FAIRMol

OHD_TB2020_27

Pose ID 1408 Compound 1305 Pose 53

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
T03
L. major DHFR L. major
Ligand OHD_TB2020_27

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
65.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.70, Jaccard 0.56, H-bond role recall 0.20
Burial
73%
Hydrophobic fit
82%
Reason: strain 65.1 kcal/mol
strain ΔE 65.1 kcal/mol 4 protein-contact clashes 4 intramolecular clashes 54% of hydrophobic surface appears solvent-exposed (21/39 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
vB — Very bioaccumulative (BCF>5000)
Persistent
Yes
ADMET alerts (in-silico)
hERG High Ames Clear DILI Risk
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.328 kcal/mol/HA) ✓ Good fit quality (FQ -3.62) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Extreme strain energy (65.1 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (19)
Score
-16.748
kcal/mol
LE
-0.328
kcal/mol/HA
Fit Quality
-3.62
FQ (Leeson)
HAC
51
heavy atoms
MW
741
Da
LogP
6.36
cLogP
Final rank
2.5634
rank score
Inter norm
-0.534
normalised
Contacts
19
H-bonds 3
Strain ΔE
65.1 kcal/mol
SASA buried
73%
Lipo contact
82% BSA apolar/total
SASA unbound
1109 Ų
Apolar buried
668 Ų

Interaction summary

HBA 1 HY 6 PI 1 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

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.
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 overlap14Native recall0.70
Jaccard0.56RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
51 2.3367390353755515 -0.464314 -19.6831 3 22 0 0.00 0.00 - no Open
53 2.5633739943125504 -0.533989 -16.7478 3 19 14 0.70 0.20 - no Current
36 5.822086808893963 -0.5059 -21.6119 6 17 1 0.05 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 -16.748kcal/mol
Ligand efficiency (LE) -0.3284kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -3.623
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 51HA

Physicochemical properties
Molecular weight 741.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.36
Lipinski: ≤ 5
Rotatable bonds 16

Conformational strain (MMFF94s)
Strain energy (ΔE) 65.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 6.47kcal/mol
Minimised FF energy -58.63kcal/mol

SASA & burial

✓ computed
SASA (unbound) 1109.3Ų
Total solvent-accessible surface area of free ligand
BSA total 813.0Ų
Buried surface area upon binding
BSA apolar 667.9Ų
Hydrophobic contacts buried
BSA polar 145.1Ų
Polar contacts buried
Fraction buried 73.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1912.5Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 844.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)