FAIRMol

Z56779856

Pose ID 10783 Compound 2286 Pose 618

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
T16
T. brucei TR (Dimer interface (site 2)) T. brucei Dimer interface (site 2)
Ligand Z56779856
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 strong SASA done
Strain ΔE
34.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.37
Burial
66%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.746 kcal/mol/HA) ✓ Good fit quality (FQ -7.26) ✓ Good H-bonds (5 bonds) ✓ Deep burial (66% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Very high strain energy (34.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-23.113
kcal/mol
LE
-0.746
kcal/mol/HA
Fit Quality
-7.26
FQ (Leeson)
HAC
31
heavy atoms
MW
407
Da
LogP
5.25
cLogP
Final rank
2.7809
rank score
Inter norm
-0.756
normalised
Contacts
14
H-bonds 5
Strain ΔE
34.0 kcal/mol
SASA buried
66%
Lipo contact
81% BSA apolar/total
SASA unbound
687 Ų
Apolar buried
368 Ų

Interaction summary

HBA 5 HY 6 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

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

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name6RB5Contacts12
PoseOpen native poseHB0
IFP residues
ALA90 ARG74 GLY85 LEU73 LYS89 MET70 PHE83 PRO212 PRO213 SER86 SER87 VAL88
Current overlap7Native recall0.58
Jaccard0.37RMSD-
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
618 2.7809451592393097 -0.756201 -23.113 5 14 7 0.58 - - no Current
625 2.7945369204124924 -0.609663 -20.239 5 10 0 0.00 - - no Open
629 2.9601670035022902 -0.694595 -21.1592 2 15 0 0.00 - - no Open
610 3.9280906801648916 -0.927958 -27.8575 10 15 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 -23.113kcal/mol
Ligand efficiency (LE) -0.7456kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.264
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 407.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.25
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 120.07kcal/mol
Minimised FF energy 86.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 687.2Ų
Total solvent-accessible surface area of free ligand
BSA total 455.7Ų
Buried surface area upon binding
BSA apolar 367.6Ų
Hydrophobic contacts buried
BSA polar 88.2Ų
Polar contacts buried
Fraction buried 66.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3154.5Ų
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 1497.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)