FAIRMol

OHD_Babesia_20

Pose ID 8853 Compound 660 Pose 45

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_20
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
57.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.47, Jaccard 0.28, H-bond role recall 0.20
Burial
63%
Hydrophobic fit
72%
Reason: strain 57.2 kcal/mol
strain ΔE 57.2 kcal/mol 5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.510 kcal/mol/HA) ✓ Good fit quality (FQ -5.30) ✓ Strong H-bond network (8 bonds) ✓ Good burial (63% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Extreme strain energy (57.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (25)
Score
-19.910
kcal/mol
LE
-0.510
kcal/mol/HA
Fit Quality
-5.30
FQ (Leeson)
HAC
39
heavy atoms
MW
543
Da
LogP
0.62
cLogP
Strain ΔE
57.2 kcal/mol
SASA buried
63%
Lipo contact
72% BSA apolar/total
SASA unbound
780 Ų
Apolar buried
355 Ų

Interaction summary

HB 8 HY 9 PI 0 CLASH 5

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank4.966Score-19.910
Inter norm-0.642Intra norm0.132
Top1000noExcludedno
Contacts17H-bonds8
Artifact reasongeometry warning; 25 clashes; 1 protein clash; high strain Δ 57.2
Residues
ARG22 ARG50 ASN20 ASP44 CYS26 GLN341 GLU343 GLU384 ILE345 LEU25 LEU339 LEU382 PRO344 SER410 THR21 THR285 VAL408

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 overlap7Native recall0.47
Jaccard0.28RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
36 4.891546851860806 -0.56057 -19.6797 7 16 0 0.00 0.00 - no Open
45 4.966403150445621 -0.642243 -19.9102 8 17 7 0.47 0.20 - no Current
49 6.567048991533472 -0.682598 -23.6514 8 17 0 0.00 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 -19.910kcal/mol
Ligand efficiency (LE) -0.5105kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.298
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) 57.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 147.47kcal/mol
Minimised FF energy 90.23kcal/mol

SASA & burial

✓ computed
SASA (unbound) 780.4Ų
Total solvent-accessible surface area of free ligand
BSA total 494.9Ų
Buried surface area upon binding
BSA apolar 355.0Ų
Hydrophobic contacts buried
BSA polar 139.9Ų
Polar contacts buried
Fraction buried 63.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2547.8Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1407.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)