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 (-0.832 kcal/mol/HA)
✓ Good fit quality (FQ -7.34)
✓ Strong H-bond network (6 bonds)
✗ High strain energy (16.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-19.132
kcal/mol
LE
-0.832
kcal/mol/HA
Fit Quality
-7.34
FQ (Leeson)
HAC
23
heavy atoms
MW
341
Da
LogP
-1.28
cLogP
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 5
π–π 0
Clashes 8
Severe clashes 0
⚠ Hydrophobic exposure 57%
Partial hydrophobic solvent exposure
57% of hydrophobic surface appears solvent-exposed (8/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 14
Buried (contacted) 6
Exposed 8
LogP -1.28
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.520951292421721 | Score | -19.1319 |
|---|---|---|---|
| Inter norm | -0.836852 | Intra norm | 0.00503191 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 6 |
| Artifact reason | geometry warning; 3 clashes; 8 protein contact clashes; high strain Δ 25.9 | ||
| Residues | A:ASN402;A:GLU466;A:GLU467;A:LEU399;A:LYS407;A:PHE396;A:PRO398;A:SER464;A:THR397;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 | 6 | Native recall | 0.75 |
| Jaccard | 0.50 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1382 | 3.520951292421721 | -0.836852 | -19.1319 | 6 | 10 | 6 | 0.75 | 0.00 | - | no | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.132kcal/mol
Ligand efficiency (LE)
-0.8318kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.341
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
341.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.28
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-8.12kcal/mol
Minimised FF energy
-24.28kcal/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.