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 (-0.688 kcal/mol/HA)
✓ Good fit quality (FQ -6.82)
✓ Good H-bonds (4 bonds)
✗ High strain energy (13.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-22.688
kcal/mol
LE
-0.688
kcal/mol/HA
Fit Quality
-6.82
FQ (Leeson)
HAC
33
heavy atoms
MW
452
Da
LogP
4.67
cLogP
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 3
Severe clashes 0
| Final rank | 3.2619614091759104 | Score | -22.6879 |
|---|---|---|---|
| Inter norm | -0.738143 | Intra norm | 0.0506311 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | geometry warning; 11 clashes; 3 protein contact clashes; high strain Δ 22.1 | ||
| Residues | A:ALA10;A:ARG29;A:ASN65;A:GLU31;A:ILE61;A:ILE8;A:LEU23;A:LEU28;A:NAP201;A:PHE32;A:PHE35;A:PRO27;A:PRO62;A:SER60;A:THR137;A:TYR122;A:VAL116;A:VAL9 | ||
Protein summary
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 5 |
| IFP residues | A:ALA10; A:ASN65; A:ASP22; A:GLN36; A:GLU31; A:GLY117; A:GLY21; A:ILE61; A:ILE8; A:LEU23; A:LEU68; A:NAP201; A:PHE32; A:PHE35; A:PRO62; A:SER60; A:THR137; A:THR57; A:TYR122; A:VAL116; A:VAL9 | ||
| Current overlap | 15 | Native recall | 0.71 |
| Jaccard | 0.62 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.20 |
| 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2112 | 3.2619614091759104 | -0.738143 | -22.6879 | 4 | 18 | 15 | 0.71 | 0.20 | - | no | Current |
| 2113 | 3.622513906167073 | -0.733401 | -20.9915 | 6 | 20 | 17 | 0.81 | 0.20 | - | no | Open |
| 1027 | 3.832733786417633 | -0.753355 | -22.1827 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1028 | 8.012306474366065 | -0.684168 | -19.5459 | 2 | 16 | 0 | 0.00 | 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
-22.688kcal/mol
Ligand efficiency (LE)
-0.6875kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.821
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
451.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.67
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
46.18kcal/mol
Minimised FF energy
32.72kcal/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.