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 (-1.395 kcal/mol/HA)
✓ Good fit quality (FQ -12.31)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (24.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-32.077
kcal/mol
LE
-1.395
kcal/mol/HA
Fit Quality
-12.31
FQ (Leeson)
HAC
23
heavy atoms
MW
353
Da
LogP
1.43
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 24.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 20
π–π 2
Clashes 7
Severe clashes 0
| Final rank | 3.500720688483656 | Score | -32.0766 |
|---|---|---|---|
| Inter norm | -1.38593 | Intra norm | -0.00870317 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 10 |
| Artifact reason | geometry warning; 6 clashes; 7 protein contact clashes; high strain Δ 31.2 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:GLY157;A:ILE45;A:MET53;A:NDP301;A:PHE56;A:SER44;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49 | ||
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 | 10 | Native recall | 0.50 |
| Jaccard | 0.40 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.57 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2224 | 3.500720688483656 | -1.38593 | -32.0766 | 10 | 15 | 10 | 0.50 | 0.80 | - | no | Current |
| 2860 | 3.72559174762444 | -0.909455 | -21.7366 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2984 | 4.093514725097359 | -1.1536 | -27.6164 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2858 | 4.6588634379915055 | -1.16524 | -26.8762 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1398 | 4.915164110401625 | -0.936024 | -21.449 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1395 | 5.137850874866332 | -0.911847 | -20.8778 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2859 | 5.138729590361963 | -1.04571 | -24.4591 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1396 | 5.877747627516784 | -0.900102 | -20.7012 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1397 | 9.418646113841856 | -0.864953 | -19.8105 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-32.077kcal/mol
Ligand efficiency (LE)
-1.3946kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.309
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
353.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.43
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-28.34kcal/mol
Minimised FF energy
-52.57kcal/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.