FAIRMol

GemmaOHDUnisi_38

Pose ID 13906 Compound 3024 Pose 348

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_38
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
19.6 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.93, Jaccard 0.87, H-bond role recall 0.67
Burial
66%
Hydrophobic fit
76%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.499 kcal/mol/HA) ✓ Good fit quality (FQ -4.66) ✓ Good H-bonds (5 bonds) ✓ Deep burial (66% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Moderate strain (19.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-13.477
kcal/mol
LE
-0.499
kcal/mol/HA
Fit Quality
-4.66
FQ (Leeson)
HAC
27
heavy atoms
MW
356
Da
LogP
5.41
cLogP
Final rank
4.0234
rank score
Inter norm
-0.910
normalised
Contacts
14
H-bonds 8
Strain ΔE
19.6 kcal/mol
SASA buried
66%
Lipo contact
76% BSA apolar/total
SASA unbound
651 Ų
Apolar buried
326 Ų

Interaction summary

HBD 2 HBA 3 HY 3 PI 3 CLASH 6

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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: strict.
Name3K7OContacts14
PoseOpen native poseHB0
IFP residues
ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap13Native recall0.93
Jaccard0.87RMSD-
HB strict7Strict recall0.58
HB same residue+role6HB role recall0.67
HB same residue6HB residue recall0.75

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
322 0.8278075936041438 -1.32071 -32.9059 6 14 0 0.00 0.00 - no Open
356 0.9693317372851367 -0.896093 -18.51 4 17 0 0.00 0.00 - no Open
339 3.6612808815022593 -0.956451 -23.6271 4 17 0 0.00 0.00 - no Open
348 4.023415965506665 -0.910424 -13.4768 8 14 13 0.93 0.67 - no Current
338 4.349104779598979 -1.12272 -24.8121 10 18 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 -13.477kcal/mol
Ligand efficiency (LE) -0.4991kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.657
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) 19.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 81.90kcal/mol
Minimised FF energy 62.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 650.6Ų
Total solvent-accessible surface area of free ligand
BSA total 425.9Ų
Buried surface area upon binding
BSA apolar 325.6Ų
Hydrophobic contacts buried
BSA polar 100.2Ų
Polar contacts buried
Fraction buried 65.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2217.4Ų
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 808.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)