FAIRMol

Z44426342

Pose ID 13424 Compound 1266 Pose 545

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 Z44426342
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
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
31.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 1.00, Jaccard 0.57, H-bond role recall 1.00
Burial
58%
Hydrophobic fit
91%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.558 kcal/mol/HA) ✓ Good fit quality (FQ -5.67) ✓ Good H-bonds (3 bonds) ✓ Good burial (58% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ Very high strain energy (31.5 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (22)
Score
-20.102
kcal/mol
LE
-0.558
kcal/mol/HA
Fit Quality
-5.67
FQ (Leeson)
HAC
36
heavy atoms
MW
501
Da
LogP
5.91
cLogP
Strain ΔE
31.5 kcal/mol
SASA buried
58%
Lipo contact
91% BSA apolar/total
SASA unbound
799 Ų
Apolar buried
423 Ų

Interaction summary

HB 3 HY 16 PI 3 CLASH 5

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 rank2.910Score-20.102
Inter norm-0.557Intra norm-0.007
Top1000noExcludedno
Contacts14H-bonds3
Artifact reasongeometry warning; 22 clashes; 7 protein contact clashes; high strain Δ 31.5
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 PHE396 PRO398 PRO462 SER394 SER395 SER464 SER470 THR397 THR463

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
Jaccard0.57RMSD-
HB strict1Strict recall0.50
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
551 2.2430881686606607 -0.746127 -24.7422 3 22 0 0.00 0.00 - no Open
545 2.9098520734152262 -0.557097 -20.1019 3 14 8 1.00 1.00 - no Current
527 4.377424192032045 -0.76659 -25.4848 7 16 0 0.00 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 -20.102kcal/mol
Ligand efficiency (LE) -0.5584kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.675
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 501.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.91
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 76.25kcal/mol
Minimised FF energy 44.77kcal/mol

SASA & burial

✓ computed
SASA (unbound) 799.2Ų
Total solvent-accessible surface area of free ligand
BSA total 464.3Ų
Buried surface area upon binding
BSA apolar 422.6Ų
Hydrophobic contacts buried
BSA polar 41.7Ų
Polar contacts buried
Fraction buried 58.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3239.1Ų
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 1543.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)