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 (-0.531 kcal/mol/HA)
✓ Good fit quality (FQ -5.40)
✗ Very high strain energy (35.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-19.116
kcal/mol
LE
-0.531
kcal/mol/HA
Fit Quality
-5.40
FQ (Leeson)
HAC
36
heavy atoms
MW
489
Da
LogP
1.10
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 35.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 0
Clashes 8
Severe clashes 1
| Final rank | 56.04509772837666 | Score | -19.1156 |
|---|---|---|---|
| Inter norm | -0.529835 | Intra norm | -0.00115434 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 13 clashes; 1 protein clash | ||
| Residues | A:ARG48;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR83;A:TRP47;A:VAL156;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 | 12 | Native recall | 0.60 |
| Jaccard | 0.52 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| 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
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1326 | 4.602018481241874 | -0.629637 | -24.3257 | 0 | 21 | 18 | 0.90 | 0.00 | - | no | Open |
| 1322 | 5.205125837797029 | -0.735088 | -26.262 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1323 | 5.540528703381871 | -0.723736 | -24.582 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1334 | 6.297800712726597 | -0.683268 | -26.5183 | 1 | 14 | 11 | 0.55 | 0.00 | - | no | Open |
| 1331 | 6.546825397264573 | -0.728936 | -24.482 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1332 | 7.592079784702666 | -0.638139 | -21.1338 | 1 | 19 | 18 | 0.90 | 0.00 | - | no | Open |
| 1321 | 54.8996813117031 | -0.62467 | -20.5225 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1327 | 54.90760247093767 | -0.654613 | -24.618 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1325 | 55.07803929523387 | -0.602244 | -24.9353 | 1 | 16 | 15 | 0.75 | 0.00 | - | no | Open |
| 1328 | 55.0971827192367 | -0.654138 | -24.6725 | 1 | 16 | 13 | 0.65 | 0.00 | - | no | Open |
| 1324 | 56.04509772837666 | -0.529835 | -19.1156 | 1 | 15 | 12 | 0.60 | 0.20 | - | yes | Current |
| 1333 | 56.567713421730375 | -0.574165 | -23.511 | 0 | 11 | 9 | 0.45 | 0.00 | - | yes | Open |
| 1329 | 56.6890068989602 | -0.615056 | -21.267 | 0 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1330 | 57.15601895077896 | -0.703412 | -24.8684 | 1 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1336 | 57.72511530461719 | -0.745056 | -27.5138 | 2 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1335 | 58.1900674430388 | -0.628006 | -22.7609 | 1 | 20 | 16 | 0.80 | 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
-19.116kcal/mol
Ligand efficiency (LE)
-0.5310kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.397
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
488.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.10
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
202.86kcal/mol
Minimised FF energy
167.31kcal/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.