FAIRMol

NMT-TY0543

Pose ID 3671 Compound 2637 Pose 285

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-TY0543
PDB8RHT↗

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
62.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.81, Jaccard 0.77, H-bond role recall 1.00
Burial
100%
Hydrophobic fit
62%
Reason: strain 62.8 kcal/mol
strain ΔE 62.8 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.935 kcal/mol/HA) ✓ Good fit quality (FQ -8.12) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (100% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ Extreme strain energy (62.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-20.580
kcal/mol
LE
-0.935
kcal/mol/HA
Fit Quality
-8.12
FQ (Leeson)
HAC
22
heavy atoms
MW
327
Da
LogP
-0.76
cLogP
Strain ΔE
62.8 kcal/mol
SASA buried
100%
Lipo contact
62% BSA apolar/total
SASA unbound
514 Ų
Apolar buried
317 Ų

Interaction summary

HB 12 HY 19 PI 2 CLASH 3

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 rank3.038Score-20.580
Inter norm-1.030Intra norm0.095
Top1000noExcludedno
Contacts18H-bonds12
Artifact reasongeometry warning; 9 clashes; 2 protein clashes; high strain Δ 62.8
Residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 MET82 NDP301 PHE58 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 overlap17Native recall0.81
Jaccard0.77RMSD-
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
291 1.4665335177179741 -1.4222 -30.7212 13 16 0 0.00 0.00 - no Open
285 3.0376044302499703 -1.03006 -20.5804 12 18 17 0.81 1.00 - 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 -20.580kcal/mol
Ligand efficiency (LE) -0.9355kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.122
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 327.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.76
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 62.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -3.64kcal/mol
Minimised FF energy -66.41kcal/mol

SASA & burial

✓ computed
SASA (unbound) 514.1Ų
Total solvent-accessible surface area of free ligand
BSA total 512.6Ų
Buried surface area upon binding
BSA apolar 316.8Ų
Hydrophobic contacts buried
BSA polar 195.8Ų
Polar contacts buried
Fraction buried 99.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 61.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1531.7Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 594.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)