3-[(2s)-2-{[(4-methylphenyl)sulfonyl]amino}-3-oxo-3-piperidin-1-ylpropyl]benzenecarboximidamide (0ZG) 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 | 59 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 1853 |
| 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 | 0.79 | 0.80 | 0.80 | 0.81 | 0.82 | 0.82 | 0.82 | 0.82 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 |
| # Exchanges | 3943 | 4002 | 3985 | 4073 | 4031 | 4074 | 4107 | 4127 | 4141 | 4207 | 4208 | 4177 | 4151 | 4260 | 4207 |
| Avg. # Exchanges | 0.79 | 0.80 | 0.80 | 0.81 | 0.81 | 0.81 | 0.82 | 0.83 | 0.83 | 0.84 | 0.84 | 0.84 | 0.83 | 0.85 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.3679 | 0.5117 |
| RMSd_exp | 2.8349 | 0.4508 |
| RMSdist_first | 1.4283 | 0.3621 |
| RMSdist_exp | 1.4750 | 0.3604 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.3168 | 0.2393 |
| RgyrX | 2.3901 | 0.2813 |
| RgyrY | 3.9286 | 0.3821 |
| RgyrZ | 3.9937 | 0.2519 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.5247 |
| Standard deviation (Å) | 0.5532 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| S | 1.334 |
| O | 2.149 |
| O1 | 2.063 |
| C | 0.68 |
| C1 | 1.475 |
| C2 | 2.034 |
| C3 | 2.142 |
| C4 | 2.101 |
| C5 | 1.515 |
| C6 | 3.169 |
| N | 0.963 |
| C7 | 1.269 |
| C8 | 1.763 |
| C9 | 2.068 |
| C10 | 1.922 |
| C11 | 1.385 |
| N1 | 1.201 |
| C12 | 0.918 |
| C13 | 0.777 |
| O2 | 1.035 |
| C14 | 1.407 |
| C15 | 0.794 |
| C16 | 1.344 |
| C17 | 1.305 |
| C18 | 1.32 |
| C19 | 1.313 |
| C20 | 0.773 |
| C21 | 1.386 |
| N2 | 2.086 |
| N3 | 2.049 |
3D View
Fluctuation Plot