FAIRMol

Z45925616

Pose ID 13411 Compound 1370 Pose 532

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 Z45925616
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
8.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.54, H-bond role recall 0.00
Burial
62%
Hydrophobic fit
83%
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 (-0.628 kcal/mol/HA) ✓ Good fit quality (FQ -5.93) ✓ Good H-bonds (3 bonds) ✓ Good burial (62% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (8.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-17.579
kcal/mol
LE
-0.628
kcal/mol/HA
Fit Quality
-5.93
FQ (Leeson)
HAC
28
heavy atoms
MW
407
Da
LogP
5.83
cLogP
Strain ΔE
8.4 kcal/mol
SASA buried
62%
Lipo contact
83% BSA apolar/total
SASA unbound
655 Ų
Apolar buried
338 Ų

Interaction summary

HB 3 HY 19 PI 1 CLASH 1

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 rank3.351Score-17.579
Inter norm-0.669Intra norm0.042
Top1000noExcludedno
Contacts12H-bonds3
Artifact reasongeometry warning; 11 clashes; 2 protein clashes
Residues
ASN402 GLU466 GLU467 LEU399 MET393 PHE396 PRO398 PRO462 SER394 SER395 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 overlap7Native recall0.88
Jaccard0.54RMSD-
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
518 0.6120157704450939 -1.27329 -33.9374 6 22 0 0.00 0.00 - no Open
543 3.092241781824182 -1.06292 -27.7872 2 16 0 0.00 0.00 - no Open
532 3.350782921649517 -0.669419 -17.579 3 12 7 0.88 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 -17.579kcal/mol
Ligand efficiency (LE) -0.6278kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.927
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 406.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.83
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 8.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 55.44kcal/mol
Minimised FF energy 47.01kcal/mol

SASA & burial

✓ computed
SASA (unbound) 655.1Ų
Total solvent-accessible surface area of free ligand
BSA total 405.6Ų
Buried surface area upon binding
BSA apolar 338.3Ų
Hydrophobic contacts buried
BSA polar 67.3Ų
Polar contacts buried
Fraction buried 61.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3072.1Ų
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 1559.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)