N-[(4s,8e,11s)-4-[(1r)-1-hydroxy-2-{[3-(propan-2-yl)benzyl]amino}ethyl]-2,13-dioxo-11-phenyl-6-oxa-3,12-diazabicyclo[12.3.1]octadeca-1(18),8,14,16-tetraen-16-yl]-n-methylmethanesulfonamide (0LG) 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 | 91 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 3871 |
| 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 | 0.80 | 0.80 | 0.81 | 0.81 | 0.81 | 0.81 | 0.82 | 0.82 | 0.81 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.83 |
| # Exchanges | 4012 | 3992 | 4032 | 4058 | 4069 | 4002 | 4062 | 4051 | 4072 | 4079 | 4145 | 4136 | 4100 | 4166 | 4166 |
| Avg. # Exchanges | 0.80 | 0.80 | 0.81 | 0.81 | 0.81 | 0.80 | 0.81 | 0.81 | 0.81 | 0.82 | 0.83 | 0.83 | 0.82 | 0.83 | 0.83 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.6502 | 0.7735 |
| RMSd_exp | 2.6830 | 0.6757 |
| RMSdist_first | 2.0275 | 0.9361 |
| RMSdist_exp | 1.7494 | 0.6723 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.5759 | 0.5804 |
| RgyrX | 4.4112 | 0.4834 |
| RgyrY | 4.3390 | 0.3283 |
| RgyrZ | 4.8757 | 0.6746 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.8103 |
| Standard deviation (Å) | 1.1332 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| O14 | 2.183 |
| S11 | 1.502 |
| O13 | 2.236 |
| C12 | 2.362 |
| N7 | 1.278 |
| C10 | 2.236 |
| C6 | 1.111 |
| C1 | 1.017 |
| C2 | 0.906 |
| C5 | 1.117 |
| C4 | 1.015 |
| C3 | 0.904 |
| C8 | 1.108 |
| O15 | 1.2 |
| N16 | 1.197 |
| C17 | 1.272 |
| C18 | 1.491 |
| C19 | 1.133 |
| N20 | 1.126 |
| C37 | 1.472 |
| C38 | 1.867 |
| C39 | 2.47 |
| C40 | 3.523 |
| C44 | 4.612 |
| C45 | 5.268 |
| C46 | 5.272 |
| C41 | 4.001 |
| C42 | 3.713 |
| C43 | 2.746 |
| O21 | 2.273 |
| C22 | 1.327 |
| O34 | 1.101 |
| C35 | 1.168 |
| C36 | 1.152 |
| C33 | 1.002 |
| C26 | 1.201 |
| C25 | 0.952 |
| N23 | 0.874 |
| C9 | 0.91 |
| O24 | 1.102 |
| C27 | 0.899 |
| C28 | 1.561 |
| C29 | 1.746 |
| C30 | 1.425 |
| C31 | 1.714 |
| C32 | 1.527 |
3D View
Fluctuation Plot