7-(1,1-dioxo-1h-benzo[d]isothiazol-3-yloxymethyl)-2-(oxalyl-amino)-4,7-dihydro-5h-thieno[2,3-c]pyran-3-carboxylic acid (DBD) Summary
TRAJECTORIES
METADATA
| Parameter | Value |
|---|---|
| Method | HamiltonianREMD |
| Number of MD replicas | 16 |
| Length of the MD simulations (ns) | 10 |
| Number of steps between exchanges | 100 |
| Force Field | General Amber Force Field (GAFF) |
| Charge scheme | Semi-Empirical (AM1) |
| REMD Progression | Geometric Progression |
| Initial (low) temperature (K) / Scaling factor | 298 / 1 |
| Final (high) temperature (K) / Scaling factor | 498 / 0.59 |
| Molecule number of atoms | 43 |
| Molecule charge (simulated) | -2 |
| System number of atoms | 2413 |
| Box size in simulations (nm) | 0.8 |
| Solvent model | TIP3P |
| Box type in simulations | Octahedron |
| MD ensemble | NVT |
REMD stats
| 1-2 | 2-3 | 3-4 | 4-5 | 5-6 | 6-7 | 7-8 | 8-9 | 9-10 | 10-11 | 11-12 | 12-13 | 13-14 | 14-15 | 15-16 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Probabilities | 0.76 | 0.77 | 0.77 | 0.77 | 0.77 | 0.78 | 0.78 | 0.77 | 0.79 | 0.79 | 0.79 | 0.80 | 0.80 | 0.81 | 0.80 |
| # Exchanges | 3834 | 3856 | 3866 | 3859 | 3825 | 3892 | 3888 | 3853 | 3927 | 3968 | 3980 | 3982 | 3996 | 4024 | 3983 |
| Avg. # Exchanges | 0.77 | 0.77 | 0.77 | 0.77 | 0.77 | 0.78 | 0.78 | 0.77 | 0.79 | 0.79 | 0.80 | 0.80 | 0.80 | 0.80 | 0.80 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.7548 | 0.7493 |
| RMSd_exp | 2.7699 | 0.6472 |
| RMSdist_first | 2.2256 | 0.8131 |
| RMSdist_exp | 1.9610 | 0.6548 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.0229 | 0.4388 |
| RgyrX | 3.5389 | 0.4022 |
| RgyrY | 2.6391 | 0.3040 |
| RgyrZ | 3.5733 | 0.4902 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.2685 |
| Standard deviation (Å) | 0.5832 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| O1 | 1.117 |
| C2 | 0.922 |
| C3 | 0.687 |
| C4 | 0.699 |
| C5 | 0.981 |
| C6 | 0.998 |
| S7 | 0.704 |
| C8 | 0.553 |
| C9 | 0.702 |
| C10 | 1.075 |
| O11 | 1.353 |
| O12 | 1.212 |
| N13 | 0.671 |
| C14 | 0.771 |
| C15 | 1.063 |
| O16 | 1.599 |
| O17 | 1.611 |
| O18 | 0.909 |
| C19 | 1.343 |
| O20 | 1.283 |
| C21 | 0.642 |
| C22 | 1.148 |
| C23 | 1.23 |
| S24 | 1.376 |
| N25 | 0.917 |
| C26 | 2.125 |
| C27 | 2.771 |
| C28 | 2.642 |
| C29 | 2.004 |
| O30 | 2.056 |
| O31 | 2.158 |
3D View
Fluctuation Plot