FAIRMol

OHD_Leishmania_45

Pose ID 5421 Compound 3350 Pose 3

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
T09
L. major DHFR-TS L. major
Ligand OHD_Leishmania_45

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
71.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.64, H-bond role recall 0.17
Burial
78%
Hydrophobic fit
80%
Reason: strain 71.2 kcal/mol
strain ΔE 71.2 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.592 kcal/mol/HA) ✓ Good fit quality (FQ -6.70) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (71.2 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (11) ✗ Many internal clashes (24)
Score
-34.359
kcal/mol
LE
-0.592
kcal/mol/HA
Fit Quality
-6.70
FQ (Leeson)
HAC
58
heavy atoms
MW
811
Da
LogP
0.36
cLogP
Final rank
3.9665
rank score
Inter norm
-0.455
normalised
Contacts
20
H-bonds 9
Strain ΔE
71.2 kcal/mol
SASA buried
78%
Lipo contact
80% BSA apolar/total
SASA unbound
1067 Ų
Apolar buried
673 Ų

Interaction summary

HBD 3 HBA 6 HY 11 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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: strict.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap16Native recall0.76
Jaccard0.64RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.17

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
3 3.966478600896347 -0.454895 -34.3593 9 20 16 0.76 0.17 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -34.359kcal/mol
Ligand efficiency (LE) -0.5924kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.703
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 58HA

Physicochemical properties
Molecular weight 810.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.36
Lipinski: ≤ 5
Rotatable bonds 18

Conformational strain (MMFF94s)
Strain energy (ΔE) 71.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 184.01kcal/mol
Minimised FF energy 112.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 1066.8Ų
Total solvent-accessible surface area of free ligand
BSA total 835.9Ų
Buried surface area upon binding
BSA apolar 672.6Ų
Hydrophobic contacts buried
BSA polar 163.3Ų
Polar contacts buried
Fraction buried 78.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3638.5Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1670.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)