FAIRMol

Z56768366

Pose ID 5921 Compound 194 Pose 503

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 Z56768366

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 medium Native mixed SASA done
Strain ΔE
18.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.52, Jaccard 0.42, H-bond role recall 0.00
Burial
89%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.829 kcal/mol/HA) ✓ Good fit quality (FQ -7.92) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (18.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-24.051
kcal/mol
LE
-0.829
kcal/mol/HA
Fit Quality
-7.92
FQ (Leeson)
HAC
29
heavy atoms
MW
426
Da
LogP
5.37
cLogP
Strain ΔE
18.0 kcal/mol
SASA buried
89%
Lipo contact
83% BSA apolar/total
SASA unbound
629 Ų
Apolar buried
461 Ų

Interaction summary

HB 6 HY 24 PI 1 CLASH 3
Final rank2.699Score-24.051
Inter norm-0.910Intra norm0.081
Top1000noExcludedno
Contacts16H-bonds6
Artifact reasongeometry warning; 14 clashes; 1 protein clash
Residues
NDP301 ALA32 ARG48 ASP52 ILE182 ILE45 MET53 PHE56 PRO88 SER44 SER86 TRP47 TYR162 VAL31 VAL49 VAL87

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

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
Jaccard0.42RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
487 1.088329866091016 -1.17165 -32.6657 5 19 0 0.00 0.00 - no Open
511 1.2374971441566485 -1.20348 -26.4937 4 18 0 0.00 0.00 - no Open
548 1.4904529892984921 -0.920653 -22.5653 9 17 0 0.00 0.00 - no Open
521 1.81825799653337 -0.897538 -26.5745 4 17 0 0.00 0.00 - no Open
565 2.2544588790717133 -0.826268 -25.3055 8 11 0 0.00 0.00 - no Open
530 2.3192700841994296 -0.96341 -25.2468 1 20 1 0.05 0.00 - no Open
512 2.4932728018700403 -1.10026 -30.6157 5 16 0 0.00 0.00 - no Open
541 2.508845732894417 -0.876449 -24.5843 1 18 0 0.00 0.00 - no Open
522 2.531497306555514 -0.838818 -22.236 1 15 0 0.00 0.00 - no Open
543 2.556193085876479 -0.766219 -16.5141 5 18 0 0.00 0.00 - no Open
503 2.6989153506438197 -0.909917 -24.0506 6 16 11 0.52 0.00 - no Current
508 3.0900948345735757 -0.897584 -21.3907 7 15 0 0.00 0.00 - no Open
516 3.307089045836197 -0.707354 -18.8371 3 12 0 0.00 0.00 - no Open
499 3.642356120158013 -1.12423 -30.5543 8 18 0 0.00 0.00 - no Open
511 3.6596004503079134 -0.851044 -25.8511 6 13 0 0.00 0.00 - no Open
504 4.110164392350293 -1.09071 -27.3774 9 16 0 0.00 0.00 - no Open
550 4.159361593789174 -0.833109 -22.8091 6 11 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 -24.051kcal/mol
Ligand efficiency (LE) -0.8293kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.917
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 425.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.37
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 72.49kcal/mol
Minimised FF energy 54.51kcal/mol

SASA & burial

✓ computed
SASA (unbound) 629.5Ų
Total solvent-accessible surface area of free ligand
BSA total 558.0Ų
Buried surface area upon binding
BSA apolar 460.9Ų
Hydrophobic contacts buried
BSA polar 97.1Ų
Polar contacts buried
Fraction buried 88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3247.4Ų
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 1688.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)