FAIRMol

OHD_Babesia_20

Pose ID 10883 Compound 4827 Pose 40

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_Babesia_20
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
46.4 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.83, Jaccard 0.50, H-bond role recall 0.00
Burial
74%
Hydrophobic fit
73%
Reason: 7 internal clashes, strain 46.4 kcal/mol
strain ΔE 46.4 kcal/mol 7 protein-contact clashes 7 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.523 kcal/mol/HA) ✓ Good fit quality (FQ -5.43) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Extreme strain energy (46.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (20)
Score
-20.418
kcal/mol
LE
-0.523
kcal/mol/HA
Fit Quality
-5.43
FQ (Leeson)
HAC
39
heavy atoms
MW
542
Da
LogP
1.33
cLogP
Final rank
5.5145
rank score
Inter norm
-0.591
normalised
Contacts
18
H-bonds 8
Strain ΔE
46.4 kcal/mol
SASA buried
74%
Lipo contact
73% BSA apolar/total
SASA unbound
793 Ų
Apolar buried
427 Ų

Interaction summary

HBD 2 HBA 4 HY 5 PI 1 CLASH 7

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

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap10Native recall0.83
Jaccard0.50RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
40 5.514467172334284 -0.591294 -20.4183 8 18 10 0.83 0.00 - no Current
42 6.479097730088883 -0.510582 -22.0793 9 11 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 -20.418kcal/mol
Ligand efficiency (LE) -0.5235kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.433
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 39HA

Physicochemical properties
Molecular weight 541.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.33
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 46.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 166.67kcal/mol
Minimised FF energy 120.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 793.1Ų
Total solvent-accessible surface area of free ligand
BSA total 588.2Ų
Buried surface area upon binding
BSA apolar 427.4Ų
Hydrophobic contacts buried
BSA polar 160.9Ų
Polar contacts buried
Fraction buried 74.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6605.5Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2073.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)