FAIRMol

Z56778002

Pose ID 10648 Compound 4677 Pose 483

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 Z56778002
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 mixed SASA done
Strain ΔE
49.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.42, Jaccard 0.23
Burial
57%
Hydrophobic fit
73%
Reason: strain 49.8 kcal/mol
strain ΔE 49.8 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.474 kcal/mol/HA) ✓ Good fit quality (FQ -4.89) ✓ Good H-bonds (5 bonds) ✓ Good burial (57% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Extreme strain energy (49.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-18.013
kcal/mol
LE
-0.474
kcal/mol/HA
Fit Quality
-4.89
FQ (Leeson)
HAC
38
heavy atoms
MW
562
Da
LogP
3.55
cLogP
Strain ΔE
49.8 kcal/mol
SASA buried
57%
Lipo contact
73% BSA apolar/total
SASA unbound
836 Ų
Apolar buried
346 Ų

Interaction summary

HB 5 HY 22 PI 0 CLASH 3

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
Final rank4.176Score-18.013
Inter norm-0.625Intra norm0.151
Top1000noExcludedno
Contacts15H-bonds5
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; high strain Δ 49.8
Residues
ALA209 ALA90 ASN91 GLU186 GLY214 GLY215 LYS211 LYS89 LYS93 MET70 PRO187 PRO212 PRO213 TRP92 TYR210

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 overlap5Native recall0.42
Jaccard0.23RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
449 2.7946875374172264 -0.63601 -18.9238 8 20 0 0.00 - - no Open
413 2.9810047788499694 -0.525751 -19.8922 4 15 0 0.00 - - no Open
483 4.175862271338297 -0.625381 -18.0133 5 15 5 0.42 - - 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 -18.013kcal/mol
Ligand efficiency (LE) -0.4740kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.887
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 38HA

Physicochemical properties
Molecular weight 561.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.55
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 49.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 3.75kcal/mol
Minimised FF energy -46.04kcal/mol

SASA & burial

✓ computed
SASA (unbound) 836.4Ų
Total solvent-accessible surface area of free ligand
BSA total 473.5Ų
Buried surface area upon binding
BSA apolar 346.5Ų
Hydrophobic contacts buried
BSA polar 127.0Ų
Polar contacts buried
Fraction buried 56.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3273.8Ų
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 1451.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)