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 (-0.990 kcal/mol/HA)
✓ Good fit quality (FQ -9.00)
✗ High strain energy (16.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.741
kcal/mol
LE
-0.990
kcal/mol/HA
Fit Quality
-9.00
FQ (Leeson)
HAC
25
heavy atoms
MW
348
Da
LogP
4.71
cLogP
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 20
π–π 3
Clashes 4
Severe clashes 0
| Final rank | 2.91362615658808 | Score | -24.7414 |
|---|---|---|---|
| Inter norm | -0.963719 | Intra norm | -0.0259356 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 1 |
| Artifact reason | geometry warning; 10 clashes; 4 protein contact clashes; moderate strain Δ 16.3 | ||
| Residues | A:ARG17;A:HIS241;A:LEU188;A:LEU226;A:LEU229;A:NDP302;A:PHE113;A:PRO115;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 | 11 | Native recall | 0.58 |
| Jaccard | 0.58 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 260 | 2.91362615658808 | -0.963719 | -24.7414 | 1 | 11 | 11 | 0.58 | 0.20 | - | no | Current |
| 259 | 3.128417788719187 | -0.836556 | -18.904 | 1 | 13 | 12 | 0.63 | 0.00 | - | no | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.741kcal/mol
Ligand efficiency (LE)
-0.9897kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.997
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
348.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.71
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
38.67kcal/mol
Minimised FF energy
22.40kcal/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.