FAIRMol

Z56842660

Pose ID 10733 Compound 91 Pose 568

DB SELECTIONDocking 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
T16
T. brucei TR (Dimer interface (site 2)) T. brucei Dimer interface (site 2)
Ligand Z56842660
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
Likely artefact or unreliable pose
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
31.6 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.50, Jaccard 0.29
Burial
73%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.938 kcal/mol/HA) ✓ Good fit quality (FQ -8.64) ✓ Good H-bonds (5 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Very high strain energy (31.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Internal clashes (8)
Score
-24.389
kcal/mol
LE
-0.938
kcal/mol/HA
Fit Quality
-8.64
FQ (Leeson)
HAC
26
heavy atoms
MW
383
Da
LogP
5.02
cLogP
Strain ΔE
31.6 kcal/mol
SASA buried
73%
Lipo contact
77% BSA apolar/total
SASA unbound
603 Ų
Apolar buried
339 Ų

Interaction summary

HB 5 HY 24 PI 0 CLASH 5
Final rank1.504Score-24.389
Inter norm-0.924Intra norm-0.014
Top1000noExcludedno
Contacts15H-bonds5
Artifact reasongeometry warning; 8 clashes; 9 protein contact clashes; high strain Δ 31.6
Residues
ALA209 ALA90 ASN91 GLY214 GLY215 LYS211 LYS89 LYS93 MET70 PRO187 PRO212 PRO213 TRP92 TYR210 VAL88

Protein summary

493 residues
Protein targetT16Atoms7551
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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts12
PoseOpen native poseHB0
IFP residues
ALA90 ARG74 GLY85 LEU73 LYS89 MET70 PHE83 PRO212 PRO213 SER86 SER87 VAL88
Current overlap6Native recall0.50
Jaccard0.29RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
571 0.9094118158195158 -1.01549 -27.4673 4 13 0 0.00 - - no Open
560 1.0185294571365404 -1.01104 -27.3748 4 13 0 0.00 - - no Open
568 1.504258611655206 -0.923793 -24.3892 5 15 6 0.50 - - 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 -24.389kcal/mol
Ligand efficiency (LE) -0.9380kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.643
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 383.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.02
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 99.18kcal/mol
Minimised FF energy 67.60kcal/mol

SASA & burial

✓ computed
SASA (unbound) 603.3Ų
Total solvent-accessible surface area of free ligand
BSA total 439.0Ų
Buried surface area upon binding
BSA apolar 339.2Ų
Hydrophobic contacts buried
BSA polar 99.8Ų
Polar contacts buried
Fraction buried 72.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3066.8Ų
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 1492.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)