FAIRMol

NMT-TY0564

Pose ID 11826 Compound 1840 Pose 305

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
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand NMT-TY0564
PDB6RB5↗

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 mixed SASA done
Strain ΔE
32.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.54, Jaccard 0.37
Burial
74%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.865 kcal/mol/HA) ✓ Good fit quality (FQ -7.50) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Very high strain energy (32.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-19.019
kcal/mol
LE
-0.865
kcal/mol/HA
Fit Quality
-7.50
FQ (Leeson)
HAC
22
heavy atoms
MW
323
Da
LogP
0.11
cLogP
Strain ΔE
32.0 kcal/mol
SASA buried
74%
Lipo contact
70% BSA apolar/total
SASA unbound
530 Ų
Apolar buried
277 Ų

Interaction summary

HB 6 HY 19 PI 2 CLASH 1

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 rank1.887Score-19.019
Inter norm-0.956Intra norm0.092
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 11 clashes; 1 protein clash; high strain Δ 32.0
Residues
CYS52 GLU18 GLY13 GLY49 GLY50 ILE339 LEU17 MET113 SER14 THR335 TRP21 TYR110 VAL53

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap7Native recall0.54
Jaccard0.37RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT18Atoms7550
Residues493Chains1
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:276; MET:221

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:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
310 1.6885218190337798 -1.24097 -25.6825 9 12 0 0.00 - - no Open
305 1.8869440985078745 -0.956203 -19.0189 6 13 7 0.54 - - no Current
276 3.5289317786568315 -1.50032 -32.3513 16 19 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 -19.019kcal/mol
Ligand efficiency (LE) -0.8645kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.505
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 323.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.11
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -15.37kcal/mol
Minimised FF energy -47.40kcal/mol

SASA & burial

✓ computed
SASA (unbound) 529.6Ų
Total solvent-accessible surface area of free ligand
BSA total 392.7Ų
Buried surface area upon binding
BSA apolar 276.7Ų
Hydrophobic contacts buried
BSA polar 116.0Ų
Polar contacts buried
Fraction buried 74.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2972.4Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1451.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)