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 (-0.842 kcal/mol/HA)
✓ Good fit quality (FQ -7.95)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (31.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-23.567
kcal/mol
LE
-0.842
kcal/mol/HA
Fit Quality
-7.95
FQ (Leeson)
HAC
28
heavy atoms
MW
462
Da
LogP
3.91
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 31.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 3
Clashes 14
Severe clashes 1
| Final rank | 8.908880953336688 | Score | -23.5667 |
|---|---|---|---|
| Inter norm | -0.938985 | Intra norm | 0.0973169 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 13 clashes; 1 protein clash; high strain Δ 36.3 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:GLY157;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:THR180;A:THR83;A:TYR162;A:VAL156;A:VAL30;A:VAL31 | ||
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 | 0.73 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.43 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1345 | 4.907822553657604 | -0.795764 | -20.3634 | 0 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1344 | 4.922488778414525 | -0.708949 | -18.8397 | 0 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1885 | 5.096041750193326 | -0.908136 | -23.753 | 3 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 2759 | 5.976471539373534 | -0.896591 | -22.0726 | 3 | 18 | 17 | 0.85 | 0.20 | - | no | Open |
| 1719 | 6.1595454428874366 | -0.760538 | -19.4391 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1720 | 6.421137510019689 | -0.804011 | -18.6356 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1886 | 6.930408349349774 | -0.817571 | -20.2028 | 4 | 12 | 1 | 0.05 | 0.00 | - | no | Open |
| 2758 | 8.908880953336688 | -0.938985 | -23.5667 | 4 | 18 | 16 | 0.80 | 0.40 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.567kcal/mol
Ligand efficiency (LE)
-0.8417kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.946
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
462.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.91
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.54kcal/mol
Minimised FF energy
24.21kcal/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.