FAIRMol

Z19352754

Pose ID 13546 Compound 2219 Pose 667

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 Z19352754
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
17.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.50, H-bond role recall 0.00
Burial
52%
Hydrophobic fit
67%
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 (-0.807 kcal/mol/HA) ✓ Good fit quality (FQ -7.53) ✓ Strong H-bond network (6 bonds) ✓ Good burial (52% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Moderate strain (17.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-21.797
kcal/mol
LE
-0.807
kcal/mol/HA
Fit Quality
-7.53
FQ (Leeson)
HAC
27
heavy atoms
MW
381
Da
LogP
1.83
cLogP
Strain ΔE
17.1 kcal/mol
SASA buried
52%
Lipo contact
67% BSA apolar/total
SASA unbound
625 Ų
Apolar buried
221 Ų

Interaction summary

HB 6 HY 13 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 rank3.994Score-21.797
Inter norm-0.746Intra norm-0.061
Top1000noExcludedno
Contacts10H-bonds6
Artifact reasongeometry warning; 13 clashes; 2 protein clashes
Residues
ASN402 GLU466 GLU467 LEU399 LYS410 PHE396 PRO398 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 overlap6Native recall0.75
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
662 2.387234550870066 -0.875978 -25.1448 3 13 0 0.00 0.00 - no Open
676 2.7504368620559965 -1.1322 -31.8335 10 20 0 0.00 0.00 - no Open
665 2.9348303597234553 -1.04997 -30.5922 4 16 0 0.00 0.00 - no Open
668 3.054569518894309 -1.19774 -32.9591 8 16 0 0.00 0.00 - no Open
667 3.994413850524842 -0.746194 -21.7975 6 10 6 0.75 0.00 - no Current
661 5.153622008531141 -1.22703 -35.7123 13 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 -21.797kcal/mol
Ligand efficiency (LE) -0.8073kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.532
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 381.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.83
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 60.22kcal/mol
Minimised FF energy 43.16kcal/mol

SASA & burial

✓ computed
SASA (unbound) 625.4Ų
Total solvent-accessible surface area of free ligand
BSA total 328.5Ų
Buried surface area upon binding
BSA apolar 221.3Ų
Hydrophobic contacts buried
BSA polar 107.2Ų
Polar contacts buried
Fraction buried 52.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3018.0Ų
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 1505.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)