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 (-0.980 kcal/mol/HA)
✓ Good fit quality (FQ -9.35)
✗ Very high strain energy (39.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.408
kcal/mol
LE
-0.980
kcal/mol/HA
Fit Quality
-9.35
FQ (Leeson)
HAC
29
heavy atoms
MW
409
Da
LogP
3.65
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 39.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 1
Clashes 4
Severe clashes 0
| Final rank | 4.547267273473343 | Score | -28.4082 |
|---|---|---|---|
| Inter norm | -0.975299 | Intra norm | -0.00429472 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 1 |
| Artifact reason | geometry warning; 10 clashes; 4 protein contact clashes; high strain Δ 43.4 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:MET79;A:NDP301;A:PHE56;A:PHE91;A:THR180;A:THR83;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.76 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2 | 3.3251036420755127 | -0.906528 | -29.5088 | 1 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 1 | 4.141406995109392 | -1.08314 | -31.611 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 4.264027414218005 | -0.68424 | -20.1382 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2 | 4.296770971904215 | -0.883123 | -25.7635 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 4.547267273473343 | -0.975299 | -28.4082 | 1 | 17 | 16 | 0.80 | 0.20 | - | no | Current |
| 1 | 4.564811526341932 | -0.743299 | -21.2749 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 4.605424146963149 | -1.05236 | -29.5551 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 5.264422702240426 | -0.938475 | -27.9713 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 5.394435682618549 | -0.875528 | -26.8438 | 2 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 2 | 5.790928348698166 | -0.691287 | -17.0459 | 3 | 13 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2 | 6.671495795077168 | -0.710854 | -21.2765 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2 | 6.748914709704543 | -0.989913 | -25.1312 | 4 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2 | 8.579256814021038 | -1.17383 | -32.9705 | 9 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2 | 11.678464002473296 | -0.829796 | -25.0241 | 4 | 13 | 11 | 0.55 | 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
-28.408kcal/mol
Ligand efficiency (LE)
-0.9796kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.351
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
408.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.65
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
90.31kcal/mol
Minimised FF energy
50.38kcal/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.