FAIRMol

Z56174682

Pose ID 13362 Compound 3758 Pose 483

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 Z56174682
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
17.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.67, H-bond role recall 0.00
Burial
51%
Hydrophobic fit
78%
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 (-0.771 kcal/mol/HA) ✓ Good fit quality (FQ -6.91) ✓ Strong H-bond network (6 bonds) ✓ Good burial (51% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Moderate strain (17.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-18.512
kcal/mol
LE
-0.771
kcal/mol/HA
Fit Quality
-6.91
FQ (Leeson)
HAC
24
heavy atoms
MW
334
Da
LogP
3.99
cLogP
Strain ΔE
17.4 kcal/mol
SASA buried
51%
Lipo contact
78% BSA apolar/total
SASA unbound
559 Ų
Apolar buried
222 Ų

Interaction summary

HB 6 HY 17 PI 1 CLASH 1
Final rank4.208Score-18.512
Inter norm-0.904Intra norm0.133
Top1000noExcludedno
Contacts7H-bonds6
Artifact reasongeometry warning; 11 clashes; 3 protein clashes
Residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER395 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 overlap6Native recall0.75
Jaccard0.67RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
542 2.3265616095440724 -0.974797 -23.4667 6 13 0 0.00 0.00 - no Open
468 3.082846827730011 -1.01644 -20.1492 6 12 0 0.00 0.00 - no Open
483 4.207837023752851 -0.904172 -18.5122 6 7 6 0.75 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 -18.512kcal/mol
Ligand efficiency (LE) -0.7713kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.913
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 334.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.99
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 55.06kcal/mol
Minimised FF energy 37.61kcal/mol

SASA & burial

✓ computed
SASA (unbound) 559.3Ų
Total solvent-accessible surface area of free ligand
BSA total 283.2Ų
Buried surface area upon binding
BSA apolar 222.3Ų
Hydrophobic contacts buried
BSA polar 60.9Ų
Polar contacts buried
Fraction buried 50.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3009.7Ų
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 1518.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)