(5r,8s,11s)-5-methyl-8-(propan-2-yl)-11-[(1e)-4-sulfanylbut-1-en-1-yl]-3,17-dithia-7,10,14,19,20-pentaazatricyclo[14.2.1.1~2,5~]icosa-1(18),2(20),16(19)-triene-6,9,13-trione (L6G) 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 | 61 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 2014 |
| 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 | 0.85 | 0.85 | 0.85 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 |
| # Exchanges | 4240 | 4229 | 4214 | 4269 | 4315 | 4293 | 4284 | 4286 | 4338 | 4304 | 4332 | 4370 | 4342 | 4330 | 4369 |
| Avg. # Exchanges | 0.85 | 0.85 | 0.84 | 0.85 | 0.86 | 0.86 | 0.86 | 0.86 | 0.87 | 0.86 | 0.87 | 0.87 | 0.87 | 0.87 | 0.87 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 1.1355 | 0.4336 |
| RMSd_exp | 0.9730 | 0.4142 |
| RMSdist_first | 0.5673 | 0.2636 |
| RMSdist_exp | 0.5998 | 0.2835 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.2932 | 0.1787 |
| RgyrX | 3.5738 | 0.1803 |
| RgyrY | 3.6670 | 0.1970 |
| RgyrZ | 3.2585 | 0.1408 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 0.7394 |
| Standard deviation (Å) | 0.3315 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 1.312 |
| C1 | 1.102 |
| C2 | 0.905 |
| C3 | 0.676 |
| C4 | 0.601 |
| C5 | 0.583 |
| C6 | 0.56 |
| C7 | 0.696 |
| C8 | 0.974 |
| C9 | 1.029 |
| C10 | 0.516 |
| C11 | 0.528 |
| C12 | 0.809 |
| C13 | 0.567 |
| C14 | 0.43 |
| C15 | 0.448 |
| C16 | 0.702 |
| C17 | 0.515 |
| C18 | 0.641 |
| C19 | 0.554 |
| C20 | 0.887 |
| N | 0.564 |
| N1 | 0.467 |
| N2 | 0.495 |
| N3 | 0.472 |
| N4 | 0.705 |
| O | 0.736 |
| O1 | 0.716 |
| O2 | 0.945 |
| S | 2.178 |
| S1 | 0.565 |
| S2 | 0.782 |
3D View
Fluctuation Plot