Table 2.
Summary of the molecular dynamics simulation system.
| MD system | Total atoms | Simulation time (ns) | |
|---|---|---|---|
| Medial binding pose | WT SP-D•Trimannose | 67,194 | 3000 |
| Asp325Ala SP-D•Trimannose | 67,187 | 3000 | |
| Arg343Val SP-D•Trimannose | 67,279 | 3000 | |
| DM SP-D•Trimannose | 67,280 | 3000 | |
| Terminal binding pose | WT SP-D•Trimannose | 73,823 | 3000 |
| Asp325Ala SP-D•Trimannose | 73,844 | 3000 | |
| Arg343Val SP-D•Trimannose | 73,968 | 3000 | |
| DM SP-D•Trimannose | 73,981 | 3000 | |
| Without Trimannose | WT SP-D | 71,840 | 500 |
| Asp325Ala SP-D | 70,348 | 500 | |
| Arg343Val SP-D | 70,766 | 500 | |
| DM SP-D | 69,434 | 500 | |
| Simulation of Trimannose in Water | Trimannose | 3920 | 1250 |