FAIRMol

GemmaOHDUnisi_18

Pose ID 3729 Compound 2373 Pose 343

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 GemmaOHDUnisi_18
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
58.0 kcal/mol
Protein clashes
2
Internal clashes
7
Native overlap
contact recall 0.76, Jaccard 0.70, H-bond role recall 0.25
Burial
97%
Hydrophobic fit
68%
Reason: 7 internal clashes, strain 58.0 kcal/mol
strain ΔE 58.0 kcal/mol 2 protein-contact clashes 7 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.862 kcal/mol/HA) ✓ Good fit quality (FQ -7.95) ✓ Good H-bonds (3 bonds) ✓ Deep burial (97% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Extreme strain energy (58.0 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (7)
Score
-22.422
kcal/mol
LE
-0.862
kcal/mol/HA
Fit Quality
-7.95
FQ (Leeson)
HAC
26
heavy atoms
MW
390
Da
LogP
3.96
cLogP
Final rank
0.2801
rank score
Inter norm
-0.918
normalised
Contacts
18
H-bonds 4
Strain ΔE
58.0 kcal/mol
SASA buried
97%
Lipo contact
68% BSA apolar/total
SASA unbound
628 Ų
Apolar buried
417 Ų

Interaction summary

HBD 2 HBA 1 HY 9 PI 3 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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 overlap16Native recall0.76
Jaccard0.70RMSD-
HB strict1Strict recall0.20
HB same residue+role1HB role recall0.25
HB same residue1HB residue recall0.25

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
343 0.28008345492833986 -0.918014 -22.422 4 18 16 0.76 0.25 - no Current
337 2.5893131337053408 -0.927259 -24.9952 2 14 0 0.00 0.00 - no Open
294 2.967317013168541 -0.943238 -24.5916 8 15 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 -22.422kcal/mol
Ligand efficiency (LE) -0.8624kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.945
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 390.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.96
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 58.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 36.90kcal/mol
Minimised FF energy -21.14kcal/mol

SASA & burial

✓ computed
SASA (unbound) 628.1Ų
Total solvent-accessible surface area of free ligand
BSA total 610.8Ų
Buried surface area upon binding
BSA apolar 416.6Ų
Hydrophobic contacts buried
BSA polar 194.2Ų
Polar contacts buried
Fraction buried 97.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1664.8Ų
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 578.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)