FAIRMol

Z24565962

Pose ID 12061 Compound 1264 Pose 540

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
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand Z24565962
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
24.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.69, Jaccard 0.50
Burial
71%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.701 kcal/mol/HA) ✓ Good fit quality (FQ -6.96) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (71% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (24.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-23.133
kcal/mol
LE
-0.701
kcal/mol/HA
Fit Quality
-6.96
FQ (Leeson)
HAC
33
heavy atoms
MW
483
Da
LogP
4.38
cLogP
Strain ΔE
24.3 kcal/mol
SASA buried
71%
Lipo contact
82% BSA apolar/total
SASA unbound
741 Ų
Apolar buried
432 Ų

Interaction summary

HB 7 HY 24 PI 3 CLASH 2
Final rank2.711Score-23.133
Inter norm-0.642Intra norm-0.059
Top1000noExcludedno
Contacts14H-bonds3
Artifact reasongeometry warning; 7 clashes; 2 protein clashes; moderate strain Δ 21.5
Residues
ASP116 CYS52 GLU18 GLY13 GLY49 ILE106 ILE339 LEU17 MET113 SER109 SER14 TRP21 TYR110 VAL53

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

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 overlap9Native recall0.69
Jaccard0.50RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

HB · H-bonds
Mode: permissive. 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
500 2.0498656463321923 -0.829319 -28.8676 10 16 0 0.00 - - no Open
527 2.2281217810212235 -0.893909 -32.4636 4 13 0 0.00 - - no Open
540 2.711073966387919 -0.641849 -23.1334 3 14 9 0.69 - - 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 -23.133kcal/mol
Ligand efficiency (LE) -0.7010kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.955
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 482.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.38
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 27.24kcal/mol
Minimised FF energy 2.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 740.8Ų
Total solvent-accessible surface area of free ligand
BSA total 524.1Ų
Buried surface area upon binding
BSA apolar 432.4Ų
Hydrophobic contacts buried
BSA polar 91.7Ų
Polar contacts buried
Fraction buried 70.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3174.8Ų
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 1488.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)