FAIRMol

OHD_Babesia_19

Pose ID 8852 Compound 3354 Pose 44

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand OHD_Babesia_19
PDB1NJJ↗

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 mixed SASA done
Strain ΔE
44.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.40, Jaccard 0.32, H-bond role recall 0.40
Burial
60%
Hydrophobic fit
71%
Reason: strain 44.6 kcal/mol
strain ΔE 44.6 kcal/mol 4 protein-contact clashes 4 intramolecular clashes 81% of hydrophobic surface is solvent-exposed (21/26 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.578 kcal/mol/HA) ✓ Good fit quality (FQ -5.87) ✓ Good H-bonds (4 bonds) ✓ Good burial (60% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Extreme strain energy (44.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (20)
Score
-20.796
kcal/mol
LE
-0.578
kcal/mol/HA
Fit Quality
-5.87
FQ (Leeson)
HAC
36
heavy atoms
MW
498
Da
LogP
1.02
cLogP
Final rank
6.0047
rank score
Inter norm
-0.678
normalised
Contacts
10
H-bonds 11
Strain ΔE
44.6 kcal/mol
SASA buried
60%
Lipo contact
71% BSA apolar/total
SASA unbound
726 Ų
Apolar buried
313 Ų

Interaction summary

HBD 3 HBA 1 HY 1 PI 0 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap6Native recall0.40
Jaccard0.32RMSD-
HB strict1Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

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:ORX602

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
35 4.325126977199668 -0.75832 -24.4142 7 13 0 0.00 0.00 - no Open
35 5.730150167730409 -0.580774 -21.1521 8 16 0 0.00 0.00 - no Open
44 6.004742592877343 -0.677685 -20.7958 11 10 6 0.40 0.40 - 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 -20.796kcal/mol
Ligand efficiency (LE) -0.5777kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.871
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 497.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.02
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 44.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 140.17kcal/mol
Minimised FF energy 95.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 726.1Ų
Total solvent-accessible surface area of free ligand
BSA total 438.8Ų
Buried surface area upon binding
BSA apolar 312.8Ų
Hydrophobic contacts buried
BSA polar 125.9Ų
Polar contacts buried
Fraction buried 60.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2459.2Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1432.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)