FAIRMol

NMT-TY0625

Pose ID 9912 Compound 587 Pose 426

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-TY0625
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 high Native strong SASA done
Strain ΔE
25.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.50
Burial
74%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
2 protein-contact clashes 41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.895 kcal/mol/HA) ✓ Good fit quality (FQ -8.35) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (25.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-24.163
kcal/mol
LE
-0.895
kcal/mol/HA
Fit Quality
-8.35
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
25.3 kcal/mol
SASA buried
74%
Lipo contact
71% BSA apolar/total
SASA unbound
659 Ų
Apolar buried
347 Ų

Interaction summary

HB 10 HY 20 PI 1 CLASH 2 ⚠ Exposure 41%

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
⚠️Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 10 Exposed 7 LogP 2.03 H-bonds 10
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank2.491Score-24.163
Inter norm-0.907Intra norm0.012
Top1000noExcludedno
Contacts17H-bonds10
Artifact reasongeometry warning; 10 clashes; 1 protein clash; moderate strain Δ 25.3
Residues
ALA209 ALA67 ALA90 ASN208 GLY214 GLY215 GLY66 LEU73 LYS211 LYS216 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
Jaccard0.50RMSD-
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
324 0.20723889343453514 -0.951386 -23.6661 1 14 0 0.00 - - no Open
275 0.9061196009967781 -1.22993 -32.9032 9 20 0 0.00 - - no Open
292 1.1768621845493887 -1.20358 -35.0455 10 11 0 0.00 - - no Open
291 1.218230612835466 -1.06543 -26.4823 10 13 0 0.00 - - no Open
310 1.511827099897129 -0.901999 -22.8948 4 17 0 0.00 - - no Open
330 1.9924960648131407 -0.979613 -23.342 4 14 0 0.00 - - no Open
343 2.359267355874073 -0.89635 -23.6694 9 12 0 0.00 - - no Open
426 2.4909161669113518 -0.907217 -24.1632 10 17 10 0.77 - - no Current
278 2.509428388171617 -1.0319 -28.1397 6 13 0 0.00 - - no Open
297 2.63967730557778 -1.25147 -33.606 12 23 0 0.00 - - no Open
355 3.229453768262364 -1.09247 -22.9997 10 19 0 0.00 - - no Open
311 3.2950567359488305 -0.981974 -28.1708 9 14 0 0.00 - - no Open
395 3.4109746243775096 -0.855223 -23.6426 8 13 0 0.00 - - no Open
350 3.483682559989441 -0.96476 -27.5634 8 19 0 0.00 - - no Open
381 3.5214059746730104 -1.11325 -28.0276 6 14 0 0.00 - - no Open
364 4.0288364719309 -1.09005 -30.4446 8 17 0 0.00 - - no Open
272 4.1996467964885476 -1.16921 -29.9755 9 17 0 0.00 - - no Open
332 4.352390042161908 -0.822496 -24.9609 10 15 0 0.00 - - no Open
271 4.392965189680496 -1.27398 -34.4428 11 15 0 0.00 - - no Open
330 5.564206722433145 -0.904232 -20.3369 11 17 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 -24.163kcal/mol
Ligand efficiency (LE) -0.8949kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.349
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.03
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -88.79kcal/mol
Minimised FF energy -114.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 659.4Ų
Total solvent-accessible surface area of free ligand
BSA total 485.3Ų
Buried surface area upon binding
BSA apolar 346.7Ų
Hydrophobic contacts buried
BSA polar 138.6Ų
Polar contacts buried
Fraction buried 73.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2948.7Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1543.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)