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.
✓ Excellent LE (-0.454 kcal/mol/HA)
✓ Good fit quality (FQ -4.38)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (23.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-13.607
kcal/mol
LE
-0.454
kcal/mol/HA
Fit Quality
-4.38
FQ (Leeson)
HAC
30
heavy atoms
MW
449
Da
LogP
1.13
cLogP
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 5
π–π 2
Clashes 7
Severe clashes 0
| Final rank | 5.68051943962044 | Score | -13.6072 |
|---|---|---|---|
| Inter norm | -0.526032 | Intra norm | 0.072457 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 15 clashes; 7 protein contact clashes; high strain Δ 25.9 | ||
| Residues | A:GLU466;A:GLU467;A:HIS461;A:PHE396;A:PRO398;A:PRO462;A:SER394;A:SER395;A:SER464;A:SER470;A:THR463 | ||
Protein summary
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | 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:264; MET:221 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 2 |
| IFP residues | A:ASN402; A:GLU467; A:LEU399; A:PHE396; A:PRO398; A:SER394; A:SER470; A:THR397 | ||
| Current overlap | 5 | Native recall | 0.62 |
| Jaccard | 0.36 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1408 | 5.68051943962044 | -0.526032 | -13.6072 | 4 | 11 | 5 | 0.62 | 0.00 | - | no | Current |
| 1407 | 7.77342488325223 | -0.601401 | -16.8071 | 5 | 10 | 7 | 0.88 | 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
-13.607kcal/mol
Ligand efficiency (LE)
-0.4536kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.375
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
448.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.13
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
49.91kcal/mol
Minimised FF energy
26.61kcal/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.