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 (-0.472 kcal/mol/HA)
✓ Good fit quality (FQ -4.83)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (33.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-17.451
kcal/mol
LE
-0.472
kcal/mol/HA
Fit Quality
-4.83
FQ (Leeson)
HAC
37
heavy atoms
MW
503
Da
LogP
1.49
cLogP
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 16
π–π 1
Clashes 2
Severe clashes 0
| Final rank | 5.4775496321168635 | Score | -17.4508 |
|---|---|---|---|
| Inter norm | -0.430721 | Intra norm | -0.0409208 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | geometry warning; 14 clashes; 2 protein contact clashes; high strain Δ 46.0 | ||
| Residues | A:ASN402;A:GLU466;A:GLU467;A:HIS461;A:LEU399;A:MET400;A:PHE396;A:PRO398;A:PRO462;A:SER394;A:SER395;A:THR397;A:THR463 | ||
Protein summary
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | 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:264; MET:221 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 2 |
| IFP residues | A:ASN402; A:GLU467; A:LEU399; A:PHE396; A:PRO398; A:SER394; A:SER470; A:THR397 | ||
| Current overlap | 7 | Native recall | 0.88 |
| Jaccard | 0.50 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.50 |
| H-bond same residue+role | 1 | Role recall | 1.00 |
| H-bond same residue | 1 | Residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 818 | 4.334055767654448 | -0.400838 | -15.7838 | 2 | 13 | 6 | 0.75 | 1.00 | - | no | Open |
| 819 | 4.458765365284852 | -0.361306 | -13.4756 | 2 | 14 | 8 | 1.00 | 1.00 | - | no | Open |
| 817 | 4.697065193936815 | -0.386897 | -14.2773 | 2 | 10 | 5 | 0.62 | 1.00 | - | no | Open |
| 806 | 4.895129712041564 | -0.45368 | -17.1294 | 2 | 13 | 7 | 0.88 | 1.00 | - | no | Open |
| 809 | 5.325353534483452 | -0.469172 | -18.392 | 3 | 12 | 7 | 0.88 | 0.00 | - | no | Open |
| 805 | 5.4775496321168635 | -0.430721 | -17.4508 | 3 | 13 | 7 | 0.88 | 1.00 | - | no | Current |
| 804 | 53.67538422447687 | -0.49964 | -15.5715 | 2 | 12 | 7 | 0.88 | 1.00 | - | no | Open |
| 810 | 53.700580361685034 | -0.469246 | -16.4261 | 2 | 12 | 6 | 0.75 | 1.00 | - | no | Open |
| 815 | 53.89692428958918 | -0.383642 | -13.7993 | 2 | 12 | 7 | 0.88 | 0.00 | - | no | Open |
| 814 | 54.03799527984407 | -0.506004 | -15.3056 | 3 | 11 | 7 | 0.88 | 0.00 | - | no | Open |
| 812 | 54.176280369546426 | -0.449082 | -16.9722 | 4 | 10 | 5 | 0.62 | 0.00 | - | no | Open |
| 813 | 54.653517013824256 | -0.404507 | -15.6536 | 3 | 8 | 5 | 0.62 | 0.00 | - | no | Open |
| 811 | 55.06101472748635 | -0.46506 | -14.4093 | 3 | 13 | 6 | 0.75 | 1.00 | - | no | Open |
| 808 | 55.35957025009879 | -0.374323 | -13.5829 | 3 | 11 | 5 | 0.62 | 0.00 | - | no | Open |
| 807 | 55.32786280317548 | -0.579961 | -16.4144 | 3 | 13 | 8 | 1.00 | 0.00 | - | yes | Open |
| 816 | 58.435001912920086 | -0.420743 | -12.1343 | 2 | 15 | 8 | 1.00 | 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
-17.451kcal/mol
Ligand efficiency (LE)
-0.4716kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.829
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
502.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.49
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
158.12kcal/mol
Minimised FF energy
124.45kcal/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.