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 (-0.853 kcal/mol/HA)
✓ Good fit quality (FQ -7.86)
✓ Good H-bonds (5 bonds)
✗ High strain energy (19.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-22.184
kcal/mol
LE
-0.853
kcal/mol/HA
Fit Quality
-7.86
FQ (Leeson)
HAC
26
heavy atoms
MW
344
Da
LogP
3.80
cLogP
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 16
π–π 3
Clashes 7
Severe clashes 0
| Final rank | 5.083538880826211 | Score | -22.1843 |
|---|---|---|---|
| Inter norm | -0.648994 | Intra norm | -0.204247 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 15 clashes; 7 protein contact clashes; moderate strain Δ 19.9 | ||
| Residues | A:ASN402;A:GLU466;A:GLU467;A:HIS461;A:LEU399;A:PHE396;A:PRO398;A:PRO462;A:SER394;A:SER395;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 | 7 | Native recall | 0.88 |
| Jaccard | 0.54 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2258 | 4.432800924488171 | -0.535128 | -19.4395 | 5 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 2257 | 4.835953911856199 | -0.744747 | -19.5352 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2418 | 4.880178323318226 | -0.53481 | -16.8962 | 3 | 10 | 8 | 1.00 | 0.00 | - | no | Open |
| 2422 | 5.083538880826211 | -0.648994 | -22.1843 | 5 | 12 | 7 | 0.88 | 0.00 | - | no | Current |
| 2414 | 5.111839317552878 | -0.724754 | -21.3757 | 5 | 12 | 7 | 0.88 | 0.00 | - | no | Open |
| 2262 | 5.269524950228686 | -0.519459 | -17.7185 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2420 | 5.484780132869905 | -0.583976 | -18.8854 | 4 | 11 | 7 | 0.88 | 0.00 | - | no | Open |
| 2263 | 5.700764560190182 | -0.585764 | -12.6616 | 3 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 2423 | 5.977953095303983 | -0.51653 | -10.2878 | 4 | 9 | 6 | 0.75 | 0.00 | - | no | Open |
| 2416 | 5.521791695792289 | -0.621012 | -21.9887 | 4 | 8 | 7 | 0.88 | 0.00 | - | yes | Open |
| 2419 | 5.594801201247525 | -0.590564 | -13.9392 | 3 | 13 | 8 | 1.00 | 0.00 | - | yes | Open |
| 2261 | 5.62039704457523 | -0.797512 | -19.6201 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2415 | 6.120347422726654 | -0.674279 | -15.7188 | 3 | 13 | 8 | 1.00 | 0.00 | - | yes | Open |
| 2424 | 6.7205022423280765 | -0.725098 | -24.6134 | 5 | 11 | 7 | 0.88 | 0.00 | - | yes | Open |
| 2255 | 7.208832376833763 | -0.633863 | -12.6031 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2259 | 7.5292507820024985 | -0.549638 | -12.3161 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2264 | 8.646106306293484 | -0.609641 | -19.9337 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2256 | 9.651344200099961 | -0.852122 | -18.7429 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2417 | 56.04513878602127 | -0.717115 | -23.5487 | 5 | 12 | 7 | 0.88 | 0.00 | - | yes | Open |
| 2421 | 56.32837484254128 | -0.608588 | -24.2175 | 4 | 12 | 7 | 0.88 | 0.00 | - | yes | Open |
| 2425 | 56.46456058031302 | -0.694483 | -24.6973 | 5 | 12 | 7 | 0.88 | 0.00 | - | yes | Open |
| 2265 | 57.1115727236319 | -0.664429 | -16.337 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2254 | 58.505358458890775 | -0.549167 | -18.9903 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2260 | 58.95205146539992 | -0.723753 | -20.0449 | 3 | 14 | 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
-22.184kcal/mol
Ligand efficiency (LE)
-0.8532kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.861
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
105.70kcal/mol
Minimised FF energy
86.16kcal/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.