3-chloro-n-[4-chloro-2-[[(5-chloro-2-pyridinyl)amino]carbonyl]-6-methoxyphenyl]-4-[[(4,5-dihydro-2-oxazolyl)methylamino]methyl]-2-thiophenecarboxamide (XLD) 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 | 56 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 2399 |
| 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 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.88 |
| # Exchanges | 4282 | 4191 | 4267 | 4239 | 4252 | 4276 | 4313 | 4285 | 4337 | 4329 | 4343 | 4364 | 4355 | 4364 | 4372 |
| Avg. # Exchanges | 0.86 | 0.84 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.1885 | 0.5060 |
| RMSd_exp | 1.7526 | 0.5062 |
| RMSdist_first | 1.6913 | 0.5069 |
| RMSdist_exp | 1.1631 | 0.5045 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.8201 | 0.2767 |
| RgyrX | 3.3862 | 0.4615 |
| RgyrY | 3.7574 | 0.1987 |
| RgyrZ | 4.5496 | 0.2901 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.2518 |
| Standard deviation (Å) | 0.6320 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 0.972 |
| N | 1.678 |
| C1 | 1.879 |
| C2 | 1.573 |
| CL | 2.013 |
| C3 | 1.799 |
| C4 | 1.564 |
| N1 | 0.779 |
| C5 | 0.687 |
| O | 1.639 |
| C6 | 0.504 |
| C7 | 0.468 |
| C8 | 0.63 |
| C9 | 0.734 |
| C10 | 0.725 |
| CL1 | 1.051 |
| C11 | 0.647 |
| O1 | 0.871 |
| C12 | 1.399 |
| N2 | 0.544 |
| C13 | 0.66 |
| O2 | 0.92 |
| C14 | 0.712 |
| S | 1.119 |
| C15 | 1.048 |
| C16 | 0.915 |
| C17 | 0.779 |
| CL2 | 1.154 |
| C18 | 1.201 |
| N3 | 1.057 |
| C19 | 2.336 |
| C20 | 1.243 |
| N4 | 2.036 |
| C21 | 2.875 |
| C22 | 2.867 |
| O3 | 1.988 |
3D View
Fluctuation Plot