FAIRMol

Z25831748

Pose ID 3797 Compound 1909 Pose 411

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 Z25831748
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
38.5 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.67, Jaccard 0.58, H-bond role recall 0.00
Burial
91%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.081 kcal/mol/HA) ✓ Good fit quality (FQ -10.42) ✓ Good H-bonds (3 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (38.5 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (12)
Score
-32.418
kcal/mol
LE
-1.081
kcal/mol/HA
Fit Quality
-10.42
FQ (Leeson)
HAC
30
heavy atoms
MW
447
Da
LogP
2.67
cLogP
Strain ΔE
38.5 kcal/mol
SASA buried
91%
Lipo contact
68% BSA apolar/total
SASA unbound
712 Ų
Apolar buried
438 Ų

Interaction summary

HB 3 HY 24 PI 4 CLASH 4

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 rank1.224Score-32.418
Inter norm-0.805Intra norm-0.309
Top1000noExcludedno
Contacts17H-bonds3
Artifact reasongeometry warning; 12 clashes; 4 protein contact clashes; 1 cofactor-context clash; high strain Δ 38.5
Residues
ALA34 ARG100 ARG59 ASP54 GLN56 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 THR184 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 overlap14Native recall0.67
Jaccard0.58RMSD-
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
411 1.2238300291495845 -0.8053 -32.4178 3 17 14 0.67 0.00 - no Current
453 2.5515372806796917 -0.693794 -25.6657 6 13 0 0.00 0.00 - no Open
424 2.5699954615836487 -1.04947 -38.2072 3 10 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 -32.418kcal/mol
Ligand efficiency (LE) -1.0806kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.424
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 446.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.67
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 32.11kcal/mol
Minimised FF energy -6.37kcal/mol

SASA & burial

✓ computed
SASA (unbound) 712.1Ų
Total solvent-accessible surface area of free ligand
BSA total 646.9Ų
Buried surface area upon binding
BSA apolar 437.6Ų
Hydrophobic contacts buried
BSA polar 209.3Ų
Polar contacts buried
Fraction buried 90.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1724.5Ų
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 582.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)