FAIRMol

OHD_Leishmania_380

Pose ID 12213 Compound 639 Pose 12

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
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand OHD_Leishmania_380
PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
24.6 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.33, Jaccard 0.27, H-bond role recall 0.20
Burial
76%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
1 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.854 kcal/mol/HA) ✓ Good fit quality (FQ -8.92) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ High strain energy (24.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-34.157
kcal/mol
LE
-0.854
kcal/mol/HA
Fit Quality
-8.92
FQ (Leeson)
HAC
40
heavy atoms
MW
538
Da
LogP
5.13
cLogP
Strain ΔE
24.6 kcal/mol
SASA buried
76%
Lipo contact
66% BSA apolar/total
SASA unbound
763 Ų
Apolar buried
382 Ų

Interaction summary

HB 6 HY 11 PI 0 CLASH 3

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank3.268Score-34.157
Inter norm-0.927Intra norm0.073
Top1000noExcludedno
Contacts15H-bonds6
Artifact reasongeometry warning; 17 clashes; 2 protein clashes; 3 severe cofactor-context clashes; moderate strain Δ 24.6
Residues
ARG228 ARG287 ASP330 GLY196 GLY197 ILE288 LEU227 LEU332 LYS306 MET333 NDP800 PHE198 PHE230 PRO289 TYR221

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name2WOVContacts27
PoseOpen native poseHB0
IFP residues
ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap9Native recall0.33
Jaccard0.27RMSD-
HB strict1Strict recall0.08
HB same residue+role1HB role recall0.20
HB same residue2HB residue recall0.50

Protein summary

493 residues
Protein targetT19Atoms7541
Residues493Chains1
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:330; 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
C:NDP800

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 9 0.33 0.20 - no Current
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 0 0.00 0.00 - no Open
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 -34.157kcal/mol
Ligand efficiency (LE) -0.8539kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.918
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 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 145.38kcal/mol
Minimised FF energy 120.81kcal/mol

SASA & burial

✓ computed
SASA (unbound) 763.4Ų
Total solvent-accessible surface area of free ligand
BSA total 577.4Ų
Buried surface area upon binding
BSA apolar 381.8Ų
Hydrophobic contacts buried
BSA polar 195.6Ų
Polar contacts buried
Fraction buried 75.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3065.9Ų
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 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1540.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)