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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.721 kcal/mol/HA)
✓ Good fit quality (FQ -16.92)
✓ Strong H-bond network (6 bonds)
✗ High strain energy (16.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-55.068
kcal/mol
LE
-1.721
kcal/mol/HA
Fit Quality
-16.92
FQ (Leeson)
HAC
32
heavy atoms
MW
472
Da
LogP
3.88
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 16.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 1
Clashes 10
Severe clashes 1
| Final rank | 6.356233933602512 | Score | -55.0677 |
|---|---|---|---|
| Inter norm | -0.86598 | Intra norm | -0.854885 |
| Top1000 | no | Excluded | yes |
| Contacts | 19 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 10 clashes; 1 protein clash; very favorable intra outlier; moderate strain Δ 17.1 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PRO88;A:SER44;A:SER86;A:THR83;A:TRP47;A:TRP84;A:TYR162;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 | 14 | Native recall | 0.70 |
| Jaccard | 0.56 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 492 | 6.338660869457627 | -0.733929 | -40.2547 | 4 | 17 | 16 | 0.80 | 0.20 | - | no | Open |
| 493 | 6.356233933602512 | -0.86598 | -55.0677 | 6 | 19 | 14 | 0.70 | 0.20 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-55.068kcal/mol
Ligand efficiency (LE)
-1.7209kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-16.923
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
472.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.88
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
79.75kcal/mol
Minimised FF energy
63.37kcal/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.