FAIRMol

OHD_TB2021_23

Pose ID 8159 Compound 4074 Pose 29

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand OHD_TB2021_23
PDB1F3T↗

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
69.7 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.89, Jaccard 0.74, H-bond role recall 0.57
Burial
80%
Hydrophobic fit
80%
Reason: 10 protein-contact clashes, 10 internal clashes, strain 69.7 kcal/mol
strain ΔE 69.7 kcal/mol 10 protein-contact clashes 10 intramolecular clashes 39% of hydrophobic surface appears solvent-exposed (9/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.651 kcal/mol/HA) ✓ Good fit quality (FQ -6.40) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (69.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-20.829
kcal/mol
LE
-0.651
kcal/mol/HA
Fit Quality
-6.40
FQ (Leeson)
HAC
32
heavy atoms
MW
463
Da
LogP
3.42
cLogP
Final rank
5.5103
rank score
Inter norm
-0.904
normalised
Contacts
21
H-bonds 8
Strain ΔE
69.7 kcal/mol
SASA buried
80%
Lipo contact
80% BSA apolar/total
SASA unbound
811 Ų
Apolar buried
518 Ų

Interaction summary

HBD 3 HBA 3 HY 4 PI 3 CLASH 10

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap17Native recall0.89
Jaccard0.74RMSD-
HB strict4Strict recall0.44
HB same residue+role4HB role recall0.57
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
29 5.510305352267977 -0.903994 -20.8293 8 21 17 0.89 0.57 - 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 -20.829kcal/mol
Ligand efficiency (LE) -0.6509kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.401
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 462.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.42
Lipinski: ≤ 5
Rotatable bonds 12

Conformational strain (MMFF94s)
Strain energy (ΔE) 69.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 63.53kcal/mol
Minimised FF energy -6.22kcal/mol

SASA & burial

✓ computed
SASA (unbound) 810.6Ų
Total solvent-accessible surface area of free ligand
BSA total 646.3Ų
Buried surface area upon binding
BSA apolar 518.4Ų
Hydrophobic contacts buried
BSA polar 127.8Ų
Polar contacts buried
Fraction buried 79.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2742.3Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1387.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)