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.
✓ Good LE (-0.383 kcal/mol/HA)
✓ Good fit quality (FQ -3.95)
✗ Very high strain energy (29.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-14.563
kcal/mol
LE
-0.383
kcal/mol/HA
Fit Quality
-3.95
FQ (Leeson)
HAC
38
heavy atoms
MW
517
Da
LogP
1.88
cLogP
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 10
π–π 0
Clashes 4
Severe clashes 0
⚠ Hydrophobic exposure 48%
Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (16/33 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 33
Buried (contacted) 17
Exposed 16
LogP 1.88
H-bonds 2
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 55.00743541524278 | Score | -14.5629 |
|---|---|---|---|
| Inter norm | -0.432147 | Intra norm | 0.0489117 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 2 |
| Artifact reason | geometry warning; 20 clashes; 4 protein contact clashes | ||
| Residues | A:GLU466;A:GLU467;A:HIS461;A:LEU399;A:MET393;A:MET400;A:PHE396;A:PRO398;A:SER394;A:SER395;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 | 0.43 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.50 |
| H-bond same residue+role | 1 | Role recall | 1.00 |
| H-bond same residue | 1 | Residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1087 | 4.3225639031029095 | -0.469067 | -15.5351 | 2 | 12 | 6 | 0.75 | 1.00 | - | no | Open |
| 1682 | 4.822428782793232 | -0.574973 | -20.0078 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1086 | 5.101010899152662 | -0.371815 | -12.4097 | 1 | 13 | 7 | 0.88 | 0.00 | - | no | Open |
| 1295 | 5.39625897207715 | -0.573677 | -19.4394 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1081 | 5.58153289922701 | -0.390228 | -16.9009 | 2 | 14 | 6 | 0.75 | 1.00 | - | no | Open |
| 1683 | 6.25042891583922 | -0.632302 | -24.5332 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1681 | 6.668996345435847 | -0.58732 | -20.2461 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1293 | 7.0457761337255125 | -0.617927 | -20.7888 | 0 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 1290 | 8.325171038175231 | -0.602483 | -21.9589 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1088 | 54.635239060174506 | -0.327996 | -12.1045 | 3 | 14 | 6 | 0.75 | 1.00 | - | no | Open |
| 1083 | 54.65827673669226 | -0.398049 | -12.2755 | 3 | 13 | 8 | 1.00 | 0.00 | - | no | Open |
| 1084 | 55.00743541524278 | -0.432147 | -14.5629 | 2 | 12 | 6 | 0.75 | 1.00 | - | no | Current |
| 1082 | 55.03045979470512 | -0.479943 | -17.464 | 2 | 12 | 7 | 0.88 | 0.00 | - | no | Open |
| 1679 | 55.231811450195046 | -0.491455 | -18.9609 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1680 | 55.946621095636715 | -0.494738 | -15.8783 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1677 | 56.948725080742264 | -0.609203 | -20.8517 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1292 | 55.72704045128034 | -0.582274 | -22.0607 | 0 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1085 | 55.89650249869848 | -0.36287 | -11.9186 | 3 | 16 | 8 | 1.00 | 0.00 | - | yes | Open |
| 1678 | 56.04238587597847 | -0.732998 | -25.1507 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1289 | 57.50156813780052 | -0.664958 | -26.7266 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1676 | 57.83556884909578 | -0.588264 | -25.1347 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1296 | 57.85165481072552 | -0.569824 | -17.2283 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1291 | 58.29120286658544 | -0.589616 | -19.5994 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1294 | 60.273316324365645 | -0.58113 | -21.5496 | 1 | 12 | 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
-14.563kcal/mol
Ligand efficiency (LE)
-0.3832kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.951
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
516.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.88
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
157.45kcal/mol
Minimised FF energy
127.64kcal/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.