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.
✓ Excellent LE (-0.494 kcal/mol/HA)
✓ Good fit quality (FQ -5.34)
✗ Very high strain energy (21.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-22.741
kcal/mol
LE
-0.494
kcal/mol/HA
Fit Quality
-5.34
FQ (Leeson)
HAC
46
heavy atoms
MW
643
Da
LogP
5.51
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 21.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 12
Severe clashes 0
| Final rank | 7.5349379991336365 | Score | -22.7408 |
|---|---|---|---|
| Inter norm | -0.54337 | Intra norm | 0.0490057 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 1 |
| Artifact reason | geometry warning; 17 clashes; 12 protein contact clashes; high strain Δ 27.1 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS90;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:TYR162;A:VAL30;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 291 | 6.987083356985705 | -0.620325 | -25.7692 | 0 | 22 | 17 | 0.85 | 0.00 | - | no | Open |
| 294 | 7.5349379991336365 | -0.54337 | -22.7408 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Current |
| 290 | 8.930538036087817 | -0.642406 | -25.1905 | 4 | 22 | 16 | 0.80 | 0.00 | - | yes | Open |
| 295 | 59.67978943418602 | -0.583397 | -22.2193 | 0 | 20 | 15 | 0.75 | 0.00 | - | yes | Open |
| 292 | 59.70766794168428 | -0.546486 | -17.6386 | 2 | 20 | 16 | 0.80 | 0.20 | - | yes | Open |
| 288 | 60.36052805363736 | -0.526021 | -21.7073 | 1 | 19 | 17 | 0.85 | 0.20 | - | yes | Open |
| 293 | 62.48463174387422 | -0.642852 | -20.2797 | 4 | 19 | 16 | 0.80 | 0.20 | - | yes | Open |
| 289 | 63.22056462250745 | -0.597418 | -24.5155 | 3 | 18 | 17 | 0.85 | 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
-22.741kcal/mol
Ligand efficiency (LE)
-0.4944kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.336
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
46HA
Physicochemical properties
Molecular weight
642.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.51
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
109.75kcal/mol
Minimised FF energy
88.48kcal/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.