4-hydroxy-3-[2-oxo-3-(thieno[3,2-b]pyridine-2-sulfonylamino)-pyrrolidin-1-ylmethyl]-benzamidine (PR1) 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 | 49 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1954 |
| 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 | 0.80 | 0.81 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 |
| # Exchanges | 3973 | 4070 | 4051 | 4099 | 4112 | 4157 | 4163 | 4154 | 4157 | 4228 | 4240 | 4241 | 4256 | 4233 | 4333 |
| Avg. # Exchanges | 0.79 | 0.81 | 0.81 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.87 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.3412 | 0.8604 |
| RMSd_exp | 2.5345 | 0.3966 |
| RMSdist_first | 1.3299 | 0.8188 |
| RMSdist_exp | 1.3377 | 0.2651 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.7160 | 0.4153 |
| RgyrX | 2.7356 | 0.1318 |
| RgyrY | 4.1868 | 0.4489 |
| RgyrZ | 4.3951 | 0.5271 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.6986 |
| Standard deviation (Å) | 0.5283 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 1.789 |
| C2 | 2.127 |
| C3 | 1.615 |
| C4 | 0.807 |
| C5 | 1.006 |
| C6 | 1.284 |
| C10 | 2.083 |
| N11 | 2.782 |
| N12 | 2.552 |
| C13 | 1.395 |
| O44 | 2.452 |
| C16 | 1.275 |
| C17 | 2.03 |
| C18 | 2.102 |
| C19 | 2.18 |
| N20 | 2.087 |
| C21 | 1.233 |
| C25 | 1.315 |
| C26 | 0.728 |
| S27 | 1.662 |
| N28 | 1.242 |
| C29 | 1.127 |
| C30 | 1.415 |
| C31 | 2.271 |
| C32 | 2.084 |
| N37 | 1.176 |
| S38 | 1.269 |
| O39 | 2.096 |
| O40 | 2.107 |
| O41 | 1.668 |
3D View
Fluctuation Plot