FAIRMol

NMT-TY0601

Pose ID 7710 Compound 15 Pose 258

DB SELECTIONDocking 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
T12
T. brucei R5P T. brucei
Ligand NMT-TY0601
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
46.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.94, Jaccard 0.88, H-bond role recall 0.50
Burial
68%
Hydrophobic fit
69%
Reason: strain 46.7 kcal/mol
strain ΔE 46.7 kcal/mol 4 protein-contact clashes 4 intramolecular clashes 47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.847 kcal/mol/HA) ✓ Good fit quality (FQ -8.17) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Extreme strain energy (46.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-25.403
kcal/mol
LE
-0.847
kcal/mol/HA
Fit Quality
-8.17
FQ (Leeson)
HAC
30
heavy atoms
MW
446
Da
LogP
2.65
cLogP
Strain ΔE
46.7 kcal/mol
SASA buried
68%
Lipo contact
69% BSA apolar/total
SASA unbound
707 Ų
Apolar buried
332 Ų

Interaction summary

HB 9 HY 10 PI 4 CLASH 4 ⚠ Exposure 47%
⚠️Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19 Buried (contacted) 10 Exposed 9 LogP 2.65 H-bonds 9
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank2.861Score-25.403
Inter norm-1.001Intra norm0.118
Top1000noExcludedno
Contacts16H-bonds9
Artifact reasongeometry warning; 10 clashes; 1 protein clash; high strain Δ 46.7
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 ARG46 ASP13 CYS72 GLY73 GLY77 HIS14 ILE15 ILE76 SER74 TYR49

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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
A:CSD72

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap15Native recall0.94
Jaccard0.88RMSD-
HB strict7Strict recall0.58
HB same residue+role5HB role recall0.50
HB same residue5HB residue recall0.50

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
363 0.3236686833943817 -0.922656 -24.2954 3 19 0 0.00 0.00 - no Open
318 0.5313914739558929 -0.916521 -26.3515 1 14 0 0.00 0.00 - no Open
296 1.340576599260557 -0.866114 -23.6414 3 20 0 0.00 0.00 - no Open
313 1.395589756323132 -0.754263 -20.827 5 15 0 0.00 0.00 - no Open
284 1.7396787330526 -1.11044 -33.9659 13 23 0 0.00 0.00 - no Open
281 1.85607159171697 -1.14564 -34.7998 11 16 0 0.00 0.00 - no Open
348 2.510631852879237 -0.8762 -24.8059 8 14 0 0.00 0.00 - no Open
258 2.860860253450067 -1.00124 -25.4028 9 16 15 0.94 0.50 - no Current
271 2.8833662991378333 -0.970487 -29.5939 10 15 0 0.00 0.00 - no Open
273 3.372067864906788 -0.984025 -30.8549 11 15 0 0.00 0.00 - no Open
413 3.9499962992021005 -0.803776 -21.0277 6 18 0 0.00 0.00 - no Open
336 3.9850996762335 -0.846144 -23.7714 8 19 0 0.00 0.00 - no Open
296 4.196552406559037 -0.888004 -22.2524 5 13 0 0.00 0.00 - no Open
327 4.734313839890531 -0.780717 -23.4612 7 14 0 0.00 0.00 - no Open
318 5.396631318612632 -0.860345 -25.47 12 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 -25.403kcal/mol
Ligand efficiency (LE) -0.8468kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.168
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 445.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.65
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 46.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -66.71kcal/mol
Minimised FF energy -113.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 707.2Ų
Total solvent-accessible surface area of free ligand
BSA total 483.4Ų
Buried surface area upon binding
BSA apolar 332.4Ų
Hydrophobic contacts buried
BSA polar 151.1Ų
Polar contacts buried
Fraction buried 68.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2188.6Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 782.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)