FAIRMol

OHD_TB2020_17

Pose ID 3431 Compound 2601 Pose 45

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 OHD_TB2020_17
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
55.5 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.71, Jaccard 0.58, H-bond role recall 0.00
Burial
91%
Hydrophobic fit
78%
Reason: 7 internal clashes, strain 55.5 kcal/mol
strain ΔE 55.5 kcal/mol 7 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.541 kcal/mol/HA) ✓ Good fit quality (FQ -5.45) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (55.5 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (14)
Score
-18.926
kcal/mol
LE
-0.541
kcal/mol/HA
Fit Quality
-5.45
FQ (Leeson)
HAC
35
heavy atoms
MW
496
Da
LogP
4.39
cLogP
Strain ΔE
55.5 kcal/mol
SASA buried
91%
Lipo contact
78% BSA apolar/total
SASA unbound
773 Ų
Apolar buried
552 Ų

Interaction summary

HB 2 HY 24 PI 3 CLASH 7

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 rank2.074Score-18.926
Inter norm-0.662Intra norm0.120
Top1000noExcludedno
Contacts20H-bonds2
Artifact reasongeometry warning; 14 clashes; 7 protein contact clashes; high strain Δ 55.1
Residues
ALA34 ARG100 ARG59 ASP54 GLN56 GLU50 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 PRO52 PRO91 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 overlap15Native recall0.71
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
45 2.074274147786298 -0.661547 -18.9256 2 20 15 0.71 0.00 - no Current
38 3.6771447614901684 -0.781966 -28.0582 12 15 0 0.00 0.00 - no Open
22 6.122942433269545 -0.809266 -24.8972 11 23 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 -18.926kcal/mol
Ligand efficiency (LE) -0.5407kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.454
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 495.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.39
Lipinski: ≤ 5
Rotatable bonds 11

Conformational strain (MMFF94s)
Strain energy (ΔE) 55.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 98.84kcal/mol
Minimised FF energy 43.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 773.1Ų
Total solvent-accessible surface area of free ligand
BSA total 703.2Ų
Buried surface area upon binding
BSA apolar 551.8Ų
Hydrophobic contacts buried
BSA polar 151.4Ų
Polar contacts buried
Fraction buried 91.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1850.2Ų
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 574.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)