FAIRMol

NMT-TY0558

Pose ID 7704 Compound 29 Pose 252

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
T12
T. brucei R5P T. brucei
Ligand NMT-TY0558
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
57.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.88, Jaccard 0.67, H-bond role recall 0.60
Burial
90%
Hydrophobic fit
59%
Reason: strain 57.4 kcal/mol
strain ΔE 57.4 kcal/mol 5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.041 kcal/mol/HA) ✓ Good fit quality (FQ -9.19) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (90% SASA buried) ✗ Extreme strain energy (57.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-23.952
kcal/mol
LE
-1.041
kcal/mol/HA
Fit Quality
-9.19
FQ (Leeson)
HAC
23
heavy atoms
MW
339
Da
LogP
-0.18
cLogP
Strain ΔE
57.4 kcal/mol
SASA buried
90%
Lipo contact
59% BSA apolar/total
SASA unbound
528 Ų
Apolar buried
278 Ų

Interaction summary

HB 13 HY 10 PI 2 CLASH 5

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 rank4.427Score-23.952
Inter norm-1.205Intra norm0.163
Top1000noExcludedno
Contacts19H-bonds13
Artifact reasongeometry warning; 12 clashes; 2 protein clashes; high strain Δ 57.4
Residues
ARG144 ASN106 HIS105 HIS141 MET101 TYR97 ARG116 ASP13 ASP48 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49 VAL47

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 overlap14Native recall0.88
Jaccard0.67RMSD-
HB strict5Strict recall0.42
HB same residue+role6HB role recall0.60
HB same residue6HB residue recall0.60

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
355 0.53720823906409 -1.13196 -24.8857 8 18 0 0.00 0.00 - no Open
308 2.8856867920569327 -1.08579 -24.3497 12 16 0 0.00 0.00 - no Open
252 4.427465460607502 -1.20452 -23.952 13 19 14 0.88 0.60 - 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 -23.952kcal/mol
Ligand efficiency (LE) -1.0414kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.191
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 339.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.18
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 57.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -83.72kcal/mol
Minimised FF energy -141.08kcal/mol

SASA & burial

✓ computed
SASA (unbound) 528.4Ų
Total solvent-accessible surface area of free ligand
BSA total 473.4Ų
Buried surface area upon binding
BSA apolar 277.6Ų
Hydrophobic contacts buried
BSA polar 195.8Ų
Polar contacts buried
Fraction buried 89.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 58.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2019.0Ų
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 761.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)