FAIRMol

Z56960414

Pose ID 14119 Compound 2056 Pose 561

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 Z56960414
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
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
16.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.82, H-bond role recall 0.44
Burial
87%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.170 kcal/mol/HA) ✓ Good fit quality (FQ -10.49) ✓ Strong H-bond network (15 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Moderate strain (16.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-28.087
kcal/mol
LE
-1.170
kcal/mol/HA
Fit Quality
-10.49
FQ (Leeson)
HAC
24
heavy atoms
MW
331
Da
LogP
4.04
cLogP
Strain ΔE
16.7 kcal/mol
SASA buried
87%
Lipo contact
75% BSA apolar/total
SASA unbound
513 Ų
Apolar buried
334 Ų

Interaction summary

HB 15 HY 7 PI 3 CLASH 2
Final rank2.311Score-28.087
Inter norm-1.071Intra norm-0.099
Top1000noExcludedno
Contacts17H-bonds8
Artifact reasongeometry warning; 11 clashes; 1 protein clash
Residues
ARG137 ARG141 ASN103 HIS102 HIS138 MET98 ARG113 ASP10 CYS69 GLY70 GLY72 GLY74 HIS11 ILE73 PRO12 SER71 TYR46

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

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 overlap14Native recall1.00
Jaccard0.82RMSD-
HB strict5Strict recall0.42
HB same residue+role4HB role recall0.44
HB same residue3HB residue recall0.38

HB · H-bonds
Mode: permissive. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
527 1.492359396143117 -1.18351 -26.9373 3 12 0 0.00 0.00 - no Open
561 2.3113373325072017 -1.07145 -28.0873 8 17 14 1.00 0.44 - 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 -28.087kcal/mol
Ligand efficiency (LE) -1.1703kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.488
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 331.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.04
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 167.03kcal/mol
Minimised FF energy 150.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 513.2Ų
Total solvent-accessible surface area of free ligand
BSA total 447.3Ų
Buried surface area upon binding
BSA apolar 333.6Ų
Hydrophobic contacts buried
BSA polar 113.7Ų
Polar contacts buried
Fraction buried 87.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2133.4Ų
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 748.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)