FAIRMol

GemmaOHDUnisi_37

Pose ID 13905 Compound 5351 Pose 347

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
T21
T. cruzi R5P T. cruzi
Ligand GemmaOHDUnisi_37
PDB3K7O↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
5.3 kcal/mol
Protein clashes
4
Internal clashes
13
Native overlap
contact recall 0.93, Jaccard 0.76, H-bond role recall 0.33
Burial
64%
Hydrophobic fit
88%
Reason: 13 internal clashes
4 protein-contact clashes 13 intramolecular clashes 39% of hydrophobic surface appears solvent-exposed (9/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Low conformational strain (5.3 kcal/mol) ✓ Excellent LE (-0.891 kcal/mol/HA) ✓ Good fit quality (FQ -8.31) ✓ Good H-bonds (3 bonds) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (13)
Score
-24.061
kcal/mol
LE
-0.891
kcal/mol/HA
Fit Quality
-8.31
FQ (Leeson)
HAC
27
heavy atoms
MW
356
Da
LogP
5.41
cLogP
Final rank
1.2635
rank score
Inter norm
-0.888
normalised
Contacts
16
H-bonds 6
Strain ΔE
5.3 kcal/mol
SASA buried
64%
Lipo contact
88% BSA apolar/total
SASA unbound
631 Ų
Apolar buried
356 Ų

Interaction summary

HBD 1 HBA 2 HY 3 PI 4 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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

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: permissive.
Name3K7OContacts14
PoseOpen native poseHB0
IFP residues
ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap13Native recall0.93
Jaccard0.76RMSD-
HB strict3Strict recall0.25
HB same residue+role3HB role recall0.33
HB same residue4HB residue recall0.50

Protein summary

305 residues
Protein targetT21Atoms4646
Residues305Chains2
Residue summaryARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
347 1.2635489158459152 -0.887937 -24.061 6 16 13 0.93 0.33 - 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 -24.061kcal/mol
Ligand efficiency (LE) -0.8911kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.314
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 356.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.41
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 5.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 71.92kcal/mol
Minimised FF energy 66.64kcal/mol

SASA & burial

✓ computed
SASA (unbound) 630.8Ų
Total solvent-accessible surface area of free ligand
BSA total 406.3Ų
Buried surface area upon binding
BSA apolar 356.0Ų
Hydrophobic contacts buried
BSA polar 50.4Ų
Polar contacts buried
Fraction buried 64.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2213.8Ų
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 2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 809.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)