FAIRMol

NMT-TY0601

Pose ID 13876 Compound 15 Pose 318

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-TY0601
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
42.8 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 1.00, Jaccard 0.82, H-bond role recall 0.56
Burial
73%
Hydrophobic fit
62%
Reason: strain 42.8 kcal/mol
strain ΔE 42.8 kcal/mol 5 protein-contact clashes 5 intramolecular clashes 47% of hydrophobic surface appears solvent-exposed (9/19 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 (-0.849 kcal/mol/HA) ✓ Good fit quality (FQ -8.19) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ Extreme strain energy (42.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-25.470
kcal/mol
LE
-0.849
kcal/mol/HA
Fit Quality
-8.19
FQ (Leeson)
HAC
30
heavy atoms
MW
446
Da
LogP
2.40
cLogP
Strain ΔE
42.8 kcal/mol
SASA buried
73%
Lipo contact
62% BSA apolar/total
SASA unbound
656 Ų
Apolar buried
299 Ų

Interaction summary

HB 12 HY 8 PI 2 CLASH 5 ⚠ Exposure 47%
⚠️Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19 Buried (contacted) 10 Exposed 9 LogP 2.4 H-bonds 12
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank5.397Score-25.470
Inter norm-0.860Intra norm0.011
Top1000noExcludedno
Contacts17H-bonds12
Artifact reasongeometry warning; 16 clashes; 3 protein clashes; high strain Δ 42.8
Residues
ARG137 ARG141 ASN103 HIS102 HIS138 MET98 TYR94 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: 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
Jaccard0.82RMSD-
HB strict6Strict recall0.50
HB same residue+role5HB role recall0.56
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
363 0.3236686833943817 -0.922656 -24.2954 3 19 0 0.00 0.00 - no Open
318 0.5313914739558929 -0.916521 -26.3515 1 14 0 0.00 0.00 - no Open
296 1.340576599260557 -0.866114 -23.6414 3 20 0 0.00 0.00 - no Open
313 1.395589756323132 -0.754263 -20.827 5 15 0 0.00 0.00 - no Open
284 1.7396787330526 -1.11044 -33.9659 13 23 0 0.00 0.00 - no Open
281 1.85607159171697 -1.14564 -34.7998 11 16 0 0.00 0.00 - no Open
348 2.510631852879237 -0.8762 -24.8059 8 14 0 0.00 0.00 - no Open
258 2.860860253450067 -1.00124 -25.4028 9 16 0 0.00 0.00 - no Open
271 2.8833662991378333 -0.970487 -29.5939 10 15 0 0.00 0.00 - no Open
273 3.372067864906788 -0.984025 -30.8549 11 15 0 0.00 0.00 - no Open
413 3.9499962992021005 -0.803776 -21.0277 6 18 0 0.00 0.00 - no Open
336 3.9850996762335 -0.846144 -23.7714 8 19 0 0.00 0.00 - no Open
296 4.196552406559037 -0.888004 -22.2524 5 13 0 0.00 0.00 - no Open
327 4.734313839890531 -0.780717 -23.4612 7 14 0 0.00 0.00 - no Open
318 5.396631318612632 -0.860345 -25.47 12 17 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 -25.470kcal/mol
Ligand efficiency (LE) -0.8490kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.190
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 445.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.40
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 42.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -54.37kcal/mol
Minimised FF energy -97.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 656.2Ų
Total solvent-accessible surface area of free ligand
BSA total 481.2Ų
Buried surface area upon binding
BSA apolar 298.9Ų
Hydrophobic contacts buried
BSA polar 182.3Ų
Polar contacts buried
Fraction buried 73.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2182.2Ų
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 763.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)