FAIRMol

OHD_Leishmania_61

Pose ID 8811 Compound 4082 Pose 3

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand OHD_Leishmania_61
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 strong SASA done
Strain ΔE
50.0 kcal/mol
Protein clashes
2
Internal clashes
0
Native overlap
contact recall 0.67, Jaccard 0.45, H-bond role recall 0.60
Burial
59%
Hydrophobic fit
84%
Reason: strain 50.0 kcal/mol
strain ΔE 50.0 kcal/mol 2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.395 kcal/mol/HA) ✓ Good fit quality (FQ -4.41) ✓ Good H-bonds (4 bonds) ✓ Good burial (59% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Extreme strain energy (50.0 kcal/mol) ✗ Minor protein-contact clashes (2)
Score
-21.345
kcal/mol
LE
-0.395
kcal/mol/HA
Fit Quality
-4.41
FQ (Leeson)
HAC
54
heavy atoms
MW
773
Da
LogP
7.32
cLogP
Final rank
0.0546
rank score
Inter norm
-0.405
normalised
Contacts
17
H-bonds 5
Strain ΔE
50.0 kcal/mol
SASA buried
59%
Lipo contact
84% BSA apolar/total
SASA unbound
1112 Ų
Apolar buried
553 Ų

Interaction summary

HBD 4 HY 3 PI 0 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

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 overlap10Native recall0.67
Jaccard0.45RMSD-
HB strict3Strict recall0.50
HB same residue+role3HB role recall0.60
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
3 0.05460892026359143 -0.404814 -21.3448 5 17 10 0.67 0.60 - 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 -21.345kcal/mol
Ligand efficiency (LE) -0.3953kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.412
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 54HA

Physicochemical properties
Molecular weight 773.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 7.32
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 49.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 97.34kcal/mol
Minimised FF energy 47.36kcal/mol

SASA & burial

✓ computed
SASA (unbound) 1112.1Ų
Total solvent-accessible surface area of free ligand
BSA total 660.7Ų
Buried surface area upon binding
BSA apolar 552.6Ų
Hydrophobic contacts buried
BSA polar 108.1Ų
Polar contacts buried
Fraction buried 59.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2932.5Ų
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 1360.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)