FAIRMol

NMT-TY0957

Pose ID 12490 Compound 264 Pose 289

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-TY0957
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
31.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.30, Jaccard 0.20, H-bond role recall 0.40
Burial
91%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.104 kcal/mol/HA) ✓ Good fit quality (FQ -10.42) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (31.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-30.909
kcal/mol
LE
-1.104
kcal/mol/HA
Fit Quality
-10.42
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Strain ΔE
31.6 kcal/mol
SASA buried
91%
Lipo contact
74% BSA apolar/total
SASA unbound
663 Ų
Apolar buried
450 Ų

Interaction summary

HB 9 HY 21 PI 1 CLASH 2

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 rank3.009Score-30.909
Inter norm-1.248Intra norm0.144
Top1000noExcludedno
Contacts21H-bonds9
Artifact reasongeometry warning; 11 clashes; 2 protein clashes; high strain Δ 31.6
Residues
ALA365 CYS52 CYS57 GLU202 GLY56 ILE199 ILE438 LEU334 LYS60 MET333 NDP800 PHE182 PHE203 PHE367 PRO336 PRO435 SER178 SER364 THR335 THR51 VAL55

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 overlap8Native recall0.30
Jaccard0.20RMSD-
HB strict3Strict recall0.25
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
349 0.7278409086070636 -0.881455 -21.5148 2 14 0 0.00 0.00 - no Open
311 1.3229509224018154 -1.16017 -29.6884 9 15 0 0.00 0.00 - no Open
334 1.51730203346956 -0.851135 -24.9989 8 16 0 0.00 0.00 - no Open
335 1.7260732089299 -0.999198 -26.3291 6 21 0 0.00 0.00 - no Open
403 1.7481430375200544 -0.991243 -27.3069 7 18 0 0.00 0.00 - no Open
347 2.3447902198011827 -0.753436 -19.3121 7 15 0 0.00 0.00 - no Open
389 2.786111419208295 -1.0956 -28.7016 6 16 0 0.00 0.00 - no Open
289 3.0086401503696756 -1.24814 -30.9089 9 21 8 0.30 0.40 - no Current
301 3.1451083125642456 -1.02377 -27.2511 8 23 0 0.00 0.00 - no Open
357 3.2475516904388395 -0.897972 -24.0584 9 11 0 0.00 0.00 - no Open
377 3.304488419434868 -0.914277 -26.47 6 16 0 0.00 0.00 - no Open
379 3.3253823915120413 -1.07446 -31.7967 5 19 0 0.00 0.00 - no Open
414 3.598164167482077 -0.922403 -23.4985 9 14 0 0.00 0.00 - no Open
332 3.624289409705216 -0.937648 -25.3511 7 11 0 0.00 0.00 - no Open
330 4.212597954691834 -0.897031 -24.2894 4 14 0 0.00 0.00 - no Open
451 4.456710646262987 -0.898418 -22.7057 8 16 0 0.00 0.00 - no Open
324 5.157273396991818 -1.11879 -29.0355 13 26 0 0.00 0.00 - no Open
284 5.171548217517241 -0.94018 -23.463 14 15 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 -30.909kcal/mol
Ligand efficiency (LE) -1.1039kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.421
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.31
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -54.88kcal/mol
Minimised FF energy -86.52kcal/mol

SASA & burial

✓ computed
SASA (unbound) 663.4Ų
Total solvent-accessible surface area of free ligand
BSA total 606.2Ų
Buried surface area upon binding
BSA apolar 449.9Ų
Hydrophobic contacts buried
BSA polar 156.3Ų
Polar contacts buried
Fraction buried 91.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3078.4Ų
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 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1478.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)