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 (-1.151 kcal/mol/HA)
✓ Good fit quality (FQ -9.43)
✗ Moderate strain (8.0 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-21.866
kcal/mol
LE
-1.151
kcal/mol/HA
Fit Quality
-9.43
FQ (Leeson)
HAC
19
heavy atoms
MW
268
Da
LogP
3.48
cLogP
Interaction summary
Collapsible panels
H-bonds 0
Hydrophobic 18
π–π 3
Clashes 7
Severe clashes 0
| Final rank | 2.682053947476713 | Score | -21.8656 |
|---|---|---|---|
| Inter norm | -1.1891 | Intra norm | 0.0382818 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 0 |
| Artifact reason | geometry warning; 7 clashes; 7 protein contact clashes | ||
| Residues | A:ARG17;A:HIS241;A:LEU188;A:LEU226;A:LEU229;A:NDP302;A:PHE113;A:TYR191;A:TYR194;D:ARG287 | ||
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 8 |
| IFP residues | A:ARG17; A:ASP181; A:GLY225; A:HIS241; A:LEU188; A:LEU226; A:LEU229; A:LYS198; A:MET233; A:NDP302; A:PHE113; A:PRO115; A:SER111; A:SER112; A:SER227; A:TYR191; A:TYR194; A:VAL230; D:ARG287 | ||
| Current overlap | 10 | Native recall | 0.53 |
| Jaccard | 0.53 | 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
No hydrogen bonds detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1158 | 2.682053947476713 | -1.1891 | -21.8656 | 0 | 10 | 10 | 0.53 | 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
-21.866kcal/mol
Ligand efficiency (LE)
-1.1508kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.433
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
268.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.48
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
34.51kcal/mol
Minimised FF energy
26.55kcal/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.