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 (-0.722 kcal/mol/HA)
✓ Good fit quality (FQ -7.34)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (37.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.987
kcal/mol
LE
-0.722
kcal/mol/HA
Fit Quality
-7.34
FQ (Leeson)
HAC
36
heavy atoms
MW
495
Da
LogP
3.93
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 37.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 1
Clashes 5
Severe clashes 1
| Final rank | 7.094310846808231 | Score | -25.9868 |
|---|---|---|---|
| Inter norm | -0.729906 | Intra norm | 0.0080505 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash; high strain Δ 40.6 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:THR83;A:TYR162;A:VAL156;A:VAL31;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 | 0.71 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2139 | 5.5362854624508095 | -0.64905 | -22.1944 | 2 | 14 | 11 | 0.55 | 0.00 | - | no | Open |
| 1039 | 6.592745149494084 | -0.581676 | -19.1245 | 3 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 2137 | 7.350276827744787 | -0.743905 | -25.0423 | 4 | 15 | 10 | 0.50 | 0.00 | - | no | Open |
| 1043 | 9.392372717268739 | -0.597623 | -18.4221 | 3 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 2142 | 7.094310846808231 | -0.729906 | -25.9868 | 3 | 16 | 15 | 0.75 | 0.40 | - | yes | Current |
| 2141 | 8.336995967038263 | -0.664932 | -23.6589 | 3 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1042 | 9.094485776482546 | -0.664896 | -23.662 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2136 | 9.925224171279485 | -0.709942 | -23.985 | 4 | 13 | 9 | 0.45 | 0.00 | - | yes | Open |
| 2138 | 11.001599315788742 | -0.812204 | -30.6436 | 6 | 13 | 8 | 0.40 | 0.00 | - | yes | Open |
| 2135 | 11.921673994238258 | -0.733858 | -27.1507 | 6 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1044 | 12.000924412905848 | -0.741356 | -28.5902 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2140 | 13.341195533218755 | -0.81948 | -28.9361 | 5 | 20 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1041 | 14.020095673782091 | -0.701109 | -11.6526 | 8 | 20 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1040 | 14.208941346957896 | -0.6384 | -21.8212 | 6 | 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
-25.987kcal/mol
Ligand efficiency (LE)
-0.7219kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.337
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
494.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.93
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
147.68kcal/mol
Minimised FF energy
109.98kcal/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.