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 (-0.796 kcal/mol/HA)
✓ Good fit quality (FQ -7.68)
✓ Good H-bonds (5 bonds)
✗ High strain energy (11.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-23.873
kcal/mol
LE
-0.796
kcal/mol/HA
Fit Quality
-7.68
FQ (Leeson)
HAC
30
heavy atoms
MW
420
Da
LogP
4.52
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 11.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 3
Clashes 13
Severe clashes 1
| Final rank | 7.2101202371091855 | Score | -23.8735 |
|---|---|---|---|
| Inter norm | -0.859099 | Intra norm | 0.0633138 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 13 clashes; 1 protein clash; moderate strain Δ 14.3 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR180;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 | 3 | Strict recall | 0.43 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3129 | 5.30553003506395 | -0.954123 | -26.6523 | 3 | 17 | 17 | 0.85 | 0.40 | - | no | Open |
| 3167 | 6.173291032914957 | -0.682302 | -19.513 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3124 | 6.215417197943953 | -0.861558 | -23.485 | 3 | 18 | 17 | 0.85 | 0.20 | - | no | Open |
| 3666 | 6.246697130747643 | -0.707757 | -20.5324 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 3670 | 6.272432463998912 | -0.845636 | -25.0388 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 3669 | 6.322932638041371 | -0.748965 | -21.3557 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 3668 | 6.6598710599952575 | -0.849058 | -23.1853 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3665 | 6.025346247140044 | -0.740679 | -21.9125 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3667 | 6.7566606423586 | -0.754286 | -22.124 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3126 | 7.2101202371091855 | -0.859099 | -23.8735 | 5 | 18 | 17 | 0.85 | 0.40 | - | yes | Current |
| 3127 | 8.241268674929234 | -0.810159 | -23.3605 | 4 | 18 | 17 | 0.85 | 0.20 | - | yes | Open |
| 3166 | 9.2308098260559 | -0.854714 | -23.6189 | 3 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3125 | 9.317699948251644 | -0.863629 | -23.5269 | 2 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 3128 | 10.682020037457598 | -0.875906 | -22.7817 | 4 | 13 | 10 | 0.50 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.873kcal/mol
Ligand efficiency (LE)
-0.7958kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.676
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
419.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.52
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
56.93kcal/mol
Minimised FF energy
45.83kcal/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.