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 (-0.547 kcal/mol/HA)
✓ Good fit quality (FQ -5.64)
✓ Strong H-bond network (11 bonds)
✗ Very high strain energy (28.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.793
kcal/mol
LE
-0.547
kcal/mol/HA
Fit Quality
-5.64
FQ (Leeson)
HAC
38
heavy atoms
MW
515
Da
LogP
5.18
cLogP
Interaction summary
Collapsible panels
H-bonds 11
Hydrophobic 8
π–π 5
Clashes 11
Severe clashes 0
⚠ Hydrophobic exposure 73%
Solvent-exposed hydrophobic surface — desolvation penalty likely
73% of hydrophobic surface is solvent-exposed (22/30 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 30
Buried (contacted) 8
Exposed 22
LogP 5.18
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (8 atoms exposed)
| Final rank | 7.080947801614865 | Score | -20.7934 |
|---|---|---|---|
| Inter norm | -0.653011 | Intra norm | 0.105784 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 11 |
| Artifact reason | geometry warning; 16 clashes; 11 protein contact clashes; high strain Δ 31.1 | ||
| Residues | A:ARG137;A:ARG141;A:ASN103;A:GLU135;A:HIS102;A:HIS138;B:ASP10;B:CYS69;B:GLY70;B:GLY72;B:GLY74;B:HIS11;B:ILE73;B:MET75;B:PRO12;B:SER43;B:SER71;B:TYR46 | ||
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 16 |
| IFP residues | A:ARG137; A:ARG141; A:ASN103; A:HIS102; A:HIS138; B:ASP10; B:CYS69; B:GLY70; B:GLY74; B:HIS11; B:ILE73; B:PRO12; B:SER71; B:TYR46 | ||
| Current overlap | 14 | Native recall | 1.00 |
| Jaccard | 0.78 | RMSD | - |
| H-bond strict | 5 | Strict recall | 0.42 |
| H-bond same residue+role | 5 | Role recall | 0.56 |
| H-bond same residue | 6 | Residue recall | 0.75 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1121 | 7.080947801614865 | -0.653011 | -20.7934 | 11 | 18 | 14 | 1.00 | 0.56 | - | no | Current |
| 1123 | 9.05230394188456 | -0.696447 | -24.4191 | 8 | 17 | 13 | 0.93 | 0.44 | - | yes | Open |
| 1124 | 9.460327742504987 | -0.744518 | -23.7371 | 10 | 16 | 12 | 0.86 | 0.44 | - | yes | Open |
| 1125 | 11.873513211532213 | -0.691513 | -20.794 | 16 | 17 | 13 | 0.93 | 0.56 | - | yes | Open |
| 1122 | 12.141008849809587 | -0.706585 | -24.8159 | 10 | 19 | 13 | 0.93 | 0.44 | - | yes | Open |
| 1126 | 60.6005421409685 | -0.611816 | -19.7613 | 9 | 12 | 9 | 0.64 | 0.33 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.793kcal/mol
Ligand efficiency (LE)
-0.5472kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.641
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
514.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.18
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
134.72kcal/mol
Minimised FF energy
106.56kcal/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.