FAIRMol

Z49712358

Pose ID 12096 Compound 3423 Pose 575

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 Z49712358
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 high Native strong SASA done
Strain ΔE
7.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.42
Burial
73%
Hydrophobic fit
91%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Low conformational strain (7.5 kcal/mol) ✓ Excellent LE (-1.143 kcal/mol/HA) ✓ Good fit quality (FQ -9.75) ✓ Good H-bonds (3 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-24.008
kcal/mol
LE
-1.143
kcal/mol/HA
Fit Quality
-9.75
FQ (Leeson)
HAC
21
heavy atoms
MW
277
Da
LogP
3.78
cLogP
Final rank
2.5838
rank score
Inter norm
-1.035
normalised
Contacts
14
H-bonds 5
Strain ΔE
7.5 kcal/mol
SASA buried
73%
Lipo contact
91% BSA apolar/total
SASA unbound
519 Ų
Apolar buried
345 Ų

Interaction summary

HBD 2 HBA 1 HY 8 PI 2 CLASH 2

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.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap8Native recall0.62
Jaccard0.42RMSD-
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
571 2.0935925308309 -1.06981 -24.8203 4 14 0 0.00 - - no Open
575 2.5837901059382946 -1.03463 -24.0075 5 14 8 0.62 - - no Current
545 2.674304460927894 -1.13412 -26.138 7 13 0 0.00 - - no Open
575 3.1841179957797565 -1.13473 -22.6938 4 11 0 0.00 - - no Open
567 4.607903799469551 -1.16439 -21.1887 7 14 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 -24.008kcal/mol
Ligand efficiency (LE) -1.1432kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.751
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 277.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.78
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 7.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 89.72kcal/mol
Minimised FF energy 82.21kcal/mol

SASA & burial

✓ computed
SASA (unbound) 519.0Ų
Total solvent-accessible surface area of free ligand
BSA total 380.2Ų
Buried surface area upon binding
BSA apolar 344.5Ų
Hydrophobic contacts buried
BSA polar 35.6Ų
Polar contacts buried
Fraction buried 73.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3086.4Ų
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 1473.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)