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 (-0.901 kcal/mol/HA)
✓ Good fit quality (FQ -7.96)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (21.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.735
kcal/mol
LE
-0.901
kcal/mol/HA
Fit Quality
-7.96
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
0.77
cLogP
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 15
π–π 3
Clashes 4
Severe clashes 0
| Final rank | 3.0588603925441076 | Score | -20.7354 |
|---|---|---|---|
| Inter norm | -0.93956 | Intra norm | 0.0380196 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 8 |
| Artifact reason | geometry warning; 8 clashes; 4 protein contact clashes; high strain Δ 25.5 | ||
| Residues | A:CYS52;A:GLU18;A:GLY15;A:ILE339;A:LEU17;A:MET113;A:SER109;A:SER14;A:THR335;A:TRP21;A:TYR110;A:VAL53 | ||
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| Residues | 493 | 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:276; MET:221 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 0 |
| IFP residues | A:ASP116; A:GLU18; A:GLY112; A:ILE106; A:LEU17; A:MET113; A:SER109; A:THR117; A:THR335; A:TRP21; A:TYR110; A:VAL53; A:VAL58 | ||
| Current overlap | 8 | Native recall | 0.62 |
| Jaccard | 0.47 | RMSD | - |
| H-bond strict | 0 | Strict recall | - |
| H-bond same residue+role | 0 | Role recall | - |
| H-bond same residue | 0 | Residue recall | - |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1358 | 3.0588603925441076 | -0.93956 | -20.7354 | 8 | 12 | 8 | 0.62 | - | - | no | Current |
| 915 | 3.5282542162681754 | -1.01031 | -20.3141 | 9 | 17 | 0 | 0.00 | - | - | no | Open |
| 2840 | 3.566179044751922 | -1.19433 | -22.7362 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 1359 | 3.9615194275940198 | -0.91671 | -17.8619 | 7 | 11 | 8 | 0.62 | - | - | no | Open |
| 2841 | 7.315252830580894 | -1.13265 | -23.7345 | 9 | 16 | 0 | 0.00 | - | - | yes | Open |
| 914 | 12.242555487950165 | -1.17325 | -22.5326 | 11 | 17 | 0 | 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
-20.735kcal/mol
Ligand efficiency (LE)
-0.9015kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.957
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.77
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-2.59kcal/mol
Minimised FF energy
-23.61kcal/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.