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 (-0.935 kcal/mol/HA)
✓ Good fit quality (FQ -8.12)
✓ Good H-bonds (3 bonds)
✗ High strain energy (12.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.566
kcal/mol
LE
-0.935
kcal/mol/HA
Fit Quality
-8.12
FQ (Leeson)
HAC
22
heavy atoms
MW
308
Da
LogP
3.18
cLogP
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 22
π–π 0
Clashes 8
Severe clashes 0
| Final rank | 3.927650825543325 | Score | -20.5655 |
|---|---|---|---|
| Inter norm | -0.993653 | Intra norm | 0.0588583 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 3 |
| Artifact reason | geometry warning; 10 clashes; 8 protein contact clashes; moderate strain Δ 14.0 | ||
| Residues | A:ARG342;A:CYS26;A:GLN341;A:GLU343;A:GLU348;A:LEU339;A:LEU350;A:LEU382;A:PRO340;A:PRO344;A:PRO373 | ||
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 7 |
| IFP residues | A:ARG22; A:ARG242; A:ARG337; A:ARG342; A:ASP243; A:ASP385; A:GLN341; A:GLU384; A:LEU25; A:LEU339; A:LEU382; A:PRO340; A:PRO344; A:SER282; A:THR241 | ||
| Current overlap | 6 | Native recall | 0.40 |
| Jaccard | 0.30 | 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
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2747 | 3.927650825543325 | -0.993653 | -20.5655 | 3 | 11 | 6 | 0.40 | 0.20 | - | no | Current |
| 2746 | 4.5702575415015545 | -0.961315 | -19.4994 | 5 | 13 | 8 | 0.53 | 0.20 | - | no | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.566kcal/mol
Ligand efficiency (LE)
-0.9348kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.116
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
308.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.18
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.51kcal/mol
Minimised FF energy
42.32kcal/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.