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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.972 kcal/mol/HA)
✓ Good fit quality (FQ -8.83)
✓ Strong H-bond network (9 bonds)
✗ Very high strain energy (21.8 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-24.288
kcal/mol
LE
-0.972
kcal/mol/HA
Fit Quality
-8.83
FQ (Leeson)
HAC
25
heavy atoms
MW
344
Da
LogP
1.35
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 21.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 18
π–π 1
Clashes 4
Severe clashes 1
| Final rank | 4.6521318664896825 | Score | -24.2879 |
|---|---|---|---|
| Inter norm | -1.08871 | Intra norm | 0.117198 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | excluded; geometry warning; 11 clashes; 1 protein clash; high strain Δ 21.1 | ||
| Residues | A:ALA32;A:ASP52;A:GLY157;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:SER44;A:SER86;A:THR180;A:TYR162;A:TYR178;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 | 14 | Native recall | 0.70 |
| Jaccard | 0.58 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.57 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 562 | 3.2309025778092213 | -1.17157 | -28.8912 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 597 | 3.785429015974857 | -0.934566 | -22.7562 | 10 | 19 | 16 | 0.80 | 0.80 | - | no | Open |
| 727 | 5.781011157662119 | -0.759639 | -16.2355 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 4.579218795457623 | -1.05652 | -23.4495 | 6 | 17 | 14 | 0.70 | 0.80 | - | yes | Open |
| 596 | 4.6521318664896825 | -1.08871 | -24.2879 | 9 | 18 | 14 | 0.70 | 0.80 | - | yes | Current |
| 560 | 5.159170491104661 | -1.16271 | -24.8975 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 561 | 5.235738166848403 | -1.26246 | -31.4345 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 559 | 5.341746462584855 | -1.24649 | -30.8984 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 599 | 7.128453702344347 | -0.913587 | -23.5183 | 6 | 16 | 12 | 0.60 | 0.00 | - | yes | Open |
| 726 | 8.172898536219018 | -0.728896 | -15.5353 | 7 | 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
-24.288kcal/mol
Ligand efficiency (LE)
-0.9715kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.832
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.35
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-111.88kcal/mol
Minimised FF energy
-133.68kcal/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.