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 (-0.868 kcal/mol/HA)
✓ Good fit quality (FQ -8.38)
✗ High strain energy (15.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-26.052
kcal/mol
LE
-0.868
kcal/mol/HA
Fit Quality
-8.38
FQ (Leeson)
HAC
30
heavy atoms
MW
399
Da
LogP
3.42
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 15.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 4
Clashes 8
Severe clashes 0
| Final rank | 4.453092946858444 | Score | -26.0517 |
|---|---|---|---|
| Inter norm | -0.889585 | Intra norm | 0.0211953 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 2 |
| Artifact reason | geometry warning; 12 clashes; 8 protein contact clashes; moderate strain Δ 16.9 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:PHE56;A:PHE91;A:PRO88;A:SER86;A:TRP47;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 | 12 | Native recall | 0.60 |
| Jaccard | 0.52 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1851 | 3.8182993255404902 | -0.823538 | -24.9549 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1838 | 3.851783775744816 | -0.784304 | -23.3296 | 2 | 14 | 10 | 0.50 | 0.20 | - | no | Open |
| 1845 | 3.932240772894382 | -0.792345 | -21.9982 | 3 | 18 | 15 | 0.75 | 0.00 | - | no | Open |
| 1841 | 3.9693043882536476 | -0.856792 | -25.5232 | 2 | 17 | 14 | 0.70 | 0.20 | - | no | Open |
| 1840 | 4.015419590436674 | -0.792453 | -24.5044 | 2 | 15 | 12 | 0.60 | 0.20 | - | no | Open |
| 1848 | 4.453092946858444 | -0.889585 | -26.0517 | 2 | 15 | 12 | 0.60 | 0.20 | - | no | Current |
| 1837 | 4.5265026252781935 | -0.869483 | -26.2715 | 2 | 15 | 12 | 0.60 | 0.20 | - | no | Open |
| 1842 | 4.595728687915207 | -0.881575 | -27.2034 | 2 | 14 | 11 | 0.55 | 0.20 | - | no | Open |
| 1852 | 54.21749295702919 | -0.792545 | -23.0476 | 2 | 14 | 11 | 0.55 | 0.20 | - | no | Open |
| 1847 | 54.31890771050158 | -0.843341 | -23.7744 | 2 | 14 | 11 | 0.55 | 0.20 | - | no | Open |
| 1846 | 54.33898762740591 | -0.86617 | -25.8926 | 2 | 17 | 14 | 0.70 | 0.20 | - | no | Open |
| 1839 | 54.9489556704214 | -0.906657 | -27.3562 | 1 | 18 | 15 | 0.75 | 0.20 | - | no | Open |
| 1849 | 55.15193127209628 | -0.778418 | -22.323 | 2 | 16 | 13 | 0.65 | 0.20 | - | no | Open |
| 1843 | 6.8668086425962604 | -0.857185 | -20.0271 | 2 | 16 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1850 | 56.58302472155123 | -0.855723 | -24.0582 | 1 | 19 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1844 | 56.721890434218984 | -0.732713 | -21.0884 | 1 | 18 | 15 | 0.75 | 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
-26.052kcal/mol
Ligand efficiency (LE)
-0.8684kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.377
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
398.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.42
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.90kcal/mol
Minimised FF energy
72.00kcal/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.