FAIRMol

NMT-TY0823

Pose ID 3705 Compound 2385 Pose 319

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
T06
T. brucei DHFR T. brucei
Ligand NMT-TY0823
PDB8RHT↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
28.7 kcal/mol
Protein clashes
4
Internal clashes
7
Native overlap
contact recall 0.90, Jaccard 0.90, H-bond role recall 1.00
Burial
99%
Hydrophobic fit
72%
Reason: 7 internal clashes
4 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.250 kcal/mol/HA) ✓ Good fit quality (FQ -10.24) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (99% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (28.7 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Internal clashes (7)
Score
-23.748
kcal/mol
LE
-1.250
kcal/mol/HA
Fit Quality
-10.24
FQ (Leeson)
HAC
19
heavy atoms
MW
280
Da
LogP
0.02
cLogP
Strain ΔE
28.7 kcal/mol
SASA buried
99%
Lipo contact
72% BSA apolar/total
SASA unbound
471 Ų
Apolar buried
337 Ų

Interaction summary

HB 11 HY 19 PI 2 CLASH 0

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
No clash · clashes detected for this pose.
Final rank0.364Score-23.748
Inter norm-1.215Intra norm-0.035
Top1000noExcludedno
Contacts19H-bonds11
Artifact reasongeometry warning; 7 clashes; 4 protein contact clashes; moderate strain Δ 28.7
Residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name8RHTContacts21
PoseOpen native poseHB0
IFP residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap19Native recall0.90
Jaccard0.90RMSD-
HB strict5Strict recall1.00
HB same residue+role4HB role recall1.00
HB same residue4HB residue recall1.00

Protein summary

223 residues
Protein targetT06Atoms3452
Residues223Chains1
Residue summaryARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

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:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
319 0.3637981101771606 -1.21498 -23.7482 11 19 19 0.90 1.00 - no Current
405 1.9997854384566627 -1.25872 -25.1802 8 13 0 0.00 0.00 - no Open
435 2.647455335312565 -1.234 -25.0623 9 14 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 -23.748kcal/mol
Ligand efficiency (LE) -1.2499kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.245
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.02
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -144.48kcal/mol
Minimised FF energy -173.20kcal/mol

SASA & burial

✓ computed
SASA (unbound) 470.6Ų
Total solvent-accessible surface area of free ligand
BSA total 468.0Ų
Buried surface area upon binding
BSA apolar 337.2Ų
Hydrophobic contacts buried
BSA polar 130.8Ų
Polar contacts buried
Fraction buried 99.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1558.3Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 590.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)