FAIRMol

NMT-TY0577

Pose ID 9897 Compound 577 Pose 411

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand NMT-TY0577
PDB9IFF↗

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
30.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.53
Burial
74%
Hydrophobic fit
69%
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 (-1.039 kcal/mol/HA) ✓ Good fit quality (FQ -9.17) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Very high strain energy (30.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-23.896
kcal/mol
LE
-1.039
kcal/mol/HA
Fit Quality
-9.17
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
1.24
cLogP
Strain ΔE
30.8 kcal/mol
SASA buried
74%
Lipo contact
69% BSA apolar/total
SASA unbound
587 Ų
Apolar buried
300 Ų

Interaction summary

HB 8 HY 20 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 rank1.842Score-23.896
Inter norm-1.086Intra norm0.047
Top1000noExcludedno
Contacts16H-bonds8
Artifact reasongeometry warning; 7 clashes; 1 protein clash; high strain Δ 30.8
Residues
ALA209 ALA67 ALA90 ASN208 GLY214 GLY215 GLY66 LEU73 LYS211 LYS89 MET70 PRO212 PRO213 TYR210 TYR69 VAL88

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap10Native recall0.77
Jaccard0.53RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
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:319; TYR:294; ASP:264; MET:204

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
310 1.6517756537347557 -0.923016 -23.3717 9 14 0 0.00 - - no Open
270 1.6639064795267455 -1.1777 -26.9612 10 12 0 0.00 - - no Open
411 1.842210776941111 -1.08583 -23.896 8 16 10 0.77 - - no Current
334 1.8998383924810274 -0.888361 -20.4444 8 10 0 0.00 - - no Open
343 2.0334518639712758 -1.24284 -25.2174 8 14 0 0.00 - - no Open
256 2.5392554407387005 -1.19497 -26.3836 12 12 0 0.00 - - no Open
293 2.906929042751237 -1.06321 -21.6989 6 18 0 0.00 - - no Open
346 2.9842050902607964 -1.22311 -28.2689 8 15 0 0.00 - - no Open
361 3.3942738138361097 -1.12993 -22.908 7 15 0 0.00 - - no Open
281 3.5581070657350717 -1.33462 -33.5911 16 20 0 0.00 - - no Open
244 4.77291506171667 -1.19294 -25.9697 11 14 0 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 -23.896kcal/mol
Ligand efficiency (LE) -1.0390kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.170
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.24
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -53.39kcal/mol
Minimised FF energy -84.24kcal/mol

SASA & burial

✓ computed
SASA (unbound) 587.5Ų
Total solvent-accessible surface area of free ligand
BSA total 435.5Ų
Buried surface area upon binding
BSA apolar 299.7Ų
Hydrophobic contacts buried
BSA polar 135.8Ų
Polar contacts buried
Fraction buried 74.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2906.9Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1517.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)