FAIRMol

OHD_Leishmania_481

Pose ID 12914 Compound 469 Pose 35

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand OHD_Leishmania_481
PDB9IFH↗

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
20.2 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 1.00, Jaccard 0.67, H-bond role recall 1.00
Burial
55%
Hydrophobic fit
83%
Reason: 14 internal clashes
14 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.751 kcal/mol/HA) ✓ Good fit quality (FQ -7.38) ✓ Strong H-bond network (9 bonds) ✓ Good burial (55% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (20.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-24.023
kcal/mol
LE
-0.751
kcal/mol/HA
Fit Quality
-7.38
FQ (Leeson)
HAC
32
heavy atoms
MW
466
Da
LogP
4.94
cLogP
Strain ΔE
20.2 kcal/mol
SASA buried
55%
Lipo contact
83% BSA apolar/total
SASA unbound
725 Ų
Apolar buried
331 Ų

Interaction summary

HB 9 HY 15 PI 1 CLASH 0

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
No clash · clashes detected for this pose.
Final rank4.104Score-24.023
Inter norm-0.708Intra norm-0.043
Top1000noExcludedno
Contacts12H-bonds9
Artifact reasongeometry warning; 14 clashes; 2 protein clashes; moderate strain Δ 20.2
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 PHE396 PRO398 PRO462 SER394 SER470 THR397 THR463

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap8Native recall1.00
Jaccard0.67RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221

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:FAD501

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 0 0.00 0.00 - no Open
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 8 1.00 1.00 - no Current
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 -24.023kcal/mol
Ligand efficiency (LE) -0.7507kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.383
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) 20.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 9.61kcal/mol
Minimised FF energy -10.58kcal/mol

SASA & burial

✓ computed
SASA (unbound) 725.2Ų
Total solvent-accessible surface area of free ligand
BSA total 399.7Ų
Buried surface area upon binding
BSA apolar 331.4Ų
Hydrophobic contacts buried
BSA polar 68.3Ų
Polar contacts buried
Fraction buried 55.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3105.8Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1556.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)