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 (-0.959 kcal/mol/HA)
✓ Good fit quality (FQ -9.25)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (23.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.776
kcal/mol
LE
-0.959
kcal/mol/HA
Fit Quality
-9.25
FQ (Leeson)
HAC
30
heavy atoms
MW
458
Da
LogP
2.66
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 1
| Final rank | 6.444099753091593 | Score | -28.7764 |
|---|---|---|---|
| Inter norm | -0.905993 | Intra norm | -0.0532208 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 13 clashes; 1 protein clash; high strain Δ 22.3 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:THR180;A:TYR162;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: 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 | 17 | Native recall | 0.85 |
| Jaccard | 0.81 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2085 | 3.7455999172086187 | -0.910863 | -24.5258 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2087 | 4.9305657277534 | -0.929606 | -25.0038 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2177 | 5.746147205921879 | -0.914004 | -26.8537 | 3 | 19 | 18 | 0.90 | 0.20 | - | no | Open |
| 2175 | 6.391428284754564 | -0.852881 | -26.065 | 5 | 15 | 14 | 0.70 | 0.20 | - | no | Open |
| 2088 | 7.098387350979841 | -0.867806 | -28.6497 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2176 | 5.320168698013479 | -0.874951 | -24.4856 | 4 | 18 | 17 | 0.85 | 0.20 | - | yes | Open |
| 2178 | 6.444099753091593 | -0.905993 | -28.7764 | 5 | 18 | 17 | 0.85 | 0.20 | - | yes | Current |
| 2086 | 11.452162562313429 | -0.929261 | -26.8997 | 8 | 20 | 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
-28.776kcal/mol
Ligand efficiency (LE)
-0.9592kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.253
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
43.54kcal/mol
Minimised FF energy
20.48kcal/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.