FAIRMol

Z56867851

Pose ID 13474 Compound 5263 Pose 595

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand Z56867851
PDB9IFH↗

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
52.4 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 1.00, Jaccard 0.47, H-bond role recall 1.00
Burial
63%
Hydrophobic fit
78%
Reason: strain 52.4 kcal/mol
strain ΔE 52.4 kcal/mol 4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.494 kcal/mol/HA) ✓ Good fit quality (FQ -5.06) ✓ Good H-bonds (4 bonds) ✓ Good burial (63% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (52.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-18.290
kcal/mol
LE
-0.494
kcal/mol/HA
Fit Quality
-5.06
FQ (Leeson)
HAC
37
heavy atoms
MW
497
Da
LogP
4.38
cLogP
Final rank
3.6132
rank score
Inter norm
-0.512
normalised
Contacts
17
H-bonds 8
Strain ΔE
52.4 kcal/mol
SASA buried
63%
Lipo contact
78% BSA apolar/total
SASA unbound
801 Ų
Apolar buried
397 Ų

Interaction summary

HBD 2 HBA 2 HY 4 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap8Native recall1.00
Jaccard0.47RMSD-
HB strict2Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
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:264; 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
595 3.6131909258997 -0.511809 -18.2895 8 17 8 1.00 1.00 - 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 -18.290kcal/mol
Ligand efficiency (LE) -0.4943kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.061
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 37HA

Physicochemical properties
Molecular weight 497.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.38
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 52.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 189.98kcal/mol
Minimised FF energy 137.54kcal/mol

SASA & burial

✓ computed
SASA (unbound) 800.9Ų
Total solvent-accessible surface area of free ligand
BSA total 507.3Ų
Buried surface area upon binding
BSA apolar 397.2Ų
Hydrophobic contacts buried
BSA polar 110.1Ų
Polar contacts buried
Fraction buried 63.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3172.1Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1540.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)