FAIRMol

Z56911531

Pose ID 1828 Compound 1291 Pose 473

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
T03
L. major DHFR L. major
Ligand Z56911531

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 strong SASA done
Strain ΔE
24.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.65, Jaccard 0.54, H-bond role recall 0.20
Burial
92%
Hydrophobic fit
67%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.331 kcal/mol/HA) ✓ Good fit quality (FQ -11.74) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ High strain energy (24.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-30.603
kcal/mol
LE
-1.331
kcal/mol/HA
Fit Quality
-11.74
FQ (Leeson)
HAC
23
heavy atoms
MW
347
Da
LogP
2.81
cLogP
Strain ΔE
24.4 kcal/mol
SASA buried
92%
Lipo contact
67% BSA apolar/total
SASA unbound
556 Ų
Apolar buried
343 Ų

Interaction summary

HB 8 HY 24 PI 2 CLASH 2

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
Final rank2.423Score-30.603
Inter norm-1.253Intra norm-0.078
Top1000noExcludedno
Contacts17H-bonds8
Artifact reasongeometry warning; 6 clashes; 2 protein clashes; moderate strain Δ 24.4
Residues
ALA32 ARG48 ASP52 ILE182 ILE45 MET53 NDP301 PHE56 THR180 THR83 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49 VAL87

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 overlap13Native recall0.65
Jaccard0.54RMSD-
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
473 2.4234419940035883 -1.25295 -30.6033 8 17 13 0.65 0.20 - no Current
456 2.5187955141248546 -1.23622 -30.8904 7 18 1 0.05 0.00 - no Open
433 3.4230627256185704 -1.04218 -23.1072 9 15 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 -30.603kcal/mol
Ligand efficiency (LE) -1.3306kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.743
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 347.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.81
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 96.01kcal/mol
Minimised FF energy 71.60kcal/mol

SASA & burial

✓ computed
SASA (unbound) 555.9Ų
Total solvent-accessible surface area of free ligand
BSA total 511.6Ų
Buried surface area upon binding
BSA apolar 343.3Ų
Hydrophobic contacts buried
BSA polar 168.2Ų
Polar contacts buried
Fraction buried 92.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1377.9Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 822.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)