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 (-0.868 kcal/mol/HA)
✓ Good fit quality (FQ -8.62)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (35.5 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.654
kcal/mol
LE
-0.868
kcal/mol/HA
Fit Quality
-8.62
FQ (Leeson)
HAC
33
heavy atoms
MW
444
Da
LogP
1.91
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 35.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 20
π–π 2
Clashes 14
Severe clashes 3
| Final rank | 10.252507299590931 | Score | -28.6542 |
|---|---|---|---|
| Inter norm | -0.919278 | Intra norm | 0.0509692 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 9 clashes; 3 protein clashes; high strain Δ 35.4 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:GLY96;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:THR61;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 | 0.61 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 610 | 3.9227368786597183 | -0.651244 | -21.2159 | 2 | 15 | 11 | 0.55 | 0.00 | - | no | Open |
| 696 | 4.403344250181916 | -0.500199 | -13.5077 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 698 | 5.454954305976354 | -0.55846 | -18.8801 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 615 | 6.1943138389988555 | -0.890133 | -28.1568 | 3 | 17 | 15 | 0.75 | 0.20 | - | yes | Open |
| 611 | 10.252507299590931 | -0.919278 | -28.6542 | 4 | 17 | 14 | 0.70 | 0.20 | - | yes | Current |
| 614 | 10.366814282594296 | -0.843316 | -24.7097 | 5 | 14 | 12 | 0.60 | 0.20 | - | yes | Open |
| 695 | 11.732590774908134 | -0.752914 | -25.5713 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 697 | 12.23975649193952 | -0.775301 | -24.5546 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 613 | 12.404005164513254 | -0.665891 | -21.3396 | 3 | 10 | 7 | 0.35 | 0.20 | - | yes | Open |
| 612 | 60.661231820847455 | -0.793129 | -25.5679 | 3 | 13 | 7 | 0.35 | 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
-28.654kcal/mol
Ligand efficiency (LE)
-0.8683kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.615
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
443.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.91
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
19.57kcal/mol
Minimised FF energy
-15.93kcal/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.