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 (-0.463 kcal/mol/HA)
✓ Good fit quality (FQ -4.42)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (39.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-13.426
kcal/mol
LE
-0.463
kcal/mol/HA
Fit Quality
-4.42
FQ (Leeson)
HAC
29
heavy atoms
MW
387
Da
LogP
4.55
cLogP
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 13
π–π 1
Clashes 8
Severe clashes 0
| Final rank | 8.050501809021219 | Score | -13.4264 |
|---|---|---|---|
| Inter norm | -0.606442 | Intra norm | 0.143462 |
| Top1000 | no | Excluded | no |
| Contacts | 6 | H-bonds | 7 |
| Artifact reason | geometry warning; 17 clashes; 8 protein contact clashes; high strain Δ 55.9 | ||
| Residues | A:ASN402;A:LEU399;A:LYS407;A:PHE396;A:PRO398;A:THR397 | ||
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 | 0.56 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2187 | 6.72959580888413 | -1.10709 | -27.8499 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 2844 | 6.802451193186113 | -0.661541 | -16.926 | 5 | 7 | 6 | 0.75 | 0.00 | - | no | Open |
| 2843 | 8.050501809021219 | -0.606442 | -13.4264 | 7 | 6 | 5 | 0.62 | 0.00 | - | no | Current |
| 2189 | 8.185745733851823 | -1.21552 | -33.1116 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2845 | 7.783379389481876 | -0.565641 | -15.82 | 7 | 7 | 6 | 0.75 | 0.00 | - | yes | Open |
| 2191 | 9.954485767120143 | -1.11811 | -30.5533 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2188 | 10.082435984622862 | -1.0252 | -28.9828 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2846 | 10.44678636690243 | -0.604876 | -17.3176 | 7 | 8 | 7 | 0.88 | 0.00 | - | yes | Open |
| 2190 | 11.565762983648456 | -1.06908 | -30.7692 | 4 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2186 | 12.399546710458454 | -1.06826 | -29.767 | 8 | 21 | 0 | 0.00 | 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
-13.426kcal/mol
Ligand efficiency (LE)
-0.4630kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.419
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
387.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.55
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
91.14kcal/mol
Minimised FF energy
51.97kcal/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.