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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.759 kcal/mol/HA)
✓ Good fit quality (FQ -7.60)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (46.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.824
kcal/mol
LE
-0.759
kcal/mol/HA
Fit Quality
-7.60
FQ (Leeson)
HAC
34
heavy atoms
MW
483
Da
LogP
5.37
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 46.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 1
Clashes 17
Severe clashes 1
| Final rank | 58.95174772421978 | Score | -25.8237 |
|---|---|---|---|
| Inter norm | -0.812852 | Intra norm | 0.0533317 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | excluded; hard geometry fail; 1 severe clash; 1 protein clash | ||
| Residues | A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO88;A:SER44;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 | 11 | Native recall | 0.55 |
| Jaccard | 0.44 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1905 | 5.104866815228245 | -0.710523 | -26.0124 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1907 | 6.175050330553141 | -0.635334 | -20.1282 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1987 | 6.493443960901055 | -0.667066 | -23.1803 | 3 | 19 | 18 | 0.90 | 0.20 | - | no | Open |
| 1909 | 7.101960946007024 | -0.801899 | -30.7153 | 8 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 1993 | 7.441618172275733 | -0.683262 | -20.4478 | 3 | 18 | 18 | 0.90 | 0.00 | - | no | Open |
| 1988 | 7.755716690108713 | -0.790421 | -25.5478 | 2 | 17 | 17 | 0.85 | 0.20 | - | yes | Open |
| 1906 | 55.04519385134802 | -0.670851 | -23.0018 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1991 | 56.49799754134236 | -0.645669 | -22.8663 | 4 | 14 | 10 | 0.50 | 0.20 | - | yes | Open |
| 1910 | 56.752469651210745 | -0.629057 | -21.7106 | 9 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1989 | 56.92236331963167 | -0.679926 | -24.5927 | 3 | 20 | 18 | 0.90 | 0.20 | - | yes | Open |
| 1990 | 57.10592140478446 | -0.655981 | -21.2727 | 3 | 16 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1911 | 57.26577548493912 | -0.580617 | -21.0767 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1908 | 58.39041328417018 | -0.612291 | -22.19 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1992 | 58.52225989130012 | -0.647248 | -23.4862 | 3 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1986 | 58.95174772421978 | -0.812852 | -25.8237 | 4 | 16 | 11 | 0.55 | 0.20 | - | yes | Current |
| 1904 | 60.214299205472514 | -0.626782 | -22.1073 | 9 | 19 | 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
-25.824kcal/mol
Ligand efficiency (LE)
-0.7595kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.600
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
482.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.37
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
46.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
76.92kcal/mol
Minimised FF energy
30.30kcal/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.