FAIRMol

OHD_Leishmania_12

Pose ID 8809 Compound 3727 Pose 1

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_Leishmania_12
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
42.1 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.60, Jaccard 0.41, H-bond role recall 0.20
Burial
81%
Hydrophobic fit
88%
Reason: 7 internal clashes, strain 42.1 kcal/mol
strain ΔE 42.1 kcal/mol 7 protein-contact clashes 7 intramolecular clashes 46% of hydrophobic surface appears solvent-exposed (11/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.593 kcal/mol/HA) ✓ Good fit quality (FQ -5.83) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Extreme strain energy (42.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-18.987
kcal/mol
LE
-0.593
kcal/mol/HA
Fit Quality
-5.83
FQ (Leeson)
HAC
32
heavy atoms
MW
429
Da
LogP
-0.54
cLogP
Strain ΔE
42.1 kcal/mol
SASA buried
81%
Lipo contact
88% BSA apolar/total
SASA unbound
743 Ų
Apolar buried
529 Ų

Interaction summary

HB 7 HY 3 PI 0 CLASH 7 ⚠ Exposure 45%
⚠️Partial hydrophobic solvent exposure
46% of hydrophobic surface appears solvent-exposed (11/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24 Buried (contacted) 13 Exposed 11 LogP -0.54 H-bonds 7
Exposed fragments: phenyl (5/7 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank3.949Score-18.987
Inter norm-0.755Intra norm0.159
Top1000noExcludedno
Contacts16H-bonds7
Artifact reasongeometry warning; 16 clashes; 1 protein clash; high strain Δ 42.1
Residues
ALA283 ARG22 ARG342 ASN20 ASP44 CYS26 GLN341 GLU343 GLU384 LEU25 LEU382 PRO340 PRO344 SER282 THR21 THR285

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

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 overlap9Native recall0.60
Jaccard0.41RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
1 2.7528932591503654 -0.775966 -20.3319 2 17 0 0.00 0.00 - no Open
2 3.24502420795834 -0.651353 -16.9573 3 11 0 0.00 0.00 - no Open
1 3.9494021502598833 -0.755197 -18.9873 7 16 9 0.60 0.20 - 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 -18.987kcal/mol
Ligand efficiency (LE) -0.5934kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.835
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 428.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.54
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 42.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 111.58kcal/mol
Minimised FF energy 69.48kcal/mol

SASA & burial

✓ computed
SASA (unbound) 742.9Ų
Total solvent-accessible surface area of free ligand
BSA total 600.6Ų
Buried surface area upon binding
BSA apolar 529.0Ų
Hydrophobic contacts buried
BSA polar 71.7Ų
Polar contacts buried
Fraction buried 80.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2633.6Ų
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 1378.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)