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 (-0.658 kcal/mol/HA)
✓ Good fit quality (FQ -6.64)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.038
kcal/mol
LE
-0.658
kcal/mol/HA
Fit Quality
-6.64
FQ (Leeson)
HAC
35
heavy atoms
MW
480
Da
LogP
1.45
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 24.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 1
Clashes 5
Severe clashes 0
| Final rank | 6.366358367034772 | Score | -23.0382 |
|---|---|---|---|
| Inter norm | -0.782948 | Intra norm | 0.124714 |
| Top1000 | no | Excluded | no |
| Contacts | 23 | H-bonds | 8 |
| Artifact reason | geometry warning; 17 clashes; 5 protein contact clashes; high strain Δ 46.3 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:GLU216;A:GLY157;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:PRO50;A:PRO88;A:SER44;A:SER86;A:THR180;A:TYR162;A:TYR178;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 | 0.54 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.57 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 71 | 3.8380967824303305 | -1.05128 | -36.544 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 69 | 4.730767067765323 | -1.01484 | -29.5226 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 54 | 5.1923128629157365 | -0.722873 | -25.0494 | 12 | 20 | 17 | 0.85 | 0.80 | - | no | Open |
| 70 | 5.26360611356286 | -1.04528 | -38.3918 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 55 | 6.366358367034772 | -0.782948 | -23.0382 | 8 | 23 | 15 | 0.75 | 0.80 | - | no | Current |
| 61 | 6.394843175325515 | -0.711297 | -22.2872 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 83 | 6.610935079220738 | -0.727966 | -21.56 | 10 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 81 | 6.692996863824275 | -0.650495 | -20.5848 | 11 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 43 | 8.082188569899184 | -0.698506 | -15.5277 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 82 | 6.464852845981596 | -0.723062 | -25.4146 | 11 | 20 | 1 | 0.05 | 0.00 | - | yes | Open |
| 60 | 6.839916997728094 | -0.720723 | -23.0257 | 6 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 53 | 10.264400783665268 | -0.759205 | -21.0091 | 9 | 20 | 16 | 0.80 | 0.60 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.038kcal/mol
Ligand efficiency (LE)
-0.6582kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.639
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
479.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.45
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.39kcal/mol
Minimised FF energy
62.85kcal/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.