N-cyclopropyl-3-[1-(2,4-difluorophenyl)-7-methyl-6-oxo-6,7-dihydro-1h-pyrazolo[3,4-b]pyridin-5-yl]-4-methylbenzamide (LHJ) 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 | 52 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 2890 |
| 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 | 0.87 | 0.87 | 0.87 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 |
| # Exchanges | 4316 | 4314 | 4315 | 4359 | 4307 | 4348 | 4297 | 4321 | 4329 | 4364 | 4352 | 4329 | 4318 | 4352 | 4353 |
| Avg. # Exchanges | 0.86 | 0.86 | 0.86 | 0.87 | 0.86 | 0.87 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.86 | 0.87 | 0.87 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 0.8882 | 0.3273 |
| RMSd_exp | 0.8173 | 0.3186 |
| RMSdist_first | 0.5204 | 0.2614 |
| RMSdist_exp | 0.4831 | 0.2685 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.9175 | 0.1392 |
| RgyrX | 4.6353 | 0.1925 |
| RgyrY | 2.7940 | 0.0326 |
| RgyrZ | 4.3657 | 0.1156 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.6118 |
| Standard deviation (Å) | 0.4198 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N1 | 0.35 |
| N3 | 0.352 |
| C4 | 0.31 |
| C5 | 0.412 |
| C6 | 0.597 |
| C7 | 0.581 |
| C8 | 0.302 |
| C10 | 0.407 |
| C13 | 0.594 |
| C15 | 0.346 |
| C17 | 0.419 |
| C20 | 0.557 |
| C21 | 0.542 |
| C22 | 0.955 |
| C24 | 1.941 |
| C23 | 1.942 |
| N4 | 0.801 |
| O2 | 1.539 |
| C16 | 0.373 |
| C18 | 0.461 |
| C19 | 0.394 |
| C3 | 0.364 |
| O1 | 0.535 |
| C2 | 0.303 |
| C1 | 0.41 |
| N2 | 0.547 |
| C9 | 0.23 |
| C14 | 0.468 |
| C12 | 0.521 |
| F2 | 0.774 |
| C11 | 0.502 |
| F1 | 0.749 |
3D View
Fluctuation Plot