FAIRMol

NMT-TY0939

Pose ID 13897 Compound 912 Pose 339

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-TY0939
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
72.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 1.00, Jaccard 0.93, H-bond role recall 0.89
Burial
68%
Hydrophobic fit
45%
Reason: strain 72.9 kcal/mol
strain ΔE 72.9 kcal/mol 4 protein-contact clashes 4 intramolecular clashes 58% of hydrophobic surface appears solvent-exposed (7/12 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.
✓ Excellent LE (-0.940 kcal/mol/HA) ✓ Good fit quality (FQ -8.66) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (68% SASA buried) ✗ Extreme strain energy (72.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-24.437
kcal/mol
LE
-0.940
kcal/mol/HA
Fit Quality
-8.66
FQ (Leeson)
HAC
26
heavy atoms
MW
402
Da
LogP
0.13
cLogP
Final rank
6.8109
rank score
Inter norm
-0.970
normalised
Contacts
15
H-bonds 16
Strain ΔE
72.9 kcal/mol
SASA buried
68%
Lipo contact
45% BSA apolar/total
SASA unbound
610 Ų
Apolar buried
188 Ų

Interaction summary

HBD 3 HBA 10 HY 2 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 8.

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 overlap14Native recall1.00
Jaccard0.93RMSD-
HB strict11Strict recall0.92
HB same residue+role8HB role recall0.89
HB same residue7HB residue recall0.88

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 0.47311557931133086 -0.935109 -19.2367 4 13 0 0.00 0.00 - no Open
322 1.415578661134894 -1.03243 -26.6288 12 15 0 0.00 0.00 - no Open
374 1.7236615503669714 -1.05315 -30.1239 8 13 0 0.00 0.00 - no Open
380 2.2523504511266683 -1.00941 -20.4416 7 16 0 0.00 0.00 - no Open
298 3.331173736035127 -1.11268 -26.9067 10 14 0 0.00 0.00 - no Open
327 3.4700047251715773 -0.87606 -20.3514 3 16 0 0.00 0.00 - no Open
445 3.506483242040409 -0.904121 -22.2104 13 16 0 0.00 0.00 - no Open
276 5.5461368627814105 -0.989799 -17.3373 15 17 0 0.00 0.00 - no Open
339 6.810864659394439 -0.970214 -24.4372 16 15 14 1.00 0.89 - 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 -24.437kcal/mol
Ligand efficiency (LE) -0.9399kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.660
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 402.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.13
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 72.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -45.47kcal/mol
Minimised FF energy -118.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 610.2Ų
Total solvent-accessible surface area of free ligand
BSA total 418.2Ų
Buried surface area upon binding
BSA apolar 188.2Ų
Hydrophobic contacts buried
BSA polar 230.0Ų
Polar contacts buried
Fraction buried 68.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 45.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2037.6Ų
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 757.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)