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 (-0.818 kcal/mol/HA)
✓ Good fit quality (FQ -7.89)
✗ Very high strain energy (41.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.545
kcal/mol
LE
-0.818
kcal/mol/HA
Fit Quality
-7.89
FQ (Leeson)
HAC
30
heavy atoms
MW
406
Da
LogP
1.85
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 41.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 54.68616997773502 | Score | -24.5454 |
|---|---|---|---|
| Inter norm | -0.844469 | Intra norm | 0.0262902 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 1 |
| Artifact reason | geometry warning; 14 clashes; 8 protein contact clashes | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PRO88;A:SER86;A:THR54;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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 | 17 | Native recall | 0.85 |
| Jaccard | 0.74 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1679 | 3.8211097807997416 | -0.858111 | -25.7538 | 0 | 21 | 18 | 0.90 | 0.00 | - | no | Open |
| 1682 | 3.84020984989632 | -0.710977 | -20.9194 | 0 | 16 | 16 | 0.80 | 0.00 | - | no | Open |
| 1674 | 3.934725849205876 | -0.721152 | -21.6615 | 0 | 18 | 15 | 0.75 | 0.00 | - | no | Open |
| 1681 | 4.300761839522966 | -0.688906 | -20.3079 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1678 | 4.337918151361544 | -0.681481 | -18.9776 | 0 | 18 | 15 | 0.75 | 0.00 | - | no | Open |
| 1683 | 4.410761028776333 | -0.647598 | -20.1427 | 0 | 18 | 15 | 0.75 | 0.00 | - | no | Open |
| 1688 | 53.53925770848332 | -0.702991 | -18.1506 | 2 | 19 | 16 | 0.80 | 0.20 | - | no | Open |
| 1673 | 53.59461909940166 | -0.631063 | -16.4089 | 0 | 17 | 17 | 0.85 | 0.00 | - | no | Open |
| 1680 | 54.250888920292375 | -0.703922 | -19.1243 | 1 | 18 | 17 | 0.85 | 0.00 | - | no | Open |
| 1675 | 54.557920964248666 | -0.664692 | -19.5125 | 0 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1687 | 54.68616997773502 | -0.844469 | -24.5454 | 1 | 20 | 17 | 0.85 | 0.00 | - | no | Current |
| 1676 | 54.87589185365573 | -0.68266 | -19.8441 | 0 | 15 | 11 | 0.55 | 0.00 | - | no | Open |
| 1684 | 54.9344767219574 | -0.699194 | -21.0605 | 0 | 16 | 12 | 0.60 | 0.00 | - | no | Open |
| 1685 | 55.24792418956906 | -0.719354 | -17.7936 | 1 | 19 | 16 | 0.80 | 0.20 | - | no | Open |
| 1686 | 55.796250310983375 | -0.81184 | -20.8051 | 1 | 18 | 15 | 0.75 | 0.20 | - | no | Open |
| 1677 | 54.90345637625511 | -0.726472 | -19.0427 | 0 | 18 | 15 | 0.75 | 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
-24.545kcal/mol
Ligand efficiency (LE)
-0.8182kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.892
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
405.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.85
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
106.72kcal/mol
Minimised FF energy
65.74kcal/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.