FAIRMol

NMT-TY0920

Pose ID 11204 Compound 544 Pose 361

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand NMT-TY0920
PDB5S9T↗

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
31.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.33, H-bond role recall 0.00
Burial
80%
Hydrophobic fit
71%
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 (-1.192 kcal/mol/HA) ✓ Good fit quality (FQ -11.25) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Very high strain energy (31.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-33.380
kcal/mol
LE
-1.192
kcal/mol/HA
Fit Quality
-11.25
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.07
cLogP
Strain ΔE
31.9 kcal/mol
SASA buried
80%
Lipo contact
71% BSA apolar/total
SASA unbound
646 Ų
Apolar buried
365 Ų

Interaction summary

HB 11 HY 18 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 rank5.232Score-33.380
Inter norm-0.900Intra norm-0.292
Top1000noExcludedno
Contacts16H-bonds11
Artifact reasongeometry warning; 13 clashes; 3 protein clashes; high strain Δ 31.9
Residues
ALA363 ARG361 CYS375 GLY376 HIS359 HIS428 LEU332 LEU334 LEU377 MET333 PHE198 PHE230 SER364 THR360 THR374 VAL362

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap7Native recall0.58
Jaccard0.33RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
302 0.5239567590025211 -1.18433 -30.604 9 13 0 0.00 0.00 - no Open
319 0.9940520654587742 -0.944043 -25.3008 5 13 0 0.00 0.00 - no Open
320 1.0669444827431311 -0.878088 -31.4505 3 16 0 0.00 0.00 - no Open
345 1.1134646347622539 -0.877657 -23.1229 3 15 0 0.00 0.00 - no Open
369 1.570299553280359 -0.935163 -25.1037 6 14 0 0.00 0.00 - no Open
285 1.846962516011115 -1.10054 -35.0271 11 16 0 0.00 0.00 - no Open
333 2.430240854014312 -0.961348 -34.1213 11 17 0 0.00 0.00 - no Open
313 2.7355217655896267 -0.945999 -28.0195 7 18 0 0.00 0.00 - no Open
388 3.1357764599548372 -1.01979 -35.0482 6 16 0 0.00 0.00 - no Open
366 3.33349022232488 -1.04252 -32.8619 6 15 0 0.00 0.00 - no Open
313 3.427850034969361 -1.24397 -30.3675 11 26 0 0.00 0.00 - no Open
342 3.492057571577017 -0.785111 -22.7794 9 15 0 0.00 0.00 - no Open
295 3.616137840018539 -0.981468 -32.0097 7 17 0 0.00 0.00 - no Open
437 3.855523120955258 -0.937716 -27.4849 10 13 0 0.00 0.00 - no Open
349 4.8296015227220686 -0.681525 -25.7042 8 9 0 0.00 0.00 - no Open
361 5.231781681702861 -0.899682 -33.3801 11 16 7 0.58 0.00 - 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 -33.380kcal/mol
Ligand efficiency (LE) -1.1921kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.254
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.07
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -24.89kcal/mol
Minimised FF energy -56.82kcal/mol

SASA & burial

✓ computed
SASA (unbound) 645.7Ų
Total solvent-accessible surface area of free ligand
BSA total 515.7Ų
Buried surface area upon binding
BSA apolar 365.5Ų
Hydrophobic contacts buried
BSA polar 150.3Ų
Polar contacts buried
Fraction buried 79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6478.3Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2076.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)