FAIRMol

Z56174083

Pose ID 6026 Compound 3341 Pose 608

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 Z56174083

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 mixed SASA done
Strain ΔE
11.5 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.17
Burial
89%
Hydrophobic fit
89%
Reason: 15 internal clashes
15 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.183 kcal/mol/HA) ✓ Good fit quality (FQ -11.04) ✓ Good H-bonds (3 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Moderate strain (11.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-31.937
kcal/mol
LE
-1.183
kcal/mol/HA
Fit Quality
-11.04
FQ (Leeson)
HAC
27
heavy atoms
MW
354
Da
LogP
6.17
cLogP
Final rank
3.6157
rank score
Inter norm
-0.938
normalised
Contacts
15
H-bonds 5
Strain ΔE
11.5 kcal/mol
SASA buried
89%
Lipo contact
89% BSA apolar/total
SASA unbound
602 Ų
Apolar buried
476 Ų

Interaction summary

HBD 1 HBA 2 HY 9 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
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 overlap11Native recall0.52
Jaccard0.44RMSD-
HB strict0Strict recall0.00
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
608 3.6156882569928297 -0.938264 -31.9371 5 15 11 0.52 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 -31.937kcal/mol
Ligand efficiency (LE) -1.1829kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.036
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 354.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.17
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 11.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 88.40kcal/mol
Minimised FF energy 76.86kcal/mol

SASA & burial

✓ computed
SASA (unbound) 602.3Ų
Total solvent-accessible surface area of free ligand
BSA total 537.0Ų
Buried surface area upon binding
BSA apolar 476.0Ų
Hydrophobic contacts buried
BSA polar 61.0Ų
Polar contacts buried
Fraction buried 89.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3297.8Ų
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 1672.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)