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 (-0.542 kcal/mol/HA)
✓ Good fit quality (FQ -5.28)
✓ Strong H-bond network (9 bonds)
✗ High strain energy (19.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-16.793
kcal/mol
LE
-0.542
kcal/mol/HA
Fit Quality
-5.28
FQ (Leeson)
HAC
31
heavy atoms
MW
418
Da
LogP
4.87
cLogP
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 4
π–π 3
Clashes 6
Severe clashes 0
⚠ Hydrophobic exposure 52%
Partial hydrophobic solvent exposure
52% of hydrophobic surface appears solvent-exposed (13/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 12
Exposed 13
LogP 4.87
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (7 atoms exposed)
| Final rank | 4.970431183587568 | Score | -16.7932 |
|---|---|---|---|
| Inter norm | -0.587359 | Intra norm | 0.0456417 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 9 |
| Artifact reason | geometry warning; 14 clashes; 6 protein contact clashes; high strain Δ 23.1 | ||
| Residues | A:ARG137;A:ARG141;A:ASN103;A:HIS102;A:MET98;A:TYR94;B:ARG113;B:ASP10;B:CYS69;B:GLY70;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 | 13 | Native recall | 0.93 |
| Jaccard | 0.76 | RMSD | - |
| H-bond strict | 5 | Strict recall | 0.42 |
| H-bond same residue+role | 5 | Role recall | 0.56 |
| H-bond same residue | 4 | Residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2603 | 4.970431183587568 | -0.587359 | -16.7932 | 9 | 16 | 13 | 0.93 | 0.56 | - | no | Current |
| 2459 | 5.283698177054297 | -0.568492 | -19.7534 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 2064 | 7.323797290416142 | -0.810191 | -30.4895 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2060 | 7.4413794267973445 | -0.805549 | -24.7691 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2598 | 6.057633307738709 | -0.76343 | -21.2631 | 5 | 17 | 13 | 0.93 | 0.44 | - | yes | Open |
| 2065 | 6.480752843876996 | -0.798298 | -24.4765 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2602 | 6.779895029604055 | -0.720747 | -22.7613 | 8 | 17 | 13 | 0.93 | 0.56 | - | yes | Open |
| 2461 | 6.906583323998046 | -0.577292 | -18.023 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2462 | 6.955028032851434 | -0.49098 | -15.2632 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2601 | 7.153191856958005 | -0.605953 | -19.4329 | 7 | 15 | 12 | 0.86 | 0.56 | - | yes | Open |
| 2599 | 7.307388460417495 | -0.650187 | -21.9386 | 10 | 16 | 12 | 0.86 | 0.56 | - | yes | Open |
| 2463 | 7.593777531084623 | -0.462227 | -13.502 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2062 | 7.623365461212505 | -0.689706 | -20.3921 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2063 | 8.06591193248797 | -0.812272 | -28.593 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2600 | 8.846237669105472 | -0.570156 | -15.7378 | 7 | 13 | 12 | 0.86 | 0.56 | - | yes | Open |
| 2460 | 8.997477115010753 | -0.46383 | -13.2881 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2059 | 9.123046795785138 | -0.794823 | -18.14 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2061 | 9.741765202331994 | -0.676692 | -19.0511 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2458 | 10.051436411354386 | -0.589233 | -12.4988 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2066 | 12.229632591397024 | -0.717067 | -22.6047 | 7 | 19 | 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
-16.793kcal/mol
Ligand efficiency (LE)
-0.5417kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.278
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
418.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.87
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.72kcal/mol
Minimised FF energy
85.63kcal/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.