FAIRMol

Z277540138

Pose ID 13372 Compound 360 Pose 493

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 Z277540138
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
28.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.62, H-bond role recall 0.00
Burial
50%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 48% of hydrophobic surface appears solvent-exposed (11/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.610 kcal/mol/HA) ✓ Good fit quality (FQ -6.05) ✓ Good H-bonds (4 bonds) ✓ Good burial (50% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (28.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-20.134
kcal/mol
LE
-0.610
kcal/mol/HA
Fit Quality
-6.05
FQ (Leeson)
HAC
33
heavy atoms
MW
494
Da
LogP
3.64
cLogP
Final rank
4.5664
rank score
Inter norm
-0.579
normalised
Contacts
13
H-bonds 7
Strain ΔE
28.2 kcal/mol
SASA buried
50%
Lipo contact
79% BSA apolar/total
SASA unbound
816 Ų
Apolar buried
320 Ų

Interaction summary

HBD 2 HBA 2 HY 4 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap8Native recall1.00
Jaccard0.62RMSD-
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
460 0.6519554372013339 -0.915239 -35.1703 5 17 0 0.00 0.00 - no Open
534 2.127728214395661 -0.824251 -28.5767 2 19 0 0.00 0.00 - no Open
475 2.871927623588891 -0.685703 -14.4773 3 19 0 0.00 0.00 - no Open
489 2.8906447746620816 -0.804653 -27.0185 6 15 0 0.00 0.00 - no Open
519 3.3855222369474767 -0.670185 -21.9094 6 17 0 0.00 0.00 - no Open
493 4.566432422981136 -0.578552 -20.134 7 13 8 1.00 0.00 - no Current
491 4.603364842916196 -0.786607 -26.2787 3 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 -20.134kcal/mol
Ligand efficiency (LE) -0.6101kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.054
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 494.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.64
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -141.29kcal/mol
Minimised FF energy -169.52kcal/mol

SASA & burial

✓ computed
SASA (unbound) 815.9Ų
Total solvent-accessible surface area of free ligand
BSA total 404.6Ų
Buried surface area upon binding
BSA apolar 320.1Ų
Hydrophobic contacts buried
BSA polar 84.5Ų
Polar contacts buried
Fraction buried 49.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3220.4Ų
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 1528.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)