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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.659 kcal/mol/HA)
✓ Good fit quality (FQ -6.48)
✓ Good H-bonds (3 bonds)
✗ High strain energy (19.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-21.100
kcal/mol
LE
-0.659
kcal/mol/HA
Fit Quality
-6.48
FQ (Leeson)
HAC
32
heavy atoms
MW
443
Da
LogP
3.31
cLogP
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 0
Clashes 4
Severe clashes 0
| Final rank | 3.4923915045259353 | Score | -21.0999 |
|---|---|---|---|
| Inter norm | -0.659455 | Intra norm | 8.37005e-05 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | geometry warning; 12 clashes; 4 protein contact clashes; moderate strain Δ 18.4 | ||
| Residues | A:ASP116;A:GLU18;A:GLY13;A:GLY49;A:ILE339;A:LEU17;A:MET113;A:SER109;A:SER14;A:THR335;A:TRP21;A:TYR110;A:VAL53 | ||
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 | 0.53 | 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
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1237 | 3.4923915045259353 | -0.659455 | -21.0999 | 3 | 13 | 9 | 0.69 | - | - | no | Current |
| 1236 | 5.593806858404492 | -0.671888 | -24.5081 | 3 | 14 | 9 | 0.69 | - | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.100kcal/mol
Ligand efficiency (LE)
-0.6594kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.484
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
442.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.31
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
124.14kcal/mol
Minimised FF energy
104.19kcal/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.