FAIRMol

Z56566324

Pose ID 3998 Compound 2534 Pose 612

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 Z56566324
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
26.1 kcal/mol
Protein clashes
7
Internal clashes
10
Native overlap
contact recall 0.86, Jaccard 0.75, H-bond role recall 0.00
Burial
94%
Hydrophobic fit
78%
Reason: 10 internal clashes
7 protein-contact clashes 10 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.494 kcal/mol/HA) ✓ Good fit quality (FQ -4.81) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ High strain energy (26.1 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Internal clashes (9)
Score
-15.302
kcal/mol
LE
-0.494
kcal/mol/HA
Fit Quality
-4.81
FQ (Leeson)
HAC
31
heavy atoms
MW
454
Da
LogP
5.00
cLogP
Strain ΔE
26.1 kcal/mol
SASA buried
94%
Lipo contact
78% BSA apolar/total
SASA unbound
719 Ų
Apolar buried
527 Ų

Interaction summary

HB 0 HY 24 PI 5 CLASH 10

HB · H-bonds
No hb · h-bonds detected for this pose.

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 rank1.423Score-15.302
Inter norm-0.749Intra norm0.255
Top1000noExcludedno
Contacts21H-bonds0
Artifact reasongeometry warning; 9 clashes; 7 protein contact clashes; 3 cofactor-context clashes; moderate strain Δ 26.1
Residues
ALA34 ARG59 ASP54 GLN56 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO52 PRO91 THR184 THR86 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 overlap18Native recall0.86
Jaccard0.75RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
612 1.4226843790751635 -0.748953 -15.3023 0 21 18 0.86 0.00 - no Current
625 2.8556748578086197 -0.772632 -17.3417 10 15 0 0.00 0.00 - no Open
634 3.0066692990171866 -0.767146 -19.1205 3 12 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 -15.302kcal/mol
Ligand efficiency (LE) -0.4936kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.809
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 453.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.00
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -16.17kcal/mol
Minimised FF energy -42.26kcal/mol

SASA & burial

✓ computed
SASA (unbound) 719.4Ų
Total solvent-accessible surface area of free ligand
BSA total 677.7Ų
Buried surface area upon binding
BSA apolar 527.3Ų
Hydrophobic contacts buried
BSA polar 150.4Ų
Polar contacts buried
Fraction buried 94.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1789.6Ų
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 587.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)