FAIRMol

Z49712358

Pose ID 13441 Compound 5317 Pose 562

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand Z49712358
PDB9IFH↗

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
35.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Burial
44%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.899 kcal/mol/HA) ✓ Good fit quality (FQ -7.67) ✓ Strong H-bond network (7 bonds) ✓ Good burial (44% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (35.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-18.886
kcal/mol
LE
-0.899
kcal/mol/HA
Fit Quality
-7.67
FQ (Leeson)
HAC
21
heavy atoms
MW
277
Da
LogP
3.78
cLogP
Strain ΔE
35.1 kcal/mol
SASA buried
44%
Lipo contact
79% BSA apolar/total
SASA unbound
509 Ų
Apolar buried
179 Ų

Interaction summary

HB 7 HY 12 PI 1 CLASH 3

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

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank4.906Score-18.886
Inter norm-0.908Intra norm0.009
Top1000noExcludedno
Contacts7H-bonds7
Artifact reasongeometry warning; 10 clashes; 3 protein clashes; high strain Δ 35.1
Residues
ASN402 LEU399 LYS410 PHE396 PRO398 SER395 THR397

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 overlap5Native recall0.62
Jaccard0.50RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
562 4.906302610565335 -0.908144 -18.8864 7 7 5 0.62 0.00 - 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 -18.886kcal/mol
Ligand efficiency (LE) -0.8994kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.671
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 277.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.78
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 108.39kcal/mol
Minimised FF energy 73.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 508.6Ų
Total solvent-accessible surface area of free ligand
BSA total 225.9Ų
Buried surface area upon binding
BSA apolar 178.8Ų
Hydrophobic contacts buried
BSA polar 47.1Ų
Polar contacts buried
Fraction buried 44.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2994.2Ų
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 1522.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)