3-chloro-n-[4-chloro-2-[[(4-chlorophenyl)amino]carbonyl]phenyl]-4-[(4-methyl-1-piperazinyl)methyl]-2-thiophenecarboxamide (XLC) 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 | 58 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 2686 |
| 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 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 |
| # Exchanges | 4138 | 4154 | 4152 | 4153 | 4140 | 4157 | 4168 | 4248 | 4208 | 4173 | 4189 | 4226 | 4265 | 4288 | 4300 |
| Avg. # Exchanges | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.85 | 0.84 | 0.83 | 0.84 | 0.85 | 0.85 | 0.86 | 0.86 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.0905 | 0.5600 |
| RMSd_exp | 2.3469 | 0.8015 |
| RMSdist_first | 1.0315 | 0.4043 |
| RMSdist_exp | 1.3746 | 0.6658 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.8100 | 0.2965 |
| RgyrX | 4.0043 | 0.1996 |
| RgyrY | 4.5615 | 0.2779 |
| RgyrZ | 3.0582 | 0.3680 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.5265 |
| Standard deviation (Å) | 0.6449 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 1.056 |
| C1 | 1.759 |
| C2 | 2.094 |
| C3 | 1.918 |
| CL | 2.504 |
| C4 | 2.059 |
| C5 | 1.726 |
| N | 0.753 |
| C6 | 0.651 |
| O | 1.535 |
| C7 | 0.658 |
| C8 | 0.691 |
| C9 | 1.103 |
| C10 | 1.393 |
| C11 | 1.314 |
| CL1 | 1.784 |
| C12 | 0.981 |
| N1 | 0.571 |
| C13 | 0.913 |
| O1 | 1.712 |
| C14 | 1.012 |
| S | 2.249 |
| C15 | 1.783 |
| C16 | 1.083 |
| C17 | 0.882 |
| CL2 | 1.941 |
| C18 | 1.433 |
| N2 | 0.832 |
| C19 | 1.621 |
| C20 | 2.193 |
| N3 | 2.413 |
| C21 | 2.241 |
| C22 | 1.653 |
| C23 | 3.39 |
3D View
Fluctuation Plot