FAIRMol

Z278071350

Pose ID 1274 Compound 682 Pose 596

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
T02
Human DHFR Human
Ligand Z278071350
PDB5SD8↗

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
22.4 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.76, Jaccard 0.64, H-bond role recall 0.00
Burial
79%
Hydrophobic fit
81%
Reason: 10 internal clashes
10 intramolecular clashes 62% of hydrophobic surface is solvent-exposed (13/21 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.863 kcal/mol/HA) ✓ Good fit quality (FQ -8.33) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ High strain energy (22.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-25.896
kcal/mol
LE
-0.863
kcal/mol/HA
Fit Quality
-8.33
FQ (Leeson)
HAC
30
heavy atoms
MW
426
Da
LogP
3.82
cLogP
Final rank
0.5773
rank score
Inter norm
-0.863
normalised
Contacts
20
H-bonds 3
Strain ΔE
22.4 kcal/mol
SASA buried
79%
Lipo contact
81% BSA apolar/total
SASA unbound
696 Ų
Apolar buried
449 Ų

Interaction summary

HBA 1 HY 6 PI 1 CLASH 0

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
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.
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 overlap16Native recall0.76
Jaccard0.64RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
596 0.5773062689630676 -0.862611 -25.896 3 20 16 0.76 0.00 - no Current
591 1.036432703761499 -0.853836 -24.2863 2 20 0 0.00 0.00 - no Open
605 2.0302417119039733 -0.854506 -24.5526 1 13 0 0.00 0.00 - no Open
615 2.689759316825253 -0.827482 -20.2121 4 14 0 0.00 0.00 - no Open
607 4.895650481240657 -0.715065 -17.8757 7 12 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 -25.896kcal/mol
Ligand efficiency (LE) -0.8632kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.327
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 426.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.82
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -42.16kcal/mol
Minimised FF energy -64.59kcal/mol

SASA & burial

✓ computed
SASA (unbound) 696.0Ų
Total solvent-accessible surface area of free ligand
BSA total 552.6Ų
Buried surface area upon binding
BSA apolar 449.2Ų
Hydrophobic contacts buried
BSA polar 103.5Ų
Polar contacts buried
Fraction buried 79.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1604.3Ų
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 628.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)