FAIRMol

Z27358498

Pose ID 13478 Compound 5218 Pose 599

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 Z27358498
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 high Native strong SASA done
Strain ΔE
16.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.67, H-bond role recall 1.00
Burial
58%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.799 kcal/mol/HA) ✓ Good fit quality (FQ -7.46) ✓ Strong H-bond network (8 bonds) ✓ Good burial (58% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Moderate strain (16.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-21.575
kcal/mol
LE
-0.799
kcal/mol/HA
Fit Quality
-7.46
FQ (Leeson)
HAC
27
heavy atoms
MW
386
Da
LogP
3.39
cLogP
Strain ΔE
16.2 kcal/mol
SASA buried
58%
Lipo contact
80% BSA apolar/total
SASA unbound
665 Ų
Apolar buried
309 Ų

Interaction summary

HB 8 HY 14 PI 1 CLASH 2
Final rank2.490Score-21.575
Inter norm-0.716Intra norm-0.083
Top1000noExcludedno
Contacts12H-bonds8
Artifact reasongeometry warning; 10 clashes; 1 protein clash
Residues
ASN402 GLU467 LEU399 MET393 MET471 PHE396 PRO398 SER394 SER395 SER470 SER475 THR397

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

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
Jaccard0.67RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
599 2.4902725446631746 -0.715647 -21.5749 8 12 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 -21.575kcal/mol
Ligand efficiency (LE) -0.7991kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.455
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 386.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.39
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 37.20kcal/mol
Minimised FF energy 20.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 665.0Ų
Total solvent-accessible surface area of free ligand
BSA total 385.8Ų
Buried surface area upon binding
BSA apolar 308.6Ų
Hydrophobic contacts buried
BSA polar 77.2Ų
Polar contacts buried
Fraction buried 58.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3119.5Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1495.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)