[4r--(1alpha,5alpha,7beta)]-3-[(cycloprophylmethyl)hexahydro-5,6-dihydroxy-2-oxo-4,7-bis(phenylmethyl)-1h-1,3-diazepin]methyl-2-thiazolylbenzamide (846) 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 | 79 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 3022 |
| 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 | 0.84 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 |
| # Exchanges | 4171 | 4139 | 4144 | 4185 | 4210 | 4190 | 4235 | 4206 | 4185 | 4214 | 4238 | 4251 | 4249 | 4222 | 4269 |
| Avg. # Exchanges | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.85 | 0.84 | 0.84 | 0.84 | 0.85 | 0.85 | 0.85 | 0.84 | 0.85 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.9071 | 0.8399 |
| RMSd_exp | 2.8160 | 0.6895 |
| RMSdist_first | 1.0387 | 0.4404 |
| RMSdist_exp | 1.7741 | 0.4949 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.8389 | 0.1652 |
| RgyrX | 4.4822 | 0.2148 |
| RgyrY | 3.7352 | 0.4271 |
| RgyrZ | 3.5314 | 0.3793 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.7005 |
| Standard deviation (Å) | 0.7183 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 0.807 |
| C2 | 1.612 |
| C3 | 0.825 |
| C4 | 1.034 |
| C5 | 0.953 |
| C6 | 0.668 |
| C7 | 1.135 |
| C20 | 1.71 |
| C21 | 0.932 |
| C22 | 1.233 |
| C23 | 2.463 |
| C24 | 3.266 |
| C25 | 2.87 |
| C26 | 0.818 |
| C27 | 1.634 |
| C28 | 3.245 |
| C29 | 3.072 |
| C31 | 0.918 |
| C32 | 1.13 |
| C33 | 1.647 |
| C34 | 2.016 |
| C35 | 2.002 |
| C36 | 2.13 |
| C37 | 1.779 |
| C61 | 1.046 |
| C62 | 1.371 |
| C63 | 2.008 |
| C64 | 2.462 |
| C65 | 2.433 |
| C66 | 2.439 |
| C67 | 1.987 |
| C70 | 1.54 |
| C71 | 2.198 |
| C72 | 2.183 |
| N2 | 0.892 |
| N7 | 0.594 |
| N26 | 0.97 |
| N27 | 2.606 |
| O1 | 1.341 |
| O4 | 1.599 |
| O5 | 1.51 |
| O26 | 1.745 |
| S29 | 2.297 |
3D View
Fluctuation Plot