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.
✓ Good LE (-0.366 kcal/mol/HA)
✓ Good fit quality (FQ -3.72)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (27.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-13.168
kcal/mol
LE
-0.366
kcal/mol/HA
Fit Quality
-3.72
FQ (Leeson)
HAC
36
heavy atoms
MW
489
Da
LogP
2.94
cLogP
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 3
Clashes 5
Severe clashes 0
| Final rank | 5.623963851674326 | Score | -13.1675 |
|---|---|---|---|
| Inter norm | -0.409045 | Intra norm | 0.0432815 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 3 |
| Artifact reason | geometry warning; 17 clashes; 5 protein contact clashes; high strain Δ 27.5 | ||
| Residues | A:ASN22;A:ASP116;A:GLU18;A:ILE106;A:LEU17;A:LEU26;A:MET113;A:SER109;A:TRP21;A:TYR110 | ||
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 | 0.53 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 820 | 4.963206092452358 | -0.37276 | -13.8638 | 1 | 7 | 7 | 0.54 | - | - | no | Open |
| 825 | 5.092424181054691 | -0.341943 | -11.7908 | 1 | 8 | 8 | 0.62 | - | - | no | Open |
| 821 | 5.623963851674326 | -0.409045 | -13.1675 | 3 | 10 | 8 | 0.62 | - | - | no | Current |
| 823 | 56.17876365373861 | -0.560292 | -18.5485 | 4 | 13 | 8 | 0.62 | - | - | no | Open |
| 826 | 56.648515687516664 | -0.438351 | -14.163 | 3 | 13 | 8 | 0.62 | - | - | yes | Open |
| 824 | 57.23397204518824 | -0.450712 | -14.4692 | 2 | 13 | 7 | 0.54 | - | - | yes | Open |
| 822 | 57.93142326851803 | -0.465842 | -16.4992 | 3 | 14 | 9 | 0.69 | - | - | yes | Open |
| 827 | 58.60962456131719 | -0.561005 | -16.4077 | 4 | 13 | 8 | 0.62 | - | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-13.168kcal/mol
Ligand efficiency (LE)
-0.3658kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.718
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
488.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.94
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
174.54kcal/mol
Minimised FF energy
146.64kcal/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.