Table 1.
Hydrogen bond (HB) properties during the MD simulation
| Configuration | %* | HB
no. 1
|
HB no. 2
|
HB no. 3
|
HB
no. 4
|
HB no. 5
|
HB no. 6
|
HB
no. 7
|
|---|---|---|---|---|---|---|---|---|
| W230 H–Gln-61 C⩵O | Gln-61 NH2–W230 O | Gln-61 NH2–GTP OG | W230 H–GTP OG | W230 H–Arg-789 C⩵O | Gln-61 NH2–Arg-789 C⩵O | Thr-35 NH–W230 O | ||
| During the first 250 ps of the simulation | ||||||||
| 1 | 32 | Y | N | N | Y | N | Y | N |
| 2 | 28 | Y | N | Y | Y | N | Y | Y |
| 3 | 16 | Y | N | N | Y | N | N | N |
| 4 | 12 | Y | N | N | Y | N | Y | Y |
| 5 | 8 | Y | N | Y | Y | N | Y | N |
| During the last 500 ps of the simulation | ||||||||
| 1 | 56 | N | Y | N | Y | Y | N | N |
| 2 | 10 | Y | Y | N | Y | N | N | N |
| 3 | 7 | N | Y | N | Y | N | N | N |
| 4 | 7 | N | Y | Y | Y | Y | N | N |
| 5 | 7 | N | N | Y | Y | Y | N | N |
| 6 | 6 | N | N | N | Y | Y | N | N |
Y and N respectively denote presence or absence of the hydrogen bond.
*
Shows the percentage of snapshots in which the configuration was observed.