FAIRMol

NMT-TY0538

Pose ID 13862 Compound 3240 Pose 304

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 NMT-TY0538
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
81.8 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 1.00, Jaccard 0.78, H-bond role recall 0.56
Burial
81%
Hydrophobic fit
61%
Reason: 11 internal clashes, strain 81.8 kcal/mol
strain ΔE 81.8 kcal/mol 11 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.166 kcal/mol/HA) ✓ Good fit quality (FQ -10.75) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (61%) ✗ Extreme strain energy (81.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-30.325
kcal/mol
LE
-1.166
kcal/mol/HA
Fit Quality
-10.75
FQ (Leeson)
HAC
26
heavy atoms
MW
383
Da
LogP
-0.22
cLogP
Final rank
3.5089
rank score
Inter norm
-0.934
normalised
Contacts
18
H-bonds 16
Strain ΔE
81.8 kcal/mol
SASA buried
81%
Lipo contact
61% BSA apolar/total
SASA unbound
573 Ų
Apolar buried
284 Ų

Interaction summary

HBD 2 HBA 7 HY 2 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

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: strict.
Name3K7OContacts14
PoseOpen native poseHB0
IFP residues
ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap14Native recall1.00
Jaccard0.78RMSD-
HB strict6Strict recall0.50
HB same residue+role5HB role recall0.56
HB same residue5HB residue recall0.62

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
259 1.8111479340757963 -0.976755 -29.3029 14 19 0 0.00 0.00 - no Open
304 3.5088535324803387 -0.933594 -30.325 16 18 14 1.00 0.56 - 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 -30.325kcal/mol
Ligand efficiency (LE) -1.1663kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.746
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 383.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.22
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 81.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -31.74kcal/mol
Minimised FF energy -113.58kcal/mol

SASA & burial

✓ computed
SASA (unbound) 573.4Ų
Total solvent-accessible surface area of free ligand
BSA total 463.1Ų
Buried surface area upon binding
BSA apolar 283.9Ų
Hydrophobic contacts buried
BSA polar 179.3Ų
Polar contacts buried
Fraction buried 80.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 61.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2088.6Ų
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 743.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)