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 (-0.603 kcal/mol/HA)
✓ Good fit quality (FQ -6.22)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (31.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-22.921
kcal/mol
LE
-0.603
kcal/mol/HA
Fit Quality
-6.22
FQ (Leeson)
HAC
38
heavy atoms
MW
516
Da
LogP
3.89
cLogP
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 7
π–π 3
Clashes 9
Severe clashes 0
⚠ Hydrophobic exposure 66%
Solvent-exposed hydrophobic surface — desolvation penalty likely
67% of hydrophobic surface is solvent-exposed (20/30 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) 10
Exposed 20
LogP 3.89
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 6.645777426446846 | Score | -22.9213 |
|---|---|---|---|
| Inter norm | -0.620013 | Intra norm | 0.0168205 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 7 |
| Artifact reason | geometry warning; 15 clashes; 9 protein contact clashes; high strain Δ 36.4 | ||
| Residues | A:ARG137;A:ARG141;A:ASN103;A:HIS102;A:HIS138;B:ARG113;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 | 4 | Strict recall | 0.33 |
| H-bond same residue+role | 4 | Role recall | 0.44 |
| H-bond same residue | 5 | Residue recall | 0.62 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1999 | 5.272708742707004 | -0.688351 | -26.9738 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1476 | 6.533066867450893 | -0.39315 | -12.8034 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1132 | 6.645777426446846 | -0.620013 | -22.9213 | 7 | 16 | 14 | 1.00 | 0.44 | - | no | Current |
| 1230 | 8.251839186234587 | -0.602005 | -20.5177 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1998 | 7.240843304044559 | -0.670693 | -20.9695 | 6 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1475 | 7.963916878157511 | -0.431647 | -16.7481 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1995 | 8.066526640664282 | -0.706716 | -23.0589 | 7 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1130 | 8.127098080349779 | -0.610645 | -25.2427 | 8 | 20 | 14 | 1.00 | 0.44 | - | yes | Open |
| 1996 | 8.171509757207689 | -0.553007 | -22.0349 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2000 | 8.277903328285353 | -0.572823 | -22.6152 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1227 | 8.56226667329796 | -0.60102 | -23.248 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1474 | 9.063358701677405 | -0.477076 | -15.3346 | 6 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1129 | 10.128587189751437 | -0.72436 | -29.9817 | 13 | 12 | 11 | 0.79 | 0.67 | - | yes | Open |
| 1128 | 10.1491345853552 | -0.618335 | -20.9636 | 10 | 17 | 14 | 1.00 | 0.67 | - | yes | Open |
| 1127 | 11.07141744366152 | -0.651016 | -22.819 | 11 | 20 | 13 | 0.93 | 0.22 | - | yes | Open |
| 1229 | 11.944968688966789 | -0.525331 | -24.8187 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1473 | 58.1942443400908 | -0.479533 | -17.9589 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1131 | 59.45831748221258 | -0.724881 | -29.5472 | 15 | 16 | 13 | 0.93 | 0.67 | - | yes | Open |
| 1228 | 60.55726236080507 | -0.469077 | -12.4662 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1997 | 61.51915005467398 | -0.705028 | -25.4746 | 4 | 22 | 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
-22.921kcal/mol
Ligand efficiency (LE)
-0.6032kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.218
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
515.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.89
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
105.27kcal/mol
Minimised FF energy
73.92kcal/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.