FAIRMol

OHD_Leishmania_289

Pose ID 10855 Compound 3359 Pose 12

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand OHD_Leishmania_289
PDB5S9T↗

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
53.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.39, H-bond role recall 1.00
Burial
78%
Hydrophobic fit
66%
Reason: strain 53.5 kcal/mol
strain ΔE 53.5 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.455 kcal/mol/HA) ✓ Good fit quality (FQ -4.86) ✓ Good H-bonds (4 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Extreme strain energy (53.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-20.015
kcal/mol
LE
-0.455
kcal/mol/HA
Fit Quality
-4.86
FQ (Leeson)
HAC
44
heavy atoms
MW
625
Da
LogP
-1.02
cLogP
Final rank
4.9161
rank score
Inter norm
-0.512
normalised
Contacts
20
H-bonds 11
Strain ΔE
53.5 kcal/mol
SASA buried
78%
Lipo contact
66% BSA apolar/total
SASA unbound
899 Ų
Apolar buried
462 Ų

Interaction summary

HBD 1 HBA 3 HY 7 PI 0 CLASH 3

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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap9Native recall0.75
Jaccard0.39RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
8 3.2033408266422643 -0.573234 -28.8529 12 17 0 0.00 0.00 - no Open
12 4.9161042670389214 -0.511687 -20.0147 11 20 9 0.75 1.00 - no Current
20 5.079561609865208 -0.57923 -19.1388 8 15 0 0.00 0.00 - no Open
8 5.452691758188365 -0.552019 -21.2818 14 20 0 0.00 0.00 - no Open
18 5.52295819363822 -0.667573 -20.4746 16 21 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 -20.015kcal/mol
Ligand efficiency (LE) -0.4549kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.860
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 44HA

Physicochemical properties
Molecular weight 624.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.02
Lipinski: ≤ 5
Rotatable bonds 19

Conformational strain (MMFF94s)
Strain energy (ΔE) 53.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 210.44kcal/mol
Minimised FF energy 156.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 899.1Ų
Total solvent-accessible surface area of free ligand
BSA total 704.5Ų
Buried surface area upon binding
BSA apolar 461.6Ų
Hydrophobic contacts buried
BSA polar 243.0Ų
Polar contacts buried
Fraction buried 78.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6603.8Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2065.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)