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 (-0.542 kcal/mol/HA)
✓ Good fit quality (FQ -5.47)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (23.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-18.987
kcal/mol
LE
-0.542
kcal/mol/HA
Fit Quality
-5.47
FQ (Leeson)
HAC
35
heavy atoms
MW
471
Da
LogP
4.21
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 23.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 3
Clashes 12
Severe clashes 0
| Final rank | 7.4826965659339235 | Score | -18.9868 |
|---|---|---|---|
| Inter norm | -0.625219 | Intra norm | 0.0827394 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 3 |
| Artifact reason | geometry warning; 18 clashes; 12 protein contact clashes; high strain Δ 23.4 | ||
| Residues | A:ALA32;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR180;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 | 17 | Native recall | 0.85 |
| Jaccard | 0.81 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1372 | 5.311626435603067 | -0.647113 | -20.6698 | 3 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1371 | 5.669948475886622 | -0.559592 | -19.9372 | 1 | 18 | 18 | 0.90 | 0.00 | - | no | Open |
| 1376 | 7.4826965659339235 | -0.625219 | -18.9868 | 3 | 18 | 17 | 0.85 | 0.00 | - | no | Current |
| 1374 | 57.36169557563533 | -0.782227 | -24.7766 | 1 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 1373 | 56.73500028767851 | -0.742082 | -15.15 | 1 | 19 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1370 | 57.345514048368344 | -0.679507 | -14.5826 | 3 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1375 | 59.117553014610415 | -0.735447 | -21.8849 | 1 | 19 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1369 | 59.30266864444356 | -0.591458 | -21.202 | 1 | 15 | 11 | 0.55 | 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
-18.987kcal/mol
Ligand efficiency (LE)
-0.5425kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.472
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
470.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.21
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
81.73kcal/mol
Minimised FF energy
58.18kcal/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.