FAIRMol

OHD_Leishmania_136

Pose ID 1372 Compound 636 Pose 17

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
T03
L. major DHFR L. major
Ligand OHD_Leishmania_136

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
14.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.80, Jaccard 0.67, H-bond role recall 0.60
Burial
94%
Hydrophobic fit
85%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.969 kcal/mol/HA) ✓ Good fit quality (FQ -9.35) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Moderate strain (14.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-29.074
kcal/mol
LE
-0.969
kcal/mol/HA
Fit Quality
-9.35
FQ (Leeson)
HAC
30
heavy atoms
MW
400
Da
LogP
2.26
cLogP
Strain ΔE
14.2 kcal/mol
SASA buried
94%
Lipo contact
85% BSA apolar/total
SASA unbound
680 Ų
Apolar buried
539 Ų

Interaction summary

HB 11 HY 24 PI 2 CLASH 5
Final rank3.586Score-29.074
Inter norm-0.977Intra norm0.008
Top1000noExcludedno
Contacts20H-bonds11
Artifact reasongeometry warning; 15 clashes; 1 protein clash
Residues
ALA32 ARG97 ASP52 ILE45 LEU179 LEU94 LYS57 LYS95 MET53 NDP301 PHE55 PHE56 PHE91 THR180 TYR162 TYR178 VAL156 VAL30 VAL31 VAL87

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap16Native recall0.80
Jaccard0.67RMSD-
HB strict4Strict recall0.57
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
59 1.8077656603314811 -1.33737 -41.1817 8 18 0 0.00 0.00 - no Open
21 1.8167442151259838 -1.3248 -40.6867 9 18 0 0.00 0.00 - no Open
69 2.0383590711769224 -1.31566 -36.354 9 18 0 0.00 0.00 - no Open
18 2.07494107366931 -1.35194 -41.1881 8 18 0 0.00 0.00 - no Open
51 2.4756796252970026 -0.987142 -25.1715 6 16 0 0.00 0.00 - no Open
17 2.659480533179131 -0.988025 -29.206 7 15 0 0.00 0.00 - no Open
72 2.6888440031633536 -0.750575 -21.7979 3 14 0 0.00 0.00 - no Open
17 3.58601093162473 -0.977028 -29.0743 11 20 16 0.80 0.60 - no Current
44 3.8186271411229127 -0.825732 -21.4312 7 17 0 0.00 0.00 - no Open
69 3.822991328266453 -0.994304 -25.3242 10 18 15 0.75 0.60 - no Open
15 3.9945811977562276 -1.07747 -28.4735 11 20 1 0.05 0.00 - no Open
6 4.1125363457515824 -0.789709 -22.5077 7 16 0 0.00 0.00 - no Open
59 4.174917693331722 -0.958177 -28.341 9 18 1 0.05 0.00 - no Open
51 4.210198956266459 -1.07569 -27.4595 10 20 1 0.05 0.00 - no Open
18 4.247291649628563 -0.861737 -21.7221 4 20 0 0.00 0.00 - no Open
77 4.253748462384305 -0.861034 -20.9423 10 20 0 0.00 0.00 - no Open
15 4.305552679508108 -0.796609 -24.1605 4 14 0 0.00 0.00 - no Open
14 4.938291489005273 -0.642126 -17.5617 5 14 0 0.00 0.00 - no Open
67 5.1022653534044835 -0.644701 -19.1146 6 14 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 -29.074kcal/mol
Ligand efficiency (LE) -0.9691kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.349
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 400.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.26
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 62.00kcal/mol
Minimised FF energy 47.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 680.3Ų
Total solvent-accessible surface area of free ligand
BSA total 636.9Ų
Buried surface area upon binding
BSA apolar 539.3Ų
Hydrophobic contacts buried
BSA polar 97.6Ų
Polar contacts buried
Fraction buried 93.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1588.9Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 803.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)