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 (-0.643 kcal/mol/HA)
✓ Good fit quality (FQ -6.58)
✗ Very high strain energy (40.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.776
kcal/mol
LE
-0.643
kcal/mol/HA
Fit Quality
-6.58
FQ (Leeson)
HAC
37
heavy atoms
MW
503
Da
LogP
1.49
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 40.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 5
Severe clashes 0
| Final rank | 5.995958681595984 | Score | -23.7759 |
|---|---|---|---|
| Inter norm | -0.640473 | Intra norm | -0.0021191 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 1 |
| Artifact reason | geometry warning; 14 clashes; 5 protein contact clashes; high strain Δ 43.5 | ||
| Residues | A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:TRP47;A:TYR162;A:VAL156;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 | 15 | Native recall | 0.75 |
| Jaccard | 0.62 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1302 | 5.824026275734604 | -0.620775 | -23.0327 | 2 | 15 | 11 | 0.55 | 0.00 | - | no | Open |
| 1304 | 5.995958681595984 | -0.640473 | -23.7759 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Current |
| 1298 | 6.319760569503252 | -0.760435 | -24.267 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1303 | 55.54953674524352 | -0.596642 | -18.1975 | 1 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1301 | 55.046259994510585 | -0.59874 | -21.8555 | 0 | 13 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1299 | 56.21022497611001 | -0.582735 | -16.3485 | 1 | 22 | 18 | 0.90 | 0.00 | - | yes | Open |
| 1297 | 57.493125330664355 | -0.599773 | -24.3388 | 1 | 18 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1300 | 58.692113405109595 | -0.559714 | -18.5907 | 1 | 19 | 18 | 0.90 | 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
-23.776kcal/mol
Ligand efficiency (LE)
-0.6426kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.579
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
502.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.49
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
164.40kcal/mol
Minimised FF energy
123.97kcal/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.