FAIRMol

Z56899981

Pose ID 4000 Compound 2609 Pose 614

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 Z56899981
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 high Native strong SASA done
Strain ΔE
21.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.00
Burial
96%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.579 kcal/mol/HA) ✓ Good fit quality (FQ -5.33) ✓ Good H-bonds (3 bonds) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (21.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-15.054
kcal/mol
LE
-0.579
kcal/mol/HA
Fit Quality
-5.33
FQ (Leeson)
HAC
26
heavy atoms
MW
353
Da
LogP
4.06
cLogP
Strain ΔE
21.5 kcal/mol
SASA buried
96%
Lipo contact
79% BSA apolar/total
SASA unbound
610 Ų
Apolar buried
464 Ų

Interaction summary

HB 3 HY 24 PI 3 CLASH 1

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 rank2.206Score-15.054
Inter norm-0.881Intra norm0.302
Top1000noExcludedno
Contacts19H-bonds3
Artifact reasongeometry warning; 13 clashes; 1 protein clash; moderate strain Δ 21.0
Residues
ALA34 ARG100 ARG59 ASP54 GLY161 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 PRO91 SER89 THR86 TYR166 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 overlap16Native recall0.76
Jaccard0.67RMSD-
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
622 1.7531350104233334 -1.17674 -31.2262 5 15 0 0.00 0.00 - no Open
614 2.2055198786948744 -0.88061 -15.0542 3 19 16 0.76 0.00 - no Current
612 3.5293553397063118 -1.03384 -28.1524 4 17 1 0.05 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 -15.054kcal/mol
Ligand efficiency (LE) -0.5790kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.335
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 353.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.06
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 93.71kcal/mol
Minimised FF energy 72.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 609.6Ų
Total solvent-accessible surface area of free ligand
BSA total 584.8Ų
Buried surface area upon binding
BSA apolar 464.4Ų
Hydrophobic contacts buried
BSA polar 120.4Ų
Polar contacts buried
Fraction buried 95.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1723.2Ų
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 574.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)