Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
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 (-0.740 kcal/mol/HA)
✓ Good fit quality (FQ -7.62)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (23.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.108
kcal/mol
LE
-0.740
kcal/mol/HA
Fit Quality
-7.62
FQ (Leeson)
HAC
38
heavy atoms
MW
524
Da
LogP
2.79
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 4
Severe clashes 1
| Final rank | 6.565882949078026 | Score | -28.1075 |
|---|---|---|---|
| Inter norm | -0.720195 | Intra norm | -0.0194745 |
| Top1000 | no | Excluded | yes |
| Contacts | 21 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 17 clashes; 1 protein clash; high strain Δ 24.8 | ||
| Residues | A:ALA10;A:ARG29;A:ASP22;A:GLU31;A:GLY21;A:ILE61;A:ILE8;A:LEU23;A:LEU28;A:LEU68;A:NAP201;A:PHE32;A:PHE35;A:PRO27;A:PRO62;A:SER60;A:THR137;A:THR57;A:TYR122;A:VAL116;A:VAL9 | ||
Protein summary
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 5 |
| IFP residues | A:ALA10; A:ASN65; A:ASP22; A:GLN36; A:GLU31; A:GLY117; A:GLY21; A:ILE61; A:ILE8; A:LEU23; A:LEU68; A:NAP201; A:PHE32; A:PHE35; A:PRO62; A:SER60; A:THR137; A:THR57; A:TYR122; A:VAL116; A:VAL9 | ||
| Current overlap | 18 | Native recall | 0.86 |
| Jaccard | 0.75 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.20 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 959 | 6.009302533631635 | -0.719885 | -26.0821 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 2018 | 6.410802487792158 | -0.739335 | -19.3663 | 2 | 20 | 17 | 0.81 | 0.00 | - | no | Open |
| 1495 | 7.99260184067923 | -0.472823 | -21.3694 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2017 | 6.565882949078026 | -0.720195 | -28.1075 | 4 | 21 | 18 | 0.86 | 0.20 | - | yes | Current |
| 2015 | 7.166221328245506 | -0.761462 | -25.3213 | 3 | 19 | 16 | 0.76 | 0.20 | - | yes | Open |
| 2016 | 7.349770094387949 | -0.659327 | -23.1357 | 3 | 18 | 16 | 0.76 | 0.20 | - | yes | Open |
| 2014 | 8.18183828096865 | -0.716883 | -23.8502 | 2 | 19 | 17 | 0.81 | 0.00 | - | yes | Open |
| 1496 | 8.204784729682377 | -0.397949 | -17.1292 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 960 | 10.237651560297277 | -0.582333 | -22.5166 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2019 | 12.945932220706581 | -0.782625 | -21.0419 | 6 | 24 | 19 | 0.90 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.108kcal/mol
Ligand efficiency (LE)
-0.7397kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.625
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
523.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.79
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
129.09kcal/mol
Minimised FF energy
105.80kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.