FAIRMol

OHD_Leishmania_376

Pose ID 5442 Compound 1287 Pose 24

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_376

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
31.8 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.57, Jaccard 0.48, H-bond role recall 0.00
Burial
91%
Hydrophobic fit
91%
Reason: 14 internal clashes
14 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.965 kcal/mol/HA) ✓ Good fit quality (FQ -8.89) ✓ Good H-bonds (5 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ Very high strain energy (31.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-25.099
kcal/mol
LE
-0.965
kcal/mol/HA
Fit Quality
-8.89
FQ (Leeson)
HAC
26
heavy atoms
MW
350
Da
LogP
2.08
cLogP
Final rank
3.3092
rank score
Inter norm
-1.086
normalised
Contacts
16
H-bonds 6
Strain ΔE
31.8 kcal/mol
SASA buried
91%
Lipo contact
91% BSA apolar/total
SASA unbound
617 Ų
Apolar buried
512 Ų

Interaction summary

HBD 4 HBA 1 HY 8 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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.

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 overlap12Native recall0.57
Jaccard0.48RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
33 1.6930652387964553 -1.3032 -33.8634 6 17 0 0.00 0.00 - no Open
25 2.37677582883771 -1.09051 -30.1724 6 17 1 0.05 0.00 - no Open
12 2.44585948723262 -0.900816 -20.7969 5 15 0 0.00 0.00 - no Open
35 2.5616248823522323 -0.851804 -21.5439 6 20 0 0.00 0.00 - no Open
153 2.897957358189819 -0.8562 -22.5503 4 19 0 0.00 0.00 - no Open
111 3.0202415484740994 -1.0648 -31.0336 6 17 13 0.62 0.00 - no Open
24 3.3091876015919386 -1.08568 -25.0988 6 16 12 0.57 0.00 - no Current
19 3.4171330511542393 -0.834551 -20.0158 4 11 0 0.00 0.00 - no Open
95 3.4786804256067114 -1.14676 -28.8385 7 19 0 0.00 0.00 - no Open
124 3.6213626191011485 -0.903161 -25.3504 6 14 0 0.00 0.00 - no Open
17 3.6275869878240954 -0.920544 -21.0159 12 15 0 0.00 0.00 - no Open
148 3.89202282370617 -0.806911 -21.6887 5 10 0 0.00 0.00 - no Open
25 4.022373065804421 -0.812568 -20.336 5 10 0 0.00 0.00 - no Open
27 4.286510035161286 -1.21476 -29.2815 7 19 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 -25.099kcal/mol
Ligand efficiency (LE) -0.9653kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.894
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 350.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.08
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -126.34kcal/mol
Minimised FF energy -158.11kcal/mol

SASA & burial

✓ computed
SASA (unbound) 617.4Ų
Total solvent-accessible surface area of free ligand
BSA total 559.9Ų
Buried surface area upon binding
BSA apolar 511.9Ų
Hydrophobic contacts buried
BSA polar 48.0Ų
Polar contacts buried
Fraction buried 90.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3310.5Ų
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 1677.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)