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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.092 kcal/mol/HA)
✓ Good fit quality (FQ -9.48)
✓ Strong H-bond network (9 bonds)
✗ Very high strain energy (23.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-24.027
kcal/mol
LE
-1.092
kcal/mol/HA
Fit Quality
-9.48
FQ (Leeson)
HAC
22
heavy atoms
MW
341
Da
LogP
0.85
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 13
π–π 2
Clashes 20
Severe clashes 4
| Final rank | 12.12563218092324 | Score | -24.0266 |
|---|---|---|---|
| Inter norm | -1.09615 | Intra norm | 0.00403625 |
| Top1000 | no | Excluded | yes |
| Contacts | 9 | H-bonds | 9 |
| Artifact reason | excluded; geometry warning; 7 clashes; 4 protein clashes; high strain Δ 25.3 | ||
| Residues | A:ARG97;A:LEU94;A:LYS57;A:LYS90;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO93 | ||
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 | 6 | Native recall | 0.30 |
| Jaccard | 0.26 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2861 | 3.6164297562044743 | -1.32008 | -28.8892 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2863 | 3.969540372062586 | -1.09904 | -24.9808 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2134 | 4.688193311484323 | -1.23878 | -27.6063 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2227 | 4.802075810609685 | -1.30938 | -28.0234 | 11 | 14 | 10 | 0.50 | 0.80 | - | no | Open |
| 2864 | 5.37486062420216 | -1.10854 | -25.2361 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2225 | 6.265002448680948 | -1.27167 | -28.6738 | 10 | 14 | 10 | 0.50 | 0.80 | - | yes | Open |
| 2862 | 6.514321868725696 | -1.06736 | -23.0307 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2865 | 6.732307314856408 | -1.07055 | -23.9724 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2226 | 12.12563218092324 | -1.09615 | -24.0266 | 9 | 9 | 6 | 0.30 | 0.20 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.027kcal/mol
Ligand efficiency (LE)
-1.0921kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.482
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
341.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.85
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-12.21kcal/mol
Minimised FF energy
-35.33kcal/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.