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 (-0.586 kcal/mol/HA)
✓ Good fit quality (FQ -5.65)
✗ High strain energy (14.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-17.585
kcal/mol
LE
-0.586
kcal/mol/HA
Fit Quality
-5.65
FQ (Leeson)
HAC
30
heavy atoms
MW
485
Da
LogP
5.74
cLogP
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 15
π–π 2
Clashes 2
Severe clashes 0
| Final rank | 2.438228853446348 | Score | -17.585 |
|---|---|---|---|
| Inter norm | -0.554968 | Intra norm | -0.0312005 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 1 |
| Artifact reason | geometry warning; 9 clashes; 2 protein contact clashes; moderate strain Δ 14.3 | ||
| Residues | A:GLU466;A:GLU467;A:HIS461;A:LEU399;A:PHE396;A:PRO398;A:PRO462;A:SER394;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 | 6 | Native recall | 0.75 |
| Jaccard | 0.46 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 908 | 2.1118581172448754 | -0.57751 | -18.1903 | 1 | 13 | 8 | 1.00 | 0.00 | - | no | Open |
| 905 | 2.438228853446348 | -0.554968 | -17.585 | 1 | 11 | 6 | 0.75 | 0.00 | - | no | Current |
| 664 | 2.797668238469795 | -0.876321 | -25.9602 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 901 | 2.863233654820324 | -0.570014 | -17.6209 | 1 | 12 | 6 | 0.75 | 0.00 | - | no | Open |
| 902 | 3.1806401817943404 | -0.519172 | -15.69 | 1 | 12 | 7 | 0.88 | 0.00 | - | no | Open |
| 667 | 3.5558052197595953 | -0.687097 | -19.3614 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 907 | 4.085651794314032 | -0.579886 | -18.074 | 1 | 12 | 7 | 0.88 | 0.00 | - | no | Open |
| 657 | 4.088183664443179 | -0.765743 | -21.7604 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 661 | 4.256977000304189 | -0.778385 | -18.2012 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 903 | 4.293388327213341 | -0.615565 | -19.0615 | 1 | 12 | 7 | 0.88 | 0.00 | - | no | Open |
| 665 | 4.312612217289256 | -0.789862 | -22.8014 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 668 | 4.546812767577663 | -0.876243 | -19.2179 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 6.493301175417429 | -0.708243 | -19.0372 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 906 | 54.07700204691882 | -0.584284 | -17.0563 | 1 | 12 | 7 | 0.88 | 1.00 | - | no | Open |
| 904 | 54.15332891043789 | -0.525958 | -14.1395 | 1 | 12 | 7 | 0.88 | 0.00 | - | no | Open |
| 666 | 56.08983096843325 | -0.667369 | -19.4862 | 0 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 4.751132921999191 | -0.841595 | -23.7918 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 662 | 7.768401599892968 | -0.584179 | -18.1119 | 0 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 663 | 58.02908198439054 | -0.688446 | -18.729 | 0 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 658 | 59.15661133321867 | -0.641073 | -18.6392 | 1 | 19 | 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
-17.585kcal/mol
Ligand efficiency (LE)
-0.5862kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.654
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
485.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.74
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
93.19kcal/mol
Minimised FF energy
79.11kcal/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.