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 (-0.992 kcal/mol/HA)
✓ Good fit quality (FQ -9.37)
✗ High strain energy (16.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-27.787
kcal/mol
LE
-0.992
kcal/mol/HA
Fit Quality
-9.37
FQ (Leeson)
HAC
28
heavy atoms
MW
407
Da
LogP
5.83
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 16.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 4
Clashes 13
Severe clashes 2
| Final rank | 8.288375686376511 | Score | -27.7872 |
|---|---|---|---|
| Inter norm | -1.06292 | Intra norm | 0.0705225 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 2 |
| Artifact reason | excluded; geometry warning; 11 clashes; 2 protein clashes; high strain Δ 22.3 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:THR180;A:TRP47;A:VAL30;A:VAL31;A:VAL49 | ||
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 | 13 | Native recall | 0.65 |
| Jaccard | 0.57 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2043 | 2.9963607481740455 | -0.870322 | -27.6293 | 3 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 1909 | 3.689900294712992 | -0.801575 | -22.6751 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2326 | 3.705716829060318 | -0.577223 | -16.6977 | 2 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 2870 | 4.050305824450855 | -0.790025 | -23.2398 | 3 | 11 | 9 | 0.45 | 0.00 | - | no | Open |
| 2044 | 5.069101694248104 | -0.797811 | -23.0137 | 2 | 14 | 1 | 0.05 | 0.00 | - | no | Open |
| 3464 | 5.702951618806277 | -0.760193 | -17.1572 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 3625 | 6.284865441525752 | -0.735557 | -21.605 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 3463 | 6.415741126707506 | -0.828835 | -18.3728 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 3627 | 6.663919820193825 | -0.749836 | -23.5599 | 2 | 11 | 1 | 0.05 | 0.00 | - | no | Open |
| 2327 | 5.201536113397625 | -0.669419 | -17.579 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2045 | 5.778366047235093 | -0.693995 | -21.3166 | 1 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2046 | 6.1878097351617845 | -0.74483 | -22.2983 | 2 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1907 | 6.216464626402162 | -0.914844 | -25.1026 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3465 | 6.270855112040639 | -0.784948 | -21.9872 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3628 | 6.402791360590602 | -0.694176 | -19.7207 | 4 | 14 | 1 | 0.05 | 0.00 | - | yes | Open |
| 3626 | 6.622495608429628 | -0.807393 | -24.035 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2328 | 6.820727394998152 | -0.564702 | -17.1982 | 2 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2871 | 7.10882567693303 | -0.986494 | -24.6981 | 2 | 17 | 13 | 0.65 | 0.20 | - | yes | Open |
| 3462 | 7.162171496558556 | -0.789896 | -19.4096 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2868 | 7.791682645393914 | -0.851972 | -20.1413 | 4 | 18 | 14 | 0.70 | 0.40 | - | yes | Open |
| 2869 | 8.288375686376511 | -1.06292 | -27.7872 | 2 | 16 | 13 | 0.65 | 0.20 | - | yes | Current |
| 1908 | 8.699957135349466 | -0.783758 | -15.2456 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1910 | 9.791668457905187 | -0.727799 | -12.3201 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2329 | 11.561716334351372 | -0.596354 | -14.53 | 3 | 8 | 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
-27.787kcal/mol
Ligand efficiency (LE)
-0.9924kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.369
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
406.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.83
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
71.38kcal/mol
Minimised FF energy
55.40kcal/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.