FAIRMol

OHD_Leishmania_380

Pose ID 10863 Compound 639 Pose 20

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand OHD_Leishmania_380
PDB5S9T↗

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
22.1 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.75, Jaccard 0.45, H-bond role recall 0.00
Burial
77%
Hydrophobic fit
68%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.662 kcal/mol/HA) ✓ Good fit quality (FQ -6.91) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ High strain energy (22.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)
Score
-26.470
kcal/mol
LE
-0.662
kcal/mol/HA
Fit Quality
-6.91
FQ (Leeson)
HAC
40
heavy atoms
MW
538
Da
LogP
5.13
cLogP
Strain ΔE
22.1 kcal/mol
SASA buried
77%
Lipo contact
68% BSA apolar/total
SASA unbound
739 Ų
Apolar buried
384 Ų

Interaction summary

HB 11 HY 24 PI 2 CLASH 6

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 rank5.305Score-26.470
Inter norm-0.745Intra norm0.083
Top1000noExcludedno
Contacts17H-bonds11
Artifact reasongeometry warning; 19 clashes; 2 protein clashes; moderate strain Δ 22.1
Residues
ARG331 ARG361 CYS375 FAD501 GLY229 GLY376 HIS359 ILE378 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR360 THR374 VAL362

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap9Native recall0.75
Jaccard0.45RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall1.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
34 2.037464332345491 -0.816862 -31.8466 6 16 0 0.00 0.00 - no Open
25 2.378437056644811 -0.79296 -25.1786 11 20 0 0.00 0.00 - no Open
28 3.1939535201530846 -0.720039 -24.3367 8 16 0 0.00 0.00 - no Open
12 3.2679598625087527 -0.927293 -34.1568 6 15 0 0.00 0.00 - no Open
20 3.495100387591973 -0.687709 -25.9631 8 13 0 0.00 0.00 - no Open
26 3.6318101855931193 -0.794213 -29.5742 8 21 0 0.00 0.00 - no Open
25 3.6473712664434346 -0.864399 -31.0091 12 17 0 0.00 0.00 - no Open
11 3.756350175949824 -0.818637 -30.0821 11 18 0 0.00 0.00 - no Open
36 4.328059027755822 -0.664103 -25.5651 8 12 0 0.00 0.00 - no Open
13 4.367243655754057 -0.718582 -25.2048 10 15 0 0.00 0.00 - no Open
30 4.3947619074725255 -0.797581 -32.0325 7 21 0 0.00 0.00 - no Open
27 4.675590440132758 -0.575435 -21.4762 7 13 0 0.00 0.00 - no Open
18 4.709489958919522 -0.661154 -21.8688 6 14 0 0.00 0.00 - no Open
26 4.853888287172083 -0.702973 -26.167 8 19 0 0.00 0.00 - no Open
25 5.0046255959625645 -0.602508 -21.2208 5 13 0 0.00 0.00 - no Open
20 5.305300875417073 -0.744562 -26.4698 11 17 9 0.75 0.00 - no Current
17 5.662829045447725 -0.771959 -29.8084 10 17 0 0.00 0.00 - no Open
12 6.260876601403174 -0.803018 -30.5918 10 16 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 -26.470kcal/mol
Ligand efficiency (LE) -0.6617kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.911
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 40HA

Physicochemical properties
Molecular weight 538.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.13
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 143.37kcal/mol
Minimised FF energy 121.27kcal/mol

SASA & burial

✓ computed
SASA (unbound) 738.6Ų
Total solvent-accessible surface area of free ligand
BSA total 565.5Ų
Buried surface area upon binding
BSA apolar 383.6Ų
Hydrophobic contacts buried
BSA polar 181.9Ų
Polar contacts buried
Fraction buried 76.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6476.1Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2105.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)