FAIRMol

NMT-TY0929

Pose ID 12483 Compound 484 Pose 282

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
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand NMT-TY0929
PDB2WOV↗

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 mixed SASA done
Strain ΔE
30.7 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.22, Jaccard 0.16, H-bond role recall 0.40
Burial
91%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
4 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.327 kcal/mol/HA) ✓ Good fit quality (FQ -12.38) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (30.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-35.843
kcal/mol
LE
-1.327
kcal/mol/HA
Fit Quality
-12.38
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
30.7 kcal/mol
SASA buried
91%
Lipo contact
74% BSA apolar/total
SASA unbound
622 Ų
Apolar buried
419 Ų

Interaction summary

HB 9 HY 18 PI 1 CLASH 5

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
Final rank4.021Score-35.843
Inter norm-1.239Intra norm-0.089
Top1000noExcludedno
Contacts17H-bonds9
Artifact reasongeometry warning; 11 clashes; 3 protein clashes; 3 cofactor-context clashes; high strain Δ 30.6
Residues
ALA363 ALA365 ASP327 CYS52 CYS57 GLY56 LEU334 LYS60 MET333 NDP800 PHE367 PRO336 SER14 SER364 THR335 THR51 VAL362

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name2WOVContacts27
PoseOpen native poseHB0
IFP residues
ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap6Native recall0.22
Jaccard0.16RMSD-
HB strict2Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue1HB residue recall0.25

Protein summary

493 residues
Protein targetT19Atoms7541
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
C:NDP800

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 0 0.00 0.00 - no Open
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 6 0.22 0.40 - no Current
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 -35.843kcal/mol
Ligand efficiency (LE) -1.3275kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.385
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.27
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -44.36kcal/mol
Minimised FF energy -75.02kcal/mol

SASA & burial

✓ computed
SASA (unbound) 622.3Ų
Total solvent-accessible surface area of free ligand
BSA total 568.7Ų
Buried surface area upon binding
BSA apolar 418.9Ų
Hydrophobic contacts buried
BSA polar 149.7Ų
Polar contacts buried
Fraction buried 91.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3050.7Ų
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 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1481.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)