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 (-1.083 kcal/mol/HA)
✓ Good fit quality (FQ -9.97)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (30.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.147
kcal/mol
LE
-1.083
kcal/mol/HA
Fit Quality
-9.97
FQ (Leeson)
HAC
26
heavy atoms
MW
388
Da
LogP
2.45
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 30.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 3
Clashes 13
Severe clashes 0
| Final rank | 6.889240165523834 | Score | -28.147 |
|---|---|---|---|
| Inter norm | -1.06772 | Intra norm | -0.0148593 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 3 |
| Artifact reason | geometry warning; 11 clashes; 13 protein contact clashes; high strain Δ 38.6 | ||
| Residues | A:ALA32;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:THR54;A:TYR162;A:VAL156;A:VAL30;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.73 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2969 | 4.137803645094924 | -0.93915 | -24.9209 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2242 | 4.296283153712543 | -0.968744 | -24.5432 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 798 | 4.392766722590424 | -0.91132 | -23.537 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1547 | 4.921088716085349 | -0.737209 | -20.8922 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 796 | 4.99701273232448 | -0.973938 | -25.1331 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1549 | 5.59837508517362 | -0.772639 | -18.2719 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 799 | 6.085486100632919 | -0.929838 | -22.6506 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 797 | 6.127482688751314 | -0.953386 | -20.2311 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2330 | 6.189305179927231 | -1.01133 | -23.3342 | 2 | 16 | 14 | 0.70 | 0.20 | - | no | Open |
| 1548 | 6.277837426162495 | -0.737054 | -16.8973 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1551 | 6.547854085861548 | -0.792669 | -20.1687 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1202 | 6.8709869873533185 | -0.831671 | -24.7083 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2329 | 6.889240165523834 | -1.06772 | -28.147 | 3 | 18 | 16 | 0.80 | 0.20 | - | no | Current |
| 795 | 5.668979836923617 | -0.988227 | -26.017 | 1 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 794 | 5.697140127009128 | -0.97135 | -24.7544 | 1 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1550 | 6.1154515945929795 | -0.696997 | -18.037 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2243 | 6.280150903613029 | -0.890273 | -22.9369 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1204 | 6.819337867252677 | -0.958722 | -24.8957 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1546 | 7.558494573215623 | -0.761754 | -18.7838 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1205 | 7.969771235561705 | -0.875692 | -23.7292 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1203 | 8.177415906660007 | -0.910363 | -22.6194 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2331 | 8.766428907609987 | -1.05787 | -25.1401 | 3 | 18 | 16 | 0.80 | 0.20 | - | yes | Open |
| 2332 | 10.248451867163455 | -1.07259 | -25.1657 | 3 | 18 | 16 | 0.80 | 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
-28.147kcal/mol
Ligand efficiency (LE)
-1.0826kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.974
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
388.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.45
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
1.53kcal/mol
Minimised FF energy
-28.70kcal/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.