FAIRMol

OHD_Babesia_20

Pose ID 11557 Compound 660 Pose 36

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 OHD_Babesia_20
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
43.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.53
Burial
63%
Hydrophobic fit
78%
Reason: strain 43.7 kcal/mol
strain ΔE 43.7 kcal/mol 2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.505 kcal/mol/HA) ✓ Good fit quality (FQ -5.24) ✓ Strong H-bond network (7 bonds) ✓ Good burial (63% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (43.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (22)
Score
-19.680
kcal/mol
LE
-0.505
kcal/mol/HA
Fit Quality
-5.24
FQ (Leeson)
HAC
39
heavy atoms
MW
543
Da
LogP
0.62
cLogP
Strain ΔE
43.7 kcal/mol
SASA buried
63%
Lipo contact
78% BSA apolar/total
SASA unbound
761 Ų
Apolar buried
372 Ų

Interaction summary

HB 7 HY 24 PI 2 CLASH 2

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 rank4.892Score-19.680
Inter norm-0.561Intra norm0.056
Top1000noExcludedno
Contacts16H-bonds7
Artifact reasongeometry warning; 22 clashes; 2 protein clashes; high strain Δ 43.7
Residues
CYS52 GLU18 GLY13 GLY15 GLY49 ILE106 ILE339 LEU17 MET113 SER109 SER14 THR335 TRP21 TYR110 VAL53 VAL58

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 overlap10Native recall0.77
Jaccard0.53RMSD-
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
36 4.891546851860806 -0.56057 -19.6797 7 16 10 0.77 - - no Current
45 4.966403150445621 -0.642243 -19.9102 8 17 0 0.00 - - no Open
49 6.567048991533472 -0.682598 -23.6514 8 17 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 -19.680kcal/mol
Ligand efficiency (LE) -0.5046kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.237
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 39HA

Physicochemical properties
Molecular weight 542.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.62
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 128.61kcal/mol
Minimised FF energy 84.90kcal/mol

SASA & burial

✓ computed
SASA (unbound) 761.3Ų
Total solvent-accessible surface area of free ligand
BSA total 476.9Ų
Buried surface area upon binding
BSA apolar 372.3Ų
Hydrophobic contacts buried
BSA polar 104.7Ų
Polar contacts buried
Fraction buried 62.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3209.4Ų
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 1471.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)