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 (-0.873 kcal/mol/HA)
✓ Good fit quality (FQ -8.51)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (58.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-27.064
kcal/mol
LE
-0.873
kcal/mol/HA
Fit Quality
-8.51
FQ (Leeson)
HAC
31
heavy atoms
MW
442
Da
LogP
3.53
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 58.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 3
Clashes 9
Severe clashes 0
| Final rank | 7.7517023364703235 | Score | -27.0636 |
|---|---|---|---|
| Inter norm | -0.851646 | Intra norm | -0.0213748 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 4 |
| Artifact reason | geometry warning; 14 clashes; 9 protein contact clashes; high strain Δ 59.6 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO93;A:THR180;A:THR83;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 | 17 | Native recall | 0.85 |
| Jaccard | 0.77 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1356 | 7.30919015569561 | -0.747819 | -22.4692 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2766 | 7.626560514791622 | -0.76421 | -21.2192 | 4 | 14 | 14 | 0.70 | 0.20 | - | no | Open |
| 2764 | 7.7517023364703235 | -0.851646 | -27.0636 | 4 | 19 | 17 | 0.85 | 0.20 | - | no | Current |
| 1354 | 8.091391784310396 | -0.76201 | -22.4584 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1357 | 8.286357705039862 | -0.71293 | -20.1897 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1358 | 8.509331768833594 | -0.765906 | -22.5045 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1673 | 8.575978773607371 | -0.953186 | -27.6149 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1669 | 8.816759867335094 | -1.03081 | -29.7112 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1672 | 9.362017157837828 | -0.97062 | -23.9871 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1353 | 9.570110861770155 | -0.762672 | -21.9133 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1670 | 9.58932627039659 | -0.902423 | -27.2893 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1668 | 9.675499203019521 | -0.847302 | -21.3097 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1355 | 9.982986083410468 | -0.647251 | -16.8308 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2768 | 11.772406665392056 | -0.812859 | -20.601 | 5 | 14 | 10 | 0.50 | 0.20 | - | yes | Open |
| 2765 | 13.036634138808747 | -0.69553 | -21.8898 | 3 | 14 | 9 | 0.45 | 0.20 | - | yes | Open |
| 2767 | 14.005140975277962 | -0.649309 | -18.2469 | 3 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
| 2763 | 14.712984028568691 | -0.74996 | -16.6372 | 4 | 13 | 9 | 0.45 | 0.20 | - | yes | Open |
| 1671 | 16.875902029159732 | -0.928572 | -27.141 | 7 | 17 | 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
-27.064kcal/mol
Ligand efficiency (LE)
-0.8730kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.505
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
442.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.53
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
58.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.55kcal/mol
Minimised FF energy
43.09kcal/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.