FAIRMol

Z56902329

Pose ID 11929 Compound 2846 Pose 408

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
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand Z56902329
PDB6RB5↗

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 mixed SASA done
Strain ΔE
32.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.54, Jaccard 0.44
Burial
62%
Hydrophobic fit
74%
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 (-0.782 kcal/mol/HA) ✓ Good fit quality (FQ -7.21) ✓ Good H-bonds (5 bonds) ✓ Good burial (62% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (32.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-20.337
kcal/mol
LE
-0.782
kcal/mol/HA
Fit Quality
-7.21
FQ (Leeson)
HAC
26
heavy atoms
MW
435
Da
LogP
1.98
cLogP
Strain ΔE
32.8 kcal/mol
SASA buried
62%
Lipo contact
74% BSA apolar/total
SASA unbound
613 Ų
Apolar buried
285 Ų

Interaction summary

HB 5 HY 24 PI 4 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 rank1.661Score-20.337
Inter norm-0.900Intra norm0.118
Top1000noExcludedno
Contacts10H-bonds5
Artifact reasongeometry warning; 7 clashes; 1 protein clash; high strain Δ 32.8
Residues
GLU18 GLY13 ILE106 ILE339 LEU17 MET113 SER109 SER14 TRP21 TYR110

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap7Native recall0.54
Jaccard0.44RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT18Atoms7550
Residues493Chains1
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:276; 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
355 1.3986381559687069 -1.35258 -35.2318 12 16 0 0.00 - - no Open
408 1.661138863672402 -0.8999 -20.3371 5 10 7 0.54 - - no Current
371 3.8893457067493027 -1.33147 -34.0855 12 20 0 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 -20.337kcal/mol
Ligand efficiency (LE) -0.7822kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.207
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 435.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.98
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 104.11kcal/mol
Minimised FF energy 71.35kcal/mol

SASA & burial

✓ computed
SASA (unbound) 612.8Ų
Total solvent-accessible surface area of free ligand
BSA total 383.0Ų
Buried surface area upon binding
BSA apolar 285.4Ų
Hydrophobic contacts buried
BSA polar 97.6Ų
Polar contacts buried
Fraction buried 62.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3044.4Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1517.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)