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.
✓ Good LE (-0.331 kcal/mol/HA)
✓ Good fit quality (FQ -3.36)
✗ Very high strain energy (35.8 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-11.901
kcal/mol
LE
-0.331
kcal/mol/HA
Fit Quality
-3.36
FQ (Leeson)
HAC
36
heavy atoms
MW
491
Da
LogP
3.19
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: good
Geometry reliability: low
Reason: geometry warning, clashes, strain 35.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 14
Severe clashes 1
| Final rank | 58.30911582205452 | Score | -11.9012 |
|---|---|---|---|
| Inter norm | -0.471308 | Intra norm | 0.140718 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 16 clashes; 1 protein clash | ||
| Residues | A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS90;A:LYS95;A:MET53;A:PHE91;A:PRO88;A:SER44;A:SER86;A:TRP47;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 | 10 | Native recall | 0.50 |
| Jaccard | 0.38 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1403 | 4.877137107124791 | -0.51463 | -17.6107 | 0 | 18 | 13 | 0.65 | 0.00 | - | no | Open |
| 1412 | 4.998640415975911 | -0.54482 | -17.2925 | 1 | 20 | 17 | 0.85 | 0.20 | - | no | Open |
| 1413 | 5.1564795499309835 | -0.530769 | -13.0854 | 0 | 17 | 12 | 0.60 | 0.00 | - | no | Open |
| 1416 | 5.682459418156231 | -0.725498 | -24.2474 | 1 | 19 | 15 | 0.75 | 0.20 | - | no | Open |
| 1408 | 7.102757899335591 | -0.668387 | -16.5626 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1402 | 7.5860855463520025 | -0.741921 | -23.4735 | 2 | 15 | 12 | 0.60 | 0.00 | - | no | Open |
| 1409 | 54.891361410598726 | -0.499712 | -15.0372 | 1 | 16 | 16 | 0.80 | 0.00 | - | no | Open |
| 1411 | 55.514118303168836 | -0.690938 | -22.965 | 1 | 20 | 16 | 0.80 | 0.20 | - | no | Open |
| 1407 | 56.145548799336055 | -0.64349 | -22.4519 | 1 | 18 | 13 | 0.65 | 0.00 | - | no | Open |
| 1405 | 56.657433966594915 | -0.546343 | -18.842 | 1 | 13 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1404 | 57.05719919322622 | -0.505622 | -19.0249 | 0 | 14 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1406 | 57.587599134029524 | -0.768061 | -22.1005 | 1 | 22 | 18 | 0.90 | 0.20 | - | yes | Open |
| 1401 | 57.66004617041284 | -0.505714 | -16.7854 | 1 | 16 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1410 | 58.30911582205452 | -0.471308 | -11.9012 | 1 | 16 | 10 | 0.50 | 0.00 | - | yes | Current |
| 1415 | 58.73660687944592 | -0.626569 | -17.222 | 0 | 18 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1414 | 61.57258867453939 | -0.688021 | -16.8565 | 1 | 21 | 17 | 0.85 | 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
-11.901kcal/mol
Ligand efficiency (LE)
-0.3306kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.360
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
490.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.19
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
129.57kcal/mol
Minimised FF energy
93.74kcal/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.