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 (-0.857 kcal/mol/HA)
✓ Good fit quality (FQ -8.43)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (20.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-27.420
kcal/mol
LE
-0.857
kcal/mol/HA
Fit Quality
-8.43
FQ (Leeson)
HAC
32
heavy atoms
MW
432
Da
LogP
0.83
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 20.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 2
Clashes 11
Severe clashes 0
| Final rank | 6.605912727722192 | Score | -27.4202 |
|---|---|---|---|
| Inter norm | -0.809895 | Intra norm | -0.0469893 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 5 |
| Artifact reason | geometry warning; 12 clashes; 11 protein contact clashes; high strain Δ 36.6 | ||
| Residues | A:ALA32;A:ASP52;A:ILE224;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:PRO88;A:SER44;A:SER86;A:THR180;A:THR83;A:TYR162;A:TYR178;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 | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 491 | 4.918248685407759 | -0.937426 | -26.6984 | 5 | 21 | 1 | 0.05 | 0.00 | - | no | Open |
| 595 | 5.575090899916919 | -0.7408 | -24.8635 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 414 | 6.434035714449353 | -0.717975 | -25.5926 | 4 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 485 | 6.500526567711173 | -0.675873 | -24.2658 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 6.605912727722192 | -0.809895 | -27.4202 | 5 | 20 | 16 | 0.80 | 0.20 | - | no | Current |
| 484 | 7.658521530819854 | -0.628344 | -18.6935 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 529 | 8.323509071516625 | -0.964933 | -23.9292 | 7 | 20 | 16 | 0.80 | 0.20 | - | yes | Open |
| 490 | 8.55090867045927 | -0.776061 | -19.809 | 3 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 594 | 10.819536765416256 | -0.842022 | -25.106 | 5 | 19 | 0 | 0.00 | 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
-27.420kcal/mol
Ligand efficiency (LE)
-0.8569kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.427
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.83
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
84.05kcal/mol
Minimised FF energy
63.87kcal/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.