FAIRMol

Z56893343

Pose ID 3893 Compound 142 Pose 507

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
T06
T. brucei DHFR T. brucei
Ligand Z56893343
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
47.8 kcal/mol
Protein clashes
5
Internal clashes
6
Native overlap
contact recall 0.76, Jaccard 0.70, H-bond role recall 0.00
Burial
93%
Hydrophobic fit
83%
Reason: 6 internal clashes, strain 47.8 kcal/mol
strain ΔE 47.8 kcal/mol 5 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.501 kcal/mol/HA) ✓ Good fit quality (FQ -5.02) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Extreme strain energy (47.8 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (14)
Score
-17.047
kcal/mol
LE
-0.501
kcal/mol/HA
Fit Quality
-5.02
FQ (Leeson)
HAC
34
heavy atoms
MW
479
Da
LogP
4.51
cLogP
Strain ΔE
47.8 kcal/mol
SASA buried
93%
Lipo contact
83% BSA apolar/total
SASA unbound
759 Ų
Apolar buried
590 Ų

Interaction summary

HB 2 HY 24 PI 3 CLASH 6
Final rank1.821Score-17.047
Inter norm-0.781Intra norm0.219
Top1000noExcludedno
Contacts18H-bonds2
Artifact reasongeometry warning; 14 clashes; 6 protein contact clashes; 1 cofactor-context clash; high strain Δ 47.8
Residues
ALA34 ARG100 ARG59 ASP54 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 PRO91 THR184 TYR166 TYR57 VAL32 VAL33

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

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 overlap16Native recall0.76
Jaccard0.70RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
550 1.197726939005163 -0.783787 -21.0567 2 19 0 0.00 0.00 - no Open
543 1.331348486803007 -0.769292 -20.2938 2 18 0 0.00 0.00 - no Open
507 1.8206294907843865 -0.781117 -17.0472 2 18 16 0.76 0.00 - 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 -17.047kcal/mol
Ligand efficiency (LE) -0.5014kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.017
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 478.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.51
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 47.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 88.18kcal/mol
Minimised FF energy 40.42kcal/mol

SASA & burial

✓ computed
SASA (unbound) 759.0Ų
Total solvent-accessible surface area of free ligand
BSA total 707.3Ų
Buried surface area upon binding
BSA apolar 590.1Ų
Hydrophobic contacts buried
BSA polar 117.2Ų
Polar contacts buried
Fraction buried 93.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1865.6Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 584.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)