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 (-0.710 kcal/mol/HA)
✓ Good fit quality (FQ -6.70)
✓ Strong H-bond network (11 bonds)
✗ Very high strain energy (55.9 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-19.875
kcal/mol
LE
-0.710
kcal/mol/HA
Fit Quality
-6.70
FQ (Leeson)
HAC
28
heavy atoms
MW
441
Da
LogP
-1.19
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 55.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 11
Hydrophobic 12
π–π 0
Clashes 18
Severe clashes 4
| Final rank | 13.996627871910981 | Score | -19.8747 |
|---|---|---|---|
| Inter norm | -1.02988 | Intra norm | 0.320065 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 11 |
| Artifact reason | excluded; geometry warning; 6 clashes; 4 protein clashes; high strain Δ 65.7 | ||
| Residues | A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:PHE56;A:PHE91;A:PRO50;A:PRO88;A:SER44;A:SER86;A:TRP47;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 | 11 | Native recall | 0.55 |
| Jaccard | 0.44 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| 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
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 317 | 6.365406276728072 | -1.03371 | -23.4084 | 12 | 20 | 18 | 0.90 | 0.80 | - | no | Open |
| 315 | 8.504820642863493 | -0.836689 | -17.569 | 5 | 18 | 13 | 0.65 | 0.40 | - | no | Open |
| 318 | 11.48936191913787 | -0.897955 | -26.7006 | 10 | 15 | 11 | 0.55 | 0.40 | - | yes | Open |
| 316 | 13.996627871910981 | -1.02988 | -19.8747 | 11 | 16 | 11 | 0.55 | 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
-19.875kcal/mol
Ligand efficiency (LE)
-0.7098kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.701
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
441.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.19
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
55.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
141.63kcal/mol
Minimised FF energy
85.77kcal/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.