(2s,4s)-4-hydroxy-2-(1-methylethyl)-4-[(4r,13s)-18-[methyl(methylsulfonyl)amino]-2,15-dioxo-4-phenyl-11-oxa-3,14-diazatricyclo[14.3.1.1~5,9~]henicosa-1(20),5(21),6,8,16,18-hexaen-13-yl]-n-(2-methylpropyl)butanamide (3OX) 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 | 97 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 3766 |
| 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 | 0.82 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 | 0.83 | 0.84 | 0.84 | 0.83 | 0.84 | 0.84 |
| # Exchanges | 4082 | 4063 | 4143 | 4145 | 4116 | 4057 | 4154 | 4126 | 4179 | 4126 | 4193 | 4188 | 4187 | 4200 | 4195 |
| Avg. # Exchanges | 0.82 | 0.81 | 0.83 | 0.83 | 0.82 | 0.81 | 0.83 | 0.83 | 0.84 | 0.83 | 0.84 | 0.84 | 0.84 | 0.84 | 0.84 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.1869 | 0.5479 |
| RMSd_exp | 2.1319 | 0.5333 |
| RMSdist_first | 1.5400 | 0.4030 |
| RMSdist_exp | 1.1677 | 0.3905 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.6862 | 0.1724 |
| RgyrX | 4.2273 | 0.0811 |
| RgyrY | 5.0267 | 0.1887 |
| RgyrZ | 4.6362 | 0.2290 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.2621 |
| Standard deviation (Å) | 0.8088 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N1 | 0.699 |
| C2 | 0.82 |
| C3 | 0.789 |
| C4 | 1.235 |
| C5 | 1.129 |
| C6 | 0.839 |
| C7 | 0.989 |
| O8 | 1.636 |
| C9 | 2.219 |
| C10 | 3.076 |
| C11 | 2.734 |
| O12 | 1.688 |
| O13 | 0.794 |
| C14 | 2.047 |
| C15 | 2.813 |
| C16 | 3.535 |
| C17 | 3.573 |
| N18 | 1.046 |
| C19 | 0.543 |
| C20 | 0.607 |
| C21 | 0.605 |
| C22 | 0.537 |
| C23 | 0.442 |
| C24 | 0.466 |
| C25 | 0.666 |
| C26 | 0.471 |
| N27 | 0.78 |
| C28 | 1.949 |
| S29 | 1.058 |
| C30 | 2.226 |
| O31 | 0.715 |
| O32 | 0.852 |
| O33 | 1.916 |
| O34 | 1.827 |
| N35 | 0.447 |
| C36 | 0.47 |
| C37 | 0.548 |
| C38 | 0.736 |
| C39 | 1.064 |
| C40 | 1.263 |
| C41 | 1.009 |
| C42 | 0.553 |
| C43 | 0.924 |
| C44 | 0.569 |
| C45 | 1.381 |
| C46 | 1.535 |
| C47 | 1.107 |
| C48 | 1.535 |
| C49 | 1.383 |
3D View
Fluctuation Plot