FAIRMol

Z32154728

Pose ID 6052 Compound 1008 Pose 634

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 Z32154728

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 high Native mixed SASA done
Strain ΔE
23.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.00
Burial
87%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.735 kcal/mol/HA) ✓ Good fit quality (FQ -7.23) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ High strain energy (23.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-23.529
kcal/mol
LE
-0.735
kcal/mol/HA
Fit Quality
-7.23
FQ (Leeson)
HAC
32
heavy atoms
MW
456
Da
LogP
0.55
cLogP
Final rank
2.0658
rank score
Inter norm
-0.809
normalised
Contacts
15
H-bonds 3
Strain ΔE
23.6 kcal/mol
SASA buried
87%
Lipo contact
66% BSA apolar/total
SASA unbound
704 Ų
Apolar buried
400 Ų

Interaction summary

HBA 2 HY 8 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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.
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+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
66 1.3505982434811619 -0.755698 -17.641 1 12 0 0.00 0.00 - no Open
650 1.6779348296445458 -0.763793 -24.7301 4 13 0 0.00 0.00 - no Open
634 2.0657957641371216 -0.809113 -23.5291 3 15 11 0.52 0.00 - no Current
141 3.3915646375584045 -0.794759 -23.1152 3 17 0 0.00 0.00 - no Open
83 5.420150559491577 -0.882408 -24.5321 11 19 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 -23.529kcal/mol
Ligand efficiency (LE) -0.7353kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.231
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 456.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.55
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 17.21kcal/mol
Minimised FF energy -6.40kcal/mol

SASA & burial

✓ computed
SASA (unbound) 704.2Ų
Total solvent-accessible surface area of free ligand
BSA total 610.4Ų
Buried surface area upon binding
BSA apolar 399.9Ų
Hydrophobic contacts buried
BSA polar 210.5Ų
Polar contacts buried
Fraction buried 86.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3225.6Ų
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 1678.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)