.4414 ± 54.5076 | −24508.3015 ± 50.1600 | −103.2814 ± 11.0789 |