FAIRMol

OHD_Leishmania_477

Pose ID 13579 Compound 3747 Pose 21

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
T21
T. cruzi R5P T. cruzi
Ligand OHD_Leishmania_477
PDB3K7O↗

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
44.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.93, Jaccard 0.68, H-bond role recall 0.11
Burial
62%
Hydrophobic fit
88%
Reason: strain 44.4 kcal/mol
strain ΔE 44.4 kcal/mol 2 protein-contact clashes 59% of hydrophobic surface appears solvent-exposed (17/29 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.
✓ Good LE (-0.361 kcal/mol/HA) ✓ Good fit quality (FQ -3.75) ✓ Good H-bonds (4 bonds) ✓ Good burial (62% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Extreme strain energy (44.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-14.100
kcal/mol
LE
-0.361
kcal/mol/HA
Fit Quality
-3.75
FQ (Leeson)
HAC
39
heavy atoms
MW
542
Da
LogP
6.08
cLogP
Final rank
3.0561
rank score
Inter norm
-0.634
normalised
Contacts
18
H-bonds 6
Strain ΔE
44.4 kcal/mol
SASA buried
62%
Lipo contact
88% BSA apolar/total
SASA unbound
874 Ų
Apolar buried
475 Ų

Interaction summary

HBA 4 HY 2 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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
Jaccard0.68RMSD-
HB strict2Strict recall0.17
HB same residue+role1HB role recall0.11
HB same residue1HB residue recall0.12

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
15 2.4395873276642837 -0.712507 -20.1923 6 15 0 0.00 0.00 - no Open
33 2.9201007805750137 -0.663814 -16.135 5 17 0 0.00 0.00 - no Open
33 2.94109877306006 -0.622988 -17.2062 5 14 0 0.00 0.00 - no Open
21 3.0561031500942453 -0.633908 -14.1004 6 18 13 0.93 0.11 - no Current
27 3.2499699785463396 -0.605523 -19.2965 3 22 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 -14.100kcal/mol
Ligand efficiency (LE) -0.3615kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -3.752
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 39HA

Physicochemical properties
Molecular weight 542.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.08
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 44.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 84.58kcal/mol
Minimised FF energy 40.16kcal/mol

SASA & burial

✓ computed
SASA (unbound) 874.0Ų
Total solvent-accessible surface area of free ligand
BSA total 542.1Ų
Buried surface area upon binding
BSA apolar 474.9Ų
Hydrophobic contacts buried
BSA polar 67.2Ų
Polar contacts buried
Fraction buried 62.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2428.1Ų
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 798.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)