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 (-0.830 kcal/mol/HA)
✓ Good fit quality (FQ -7.83)
✓ Good H-bonds (3 bonds)
✗ High strain energy (12.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.240
kcal/mol
LE
-0.830
kcal/mol/HA
Fit Quality
-7.83
FQ (Leeson)
HAC
28
heavy atoms
MW
407
Da
LogP
5.83
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 12.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 2
Clashes 7
Severe clashes 0
| Final rank | 4.050305824450855 | Score | -23.2398 |
|---|---|---|---|
| Inter norm | -0.790025 | Intra norm | -0.0399689 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 3 |
| Artifact reason | geometry warning; 10 clashes; 7 protein contact clashes; moderate strain Δ 17.4 | ||
| Residues | A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO93;A:THR54 | ||
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 | 9 | Native recall | 0.45 |
| Jaccard | 0.41 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | Current |
| 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 | Open |
| 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
-23.240kcal/mol
Ligand efficiency (LE)
-0.8300kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.835
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)
12.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
68.52kcal/mol
Minimised FF energy
56.03kcal/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.