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 (-1.442 kcal/mol/HA)
✓ Good fit quality (FQ -12.30)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (21.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.285
kcal/mol
LE
-1.442
kcal/mol/HA
Fit Quality
-12.30
FQ (Leeson)
HAC
21
heavy atoms
MW
327
Da
LogP
0.87
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 21.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 18
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 3.698263747816376 | Score | -30.2851 |
|---|---|---|---|
| Inter norm | -1.4266 | Intra norm | -0.0155511 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 8 protein contact clashes; high strain Δ 28.2 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:GLY157;A:ILE45;A:MET53;A:NDP301;A:PHE56;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49 | ||
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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2823 | 2.8156329434342053 | -1.09337 | -24.9759 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2202 | 3.698263747816376 | -1.4266 | -30.2851 | 10 | 14 | 10 | 0.50 | 0.80 | - | no | Current |
| 2824 | 3.798255560249272 | -1.1635 | -24.8543 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2825 | 4.264078415337873 | -1.17816 | -26.2298 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 733 | 4.690459879395728 | -1.04635 | -23.5582 | 5 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 735 | 5.985150580532946 | -1.07992 | -23.2762 | 7 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 734 | 6.265945315443796 | -1.07899 | -25.1573 | 9 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 736 | 6.799887496444368 | -1.07651 | -25.0088 | 7 | 17 | 1 | 0.05 | 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
-30.285kcal/mol
Ligand efficiency (LE)
-1.4421kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.301
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
327.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.87
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-24.99kcal/mol
Minimised FF energy
-46.53kcal/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.