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 (-1.085 kcal/mol/HA)
✓ Good fit quality (FQ -9.42)
✓ Strong H-bond network (6 bonds)
✗ Moderate strain (9.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.862
kcal/mol
LE
-1.085
kcal/mol/HA
Fit Quality
-9.42
FQ (Leeson)
HAC
22
heavy atoms
MW
290
Da
LogP
3.50
cLogP
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 9
π–π 3
Clashes 9
Severe clashes 0
| Final rank | 4.692703081182206 | Score | -23.8616 |
|---|---|---|---|
| Inter norm | -1.08745 | Intra norm | 0.00282913 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | geometry warning; 14 clashes; 9 protein contact clashes | ||
| Residues | A:ARG137;A:ARG141;A:ASN103;A:HIS102;A:HIS138;A:MET98;B:ASP10;B:CYS69;B:GLY70;B:GLY72;B:GLY74;B:HIS11;B:ILE73;B:PRO12;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 | 0.88 | RMSD | - |
| H-bond strict | 5 | Strict recall | 0.42 |
| H-bond same residue+role | 4 | Role recall | 0.44 |
| H-bond same residue | 3 | Residue recall | 0.38 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2657 | 4.692703081182206 | -1.08745 | -23.8616 | 6 | 16 | 14 | 1.00 | 0.44 | - | no | Current |
| 2658 | 5.282468483519297 | -0.775554 | -16.497 | 6 | 16 | 14 | 1.00 | 0.44 | - | no | Open |
| 2659 | 6.405454109137181 | -1.0858 | -22.919 | 6 | 15 | 13 | 0.93 | 0.44 | - | yes | Open |
| 2661 | 6.677347583907631 | -0.810838 | -17.3014 | 2 | 14 | 12 | 0.86 | 0.11 | - | yes | Open |
| 2660 | 6.910905723342648 | -1.09613 | -22.2418 | 7 | 15 | 13 | 0.93 | 0.44 | - | yes | Open |
| 2662 | 9.0769536200721 | -0.799858 | -16.7066 | 2 | 14 | 12 | 0.86 | 0.11 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.862kcal/mol
Ligand efficiency (LE)
-1.0846kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.417
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
290.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.50
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.18kcal/mol
Minimised FF energy
57.05kcal/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.