FAIRMol

NMT-TY0929

Pose ID 13896 Compound 484 Pose 338

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-TY0929
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 medium Native strong SASA done
Strain ΔE
37.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.86, Jaccard 0.71, H-bond role recall 0.22
Burial
72%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
2 protein-contact clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.925 kcal/mol/HA) ✓ Good fit quality (FQ -8.63) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Very high strain energy (37.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-24.973
kcal/mol
LE
-0.925
kcal/mol/HA
Fit Quality
-8.63
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
37.6 kcal/mol
SASA buried
72%
Lipo contact
65% BSA apolar/total
SASA unbound
612 Ų
Apolar buried
289 Ų

Interaction summary

HB 12 HY 4 PI 2 CLASH 2 ⚠ Exposure 35%

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
⚠️Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 11 Exposed 6 LogP 2.03 H-bonds 12
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank2.659Score-24.973
Inter norm-0.998Intra norm0.073
Top1000noExcludedno
Contacts15H-bonds12
Artifact reasongeometry warning; 10 clashes; 1 protein clash; high strain Δ 37.4
Residues
ARG137 ARG141 ASN103 HIS102 HIS138 MET98 TYR94 ARG113 ASP10 CYS69 GLY70 HIS11 PRO12 SER71 TYR46

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 overlap12Native recall0.86
Jaccard0.71RMSD-
HB strict4Strict recall0.33
HB same residue+role2HB role recall0.22
HB same residue2HB residue recall0.25

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
346 0.35538722495997677 -0.978913 -25.6036 2 13 0 0.00 0.00 - no Open
293 1.274900942951345 -1.03583 -28.5719 7 12 0 0.00 0.00 - no Open
323 1.3627403067812827 -0.906394 -18.7308 3 16 0 0.00 0.00 - no Open
375 2.0500114754417558 -1.04631 -29.6312 5 15 0 0.00 0.00 - no Open
318 2.0823117440239103 -1.13317 -28.9361 12 15 0 0.00 0.00 - no Open
322 2.294639162656896 -0.986167 -29.4161 5 20 0 0.00 0.00 - no Open
441 2.5220455662358785 -0.89302 -25.8372 8 15 0 0.00 0.00 - no Open
338 2.659289984590069 -0.997905 -24.9728 12 15 12 0.86 0.22 - no Current
392 2.7685730244744846 -1.12247 -31.1016 6 15 0 0.00 0.00 - no Open
333 3.6903577688505305 -0.859379 -21.1312 9 16 0 0.00 0.00 - no Open
343 3.8983164634663794 -0.849572 -21.6991 9 14 0 0.00 0.00 - no Open
372 3.9624227153920875 -1.10356 -28.0126 4 18 0 0.00 0.00 - no Open
282 4.021294943242523 -1.239 -35.8435 9 17 0 0.00 0.00 - no Open
316 4.705477255827921 -1.17836 -28.5533 9 21 0 0.00 0.00 - no Open
287 4.830955251729373 -1.16188 -25.6924 10 15 0 0.00 0.00 - no Open
353 5.092204702816937 -0.795238 -22.7627 7 12 0 0.00 0.00 - no Open
272 5.40909853377186 -0.937498 -19.6641 16 12 0 0.00 0.00 - no Open
409 5.703467463727863 -0.909529 -26.8524 10 16 0 0.00 0.00 - no Open
296 6.199766084150915 -1.0563 -30.5291 13 17 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 -24.973kcal/mol
Ligand efficiency (LE) -0.9249kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.629
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.03
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 8.86kcal/mol
Minimised FF energy -28.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 611.6Ų
Total solvent-accessible surface area of free ligand
BSA total 442.2Ų
Buried surface area upon binding
BSA apolar 289.2Ų
Hydrophobic contacts buried
BSA polar 152.9Ų
Polar contacts buried
Fraction buried 72.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2162.8Ų
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 753.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)