FAIRMol

NMT-TY0923

Pose ID 13892 Compound 1013 Pose 334

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 NMT-TY0923
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
34.9 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 1.00, Jaccard 0.78, H-bond role recall 0.67
Burial
82%
Hydrophobic fit
67%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 42% of hydrophobic surface appears solvent-exposed (8/19 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 (-0.897 kcal/mol/HA) ✓ Good fit quality (FQ -8.56) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Very high strain energy (34.9 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (13) ✗ Many internal clashes (12)
Score
-26.015
kcal/mol
LE
-0.897
kcal/mol/HA
Fit Quality
-8.56
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
2.70
cLogP
Strain ΔE
34.9 kcal/mol
SASA buried
82%
Lipo contact
67% BSA apolar/total
SASA unbound
599 Ų
Apolar buried
328 Ų

Interaction summary

HB 10 HY 8 PI 2 CLASH 6 ⚠ Exposure 42%
⚠️Partial hydrophobic solvent exposure
42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19 Buried (contacted) 11 Exposed 8 LogP 2.7 H-bonds 10
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank2.609Score-26.015
Inter norm-0.826Intra norm-0.071
Top1000noExcludedno
Contacts18H-bonds10
Artifact reasongeometry warning; 12 clashes; 13 protein contact clashes; high strain Δ 34.9
Residues
ARG137 ARG141 ASN103 HIS102 HIS138 MET98 TYR94 ARG113 ASP10 ASP45 CYS69 GLY70 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: 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+role6HB role recall0.67
HB same residue5HB residue recall0.62

HB · H-bonds
Mode: strict. 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
315 1.1613107551257762 -0.988746 -29.6316 12 16 0 0.00 0.00 - no Open
321 1.5566859020986727 -0.807286 -27.8281 8 19 0 0.00 0.00 - no Open
289 1.7875256004417812 -1.01576 -34.0347 10 17 0 0.00 0.00 - no Open
303 1.9342035494482892 -1.16396 -39.3269 9 13 0 0.00 0.00 - no Open
334 2.6091504176910982 -0.826197 -26.015 10 18 14 1.00 0.67 - no Current
367 3.0749634020371825 -0.990903 -25.5451 4 19 0 0.00 0.00 - no Open
438 3.445947979401607 -0.914081 -26.2321 6 18 0 0.00 0.00 - no Open
371 3.468473637160046 -0.952937 -25.382 5 17 0 0.00 0.00 - no Open
320 3.511127472097206 -0.833155 -22.5447 5 15 0 0.00 0.00 - no Open
407 3.597340957942763 -0.84589 -24.7448 9 14 0 0.00 0.00 - no Open
279 3.925792386612066 -1.17176 -34.1016 10 22 0 0.00 0.00 - no Open
286 4.0643906114359885 -0.970755 -26.4205 11 14 0 0.00 0.00 - no Open
307 4.098407011813724 -1.05234 -31.7217 5 14 0 0.00 0.00 - no Open
350 4.5986329465174585 -0.670614 -26.6886 7 11 0 0.00 0.00 - no Open
363 4.930702432756965 -0.921212 -24.8139 11 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 -26.015kcal/mol
Ligand efficiency (LE) -0.8971kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.563
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.70
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -26.90kcal/mol
Minimised FF energy -61.76kcal/mol

SASA & burial

✓ computed
SASA (unbound) 599.1Ų
Total solvent-accessible surface area of free ligand
BSA total 489.2Ų
Buried surface area upon binding
BSA apolar 327.9Ų
Hydrophobic contacts buried
BSA polar 161.4Ų
Polar contacts buried
Fraction buried 81.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2165.0Ų
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 754.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)