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 (-0.945 kcal/mol/HA)
✓ Good fit quality (FQ -9.37)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (20.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-31.171
kcal/mol
LE
-0.945
kcal/mol/HA
Fit Quality
-9.37
FQ (Leeson)
HAC
33
heavy atoms
MW
483
Da
LogP
3.01
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 20.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 14
Severe clashes 0
| Final rank | 5.903285916986687 | Score | -31.1707 |
|---|---|---|---|
| Inter norm | -0.803865 | Intra norm | -0.140702 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | geometry warning; 9 clashes; 14 protein contact clashes; moderate strain Δ 19.0 | ||
| Residues | A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO88;A:TRP47;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 | 10 | Native recall | 0.50 |
| Jaccard | 0.42 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1457 | 4.906031688805453 | -0.669663 | -26.9468 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2494 | 5.207639185251139 | -0.879258 | -25.5601 | 1 | 20 | 18 | 0.90 | 0.00 | - | no | Open |
| 2495 | 5.903285916986687 | -0.803865 | -31.1707 | 4 | 14 | 10 | 0.50 | 0.20 | - | no | Current |
| 2497 | 5.963036697586649 | -0.681133 | -22.5039 | 2 | 19 | 19 | 0.95 | 0.20 | - | yes | Open |
| 1458 | 6.580788726601197 | -0.701459 | -25.1583 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1460 | 8.394332398327112 | -0.634846 | -20.4106 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2496 | 55.08975206216331 | -0.673061 | -25.3774 | 1 | 19 | 18 | 0.90 | 0.00 | - | yes | Open |
| 1459 | 57.965277207560135 | -0.795828 | -27.2022 | 9 | 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
-31.171kcal/mol
Ligand efficiency (LE)
-0.9446kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.372
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
482.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.01
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-31.77kcal/mol
Minimised FF energy
-52.14kcal/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.