Amino{[(4s)-5-[(2r,4r)-2-carboxy-4-methylpiperidin-1-yl]-4-({[(3r)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}amino)-5-oxopentyl]amino}methaniminium (MIT) 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 | 71 |
| Molecule charge (simulated) | 0 |
| System number of atoms | 1694 |
| 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 | 0.76 | 0.77 | 0.78 | 0.78 | 0.79 | 0.78 | 0.79 | 0.80 | 0.80 | 0.81 | 0.81 | 0.81 | 0.82 | 0.81 | 0.82 |
| # Exchanges | 3795 | 3870 | 3914 | 3909 | 3915 | 3961 | 4009 | 3978 | 4011 | 4061 | 4061 | 4030 | 4119 | 4049 | 4043 |
| Avg. # Exchanges | 0.76 | 0.77 | 0.78 | 0.78 | 0.78 | 0.79 | 0.80 | 0.80 | 0.80 | 0.81 | 0.81 | 0.81 | 0.82 | 0.81 | 0.81 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.6191 | 0.8372 |
| RMSd_exp | 3.0492 | 0.5785 |
| RMSdist_first | 1.3365 | 0.5035 |
| RMSdist_exp | 1.3697 | 0.3807 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.1195 | 0.2768 |
| RgyrX | 3.3509 | 0.2841 |
| RgyrY | 3.0294 | 0.3968 |
| RgyrZ | 3.6453 | 0.4016 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.6696 |
| Standard deviation (Å) | 0.7452 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| S | 1.152 |
| O1 | 1.94 |
| O2 | 1.74 |
| C1 | 2.804 |
| C2 | 2.846 |
| C3 | 2.283 |
| C4 | 1.556 |
| C5 | 2.346 |
| C6 | 2.72 |
| C7 | 2.065 |
| C8 | 0.83 |
| C9 | 0.872 |
| C10 | 3.958 |
| N | 1.727 |
| N1 | 0.962 |
| CA | 0.753 |
| C | 0.668 |
| O | 0.846 |
| CB | 0.925 |
| CG | 1.163 |
| CD | 1.296 |
| NE | 1.38 |
| CZ | 1.957 |
| NH1 | 2.625 |
| NH2 | 2.629 |
| N2 | 0.849 |
| C11 | 1.082 |
| C21 | 1.409 |
| C31 | 1.559 |
| C41 | 1.441 |
| C51 | 1.123 |
| C61 | 1.306 |
| O11 | 1.781 |
| O21 | 1.786 |
| C71 | 2.057 |
3D View
Fluctuation Plot