FAIRMol

NMT-TY0563

Pose ID 13867 Compound 937 Pose 309

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-TY0563
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
36.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.93, Jaccard 0.81, H-bond role recall 0.44
Burial
81%
Hydrophobic fit
52%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.971 kcal/mol/HA) ✓ Good fit quality (FQ -8.57) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (81% SASA buried) ✗ Very high strain energy (36.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-22.334
kcal/mol
LE
-0.971
kcal/mol/HA
Fit Quality
-8.57
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
0.77
cLogP
Final rank
3.0017
rank score
Inter norm
-1.112
normalised
Contacts
15
H-bonds 10
Strain ΔE
36.6 kcal/mol
SASA buried
81%
Lipo contact
52% BSA apolar/total
SASA unbound
552 Ų
Apolar buried
232 Ų

Interaction summary

HBA 6 HY 3 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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 overlap13Native recall0.93
Jaccard0.81RMSD-
HB strict5Strict recall0.42
HB same residue+role4HB role recall0.44
HB same residue4HB residue recall0.50

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
287 2.281771617029549 -1.06786 -23.7408 5 18 0 0.00 0.00 - no Open
343 2.4562087162844173 -1.10761 -25.4402 13 17 0 0.00 0.00 - no Open
304 2.461814278287188 -0.94473 -20.9121 7 12 0 0.00 0.00 - no Open
407 2.5036253322923585 -1.19433 -22.7362 8 16 0 0.00 0.00 - no Open
266 2.5178884740350864 -1.23759 -27.3191 9 14 0 0.00 0.00 - no Open
309 3.0017361607070128 -1.11231 -22.3337 10 15 13 0.93 0.44 - no Current
328 3.3135670361627176 -0.980585 -18.4335 10 16 0 0.00 0.00 - no Open
250 4.760381988626865 -1.22455 -27.6963 12 15 0 0.00 0.00 - no Open
275 5.006226701203945 -1.35207 -29.9759 16 19 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 -22.334kcal/mol
Ligand efficiency (LE) -0.9710kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.570
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.77
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -58.16kcal/mol
Minimised FF energy -94.73kcal/mol

SASA & burial

✓ computed
SASA (unbound) 551.7Ų
Total solvent-accessible surface area of free ligand
BSA total 446.2Ų
Buried surface area upon binding
BSA apolar 231.8Ų
Hydrophobic contacts buried
BSA polar 214.3Ų
Polar contacts buried
Fraction buried 80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 52.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2030.4Ų
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 762.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)