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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.315 kcal/mol/HA)
✓ Good fit quality (FQ -3.20)
✗ Very high strain energy (40.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-11.330
kcal/mol
LE
-0.315
kcal/mol/HA
Fit Quality
-3.20
FQ (Leeson)
HAC
36
heavy atoms
MW
506
Da
LogP
2.56
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: good
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 40.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 16
Severe clashes 0
| Final rank | 9.708161019973174 | Score | -11.3302 |
|---|---|---|---|
| Inter norm | -0.492226 | Intra norm | 0.177497 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | geometry warning; 17 clashes; 16 protein contact clashes; high strain Δ 43.4 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:THR54;A:VAL156;A:VAL31;A:VAL87 | ||
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87 | ||
| Current overlap | 14 | Native recall | 0.70 |
| Jaccard | 0.64 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1528 | 6.378080916858648 | -0.56479 | -13.3664 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2305 | 7.343917661175478 | -0.683686 | -19.3219 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2304 | 7.698174361578024 | -0.714945 | -24.2064 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1529 | 8.376889525512386 | -0.644003 | -18.1525 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2367 | 9.708161019973174 | -0.492226 | -11.3302 | 1 | 16 | 14 | 0.70 | 0.00 | - | no | Current |
| 2302 | 8.785760800257554 | -0.683335 | -15.2685 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2303 | 12.730687880831763 | -0.685248 | -19.4612 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2366 | 13.927079266018765 | -0.756766 | -14.0764 | 6 | 17 | 14 | 0.70 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-11.330kcal/mol
Ligand efficiency (LE)
-0.3147kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.199
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
506.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.56
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
164.54kcal/mol
Minimised FF energy
123.70kcal/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.