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 (-0.512 kcal/mol/HA)
✓ Good fit quality (FQ -5.13)
✗ Very high strain energy (39.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-17.423
kcal/mol
LE
-0.512
kcal/mol/HA
Fit Quality
-5.13
FQ (Leeson)
HAC
34
heavy atoms
MW
491
Da
LogP
0.68
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 39.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 12
Severe clashes 1
| Final rank | 8.007040405112697 | Score | -17.4227 |
|---|---|---|---|
| Inter norm | -0.677413 | Intra norm | 0.16498 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 13 clashes; 1 protein clash; high strain Δ 30.2 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.76 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 423 | 6.235444614885987 | -0.921178 | -28.5461 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 424 | 6.5752281328867355 | -1.00078 | -28.5431 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 6.827904118123914 | -0.746868 | -24.6373 | 1 | 17 | 15 | 0.75 | 0.00 | - | no | Open |
| 601 | 7.401065038593859 | -0.779113 | -26.4587 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 6.751124317430976 | -0.70137 | -19.2185 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 602 | 7.494104916731109 | -0.827691 | -22.9203 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 467 | 8.007040405112697 | -0.677413 | -17.4227 | 1 | 17 | 16 | 0.80 | 0.00 | - | yes | Current |
| 420 | 8.66704616002394 | -0.810841 | -22.9533 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 421 | 9.458859204989842 | -0.907133 | -29.9858 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 422 | 10.017601772255048 | -0.907876 | -25.4826 | 10 | 16 | 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
-17.423kcal/mol
Ligand efficiency (LE)
-0.5124kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.127
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
490.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.68
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
165.76kcal/mol
Minimised FF energy
126.35kcal/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.