3-[(2s)-2-{[(4-methylphenyl)sulfonyl]amino}-3-oxo-3-piperidin-1-ylpropyl]benzenecarboximidamide (0ZG) 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 | 59 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 1700 |
| 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 | 0.78 | 0.79 | 0.80 | 0.80 | 0.81 | 0.81 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 |
| # Exchanges | 3901 | 3941 | 3932 | 3998 | 4027 | 4071 | 4102 | 4055 | 4128 | 4161 | 4146 | 4195 | 4197 | 4201 | 4154 |
| Avg. # Exchanges | 0.78 | 0.79 | 0.79 | 0.80 | 0.81 | 0.81 | 0.82 | 0.81 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.83 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.6608 | 0.5829 |
| RMSd_exp | 2.7289 | 0.5719 |
| RMSdist_first | 1.5346 | 0.4105 |
| RMSdist_exp | 1.4661 | 0.4127 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.1610 | 0.2381 |
| RgyrX | 3.6106 | 0.3659 |
| RgyrY | 2.6991 | 0.2081 |
| RgyrZ | 3.7668 | 0.2329 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.7837 |
| Standard deviation (Å) | 0.6531 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| S | 1.459 |
| O | 2.224 |
| O1 | 2.428 |
| C | 0.678 |
| C1 | 1.461 |
| C2 | 2.172 |
| C3 | 2.415 |
| C4 | 2.294 |
| C5 | 1.591 |
| C6 | 3.586 |
| N | 1.129 |
| C7 | 1.353 |
| C8 | 1.992 |
| C9 | 2.415 |
| C10 | 2.288 |
| C11 | 1.78 |
| N1 | 1.405 |
| C12 | 1.014 |
| C13 | 0.99 |
| O2 | 1.499 |
| C14 | 1.618 |
| C15 | 1.167 |
| C16 | 0.756 |
| C17 | 2.165 |
| C18 | 0.898 |
| C19 | 2.381 |
| C20 | 1.612 |
| C21 | 1.776 |
| N2 | 2.215 |
| N3 | 2.751 |
3D View
Fluctuation Plot