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 (-1.096 kcal/mol/HA)
✓ Good fit quality (FQ -9.68)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (37.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.217
kcal/mol
LE
-1.096
kcal/mol/HA
Fit Quality
-9.68
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
1.24
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 37.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 22
π–π 2
Clashes 13
Severe clashes 0
| Final rank | 6.012865386417346 | Score | -25.2174 |
|---|---|---|---|
| Inter norm | -1.24284 | Intra norm | 0.146434 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 8 |
| Artifact reason | geometry warning; 7 clashes; 13 protein contact clashes; high strain Δ 38.7 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:GLY157;A:ILE45;A:MET53;A:NDP301;A:PHE56;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 | 10 | Native recall | 0.50 |
| Jaccard | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2848 | 3.1609271893686097 | -1.03549 | -24.1606 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1060 | 3.336458242861153 | -1.03157 | -23.2394 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1057 | 3.6221111580558065 | -0.947237 | -21.5636 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2217 | 3.6790013135047768 | -1.14574 | -25.3553 | 6 | 14 | 8 | 0.40 | 0.40 | - | no | Open |
| 2849 | 4.123402787243458 | -1.08583 | -23.896 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1373 | 4.575019733347909 | -0.866629 | -17.6713 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1370 | 4.686958813923712 | -0.923016 | -23.3717 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1058 | 4.861752626562554 | -1.06321 | -21.6989 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2850 | 5.019088194080138 | -1.02138 | -23.492 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2218 | 6.012865386417346 | -1.24284 | -25.2174 | 8 | 14 | 10 | 0.50 | 0.80 | - | no | Current |
| 1372 | 6.180580653679305 | -0.830985 | -18.4822 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1369 | 3.8223140432413016 | -0.883037 | -20.9971 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2851 | 4.96865366664588 | -1.07326 | -24.7165 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1059 | 7.922735244763697 | -1.048 | -23.4711 | 11 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1371 | 8.553968468576814 | -0.871366 | -22.575 | 5 | 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
-25.217kcal/mol
Ligand efficiency (LE)
-1.0964kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.677
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.24
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-1.35kcal/mol
Minimised FF energy
-38.95kcal/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.