Table 3. Details of hydrogen bonds between loop bases and between loop base and quartet base.
Model | Donors | Acceptors | Occupied(%) | lifetime(ps) |
anti_bsc0 | N6@A19 | O4@T6 | 98.3 | 322.5 |
N3@T6 | N1@A19 | 98.4 | 441.5 | |
N2@G8 | O4′@A7 | 91.4a | 101.0 | |
hybrid_bsc0 | N3@T13 | N1@A24 | 99.2 | 1229.5 |
N6@A24 | O2@T13 | 99.0 | 659.8 | |
N3@T1 | N1@A20 | 99.9 | 6989.5 | |
N6@A20 | O4@T1 | 99.4 | 931.0 | |
N2@G4 | O4@T6 | 79.2 | 96.0 |
Results under parm99 force field are given in Table S2.
This hydrogen bond formed after 250 ns in the simulation, so just last 700 ns of the trajectory was used to count the hydrogen bond.