FAIRMol

Z56880482

Pose ID 3779 Compound 2421 Pose 393

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 Z56880482
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
25.8 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.67, Jaccard 0.61, H-bond role recall 0.00
Burial
96%
Hydrophobic fit
96%
Reason: 14 internal clashes
14 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.858 kcal/mol/HA) ✓ Good fit quality (FQ -7.57) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (96%) ✗ High strain energy (25.8 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-19.728
kcal/mol
LE
-0.858
kcal/mol/HA
Fit Quality
-7.57
FQ (Leeson)
HAC
23
heavy atoms
MW
367
Da
LogP
5.14
cLogP
Final rank
0.6688
rank score
Inter norm
-0.980
normalised
Contacts
16
H-bonds 0
Strain ΔE
25.8 kcal/mol
SASA buried
96%
Lipo contact
96% BSA apolar/total
SASA unbound
552 Ų
Apolar buried
507 Ų

Interaction summary

HB 0 HY 8 PI 3 CLASH 0

HBD/HBA · H-bonds (geometric)
No hbd/hba · h-bonds (geometric) 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
No clash · clashes detected for this pose.

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 overlap14Native recall0.67
Jaccard0.61RMSD-
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
393 0.6687712549936347 -0.980307 -19.7279 0 16 14 0.67 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 -19.728kcal/mol
Ligand efficiency (LE) -0.8577kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.570
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 367.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.14
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 100.54kcal/mol
Minimised FF energy 74.72kcal/mol

SASA & burial

✓ computed
SASA (unbound) 552.0Ų
Total solvent-accessible surface area of free ligand
BSA total 528.0Ų
Buried surface area upon binding
BSA apolar 507.4Ų
Hydrophobic contacts buried
BSA polar 20.6Ų
Polar contacts buried
Fraction buried 95.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 96.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1761.2Ų
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 579.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)