Table 2. MD Simulations Performed in This Work.
| simulation set | system contents | no. of ligands tested | no. of ligand poses | total no. of simulations | simulation length (ns)e |
|---|---|---|---|---|---|
| NMR1 | RNA,a ligand,c K+, Cl–, TIP3P | 12 | 1 | 12 | 232 |
| CRY1 | RNA,b ligand,c K+, Cl–, TIP3P | 12 | 1 | 12 | 218+ |
| CRY2 | RNA,b ligand,c K+, Cl–, TIP3P | 12 | 20 | 240 | 2 |
| MG | RNA,b J5R, Mg2+, K+, Cl–, TIP3P | 1 | 1 | 1 | 232 |
| RDC | RNA,b J4R, K+, Cl–, TIP3P | 1 | 1 | 1 | 5 |
| NOV | RNA,b ligand,d K+, Cl–, TIP3P | 4 | 1 | 4 | 70 |
| LIG | ligand,c K+, Cl–, TIP3P | 12 | 1 | 12 | 594+ |
a
RNA receptor in the NMR conformation.
b
RNA receptor in the crystal conformation.
c
The 12 ligands are those described in Figure 1.
d
The four ligands are those described in Figure 11.
e
Simulation length represents the simulation time for each simulation (the product of the total number of simulations and the simulation length yields the aggregate time). “+” indicates that the stated time is the minimum from among the simulation set.