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 (-0.563 kcal/mol/HA)
✓ Good fit quality (FQ -5.76)
✗ Very high strain energy (93.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.822
kcal/mol
LE
-0.563
kcal/mol/HA
Fit Quality
-5.76
FQ (Leeson)
HAC
37
heavy atoms
MW
504
Da
LogP
1.03
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 93.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 6
Severe clashes 0
| Final rank | 8.092708888080825 | Score | -20.8219 |
|---|---|---|---|
| Inter norm | -0.641587 | Intra norm | 0.0788342 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 1 |
| Artifact reason | geometry warning; 15 clashes; 6 protein contact clashes; high strain Δ 74.5 | ||
| Residues | A:ARG48;A:ASP52;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: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 | 13 | Native recall | 0.65 |
| Jaccard | 0.54 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1725 | 4.612891784941122 | -0.581194 | -19.5979 | 1 | 13 | 11 | 0.55 | 0.00 | - | no | Open |
| 1731 | 5.421028588298298 | -0.68472 | -22.0566 | 0 | 22 | 16 | 0.80 | 0.00 | - | no | Open |
| 1733 | 5.471286876358829 | -0.545653 | -22.7217 | 0 | 18 | 17 | 0.85 | 0.00 | - | no | Open |
| 1728 | 8.092708888080825 | -0.641587 | -20.8219 | 1 | 17 | 13 | 0.65 | 0.00 | - | no | Current |
| 1729 | 54.88614635171503 | -0.628169 | -20.9315 | 1 | 19 | 14 | 0.70 | 0.00 | - | no | Open |
| 1732 | 55.23839333189166 | -0.710971 | -20.7628 | 1 | 17 | 16 | 0.80 | 0.00 | - | no | Open |
| 1727 | 55.38915422514146 | -0.645377 | -19.0788 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1735 | 6.644088731945604 | -0.635424 | -22.8873 | 1 | 19 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1734 | 7.022921613411501 | -0.632344 | -20.9556 | 1 | 17 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1730 | 56.415731472060195 | -0.612127 | -20.8341 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1726 | 58.23205605313864 | -0.629934 | -19.7935 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1736 | 58.68369023909268 | -0.666683 | -15.1632 | 0 | 21 | 18 | 0.90 | 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
-20.822kcal/mol
Ligand efficiency (LE)
-0.5628kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.761
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
503.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.03
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
93.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
381.07kcal/mol
Minimised FF energy
287.87kcal/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.