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 (-0.649 kcal/mol/HA)
✓ Good fit quality (FQ -6.50)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (22.5 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-22.076
kcal/mol
LE
-0.649
kcal/mol/HA
Fit Quality
-6.50
FQ (Leeson)
HAC
34
heavy atoms
MW
476
Da
LogP
3.33
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 22.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 2
Clashes 9
Severe clashes 3
| Final rank | 10.330473319524868 | Score | -22.0761 |
|---|---|---|---|
| Inter norm | -0.645165 | Intra norm | -0.00413059 |
| Top1000 | no | Excluded | yes |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 20 clashes; 3 protein clashes; high strain Δ 21.7 | ||
| Residues | A:ALA32;A:ARG48;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR83;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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 | 15 | Native recall | 0.75 |
| Jaccard | 0.62 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1514 | 7.533781901841193 | -0.634882 | -21.4916 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1519 | 7.946048041711834 | -0.337285 | -12.4181 | 0 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1516 | 8.037752732679447 | -0.832101 | -28.9631 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2852 | 8.48620637071585 | -0.831972 | -28.6804 | 2 | 18 | 14 | 0.70 | 0.20 | - | no | Open |
| 1583 | 9.232988641186012 | -0.94457 | -33.9929 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2859 | 8.441706828631817 | -0.587213 | -21.1824 | 0 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1518 | 8.546547835918052 | -0.85907 | -28.691 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1520 | 8.565928211114365 | -0.5023 | -13.6734 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2858 | 8.61612676343768 | -0.675324 | -23.4232 | 2 | 13 | 10 | 0.50 | 0.20 | - | yes | Open |
| 1515 | 8.800782866793854 | -0.706498 | -24.139 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1584 | 9.137800022550554 | -0.902122 | -29.855 | 4 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2856 | 9.22048295162044 | -0.754895 | -24.7354 | 0 | 17 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1586 | 9.221161529299227 | -0.703799 | -25.1048 | 9 | 5 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2853 | 10.330473319524868 | -0.645165 | -22.0761 | 3 | 19 | 15 | 0.75 | 0.00 | - | yes | Current |
| 2854 | 13.695905445005074 | -0.777668 | -28.4251 | 3 | 13 | 12 | 0.60 | 0.00 | - | yes | Open |
| 1585 | 58.98715940547089 | -0.876248 | -31.2541 | 6 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1517 | 58.99014428676841 | -0.436484 | -11.9302 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2857 | 59.549788082864985 | -0.834785 | -25.7247 | 4 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
| 2855 | 62.18538355187409 | -0.659105 | -21.5791 | 3 | 13 | 9 | 0.45 | 0.20 | - | yes | Open |
| 1521 | 62.87410528533428 | -0.498737 | -17.4697 | 3 | 12 | 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
-22.076kcal/mol
Ligand efficiency (LE)
-0.6493kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.497
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
475.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.33
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
120.02kcal/mol
Minimised FF energy
97.52kcal/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.