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 (-0.844 kcal/mol/HA)
✓ Good fit quality (FQ -8.14)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (22.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.328
kcal/mol
LE
-0.844
kcal/mol/HA
Fit Quality
-8.14
FQ (Leeson)
HAC
30
heavy atoms
MW
416
Da
LogP
1.61
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 22.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 23
π–π 0
Clashes 11
Severe clashes 0
| Final rank | 5.69161726800841 | Score | -25.3284 |
|---|---|---|---|
| Inter norm | -0.855088 | Intra norm | 0.0108096 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 8 clashes; 11 protein contact clashes; high strain Δ 33.4 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:MET53;A:NDP301;A:PHE56;A:PRO88;A:SER44;A:SER86;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49 | ||
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 | 12 | Native recall | 0.60 |
| Jaccard | 0.50 | 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
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2436 | 4.619404239004076 | -0.652648 | -18.7113 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2433 | 4.76308070161585 | -0.689778 | -19.3666 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2977 | 5.69161726800841 | -0.855088 | -25.3284 | 4 | 16 | 12 | 0.60 | 0.20 | - | no | Current |
| 2434 | 6.896923322678182 | -0.661263 | -15.9357 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2974 | 7.2930489760138695 | -0.702402 | -18.0808 | 2 | 15 | 10 | 0.50 | 0.20 | - | yes | Open |
| 2976 | 8.068043716620211 | -0.790542 | -19.3977 | 4 | 13 | 12 | 0.60 | 0.20 | - | yes | Open |
| 2435 | 58.06488279945332 | -0.749386 | -19.1825 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2975 | 58.07330765868989 | -0.892561 | -22.4184 | 4 | 17 | 15 | 0.75 | 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
-25.328kcal/mol
Ligand efficiency (LE)
-0.8443kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.144
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
416.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.61
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
16.21kcal/mol
Minimised FF energy
-6.34kcal/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.