FAIRMol

Z237462396

Pose ID 10625 Compound 3802 Pose 460

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 Z237462396
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
17.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.42, Jaccard 0.25
Burial
73%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.927 kcal/mol/HA) ✓ Good fit quality (FQ -8.31) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Moderate strain (17.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-22.260
kcal/mol
LE
-0.927
kcal/mol/HA
Fit Quality
-8.31
FQ (Leeson)
HAC
24
heavy atoms
MW
316
Da
LogP
2.46
cLogP
Strain ΔE
17.6 kcal/mol
SASA buried
73%
Lipo contact
70% BSA apolar/total
SASA unbound
553 Ų
Apolar buried
282 Ų

Interaction summary

HB 6 HY 19 PI 0 CLASH 4
Final rank2.613Score-22.260
Inter norm-1.007Intra norm0.080
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 10 clashes; 1 protein clash
Residues
ALA90 ASN91 GLY214 GLY215 LYS211 LYS89 LYS93 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 overlap5Native recall0.42
Jaccard0.25RMSD-
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
460 2.6128996786723255 -1.00729 -22.2601 6 13 5 0.42 - - no Current
368 3.302336009876763 -1.05947 -20.2217 7 13 0 0.00 - - no Open
359 3.7690631860668535 -0.996286 -22.0331 7 14 0 0.00 - - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -22.260kcal/mol
Ligand efficiency (LE) -0.9275kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.312
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 316.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.46
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 71.67kcal/mol
Minimised FF energy 54.04kcal/mol

SASA & burial

✓ computed
SASA (unbound) 553.4Ų
Total solvent-accessible surface area of free ligand
BSA total 405.5Ų
Buried surface area upon binding
BSA apolar 282.4Ų
Hydrophobic contacts buried
BSA polar 123.0Ų
Polar contacts buried
Fraction buried 73.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2985.4Ų
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 1500.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)