FAIRMol

Z1501480413

Pose ID 12133 Compound 4853 Pose 612

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand Z1501480413
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
30.7 kcal/mol
Protein clashes
5
Internal clashes
9
Native overlap
contact recall 0.69, Jaccard 0.64
Burial
60%
Hydrophobic fit
82%
Reason: 9 internal clashes
5 protein-contact clashes 9 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.631 kcal/mol/HA) ✓ Good fit quality (FQ -6.26) ✓ Good H-bonds (4 bonds) ✓ Good burial (60% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Very high strain energy (30.7 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Internal clashes (9)
Score
-20.816
kcal/mol
LE
-0.631
kcal/mol/HA
Fit Quality
-6.26
FQ (Leeson)
HAC
33
heavy atoms
MW
475
Da
LogP
1.61
cLogP
Strain ΔE
30.7 kcal/mol
SASA buried
60%
Lipo contact
82% BSA apolar/total
SASA unbound
769 Ų
Apolar buried
382 Ų

Interaction summary

HB 4 HY 24 PI 2 CLASH 0

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.
Final rank1.369Score-20.816
Inter norm-0.623Intra norm-0.008
Top1000noExcludedno
Contacts10H-bonds4
Artifact reasongeometry warning; 9 clashes; 5 protein contact clashes; high strain Δ 30.3
Residues
ASP116 GLU18 GLY112 LEU17 MET113 SER109 THR117 THR25 TRP21 TYR110

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap9Native recall0.69
Jaccard0.64RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT18Atoms7550
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
612 1.3690544483299665 -0.623141 -20.8163 4 10 9 0.69 - - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -20.816kcal/mol
Ligand efficiency (LE) -0.6308kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.259
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 474.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.61
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -13.25kcal/mol
Minimised FF energy -43.94kcal/mol

SASA & burial

✓ computed
SASA (unbound) 769.1Ų
Total solvent-accessible surface area of free ligand
BSA total 463.7Ų
Buried surface area upon binding
BSA apolar 382.4Ų
Hydrophobic contacts buried
BSA polar 81.3Ų
Polar contacts buried
Fraction buried 60.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3250.4Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1460.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)