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 (-0.734 kcal/mol/HA)
✓ Good fit quality (FQ -7.28)
✗ Very high strain energy (27.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-24.218
kcal/mol
LE
-0.734
kcal/mol/HA
Fit Quality
-7.28
FQ (Leeson)
HAC
33
heavy atoms
MW
448
Da
LogP
2.55
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 27.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 3
Severe clashes 1
| Final rank | 5.514855704594468 | Score | -24.2184 |
|---|---|---|---|
| Inter norm | -0.801783 | Intra norm | 0.0678934 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash; high strain Δ 27.2 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER86;A:THR83;A:TRP47;A:VAL30;A:VAL31;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2161 | 4.3782230484754265 | -0.567269 | -19.0306 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1644 | 4.62721433170881 | -0.634089 | -21.4944 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1638 | 4.655002588446546 | -0.673674 | -22.011 | 1 | 14 | 10 | 0.50 | 0.00 | - | no | Open |
| 1637 | 4.7070361837340275 | -0.639717 | -14.2427 | 1 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 1633 | 4.729953295512503 | -0.85085 | -23.9835 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 2156 | 4.7754537615867685 | -0.585347 | -15.5436 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1642 | 4.818702465343748 | -0.60818 | -19.4837 | 1 | 19 | 14 | 0.70 | 0.00 | - | no | Open |
| 2158 | 5.502538791575042 | -0.625466 | -19.4358 | 1 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 1639 | 53.670220236953455 | -0.655876 | -22.5279 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1634 | 53.809682699443286 | -0.743176 | -21.6774 | 0 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 1636 | 53.9453954568506 | -0.660946 | -20.7646 | 0 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 2159 | 54.163381058124116 | -0.588296 | -19.5859 | 2 | 12 | 1 | 0.05 | 0.00 | - | no | Open |
| 2163 | 54.16789142741234 | -0.679053 | -20.5486 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1635 | 54.1984144159069 | -0.674292 | -21.5338 | 2 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 2157 | 54.45603665938433 | -0.582515 | -16.3419 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2162 | 54.84033681809107 | -0.564509 | -17.7505 | 0 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2160 | 54.840572484676954 | -0.521303 | -13.7567 | 3 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 1641 | 5.514855704594468 | -0.801783 | -24.2184 | 1 | 20 | 16 | 0.80 | 0.20 | - | yes | Current |
| 1640 | 55.74529969784381 | -0.68451 | -16.227 | 0 | 17 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1643 | 56.5408976991009 | -0.751697 | -20.6951 | 0 | 16 | 13 | 0.65 | 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
-24.218kcal/mol
Ligand efficiency (LE)
-0.7339kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.282
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
447.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.55
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
177.48kcal/mol
Minimised FF energy
149.91kcal/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.