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Acta Crystallogr Sect E Struct Rep Online. 2009 December 1; 65(Pt 12): o2993.
Published online 2009 November 4. doi:  10.1107/S1600536809045449
PMCID: PMC2971898

Ethyl 2-isopropyl­amino-5-methyl-4-oxo-3-phenyl-3,4-dihydro­thieno[2,3-d]pyrimidine-6-carboxyl­ate

Abstract

The title compound, C19H21N3O3S, was synthesized via an aza-Wittig reaction of a functionalized imino­phospho­rane with phenyl isocyanate under mild conditions. In the mol­ecule, the fused thienopyrimidine ring system makes a dihedral angle of 66.30 (11)° with the phenyl ring. An intra­molecular C—H(...)O hydrogen bond occurs. The terminal –OCH2CH3 group is disordered over two sites with refined occupancies of 0.537 (13) and 0.463 (13). The crystal packing is stabilized by inter­molecular C—H(...)O and N—H(...)O hydrogen bonds.

Related literature

For the biological and pharmaceutical activity of pyrimidinone derivatives, see: Modica et al. (2004 [triangle]); Panico et al. (2001 [triangle]). For related structures, see: Zheng et al. (2007 [triangle]); Hu et al. (2007 [triangle]); Xu (2008 [triangle]); Xu et al. (2006 [triangle]).

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Object name is e-65-o2993-scheme1.jpg

Experimental

Crystal data

  • C19H21N3O3S
  • M r = 371.45
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2993-efi1.jpg
  • a = 8.5995 (14) Å
  • b = 13.673 (2) Å
  • c = 15.912 (3) Å
  • V = 1871.0 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.20 mm−1
  • T = 298 K
  • 0.30 × 0.20 × 0.10 mm

Data collection

  • Bruker SMART 4K CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.943, T max = 0.981
  • 12706 measured reflections
  • 4636 independent reflections
  • 4149 reflections with I > 2σ(I)
  • R int = 0.061

Refinement

  • R[F 2 > 2σ(F 2)] = 0.050
  • wR(F 2) = 0.123
  • S = 1.10
  • 4636 reflections
  • 271 parameters
  • 6 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.33 e Å−3
  • Δρmin = −0.22 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1984 Friedel pairs
  • Flack parameter: 0.09 (8)

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SAINT-Plus (Bruker, 2001 [triangle]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: SHELXTL (Sheldrick, 2008 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809045449/bt5115sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809045449/bt5115Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We gratefully acknowledge financial support of this work by the Key Science Research Project of Hubei Provincial Department of Education (No. D20092406).

supplementary crystallographic information

Comment

Derivatives of pyrimidinone are attracting increasing attention in the synthetic chemistry community because of the important role played by such systems in many natural products, also in antibiotics and drugs (Modica et al., 2004; Panico et al., 2001). Recently, we have been interested in the synthesis of new thieno[3,2-d]pyrimidone derivatives. Some related X-ray crystal structure reports for pyrimidinone derivatives have been published (Zheng et al., 2007; Hu et al. 2007; Xu et al., 2006, 2008). Here, the structure of the title compound, which may be used as a new precursor for obtaining bioactive molecules, is reported (Fig. 1). In the molecule, the bond lengths and angles are unexceptional. The thienopyrimidinone rings are closer to coplanarity with maximum deviations 0.074 (2)Å for N3. The phenyl ring is twisted with respect to the pyrimidinone ring, with a dihedral angle of 66.30 (11)°. C18, C19 and attached hydrogen and O3 atoms are disordered over two sites, with refined occupancies of 0.537 (13) and 0.463 (13). Intramolecular C—H···O and intermolecular C—H···O, N—H···O hydrogen bonds interactions are present, which stabilize the conformation of the molecule and the crystal structure (Table 1).

Experimental

To a solution of diethyl 5-((phenylimino)methyleneamino)- 3-methylthiophene-2,4-dicarboxylate(3 mmol) in anhydrous dichloromethane (15 ml) was added iso-propan-1-amine (3 mmol). After stirring the reaction mixture for 1 h, the solvent was removed and anhydrous ethanol (10 ml) with several drops of EtONa in EtOH was added. The mixture was stirred for 5 h at room temperature. The solution was concentrated under reduced pressure and the residue was recrystallized from ethanol to give the title compound in a yield of 85%. Crystals suitable for single-crystal X-ray diffraction were obtained by recrystallization from a mixed solvent of ethanol and dichloromethane (1:1 v/v) at room temperature.

Refinement

All H-atoms bonded to C were positioned geometrically and refined using a riding model with C—H = 0.93 Å, Uiso=1.2Ueq (C) for Csp2, C—H = 0.98 Å, Uiso = 1.2Ueq (C) for CH, C—H = 0.97 Å, Uiso = 1.2Ueq (C) for CH2, C—H = 0.96 Å, Uiso = 1.5Ueq (C) for CH3. The coordinates of the amino H atom were refined with Uiso = 1.2Ueq(N). The terminal O-CH2CH3 moiety is disordered over two sites with refined occupancies of 0.537 (13) and 0.463 (13). The C-C bonds were restrained to 1.54 (1)Å, the C-O bonds to 1.45 (1)° and the O···Cmethyl distances to 2.45 (2)Å.

Figures

Fig. 1.
The molecular structure of the title compound, showing the atom-labeling scheme.

Crystal data

C19H21N3O3SF(000) = 784
Mr = 371.45Dx = 1.319 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 4510 reflections
a = 8.5995 (14) Åθ = 2.6–26.5°
b = 13.673 (2) ŵ = 0.20 mm1
c = 15.912 (3) ÅT = 298 K
V = 1871.0 (5) Å3Block, colorless
Z = 40.30 × 0.20 × 0.10 mm

Data collection

Bruker SMART 4K CCD area-detector diffractometer4636 independent reflections
Radiation source: fine-focus sealed tube4149 reflections with I > 2σ(I)
graphiteRint = 0.061
[var phi] and ω scansθmax = 28.3°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −7→11
Tmin = 0.943, Tmax = 0.981k = −18→17
12706 measured reflectionsl = −21→18

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.050H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.123w = 1/[σ2(Fo2) + (0.0601P)2] where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
4636 reflectionsΔρmax = 0.33 e Å3
271 parametersΔρmin = −0.21 e Å3
6 restraintsAbsolute structure: Flack (1983), 1984 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.09 (8)

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/UeqOcc. (<1)
C10.2137 (2)0.27871 (14)0.47156 (12)0.0406 (4)
C20.2947 (3)0.21627 (15)0.41948 (14)0.0488 (5)
H20.35780.16750.44170.059*
C30.2800 (3)0.22783 (18)0.33286 (15)0.0606 (6)
H30.33510.18690.29690.073*
C40.1855 (4)0.2987 (2)0.30019 (16)0.0694 (8)
H40.17650.30560.24230.083*
C50.1040 (4)0.3595 (2)0.35261 (17)0.0716 (8)
H50.03850.40700.33030.086*
C60.1196 (3)0.35009 (17)0.43916 (15)0.0552 (6)
H60.06630.39210.47490.066*
C70.2851 (2)0.34531 (13)0.61047 (13)0.0395 (4)
C80.2038 (2)0.27158 (14)0.72863 (12)0.0408 (4)
C90.1490 (2)0.18802 (14)0.68884 (12)0.0376 (4)
C100.1562 (2)0.18457 (13)0.59891 (13)0.0391 (4)
C110.4070 (3)0.50790 (14)0.60896 (14)0.0464 (5)
H110.32910.52700.65080.056*
C120.4122 (4)0.5855 (2)0.5416 (2)0.0834 (10)
H12A0.48230.56560.49790.125*
H12B0.44760.64600.56550.125*
H12C0.31010.59440.51850.125*
C130.5612 (3)0.4960 (2)0.6528 (2)0.0693 (7)
H13A0.55290.44590.69480.104*
H13B0.58990.55660.67900.104*
H13C0.63920.47790.61250.104*
C140.0844 (2)0.11758 (14)0.74560 (13)0.0400 (4)
C150.0934 (2)0.14955 (14)0.82673 (14)0.0446 (5)
C160.0151 (3)0.02200 (17)0.71855 (17)0.0597 (6)
H16A−0.0409−0.00650.76470.089*
H16B0.0966−0.02160.70120.089*
H16C−0.05470.03280.67240.089*
C170.0542 (3)0.09639 (19)0.90376 (15)0.0544 (6)
C18'0.0196 (9)0.1295 (7)1.0546 (4)0.065 (2)0.463 (13)
H18C−0.05350.07551.05190.078*0.463 (13)
H18D−0.02620.18091.08850.078*0.463 (13)
C19'0.1698 (11)0.0955 (10)1.0941 (7)0.099 (4)0.463 (13)
H19D0.20730.03881.06480.148*0.463 (13)
H19E0.15190.07921.15200.148*0.463 (13)
H19F0.24570.14681.09070.148*0.463 (13)
O3'0.0508 (11)0.1657 (6)0.9710 (4)0.0593 (17)0.463 (13)
C180.0891 (12)0.0864 (5)1.0496 (3)0.070 (2)0.537 (13)
H18A0.14270.02401.04840.084*0.537 (13)
H18B−0.02050.07481.06010.084*0.537 (13)
C190.1567 (16)0.1515 (7)1.1163 (5)0.106 (3)0.537 (13)
H19A0.25690.17461.09840.160*0.537 (13)
H19B0.16760.11541.16760.160*0.537 (13)
H19C0.08890.20631.12530.160*0.537 (13)
O30.1105 (10)0.1383 (5)0.9708 (3)0.0599 (15)0.537 (13)
N10.22489 (19)0.26857 (11)0.56226 (10)0.0390 (4)
N20.2725 (2)0.34924 (12)0.69284 (11)0.0414 (4)
N30.3553 (2)0.41720 (12)0.56877 (12)0.0464 (4)
H3A0.387 (3)0.4055 (18)0.5245 (18)0.056*
O10.1063 (2)0.11958 (11)0.55348 (10)0.0530 (4)
O20.0060 (2)0.01385 (13)0.90784 (12)0.0684 (5)
S10.17644 (7)0.26585 (4)0.83568 (3)0.05191 (16)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0506 (11)0.0394 (10)0.0320 (9)−0.0100 (9)0.0019 (8)−0.0027 (8)
C20.0563 (12)0.0467 (10)0.0435 (11)−0.0021 (9)−0.0007 (9)−0.0103 (9)
C30.0789 (16)0.0605 (13)0.0425 (12)−0.0130 (12)0.0112 (12)−0.0177 (12)
C40.102 (2)0.0714 (17)0.0345 (12)−0.0149 (17)−0.0017 (13)0.0018 (11)
C50.099 (2)0.0705 (16)0.0456 (15)0.0111 (15)−0.0045 (14)0.0150 (13)
C60.0710 (15)0.0511 (12)0.0434 (13)0.0092 (11)0.0073 (11)0.0047 (10)
C70.0475 (11)0.0334 (9)0.0375 (10)−0.0033 (8)0.0027 (8)−0.0061 (7)
C80.0475 (11)0.0422 (10)0.0327 (9)−0.0002 (9)0.0015 (8)−0.0026 (8)
C90.0428 (10)0.0340 (8)0.0359 (9)−0.0008 (8)−0.0028 (8)0.0014 (7)
C100.0460 (10)0.0325 (8)0.0389 (10)0.0009 (8)−0.0033 (8)−0.0008 (7)
C110.0578 (13)0.0343 (9)0.0472 (12)−0.0073 (9)0.0111 (10)−0.0077 (8)
C120.122 (3)0.0458 (13)0.082 (2)−0.0179 (16)0.0038 (19)0.0125 (14)
C130.0615 (15)0.0708 (16)0.0756 (19)−0.0120 (13)−0.0005 (14)−0.0171 (15)
C140.0424 (10)0.0358 (9)0.0418 (11)0.0007 (8)0.0007 (8)0.0052 (8)
C150.0475 (11)0.0414 (10)0.0449 (12)−0.0033 (8)−0.0007 (9)0.0060 (9)
C160.0805 (17)0.0412 (12)0.0573 (15)−0.0124 (11)0.0060 (13)0.0022 (11)
C170.0591 (14)0.0637 (14)0.0403 (12)−0.0082 (11)−0.0004 (10)0.0081 (11)
C18'0.082 (5)0.059 (4)0.053 (4)0.003 (3)0.020 (3)0.003 (3)
C19'0.099 (6)0.128 (10)0.070 (7)0.009 (7)−0.001 (5)0.028 (7)
O3'0.083 (5)0.055 (4)0.040 (2)−0.004 (3)0.006 (3)0.007 (2)
C180.107 (6)0.071 (4)0.032 (3)−0.005 (4)−0.004 (3)0.013 (3)
C190.193 (10)0.073 (5)0.054 (4)−0.001 (5)−0.024 (5)0.003 (3)
O30.090 (4)0.050 (3)0.0398 (19)0.000 (2)−0.002 (2)0.0111 (18)
N10.0515 (9)0.0339 (7)0.0315 (8)−0.0024 (7)0.0007 (7)−0.0029 (7)
N20.0549 (10)0.0348 (8)0.0345 (9)−0.0057 (7)0.0030 (7)−0.0040 (7)
N30.0623 (11)0.0403 (8)0.0365 (9)−0.0117 (8)0.0130 (8)−0.0084 (7)
O10.0762 (11)0.0409 (7)0.0420 (9)−0.0149 (7)−0.0053 (8)−0.0033 (6)
O20.0874 (13)0.0600 (10)0.0578 (11)−0.0188 (10)0.0060 (10)0.0144 (9)
S10.0734 (4)0.0499 (3)0.0324 (2)−0.0140 (3)0.0024 (2)−0.0019 (2)

Geometric parameters (Å, °)

C1—C61.369 (3)C13—H13A0.9600
C1—C21.379 (3)C13—H13B0.9600
C1—N11.453 (2)C13—H13C0.9600
C2—C31.393 (3)C14—C151.365 (3)
C2—H20.9300C14—C161.499 (3)
C3—C41.367 (4)C15—C171.464 (3)
C3—H30.9300C15—S11.749 (2)
C4—C51.371 (4)C16—H16A0.9600
C4—H40.9300C16—H16B0.9600
C5—C61.390 (3)C16—H16C0.9600
C5—H50.9300C17—O21.204 (3)
C6—H60.9300C17—O31.303 (7)
C7—N21.316 (3)C17—O3'1.429 (8)
C7—N31.331 (3)C18'—O3'1.445 (7)
C7—N11.399 (2)C18'—C19'1.510 (8)
C8—N21.342 (2)C18'—H18C0.9700
C8—C91.389 (3)C18'—H18D0.9700
C8—S11.721 (2)C19'—H19D0.9600
C9—C141.433 (3)C19'—H19E0.9600
C9—C101.433 (3)C19'—H19F0.9600
C10—O11.223 (2)C18—O31.453 (6)
C10—N11.417 (2)C18—C191.502 (7)
C11—N31.464 (3)C18—H18A0.9700
C11—C131.508 (4)C18—H18B0.9700
C11—C121.509 (4)C19—H19A0.9600
C11—H110.9800C19—H19B0.9600
C12—H12A0.9600C19—H19C0.9600
C12—H12B0.9600N3—H3A0.77 (3)
C12—H12C0.9600
C6—C1—C2120.9 (2)H13B—C13—H13C109.5
C6—C1—N1118.77 (19)C15—C14—C9111.03 (18)
C2—C1—N1120.30 (19)C15—C14—C16125.0 (2)
C1—C2—C3118.6 (2)C9—C14—C16123.99 (19)
C1—C2—H2120.7C14—C15—C17128.3 (2)
C3—C2—H2120.7C14—C15—S1113.04 (16)
C4—C3—C2120.7 (2)C17—C15—S1118.50 (17)
C4—C3—H3119.7C14—C16—H16A109.5
C2—C3—H3119.7C14—C16—H16B109.5
C3—C4—C5120.2 (2)H16A—C16—H16B109.5
C3—C4—H4119.9C14—C16—H16C109.5
C5—C4—H4119.9H16A—C16—H16C109.5
C4—C5—C6119.8 (2)H16B—C16—H16C109.5
C4—C5—H5120.1O2—C17—O3119.7 (3)
C6—C5—H5120.1O2—C17—O3'125.0 (3)
C1—C6—C5119.8 (2)O3—C17—O3'26.4 (3)
C1—C6—H6120.1O2—C17—C15126.1 (2)
C5—C6—H6120.1O3—C17—C15112.4 (3)
N2—C7—N3120.23 (18)O3'—C17—C15107.6 (3)
N2—C7—N1123.12 (18)O3'—C18'—C19'109.3 (6)
N3—C7—N1116.64 (17)O3'—C18'—H18C109.8
N2—C8—C9127.35 (18)C19'—C18'—H18C109.8
N2—C8—S1121.07 (14)O3'—C18'—H18D109.8
C9—C8—S1111.57 (14)C19'—C18'—H18D109.8
C8—C9—C14113.40 (18)H18C—C18'—H18D108.3
C8—C9—C10117.90 (18)C17—O3'—C18'117.8 (5)
C14—C9—C10128.62 (19)O3—C18—C19105.8 (5)
O1—C10—N1119.46 (18)O3—C18—H18A110.6
O1—C10—C9126.79 (19)C19—C18—H18A110.6
N1—C10—C9113.72 (17)O3—C18—H18B110.6
N3—C11—C13112.19 (19)C19—C18—H18B110.6
N3—C11—C12107.1 (2)H18A—C18—H18B108.7
C13—C11—C12112.2 (2)C18—C19—H19A109.5
N3—C11—H11108.4C18—C19—H19B109.5
C13—C11—H11108.4H19A—C19—H19B109.5
C12—C11—H11108.4C18—C19—H19C109.5
C11—C12—H12A109.5H19A—C19—H19C109.5
C11—C12—H12B109.5H19B—C19—H19C109.5
H12A—C12—H12B109.5C17—O3—C18116.4 (5)
C11—C12—H12C109.5C7—N1—C10122.44 (16)
H12A—C12—H12C109.5C7—N1—C1119.84 (16)
H12B—C12—H12C109.5C10—N1—C1117.29 (15)
C11—C13—H13A109.5C7—N2—C8115.24 (17)
C11—C13—H13B109.5C7—N3—C11123.06 (18)
H13A—C13—H13B109.5C7—N3—H3A117.6 (19)
C11—C13—H13C109.5C11—N3—H3A117.7 (19)
H13A—C13—H13C109.5C8—S1—C1590.95 (10)
C6—C1—C2—C30.6 (3)O3—C17—O3'—C18'−72.8 (10)
N1—C1—C2—C3179.51 (18)C15—C17—O3'—C18'−177.9 (5)
C1—C2—C3—C4−1.0 (4)C19'—C18'—O3'—C1785.6 (13)
C2—C3—C4—C50.1 (4)O2—C17—O3—C18−9.1 (7)
C3—C4—C5—C61.0 (5)O3'—C17—O3—C18100.6 (13)
C2—C1—C6—C50.5 (4)C15—C17—O3—C18−174.9 (5)
N1—C1—C6—C5−178.4 (2)C19—C18—O3—C17−177.4 (12)
C4—C5—C6—C1−1.4 (4)N2—C7—N1—C10−5.2 (3)
N2—C8—C9—C14178.76 (19)N3—C7—N1—C10175.90 (18)
S1—C8—C9—C14−0.3 (2)N2—C7—N1—C1167.00 (19)
N2—C8—C9—C10−4.3 (3)N3—C7—N1—C1−11.9 (3)
S1—C8—C9—C10176.67 (15)O1—C10—N1—C7−179.60 (19)
C8—C9—C10—O1−176.0 (2)C9—C10—N1—C72.4 (3)
C14—C9—C10—O10.5 (4)O1—C10—N1—C18.0 (3)
C8—C9—C10—N11.9 (3)C9—C10—N1—C1−170.04 (17)
C14—C9—C10—N1178.34 (18)C6—C1—N1—C7−62.7 (3)
C8—C9—C14—C15−0.6 (3)C2—C1—N1—C7118.4 (2)
C10—C9—C14—C15−177.1 (2)C6—C1—N1—C10109.9 (2)
C8—C9—C14—C16179.0 (2)C2—C1—N1—C10−69.0 (3)
C10—C9—C14—C162.4 (4)N3—C7—N2—C8−178.13 (19)
C9—C14—C15—C17−173.8 (2)N1—C7—N2—C83.0 (3)
C16—C14—C15—C176.7 (4)C9—C8—N2—C71.7 (3)
C9—C14—C15—S11.2 (2)S1—C8—N2—C7−179.30 (16)
C16—C14—C15—S1−178.38 (19)N2—C7—N3—C11−6.7 (3)
C14—C15—C17—O2−0.3 (4)N1—C7—N3—C11172.24 (19)
S1—C15—C17—O2−175.0 (2)C13—C11—N3—C781.3 (3)
C14—C15—C17—O3164.5 (5)C12—C11—N3—C7−155.1 (2)
S1—C15—C17—O3−10.3 (5)N2—C8—S1—C15−178.33 (18)
C14—C15—C17—O3'−167.9 (5)C9—C8—S1—C150.79 (16)
S1—C15—C17—O3'17.4 (5)C14—C15—S1—C8−1.14 (17)
O2—C17—O3'—C18'14.3 (9)C17—C15—S1—C8174.36 (18)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C16—H16A···O20.962.333.015 (3)128
C6—H6···O2i0.932.583.479 (3)164
N3—H3A···O1ii0.77 (3)2.28 (3)2.949 (2)145 (2)

Symmetry codes: (i) −x, y+1/2, −z+3/2; (ii) x+1/2, −y+1/2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT5115).

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