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 (-0.745 kcal/mol/HA)
✓ Good fit quality (FQ -7.39)
✗ Very high strain energy (23.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.571
kcal/mol
LE
-0.745
kcal/mol/HA
Fit Quality
-7.39
FQ (Leeson)
HAC
33
heavy atoms
MW
439
Da
LogP
4.29
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 23.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 1
Clashes 7
Severe clashes 0
| Final rank | 4.870780630601103 | Score | -24.5712 |
|---|---|---|---|
| Inter norm | -0.740995 | Intra norm | -0.00358766 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 2 |
| Artifact reason | geometry warning; 13 clashes; 7 protein contact clashes; high strain Δ 22.3 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:THR180;A:THR83;A:TRP47;A:VAL156;A:VAL30;A:VAL31;A:VAL49;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 | 15 | Native recall | 0.75 |
| Jaccard | 0.65 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1873 | 4.870780630601103 | -0.740995 | -24.5712 | 2 | 18 | 15 | 0.75 | 0.00 | - | no | Current |
| 1872 | 5.292901824253982 | -0.731833 | -22.0479 | 2 | 15 | 12 | 0.60 | 0.20 | - | no | Open |
| 1876 | 5.906166646816037 | -0.731787 | -22.1462 | 2 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 1870 | 55.20018696601954 | -0.648743 | -21.9213 | 1 | 13 | 12 | 0.60 | 0.00 | - | yes | Open |
| 1871 | 55.77074305297361 | -0.822958 | -26.8159 | 1 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1869 | 57.159350819689394 | -0.707027 | -20.3832 | 2 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1874 | 58.037954687303284 | -0.749818 | -24.8399 | 1 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1875 | 61.55294066457215 | -0.730887 | -20.5117 | 2 | 20 | 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
-24.571kcal/mol
Ligand efficiency (LE)
-0.7446kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.388
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
438.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.29
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
106.30kcal/mol
Minimised FF energy
82.83kcal/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.