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 (-0.742 kcal/mol/HA)
✓ Good fit quality (FQ -6.83)
✓ Good H-bonds (3 bonds)
✗ High strain energy (15.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-19.280
kcal/mol
LE
-0.742
kcal/mol/HA
Fit Quality
-6.83
FQ (Leeson)
HAC
26
heavy atoms
MW
349
Da
LogP
2.40
cLogP
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 21
π–π 0
Clashes 2
Severe clashes 0
| Final rank | 3.04881531146618 | Score | -19.2797 |
|---|---|---|---|
| Inter norm | -0.789224 | Intra norm | 0.047696 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | geometry warning; 12 clashes; 2 protein contact clashes; moderate strain Δ 16.8 | ||
| Residues | A:ALA209;A:ALA90;A:ASN208;A:GLY214;A:GLY215;A:LEU73;A:LYS211;A:LYS89;A:MET70;A:PRO212;A:PRO213;A:TYR210;A:VAL88 | ||
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 0 |
| IFP residues | A:ALA90; A:ARG74; A:GLY85; A:LEU73; A:LYS89; A:MET70; A:PHE83; A:PRO212; A:PRO213; A:SER86; A:SER87; A:VAL88 | ||
| Current overlap | 7 | Native recall | 0.58 |
| Jaccard | 0.39 | RMSD | - |
| H-bond strict | 0 | Strict recall | - |
| H-bond same residue+role | 0 | Role recall | - |
| H-bond same residue | 0 | Residue recall | - |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1312 | 3.04881531146618 | -0.789224 | -19.2797 | 3 | 13 | 7 | 0.58 | - | - | no | Current |
| 1324 | 3.335456433991353 | -0.881207 | -21.8722 | 4 | 13 | 7 | 0.58 | - | - | no | Open |
| 1315 | 3.832949461622242 | -0.869764 | -22.5535 | 3 | 14 | 9 | 0.75 | - | - | no | Open |
| 1322 | 3.838562660346953 | -0.825348 | -21.2745 | 4 | 12 | 7 | 0.58 | - | - | no | Open |
| 1318 | 3.964568238201872 | -0.700693 | -18.0911 | 4 | 10 | 5 | 0.42 | - | - | no | Open |
| 1326 | 4.017280272361394 | -0.760736 | -18.8783 | 3 | 13 | 8 | 0.67 | - | - | no | Open |
| 1313 | 53.73537365533876 | -0.780042 | -18.9905 | 3 | 13 | 7 | 0.58 | - | - | no | Open |
| 1320 | 53.92370550138362 | -0.954734 | -23.2526 | 4 | 13 | 7 | 0.58 | - | - | no | Open |
| 1321 | 54.095948950114774 | -0.770125 | -18.4558 | 2 | 13 | 7 | 0.58 | - | - | no | Open |
| 1323 | 54.229993089198935 | -0.738022 | -17.9146 | 3 | 12 | 8 | 0.67 | - | - | no | Open |
| 1316 | 54.24618337723126 | -0.791883 | -19.2566 | 2 | 14 | 8 | 0.67 | - | - | no | Open |
| 1325 | 55.003938327992266 | -0.77134 | -19.0864 | 2 | 13 | 7 | 0.58 | - | - | no | Open |
| 1327 | 55.06958616550822 | -0.752956 | -19.0502 | 2 | 15 | 10 | 0.83 | - | - | no | Open |
| 1314 | 54.23087636810456 | -0.874766 | -22.0134 | 4 | 12 | 7 | 0.58 | - | - | yes | Open |
| 1317 | 55.793383662147505 | -0.757032 | -16.132 | 2 | 14 | 9 | 0.75 | - | - | yes | Open |
| 1319 | 57.66482927389143 | -0.902158 | -21.5772 | 3 | 14 | 8 | 0.67 | - | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.280kcal/mol
Ligand efficiency (LE)
-0.7415kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.832
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
348.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.40
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
109.93kcal/mol
Minimised FF energy
94.38kcal/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.