FAIRMol

Z44847963

Pose ID 5879 Compound 386 Pose 461

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
T09
L. major DHFR-TS L. major
Ligand Z44847963

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
23.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Burial
89%
Hydrophobic fit
79%
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 (-0.728 kcal/mol/HA) ✓ Good fit quality (FQ -7.09) ✓ Good H-bonds (4 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (23.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (15)
Score
-22.555
kcal/mol
LE
-0.728
kcal/mol/HA
Fit Quality
-7.09
FQ (Leeson)
HAC
31
heavy atoms
MW
430
Da
LogP
4.70
cLogP
Strain ΔE
23.9 kcal/mol
SASA buried
89%
Lipo contact
79% BSA apolar/total
SASA unbound
699 Ų
Apolar buried
491 Ų

Interaction summary

HB 4 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 rank1.476Score-22.555
Inter norm-0.919Intra norm0.192
Top1000noExcludedno
Contacts18H-bonds4
Artifact reasongeometry warning; 15 clashes; 4 protein contact clashes; moderate strain Δ 23.8
Residues
NDP301 ALA32 ARG48 ASP52 ILE45 MET53 PHE56 PRO50 SER44 SER86 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.
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 overlap13Native recall0.62
Jaccard0.50RMSD-
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
430 1.123128311050852 -1.09943 -35.0127 9 16 0 0.00 0.00 - no Open
426 1.276767181328564 -1.03765 -27.4665 7 11 0 0.00 0.00 - no Open
461 1.476372703816213 -0.919152 -22.5547 4 18 13 0.62 0.00 - no Current
505 2.272725915955015 -0.896059 -31.1212 6 18 0 0.00 0.00 - no Open
412 2.595705842520432 -0.930582 -22.1691 7 11 0 0.00 0.00 - no Open
480 2.7191745516353594 -0.998852 -30.5149 7 16 0 0.00 0.00 - no Open
432 2.7494314954702257 -0.737507 -24.9974 1 17 1 0.05 0.00 - no Open
479 2.7843928705051484 -0.713014 -21.158 3 13 0 0.00 0.00 - no Open
500 2.791217765151704 -0.947142 -35.2818 6 18 0 0.00 0.00 - no Open
519 2.8617363901087467 -0.750125 -25.1003 6 14 0 0.00 0.00 - no Open
468 2.90635541192479 -0.798773 -25.6886 8 15 0 0.00 0.00 - no Open
441 2.9238440516247857 -0.997616 -30.3793 6 15 0 0.00 0.00 - no Open
468 3.20302513162988 -0.824135 -23.5686 7 9 0 0.00 0.00 - no Open
457 3.6279625865993608 -1.05901 -33.3892 7 17 0 0.00 0.00 - no Open
498 4.00190802340201 -0.862379 -25.6577 7 17 0 0.00 0.00 - no Open
458 5.080933656035169 -0.767574 -22.0757 6 18 0 0.00 0.00 - no Open
458 5.444083752190545 -1.06966 -30.8753 11 29 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 -22.555kcal/mol
Ligand efficiency (LE) -0.7276kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.088
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.70
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 134.01kcal/mol
Minimised FF energy 110.13kcal/mol

SASA & burial

✓ computed
SASA (unbound) 698.6Ų
Total solvent-accessible surface area of free ligand
BSA total 623.6Ų
Buried surface area upon binding
BSA apolar 491.4Ų
Hydrophobic contacts buried
BSA polar 132.2Ų
Polar contacts buried
Fraction buried 89.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3308.9Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1673.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)