4-fluoro-n-methyl-n-{1-[4-(1-methyl-1h-pyrazol-5-yl)phthalazin-1-yl]piperidin-4-yl}-2-(trifluoromethyl)benzamide (1KS) 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 | 61 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 2638 |
| 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 | 0.86 | 0.86 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 | 0.87 | 0.87 | 0.88 | 0.88 |
| # Exchanges | 4319 | 4335 | 4320 | 4285 | 4326 | 4336 | 4337 | 4346 | 4354 | 4358 | 4368 | 4429 | 4362 | 4405 | 4397 |
| Avg. # Exchanges | 0.86 | 0.87 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.89 | 0.87 | 0.88 | 0.88 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.0103 | 0.2394 |
| RMSd_exp | 1.1339 | 0.2913 |
| RMSdist_first | 0.5963 | 0.1559 |
| RMSdist_exp | 0.5930 | 0.1533 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.5701 | 0.1480 |
| RgyrX | 4.8579 | 0.1392 |
| RgyrY | 4.1164 | 0.1273 |
| RgyrZ | 4.6372 | 0.1127 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.7289 |
| Standard deviation (Å) | 0.3108 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| F1 | 0.895 |
| C1 | 0.645 |
| O1 | 0.582 |
| N1 | 0.477 |
| C10 | 0.546 |
| C11 | 0.656 |
| C12 | 0.744 |
| C13 | 0.697 |
| C14 | 0.606 |
| C15 | 0.501 |
| C16 | 0.345 |
| C17 | 0.325 |
| C18 | 0.755 |
| C19 | 1.122 |
| C2 | 0.518 |
| F2 | 1.463 |
| N2 | 0.687 |
| C20 | 1.065 |
| C21 | 0.677 |
| C22 | 0.345 |
| C23 | 0.477 |
| C24 | 0.87 |
| C25 | 0.937 |
| C26 | 1.302 |
| C3 | 0.333 |
| F3 | 1.471 |
| N3 | 0.71 |
| C4 | 0.629 |
| F4 | 1.428 |
| N4 | 0.783 |
| C5 | 0.293 |
| N5 | 0.865 |
| C6 | 0.621 |
| N6 | 0.755 |
| C7 | 0.747 |
| C8 | 0.346 |
| C9 | 0.751 |
3D View
Fluctuation Plot