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 (-2.183 kcal/mol/HA)
✓ Good fit quality (FQ -13.07)
✓ Strong H-bond network (10 bonds)
✗ Moderate strain (7.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-21.834
kcal/mol
LE
-2.183
kcal/mol/HA
Fit Quality
-13.07
FQ (Leeson)
HAC
10
heavy atoms
MW
205
Da
LogP
-0.18
cLogP
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 1
π–π 0
Clashes 7
Severe clashes 0
⚠ Hydrophobic exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (4/4 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 4
Buried (contacted) 0
Exposed 4
LogP -0.18
H-bonds 10
Exposed fragments:
aromatic ring (4/6 atoms exposed)
| Final rank | 1.3286563099559354 | Score | -21.8338 |
|---|---|---|---|
| Inter norm | -2.21009 | Intra norm | 0.0267192 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 10 |
| Artifact reason | geometry warning; 4 clashes; 7 protein contact clashes; moderate strain Δ 15.8 | ||
| Residues | A:ARG337;A:ASP243;A:ASP385;A:GLU384;A:LEU339;A:MET386;A:PHE383;A:PRO338;A:VAL336 | ||
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 | 5 | Native recall | 0.33 |
| Jaccard | 0.26 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 861 | 1.3286563099559354 | -2.21009 | -21.8338 | 10 | 9 | 5 | 0.33 | 0.60 | - | no | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.834kcal/mol
Ligand efficiency (LE)
-2.1834kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.074
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
10HA
Physicochemical properties
Molecular weight
205.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.18
Lipinski: ≤ 5
Rotatable bonds
1
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
53.13kcal/mol
Minimised FF energy
46.13kcal/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.