2-[2-hydroxy-3-(3-hydroxy-2-methyl-benzoylamino)-4-phenyl sulfanyl-butyl]-decahydro-isoquinoline-3-carboxylic acid tert-butylamide (1UN) 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 | 86 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 2381 |
| 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 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 |
| # Exchanges | 4110 | 4118 | 4159 | 4107 | 4168 | 4171 | 4166 | 4159 | 4173 | 4224 | 4149 | 4230 | 4231 | 4210 | 4220 |
| Avg. # Exchanges | 0.82 | 0.82 | 0.83 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.83 | 0.85 | 0.85 | 0.84 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 3.0300 | 0.9271 |
| RMSd_exp | 3.2386 | 0.7695 |
| RMSdist_first | 1.5775 | 0.4624 |
| RMSdist_exp | 1.6208 | 0.2636 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.9075 | 0.2266 |
| RgyrX | 4.3618 | 0.3143 |
| RgyrY | 3.6837 | 0.2334 |
| RgyrZ | 3.9308 | 0.2650 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 2.2360 |
| Standard deviation (Å) | 0.9456 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C1 | 1.81 |
| C2 | 1.283 |
| C3 | 1.607 |
| C4 | 1.797 |
| C5 | 2.579 |
| C6 | 2.272 |
| N7 | 0.68 |
| C8 | 0.755 |
| C9 | 0.773 |
| C10 | 1.602 |
| C11 | 1.737 |
| N12 | 2.513 |
| C13 | 3.604 |
| C14 | 4.246 |
| C15 | 4.291 |
| C16 | 4.28 |
| O17 | 2.302 |
| C18 | 0.896 |
| C19 | 1.334 |
| C20 | 1.278 |
| O21 | 2.322 |
| N22 | 1.205 |
| C23 | 1.605 |
| C24 | 1.562 |
| O25 | 2.028 |
| C29 | 1.796 |
| C30 | 2.366 |
| C31 | 2.792 |
| C32 | 2.699 |
| C33 | 2.589 |
| C34 | 2.207 |
| O38 | 3.324 |
| C39 | 2.9 |
| S74 | 1.849 |
| C77 | 1.743 |
| C78 | 2.383 |
| C79 | 3.241 |
| C80 | 3.552 |
| C81 | 3.24 |
| C82 | 2.399 |
3D View
Fluctuation Plot