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 (-1.467 kcal/mol/HA)
✓ Good fit quality (FQ -14.42)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (41.2 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-46.935
kcal/mol
LE
-1.467
kcal/mol/HA
Fit Quality
-14.42
FQ (Leeson)
HAC
32
heavy atoms
MW
451
Da
LogP
2.85
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 41.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 23
π–π 1
Clashes 12
Severe clashes 1
| Final rank | 9.770680662005356 | Score | -46.9355 |
|---|---|---|---|
| Inter norm | -0.684021 | Intra norm | -0.782714 |
| Top1000 | no | Excluded | yes |
| Contacts | 12 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 16 clashes; 1 protein clash; very favorable intra outlier; high strain Δ 42.8 | ||
| Residues | A:ARG97;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER86;A:THR83;A:VAL156;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 | 12 | Native recall | 0.60 |
| Jaccard | 0.60 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2623 | 6.764724992111834 | -0.680076 | -37.4835 | 2 | 10 | 10 | 0.50 | 0.20 | - | no | Open |
| 2622 | 7.231108370367019 | -0.811632 | -48.1538 | 1 | 19 | 18 | 0.90 | 0.20 | - | yes | Open |
| 2625 | 9.770680662005356 | -0.684021 | -46.9355 | 4 | 12 | 12 | 0.60 | 0.20 | - | yes | Current |
| 2624 | 12.241838564743356 | -0.74881 | -49.6017 | 4 | 15 | 11 | 0.55 | 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
-46.935kcal/mol
Ligand efficiency (LE)
-1.4667kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-14.424
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
450.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.85
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
41.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
153.21kcal/mol
Minimised FF energy
112.05kcal/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.