Table 2. Decomposition of Free Energy Differences (kcal/mol) to Bond, Angle, Dihedral, Electrostatic, and van der Waals Terms from TI Method using Molecular Dynamics with Positional Restraintsa.
| alchemical transformation | ΔG° | ΔG°bond | ΔG°angle | ΔG°dihedral | ΔG°es | ΔG°vdw |
|---|---|---|---|---|---|---|
| amber99 | ||||||
| GGAC → iGGAiC (ΔG°3, imino GA) | 110.2 ± 0.2 | −5.0 ± 0.1 | 0.4 ± 0.0 | 0.2 ± 0.0 | 113.4 ± 0.2 | 1.0 ± 0.0 |
| GGAC → iGGAiC (ΔG°2, sheared GA) | 110.0 ± 0.3 | −4.7 ± 0.1 | 0.3 ± 0.0 | 0.2 ± 0.0 | 112.7 ± 0.3 | 1.4 ± 0.0 |
| (ΔG°3 − ΔG°2) | 0.2 ± 0.4 | −0.3 ± 0.1 | 0.1 ± 0.0 | 0.0 ± 0.0 | 0.7 ± 0.4 | −0.4 ± 0.0 |
| CGAG → iCGAiG (ΔG°3, imino GA) | 110.6 ± 0.1 | −5.2 ± 0.1 | 0.6 ± 0.0 | 0.2 ± 0.0 | 114.3 ± 0.1 | 0.7 ± 0.0 |
| CGAG → iCGAiG (ΔG°2, sheared GA) | 112.5 ± 0.3 | −5.4 ± 0.2 | 0.4 ± 0.0 | 0.2 ± 0.0 | 115.9 ± 0.3 | 1.4 ± 0.0 |
| (ΔG°3 − ΔG°2) | −1.9 ± 0.3 | 0.2 ± 0.2 | 0.2 ± 0.0 | 0.0 ± 0.0 | −1.6 ± 0.3 | −0.7 ± 0.0 |
| amber99 with nonplanar G amino group in GA base pairs | ||||||
| GGAC → iGGAiC (ΔG°3, imino GA) | 110.6 ± 0.3 | −4.7 ± 0.2 | 0.3 ± 0.0 | 0.2 ± 0.0 | 113.5 ± 0.2 | 1.2 ± 0.0 |
| GGAC → iGGAiC (ΔG°2, sheared GA) | 110.0 ± 0.3 | −4.8 ± 0.1 | 0.3 ± 0.0 | 0.2 ± 0.0 | 112.9 ± 0.2 | 1.3 ± 0.0 |
| (ΔG°3 − ΔG°2) | 0.6 ± 0.4 | 0.1 ± 0.2 | 0.0 ± 0.0 | 0.0 ± 0.0 | 0.6 ± 0.3 | −0.1 ± 0.0 |
| CGAG → iCGAiG (ΔG°3, imino GA) | 110.8 ± 0.1 | −5.0 ± 0.0 | 0.6 ± 0.0 | 0.3 ± 0.0 | 114.1 ± 0.1 | 0.8 ± 0.0 |
| CGAG → iCGAiG (ΔG°2, sheared GA) | 111.9 ± 0.2 | −5.7 ± 0.2 | 0.5 ± 0.0 | 0.2 ± 0.0 | 115.6 ± 0.3 | 1.4 ± 0.0 |
| (ΔG°3 − ΔG°2) | −1.1 ± 0.2 | 0.7 ± 0.2 | 0.1 ± 0.0 | 0.1 ± 0.0 | −1.5 ± 0.3 | −0.6 ± 0.0 |
a
The values for ΔG° differ somewhat from those in Table 1 because the data set for the table includes structures generated every 50 fs, while the data set for this table contained only structures generated every 1 ps.