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.
✓ Excellent LE (-0.506 kcal/mol/HA)
✓ Good fit quality (FQ -4.60)
✗ High strain energy (16.9 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-12.659
kcal/mol
LE
-0.506
kcal/mol/HA
Fit Quality
-4.60
FQ (Leeson)
HAC
25
heavy atoms
MW
336
Da
LogP
1.80
cLogP
Interaction summary
Collapsible panels
H-bonds 0
Hydrophobic 19
π–π 2
Clashes 4
Severe clashes 0
| Final rank | 3.0731483326455593 | Score | -12.6591 |
|---|---|---|---|
| Inter norm | -0.528114 | Intra norm | 0.0217518 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 0 |
| Artifact reason | geometry warning; 9 clashes; 4 protein contact clashes; moderate strain Δ 14.8 | ||
| Residues | A:GLY240;A:HIS241;A:LEU188;A:LEU226;A:LEU229;A:LYS244;A:MET233;A:NDP302;A:PHE113;A:TYR191;A:VAL237 | ||
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 | 8 | Native recall | 0.42 |
| Jaccard | 0.36 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 249 | 3.0731483326455593 | -0.528114 | -12.6591 | 0 | 11 | 8 | 0.42 | 0.00 | - | no | Current |
| 248 | 4.102077899534413 | -0.939077 | -21.7958 | 0 | 12 | 12 | 0.63 | 0.00 | - | no | Open |
| 250 | 3.9120085327437453 | -0.674362 | -15.4654 | 0 | 10 | 10 | 0.53 | 0.00 | - | yes | Open |
| 251 | 54.11406331996647 | -0.722211 | -16.8021 | 1 | 11 | 10 | 0.53 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-12.659kcal/mol
Ligand efficiency (LE)
-0.5064kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.603
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
336.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
15.41kcal/mol
Minimised FF energy
-1.53kcal/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.