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.
✓ Acceptable LE (-0.213 kcal/mol/HA)
✓ Good fit quality (FQ -2.21)
✗ Very high strain energy (62.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-8.323
kcal/mol
LE
-0.213
kcal/mol/HA
Fit Quality
-2.21
FQ (Leeson)
HAC
39
heavy atoms
MW
532
Da
LogP
2.70
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: acceptable
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 62.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 1
Clashes 6
Severe clashes 0
| Final rank | 7.684120564277611 | Score | -8.32328 |
|---|---|---|---|
| Inter norm | -0.60545 | Intra norm | 0.392032 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 1 |
| Artifact reason | geometry warning; 17 clashes; 6 protein contact clashes; high strain Δ 58.5 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:THR83;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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 | 17 | Native recall | 0.85 |
| Jaccard | 0.85 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1388 | 4.68952802033076 | -0.564492 | -17.9877 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1390 | 5.274849379505442 | -0.596012 | -24.1528 | 1 | 18 | 13 | 0.65 | 0.20 | - | no | Open |
| 1385 | 5.7412268283381795 | -0.512528 | -17.6993 | 1 | 18 | 18 | 0.90 | 0.00 | - | no | Open |
| 1381 | 6.684190146121919 | -0.639014 | -15.2217 | 1 | 22 | 18 | 0.90 | 0.20 | - | no | Open |
| 1378 | 7.684120564277611 | -0.60545 | -8.32328 | 1 | 17 | 17 | 0.85 | 0.00 | - | no | Current |
| 1377 | 7.739744044672799 | -0.555375 | -16.9937 | 0 | 15 | 9 | 0.45 | 0.00 | - | no | Open |
| 1386 | 55.57043898071594 | -0.447338 | -11.1343 | 0 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 1389 | 55.602770679210764 | -0.59022 | -18.8315 | 2 | 19 | 14 | 0.70 | 0.20 | - | no | Open |
| 1391 | 57.115048411744084 | -0.545699 | -19.7364 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1379 | 57.86080848167939 | -0.595115 | -23.9747 | 1 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1387 | 57.916374462630685 | -0.48925 | -17.1966 | 0 | 17 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1384 | 58.2872372313345 | -0.569596 | -14.9926 | 2 | 19 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1392 | 58.29372298545407 | -0.642506 | -17.8961 | 1 | 22 | 17 | 0.85 | 0.20 | - | yes | Open |
| 1383 | 58.84704384655362 | -0.633 | -18.6424 | 1 | 17 | 12 | 0.60 | 0.20 | - | yes | Open |
| 1380 | 60.15353108448972 | -0.51107 | -5.86865 | 0 | 15 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1382 | 60.373926697166596 | -0.620718 | -23.9187 | 1 | 19 | 16 | 0.80 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-8.323kcal/mol
Ligand efficiency (LE)
-0.2134kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-2.215
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
531.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.70
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
62.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
196.99kcal/mol
Minimised FF energy
134.57kcal/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.