FAIRMol

OHD_Leishmania_380

Pose ID 8141 Compound 639 Pose 11

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_Leishmania_380
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
20.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.74, Jaccard 0.61, H-bond role recall 0.57
Burial
72%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (15/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.752 kcal/mol/HA) ✓ Good fit quality (FQ -7.85) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (20.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)
Score
-30.082
kcal/mol
LE
-0.752
kcal/mol/HA
Fit Quality
-7.85
FQ (Leeson)
HAC
40
heavy atoms
MW
538
Da
LogP
5.13
cLogP
Final rank
3.7564
rank score
Inter norm
-0.819
normalised
Contacts
18
H-bonds 11
Strain ΔE
20.4 kcal/mol
SASA buried
72%
Lipo contact
70% BSA apolar/total
SASA unbound
787 Ų
Apolar buried
397 Ų

Interaction summary

HBD 3 HBA 6 HY 3 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 8.

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 overlap14Native recall0.74
Jaccard0.61RMSD-
HB strict4Strict recall0.44
HB same residue+role4HB role recall0.57
HB same residue5HB residue recall0.71

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
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 14 0.74 0.57 - no Current
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 -30.082kcal/mol
Ligand efficiency (LE) -0.7521kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.854
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) 20.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 144.18kcal/mol
Minimised FF energy 123.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 787.0Ų
Total solvent-accessible surface area of free ligand
BSA total 565.4Ų
Buried surface area upon binding
BSA apolar 397.2Ų
Hydrophobic contacts buried
BSA polar 168.2Ų
Polar contacts buried
Fraction buried 71.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2594.1Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1411.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)