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 (-0.386 kcal/mol/HA)
✓ Good fit quality (FQ -3.95)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (37.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-14.278
kcal/mol
LE
-0.386
kcal/mol/HA
Fit Quality
-3.95
FQ (Leeson)
HAC
37
heavy atoms
MW
503
Da
LogP
1.88
cLogP
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 12
π–π 1
Clashes 4
Severe clashes 0
| Final rank | 6.801132598817804 | Score | -14.278 |
|---|---|---|---|
| Inter norm | -0.42519 | Intra norm | 0.0392969 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | geometry warning; 20 clashes; 4 protein contact clashes; high strain Δ 41.9 | ||
| Residues | A:GLU466;A:GLU467;A:HIS461;A:LEU399;A:MET393;A:MET400;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 | 6 | Native recall | 0.75 |
| Jaccard | 0.38 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1072 | 5.959432675645626 | -0.340547 | -13.2017 | 3 | 7 | 5 | 0.62 | 0.00 | - | no | Open |
| 1256 | 5.964710959533734 | -0.632258 | -18.974 | 0 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 1064 | 6.001771173684105 | -0.412686 | -8.99484 | 2 | 10 | 6 | 0.75 | 0.00 | - | no | Open |
| 1255 | 6.1959168401841325 | -0.659472 | -21.2447 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1057 | 6.346866392093182 | -0.41867 | -12.1947 | 4 | 14 | 6 | 0.75 | 1.00 | - | no | Open |
| 1263 | 6.60231951508549 | -0.683509 | -25.6179 | 1 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1059 | 6.801132598817804 | -0.42519 | -14.278 | 3 | 14 | 6 | 0.75 | 1.00 | - | no | Current |
| 1254 | 6.867978178876968 | -0.604759 | -20.4945 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1260 | 7.197183510839782 | -0.683727 | -23.4348 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1253 | 54.41658892825658 | -0.644899 | -19.8124 | 0 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1060 | 55.306999765854236 | -0.40253 | -12.7252 | 3 | 12 | 7 | 0.88 | 0.00 | - | no | Open |
| 1250 | 55.6580625884546 | -0.708155 | -20.1601 | 1 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1259 | 7.038530585043578 | -0.638988 | -20.4351 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1066 | 7.327863811853032 | -0.56779 | -20.2954 | 4 | 11 | 7 | 0.88 | 0.00 | - | yes | Open |
| 1069 | 7.340473730425458 | -0.444895 | -16.0066 | 4 | 11 | 6 | 0.75 | 0.00 | - | yes | Open |
| 1062 | 55.734685661358725 | -0.381212 | -15.1797 | 3 | 10 | 4 | 0.50 | 1.00 | - | yes | Open |
| 1252 | 55.974526153907696 | -0.608194 | -20.807 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1251 | 56.7005535894911 | -0.609644 | -24.1202 | 0 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1071 | 56.852117895408774 | -0.5053 | -14.5879 | 3 | 10 | 7 | 0.88 | 0.00 | - | yes | Open |
| 1070 | 56.902392631427915 | -0.427454 | -12.5198 | 3 | 9 | 6 | 0.75 | 0.00 | - | yes | Open |
| 1058 | 57.053999238947455 | -0.531407 | -16.739 | 3 | 10 | 7 | 0.88 | 0.00 | - | yes | Open |
| 1063 | 57.27490441539605 | -0.52151 | -16.4534 | 2 | 11 | 7 | 0.88 | 0.00 | - | yes | Open |
| 1065 | 57.402135370428766 | -0.395583 | -16.195 | 3 | 12 | 6 | 0.75 | 0.00 | - | yes | Open |
| 1262 | 57.40752138557653 | -0.566931 | -14.0268 | 1 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1068 | 57.47314862622848 | -0.582036 | -20.6788 | 3 | 10 | 7 | 0.88 | 0.00 | - | yes | Open |
| 1067 | 57.54216830387588 | -0.498979 | -16.8833 | 4 | 9 | 5 | 0.62 | 0.00 | - | yes | Open |
| 1249 | 57.60690076970691 | -0.621821 | -21.5933 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1258 | 57.7510495364424 | -0.763052 | -26.8159 | 1 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1261 | 58.140804665646584 | -0.620636 | -19.3397 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1061 | 58.444331624613994 | -0.374921 | -12.67 | 3 | 11 | 7 | 0.88 | 0.00 | - | yes | Open |
| 1257 | 58.58113556517499 | -0.59477 | -21.6424 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1264 | 58.7524435649665 | -0.781797 | -26.637 | 2 | 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
-14.278kcal/mol
Ligand efficiency (LE)
-0.3859kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.951
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
502.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.88
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
149.06kcal/mol
Minimised FF energy
111.81kcal/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.