FAIRMol

Z56778174

Pose ID 1905 Compound 671 Pose 550

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 Z56778174

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 mixed SASA done
Strain ΔE
44.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.35, Jaccard 0.30, H-bond role recall 0.20
Burial
76%
Hydrophobic fit
71%
Reason: strain 44.3 kcal/mol
strain ΔE 44.3 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.272 kcal/mol/HA) ✓ Good fit quality (FQ -11.40) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Extreme strain energy (44.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-30.531
kcal/mol
LE
-1.272
kcal/mol/HA
Fit Quality
-11.40
FQ (Leeson)
HAC
24
heavy atoms
MW
342
Da
LogP
3.04
cLogP
Strain ΔE
44.3 kcal/mol
SASA buried
76%
Lipo contact
71% BSA apolar/total
SASA unbound
557 Ų
Apolar buried
299 Ų

Interaction summary

HB 8 HY 13 PI 2 CLASH 3
Final rank2.490Score-30.531
Inter norm-1.102Intra norm-0.170
Top1000noExcludedno
Contacts10H-bonds8
Artifact reasongeometry warning; 9 clashes; 1 protein clash; high strain Δ 44.3
Residues
ARG97 LEU94 LYS57 LYS90 LYS95 MET53 PHE56 PHE91 PRO93 THR54

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

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 overlap7Native recall0.35
Jaccard0.30RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
559 0.2665955335841529 -1.07352 -26.2319 3 14 0 0.00 0.00 - no Open
550 2.4903017377618566 -1.10224 -30.5313 8 10 7 0.35 0.20 - no Current
554 3.759958976604163 -1.09088 -23.4995 7 13 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 -30.531kcal/mol
Ligand efficiency (LE) -1.2721kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.401
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 342.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.04
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 44.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 139.08kcal/mol
Minimised FF energy 94.76kcal/mol

SASA & burial

✓ computed
SASA (unbound) 557.1Ų
Total solvent-accessible surface area of free ligand
BSA total 421.0Ų
Buried surface area upon binding
BSA apolar 299.5Ų
Hydrophobic contacts buried
BSA polar 121.5Ų
Polar contacts buried
Fraction buried 75.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1392.2Ų
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 853.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)