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 (-0.715 kcal/mol/HA)
✓ Good fit quality (FQ -7.26)
✓ Strong H-bond network (16 bonds)
✗ Very high strain energy (40.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.722
kcal/mol
LE
-0.715
kcal/mol/HA
Fit Quality
-7.26
FQ (Leeson)
HAC
36
heavy atoms
MW
496
Da
LogP
0.42
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 40.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 16
Hydrophobic 24
π–π 2
Clashes 14
Severe clashes 1
| Final rank | 9.739040295876764 | Score | -25.7222 |
|---|---|---|---|
| Inter norm | -0.769883 | Intra norm | 0.0553775 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 14 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash; high strain Δ 44.7 | ||
| Residues | A:ALA32;A:ASP52;A:ILE45;A:LEU179;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:PHE91;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: permissive.
| 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 | 0.74 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.57 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
Hydrogen bonds
Mode: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| - | - | - | - | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| - | - | - | - | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 71 | 5.06926198045265 | -0.924042 | -32.8641 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 47 | 5.682540471857508 | -0.780992 | -30.7846 | 12 | 22 | 19 | 0.95 | 0.80 | - | no | Open |
| 100 | 6.730310548114257 | -0.719348 | -26.8129 | 13 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 73 | 7.936002175552865 | -0.973798 | -33.9056 | 8 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 72 | 9.413951240297864 | -1.02977 | -38.3693 | 9 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 48 | 9.739040295876764 | -0.769883 | -25.7222 | 14 | 20 | 17 | 0.85 | 0.60 | - | yes | Current |
| 49 | 14.319486327303022 | -0.724153 | -27.9119 | 6 | 19 | 15 | 0.75 | 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
-25.722kcal/mol
Ligand efficiency (LE)
-0.7145kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.262
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
495.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.42
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.11kcal/mol
Minimised FF energy
56.67kcal/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.