FAIRMol

OHD_Leishmania_481

Pose ID 8147 Compound 469 Pose 17

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand OHD_Leishmania_481
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
36.6 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.84, Jaccard 0.62, H-bond role recall 0.57
Burial
79%
Hydrophobic fit
78%
Reason: 11 internal clashes
11 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.618 kcal/mol/HA) ✓ Good fit quality (FQ -6.07) ✓ Good H-bonds (5 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Very high strain energy (36.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-19.764
kcal/mol
LE
-0.618
kcal/mol/HA
Fit Quality
-6.07
FQ (Leeson)
HAC
32
heavy atoms
MW
466
Da
LogP
4.94
cLogP
Final rank
2.9889
rank score
Inter norm
-1.003
normalised
Contacts
23
H-bonds 8
Strain ΔE
36.6 kcal/mol
SASA buried
79%
Lipo contact
78% BSA apolar/total
SASA unbound
787 Ų
Apolar buried
483 Ų

Interaction summary

HBD 3 HBA 2 HY 5 PI 3 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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
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.
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 overlap16Native recall0.84
Jaccard0.62RMSD-
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
40 0.6318633434685462 -1.05679 -25.2363 11 17 0 0.00 0.00 - no Open
32 1.1093340137788317 -0.854228 -26.2704 5 15 0 0.00 0.00 - no Open
33 1.221046822080138 -0.8404 -24.6948 5 19 0 0.00 0.00 - no Open
12 2.2763008769763395 -0.951446 -27.8948 5 20 0 0.00 0.00 - no Open
41 2.7017944339236353 -0.816536 -24.4886 6 19 0 0.00 0.00 - no Open
19 2.8062455719099972 -0.858902 -22.2054 6 17 0 0.00 0.00 - no Open
17 2.9889278715837735 -1.00267 -19.7644 8 23 16 0.84 0.57 - no Current
35 3.4599440764772713 -0.8945 -24.7699 4 15 0 0.00 0.00 - no Open
30 3.771422856064557 -0.787662 -23.0094 6 11 0 0.00 0.00 - no Open
31 4.092882811740988 -0.838847 -22.2153 6 18 0 0.00 0.00 - no Open
35 4.104329269165856 -0.708066 -24.0235 9 12 0 0.00 0.00 - no Open
29 4.699770164678327 -1.04112 -26.4163 8 17 0 0.00 0.00 - no Open
22 4.76668917309497 -0.781504 -15.2577 9 17 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 -19.764kcal/mol
Ligand efficiency (LE) -0.6176kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.074
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 466.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.94
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 28.90kcal/mol
Minimised FF energy -7.66kcal/mol

SASA & burial

✓ computed
SASA (unbound) 786.7Ų
Total solvent-accessible surface area of free ligand
BSA total 620.5Ų
Buried surface area upon binding
BSA apolar 483.0Ų
Hydrophobic contacts buried
BSA polar 137.5Ų
Polar contacts buried
Fraction buried 78.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2678.8Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1413.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)