Stability of hydrogen bonds formed between protein and ligand base during MD simulation
| Wild type | T284S/V288S/A352D | |||
| Residue | Protein–cGMP h-bonds | Water-mediated h-bonds | Protein–cGMP h-bonds | Water-mediated h-bonds |
| 284 | 2% (OG1) | 23% (OG1) | — | 10% (OG) |
| 286 | — | 35% (ND2) +20% (N) +3% (O) | 6% (ND2) | 22% (O) +9% (N) +4% (ND2) |
| 288 | — | — | 24% (OG) | 35% (OG) |
| 297 | — | — | — | — |
| 298 | — | — | — | — |
| 308 | 95% (OG) | 3% (O) | 93% (OG) | — |
| 348 | — | 6% (NE) +2% (O) | — | 2% (NE) |
| 352 | — | — | 67% (OD2) +61%(OD1) | 7% (OD1) +7% (OD2) |
| Wild type | T284S/V288S/A352D | |||
| Residue | Protein–cGMP h-bonds | Water-mediated h-bonds | Protein–cGMP h-bonds | Water-mediated h-bonds |
| 284 | 2% (OG1) | 23% (OG1) | — | 10% (OG) |
| 286 | — | 35% (ND2) +20% (N) +3% (O) | 6% (ND2) | 22% (O) +9% (N) +4% (ND2) |
| 288 | — | — | 24% (OG) | 35% (OG) |
| 297 | — | — | — | — |
| 298 | — | — | — | — |
| 308 | 95% (OG) | 3% (O) | 93% (OG) | — |
| 348 | — | 6% (NE) +2% (O) | — | 2% (NE) |
| 352 | — | — | 67% (OD2) +61%(OD1) | 7% (OD1) +7% (OD2) |
Percentages correspond to the fraction of time in the MD trajectory when a protein residue forms a hydrogen bond (h-bond) with the guanine group. The name of the protein atom participating to the h-bond is given in parentheses. Two atoms are considered part of an h-bond if donor and acceptor are closer than 3.5 Å and the donor–hydrogen–acceptor angle is below 35°.