py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Acceptable LE (-0.210 kcal/mol/HA)
✓ Good fit quality (FQ -2.29)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (39.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-10.088
kcal/mol
LE
-0.210
kcal/mol/HA
Fit Quality
-2.29
FQ (Leeson)
HAC
48
heavy atoms
MW
665
Da
LogP
3.91
cLogP
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 3
Clashes 4
Severe clashes 0
| Final rank | 6.275542488399826 | Score | -10.0884 |
|---|---|---|---|
| Inter norm | -0.230337 | Intra norm | 0.0201613 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 5 |
| Artifact reason | geometry warning; 17 clashes; 4 protein contact clashes; high strain Δ 38.3 | ||
| Residues | A:GLU18;A:ILE106;A:LEU17;A:MET113;A:SER109;A:TRP21;A:TYR110;A:VAL53;A:VAL58 | ||
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 0 |
| IFP residues | A:ASP116; A:GLU18; A:GLY112; A:ILE106; A:LEU17; A:MET113; A:SER109; A:THR117; A:THR335; A:TRP21; A:TYR110; A:VAL53; A:VAL58 | ||
| Current overlap | 9 | Native recall | 0.69 |
| Jaccard | 0.69 | RMSD | - |
| H-bond strict | 0 | Strict recall | - |
| H-bond same residue+role | 0 | Role recall | - |
| H-bond same residue | 0 | Residue recall | - |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 175 | 6.275542488399826 | -0.230337 | -10.0884 | 5 | 9 | 9 | 0.69 | - | - | no | Current |
| 177 | 6.590816676586569 | -0.297682 | -14.7996 | 4 | 13 | 10 | 0.77 | - | - | no | Open |
| 122 | 6.623908820373664 | -0.392232 | -22.8137 | 2 | 16 | 0 | 0.00 | - | - | no | Open |
| 121 | 7.38657313809238 | -0.321982 | -16.1743 | 3 | 15 | 0 | 0.00 | - | - | no | Open |
| 126 | 7.493058812238245 | -0.325898 | -13.1866 | 2 | 15 | 0 | 0.00 | - | - | no | Open |
| 174 | 7.52647633159325 | -0.296025 | -10.172 | 1 | 13 | 10 | 0.77 | - | - | no | Open |
| 233 | 7.6319290184965975 | -0.406985 | -16.0343 | 1 | 20 | 0 | 0.00 | - | - | no | Open |
| 232 | 8.98296648088481 | -0.479979 | -19.3352 | 0 | 18 | 0 | 0.00 | - | - | no | Open |
| 130 | 9.613309366169023 | -0.367896 | -20.2919 | 3 | 13 | 0 | 0.00 | - | - | no | Open |
| 124 | 54.90678412804392 | -0.446751 | -21.3675 | 4 | 17 | 0 | 0.00 | - | - | no | Open |
| 176 | 55.08095717655768 | -0.422474 | -17.7921 | 2 | 10 | 10 | 0.77 | - | - | no | Open |
| 179 | 55.441059436710546 | -0.307973 | -16.8502 | 2 | 9 | 8 | 0.62 | - | - | no | Open |
| 181 | 55.4644396591611 | -0.309166 | -16.1363 | 1 | 12 | 9 | 0.69 | - | - | no | Open |
| 123 | 56.03713740231415 | -0.361384 | -18.2614 | 3 | 12 | 0 | 0.00 | - | - | no | Open |
| 129 | 9.063943532926253 | -0.353734 | -19.554 | 3 | 14 | 0 | 0.00 | - | - | yes | Open |
| 132 | 9.21411647823986 | -0.319689 | -17.7198 | 2 | 17 | 0 | 0.00 | - | - | yes | Open |
| 235 | 9.632875282411014 | -0.40778 | -18.0707 | 0 | 20 | 0 | 0.00 | - | - | yes | Open |
| 178 | 55.54832617343075 | -0.355277 | -17.897 | 4 | 13 | 11 | 0.85 | - | - | yes | Open |
| 128 | 55.85736192058398 | -0.377757 | -22.9116 | 5 | 18 | 0 | 0.00 | - | - | yes | Open |
| 180 | 56.73329863084768 | -0.328082 | -16.7695 | 2 | 9 | 8 | 0.62 | - | - | yes | Open |
| 136 | 57.05145470516479 | -0.357664 | -15.5151 | 5 | 10 | 0 | 0.00 | - | - | yes | Open |
| 127 | 57.38136765086828 | -0.397318 | -18.2109 | 3 | 15 | 0 | 0.00 | - | - | yes | Open |
| 135 | 57.95106297431023 | -0.442919 | -19.3927 | 3 | 16 | 0 | 0.00 | - | - | yes | Open |
| 238 | 58.70619646020666 | -0.542864 | -22.7362 | 0 | 17 | 0 | 0.00 | - | - | yes | Open |
| 234 | 58.81723665573986 | -0.554031 | -24.3529 | 2 | 17 | 0 | 0.00 | - | - | yes | Open |
| 237 | 59.02381195613867 | -0.478612 | -20.8327 | 0 | 21 | 0 | 0.00 | - | - | yes | Open |
| 133 | 59.169384455664925 | -0.38743 | -14.5111 | 2 | 17 | 0 | 0.00 | - | - | yes | Open |
| 239 | 59.638485396091426 | -0.469957 | -20.6378 | 3 | 12 | 0 | 0.00 | - | - | yes | Open |
| 131 | 59.78931090831168 | -0.294202 | -15.3285 | 5 | 15 | 0 | 0.00 | - | - | yes | Open |
| 125 | 61.46460320297299 | -0.459124 | -21.609 | 3 | 17 | 0 | 0.00 | - | - | yes | Open |
| 236 | 62.04718782650286 | -0.46491 | -23.565 | 2 | 13 | 0 | 0.00 | - | - | yes | Open |
| 134 | 63.28921586966261 | -0.401364 | -20.4469 | 2 | 14 | 0 | 0.00 | - | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-10.088kcal/mol
Ligand efficiency (LE)
-0.2102kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-2.290
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
48HA
Physicochemical properties
Molecular weight
664.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.91
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
126.67kcal/mol
Minimised FF energy
87.62kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. It will be calculated automatically
the next time this pose is loaded if a receptor PDB path is stored.