FAIRMol

OHD_Leishmania_134

Pose ID 690 Compound 1020 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
T02
Human DHFR Human
Ligand OHD_Leishmania_134
PDB5SD8↗

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
49.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.81, Jaccard 0.65, H-bond role recall 0.60
Burial
85%
Hydrophobic fit
76%
Reason: strain 49.7 kcal/mol
strain ΔE 49.7 kcal/mol 1 protein-contact clashes 57% of hydrophobic surface appears solvent-exposed (13/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.913 kcal/mol/HA) ✓ Good fit quality (FQ -9.21) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Extreme strain energy (49.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-31.956
kcal/mol
LE
-0.913
kcal/mol/HA
Fit Quality
-9.21
FQ (Leeson)
HAC
35
heavy atoms
MW
481
Da
LogP
-0.59
cLogP
Strain ΔE
49.7 kcal/mol
SASA buried
85%
Lipo contact
76% BSA apolar/total
SASA unbound
775 Ų
Apolar buried
505 Ų

Interaction summary

HB 8 HY 14 PI 1 CLASH 1 ⚠ Exposure 56%

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
⚠️Partial hydrophobic solvent exposure
57% of hydrophobic surface appears solvent-exposed (13/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23 Buried (contacted) 10 Exposed 13 LogP -0.59 H-bonds 8
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.625Score-31.956
Inter norm-0.812Intra norm-0.101
Top1000noExcludedno
Contacts22H-bonds8
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; high strain Δ 46.5
Residues
ALA10 ASP22 GLU31 ILE61 ILE8 LEU23 LEU68 NAP201 PHE135 PHE32 PHE35 PRO26 PRO27 PRO62 SER60 THR137 THR57 TRP25 TYR122 TYR34 VAL116 VAL9

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5SD8Contacts21
PoseOpen native poseHB0
IFP residues
ALA10 ASN65 ASP22 GLN36 GLU31 GLY117 GLY21 ILE61 ILE8 LEU23 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9
Current overlap17Native recall0.81
Jaccard0.65RMSD-
HB strict3Strict recall0.60
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

Protein summary

200 residues
Protein targetT02Atoms3128
Residues200Chains2
Residue summaryLYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

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:NAP201

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
11 2.3326950438436285 -0.649489 -22.5313 9 16 0 0.00 0.00 - no Open
13 2.7703431775692176 -0.709407 -20.4301 6 15 0 0.00 0.00 - no Open
12 3.624857535893448 -0.812027 -31.9556 8 22 17 0.81 0.60 - 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 -31.956kcal/mol
Ligand efficiency (LE) -0.9130kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.209
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 480.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.59
Lipinski: ≤ 5
Rotatable bonds 12

Conformational strain (MMFF94s)
Strain energy (ΔE) 49.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -17.10kcal/mol
Minimised FF energy -66.77kcal/mol

SASA & burial

✓ computed
SASA (unbound) 774.5Ų
Total solvent-accessible surface area of free ligand
BSA total 661.4Ų
Buried surface area upon binding
BSA apolar 504.7Ų
Hydrophobic contacts buried
BSA polar 156.7Ų
Polar contacts buried
Fraction buried 85.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1687.9Ų
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 1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 605.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)