N-(6-Amino-3-methyl-2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidin-5-yl)-N-([beta]-D-gluco­pyran­osyl)­acet­amide

The title compound, C₁₃H₂₀N₄O₈·2H₂O, i.e. (I)·2H₂O, shows no unusual features. The structure contains two mol­ecules of water of crystallization. The absolute configuration was not determined but was known from the starting materials.

Computing details

Data collection: KappaCCD Server Software (Nonius, 1997); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); software used to prepare material for publication: SHELXL97 and WORDPERFECT macro PRPKAPPA (Ferguson, 1999).

N-(6-amino-3-methyl-2,4-dioxo-1,2,3,4-tetrahydro-5-pyrimidinyl)- N-[β-D-glucopyranosyl]acetamide

Crystal data

C13H20N4O8·2H2O	Dx = 1.476 Mg m^−3
Mr = 396.36	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121	Cell parameters from 2711 reflections
a = 7.0911 (1) Å	θ = 3.0–30.4°
b = 12.2566 (2) Å	µ = 0.13 mm^−1
c = 20.5272 (4) Å	T = 150 K
V = 1784.08 (5) Å^3	Lath, colourless
Z = 4	0.33 × 0.15 × 0.13 mm
F(000) = 840

Data collection

KappaCCD diffractometer	2711 independent reflections
Radiation source: fine-focus sealed X-ray tube	2482 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.028
φ and ω scans with κ offsets	θmax = 29.0°, θmin = 3.0°
Absorption correction: multi-scan (SORTAV; Blessing, 1995, 1997)	h = −8→9
Tmin = 0.960, Tmax = 0.984	k = −16→17
12217 measured reflections	l = −28→28

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.100	H-atom parameters constrained
S = 1.06	w = 1/[σ^2(Fo^2) + (0.0567P)^2 + 0.5011P] where P = (Fo^2 + 2Fc^2)/3
2711 reflections	(Δ/σ)max = 0.002
251 parameters	Δρmax = 0.20 e Å^−3
0 restraints	Δρmin = −0.26 e Å^−3

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

	x	y	z	Uiso*/Ueq
N1	0.2557 (3)	0.83857 (13)	0.36395 (8)	0.0211 (3)
C2	0.4044 (3)	0.83439 (15)	0.40642 (9)	0.0216 (4)
O2	0.4258 (3)	0.90595 (13)	0.44752 (7)	0.0304 (4)
N3	0.5212 (3)	0.74556 (13)	0.40075 (8)	0.0223 (4)
C31	0.6717 (4)	0.7303 (2)	0.44874 (11)	0.0369 (6)
C4	0.5047 (3)	0.66756 (15)	0.35094 (9)	0.0190 (4)
O4	0.6188 (2)	0.59105 (12)	0.34947 (7)	0.0258 (3)
C5	0.3556 (3)	0.68341 (14)	0.30588 (8)	0.0169 (3)
N5	0.3328 (2)	0.60508 (12)	0.25488 (7)	0.0155 (3)
C51	0.2248 (3)	0.51423 (15)	0.26416 (9)	0.0175 (4)
O51	0.2130 (2)	0.44259 (11)	0.22191 (7)	0.0234 (3)
C52	0.1187 (3)	0.50595 (16)	0.32728 (9)	0.0226 (4)
C6	0.2296 (3)	0.76787 (14)	0.31287 (9)	0.0179 (4)
N6	0.0784 (3)	0.78246 (14)	0.27545 (8)	0.0232 (4)
C1'	0.4273 (3)	0.62427 (14)	0.19300 (9)	0.0161 (3)
O1'	0.3373 (2)	0.71746 (11)	0.16572 (6)	0.0175 (3)
C2'	0.6390 (3)	0.64300 (15)	0.20138 (9)	0.0170 (4)
O2'	0.9189 (2)	0.69698 (12)	0.14294 (7)	0.0204 (3)
C3'	0.7228 (3)	0.67343 (15)	0.13599 (9)	0.0172 (4)
O3'	0.7273 (2)	0.54648 (11)	0.22410 (7)	0.0230 (3)
C4'	0.6213 (3)	0.77240 (15)	0.10866 (8)	0.0173 (4)
O4'	0.6982 (2)	0.80319 (13)	0.04755 (7)	0.0248 (3)
C5'	0.4104 (3)	0.74893 (15)	0.10338 (8)	0.0163 (3)
C51'	0.3006 (3)	0.84889 (16)	0.08171 (9)	0.0201 (4)
O5'	0.1210 (2)	0.82418 (13)	0.05444 (7)	0.0249 (3)
O6	0.0444 (2)	0.49349 (12)	0.10685 (7)	0.0260 (3)
O7	0.7411 (3)	0.01448 (14)	0.00626 (8)	0.0348 (4)
H1	0.1710	0.8901	0.3698	0.025*
H31A	0.7893	0.7614	0.4319	0.055*
H31B	0.6892	0.6522	0.4570	0.055*
H31C	0.6373	0.7671	0.4894	0.055*
H52A	0.0596	0.4339	0.3305	0.034*
H52B	0.0210	0.5625	0.3288	0.034*
H52C	0.2061	0.5161	0.3638	0.034*
H6A	−0.0007	0.8360	0.2839	0.028*
H6B	0.0574	0.7386	0.2423	0.028*
H1'	0.4066	0.5601	0.1638	0.019*
H2'	0.6607	0.7035	0.2332	0.020*
H2'A	0.9821	0.6408	0.1344	0.087 (14)*
H3'	0.7071	0.6108	0.1052	0.021*
H3'A	0.7089	0.5400	0.2643	0.028*
H4'	0.6391	0.8344	0.1397	0.021*
H4'A	0.6630	0.7588	0.0189	0.030*
H5'	0.3895	0.6884	0.0715	0.020*
H51A	0.2826	0.8976	0.1197	0.024*
H51B	0.3761	0.8890	0.0490	0.024*
H5'A	0.0547	0.7919	0.0823	0.030*
H6WA	0.1209	0.4725	0.1422	0.031*
H6WB	0.1136	0.4923	0.0638	0.031*
H7A	0.8597	0.0219	−0.0069	0.042*
H7B	0.7594	−0.0420	0.0235	0.042*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0232 (8)	0.0193 (7)	0.0209 (7)	0.0039 (7)	−0.0006 (7)	−0.0039 (6)
C2	0.0244 (9)	0.0197 (8)	0.0208 (8)	−0.0019 (8)	0.0010 (8)	−0.0008 (7)
O2	0.0352 (9)	0.0271 (7)	0.0289 (7)	0.0002 (7)	−0.0051 (7)	−0.0111 (6)
N3	0.0252 (9)	0.0214 (8)	0.0203 (7)	0.0020 (7)	−0.0047 (7)	−0.0025 (6)
C31	0.0389 (13)	0.0378 (12)	0.0341 (11)	0.0092 (11)	−0.0177 (11)	−0.0049 (10)
C4	0.0208 (9)	0.0186 (8)	0.0176 (8)	0.0011 (7)	0.0006 (7)	0.0012 (7)
O4	0.0284 (8)	0.0253 (7)	0.0238 (6)	0.0098 (6)	−0.0036 (6)	0.0007 (6)
C5	0.0187 (9)	0.0159 (8)	0.0160 (7)	0.0005 (7)	0.0001 (7)	−0.0002 (6)
N5	0.0164 (7)	0.0139 (6)	0.0162 (6)	−0.0010 (6)	0.0011 (6)	−0.0003 (5)
C51	0.0159 (8)	0.0185 (8)	0.0181 (7)	−0.0009 (7)	−0.0013 (7)	0.0044 (7)
O51	0.0279 (8)	0.0192 (6)	0.0230 (6)	−0.0077 (6)	0.0009 (6)	−0.0009 (5)
C52	0.0224 (9)	0.0229 (9)	0.0224 (8)	−0.0015 (8)	0.0038 (8)	0.0038 (7)
C6	0.0191 (9)	0.0177 (8)	0.0170 (7)	0.0006 (7)	0.0018 (7)	0.0007 (7)
N6	0.0227 (8)	0.0225 (8)	0.0243 (8)	0.0078 (7)	−0.0038 (7)	−0.0061 (6)
C1'	0.0157 (8)	0.0156 (8)	0.0169 (8)	0.0003 (7)	0.0013 (7)	0.0008 (6)
O1'	0.0152 (6)	0.0200 (6)	0.0171 (5)	0.0022 (5)	0.0019 (5)	0.0042 (5)
C2'	0.0148 (8)	0.0167 (8)	0.0194 (8)	0.0017 (7)	−0.0013 (7)	0.0003 (7)
O2'	0.0124 (6)	0.0232 (7)	0.0257 (6)	−0.0001 (5)	0.0012 (6)	0.0003 (6)
C3'	0.0142 (8)	0.0185 (8)	0.0188 (7)	−0.0016 (7)	0.0004 (7)	−0.0010 (7)
O3'	0.0227 (7)	0.0229 (7)	0.0233 (6)	0.0072 (6)	0.0026 (6)	0.0061 (5)
C4'	0.0167 (9)	0.0192 (8)	0.0160 (7)	−0.0024 (7)	0.0022 (7)	0.0007 (6)
O4'	0.0208 (7)	0.0328 (8)	0.0207 (6)	−0.0043 (6)	0.0042 (6)	0.0066 (6)
C5'	0.0162 (8)	0.0179 (8)	0.0149 (7)	−0.0019 (7)	0.0008 (7)	0.0010 (6)
C51'	0.0170 (9)	0.0193 (8)	0.0240 (8)	−0.0010 (7)	−0.0009 (8)	0.0040 (7)
O5'	0.0163 (7)	0.0283 (7)	0.0301 (7)	−0.0013 (6)	−0.0031 (6)	0.0064 (6)
O6	0.0236 (7)	0.0284 (7)	0.0261 (6)	0.0002 (6)	0.0010 (6)	0.0010 (6)
O7	0.0333 (9)	0.0391 (9)	0.0319 (8)	−0.0070 (8)	−0.0033 (7)	0.0075 (7)

Geometric parameters (Å, º)

N1—C2	1.369 (3)	C1'—C2'	1.528 (3)
N1—C6	1.373 (2)	C1'—H1'	1.0000
N1—H1	0.8800	O1'—C5'	1.434 (2)
C2—O2	1.226 (2)	C2'—O3'	1.417 (2)
C2—N3	1.373 (3)	C2'—C3'	1.515 (3)
N3—C4	1.405 (2)	C2'—H2'	1.0000
N3—C31	1.464 (3)	O2'—C3'	1.428 (2)
C31—H31A	0.9800	O2'—H2'A	0.8400
C31—H31B	0.9800	C3'—C4'	1.518 (3)
C31—H31C	0.9800	C3'—H3'	1.0000
C4—O4	1.239 (2)	O3'—H3'A	0.8400
C4—C5	1.418 (3)	C4'—O4'	1.419 (2)
C5—C6	1.375 (2)	C4'—C5'	1.527 (3)
C5—N5	1.430 (2)	C4'—H4'	1.0000
N5—C51	1.365 (2)	O4'—H4'A	0.8400
N5—C1'	1.455 (2)	C5'—C51'	1.518 (3)
C51—O51	1.237 (2)	C5'—H5'	1.0000
C51—C52	1.502 (3)	C51'—O5'	1.423 (2)
C52—H52A	0.9800	C51'—H51A	0.9900
C52—H52B	0.9800	C51'—H51B	0.9900
C52—H52C	0.9800	O5'—H5'A	0.8400
C6—N6	1.331 (3)	O6—H6WA	0.9419
N6—H6A	0.8800	O6—H6WB	1.0109
N6—H6B	0.8800	O7—H7A	0.8882
C1'—O1'	1.423 (2)	O7—H7B	0.7883
C2—N1—C6	124.52 (17)	N5—C1'—C2'	112.22 (15)
C2—N1—H1	117.7	O1'—C1'—H1'	109.2
C6—N1—H1	117.7	N5—C1'—H1'	109.2
O2—C2—N1	120.46 (19)	C2'—C1'—H1'	109.2
O2—C2—N3	123.41 (19)	C1'—O1'—C5'	113.89 (14)
N1—C2—N3	116.11 (16)	O3'—C2'—C3'	108.89 (15)
C2—N3—C4	123.45 (17)	O3'—C2'—C1'	110.21 (15)
C2—N3—C31	118.93 (17)	C3'—C2'—C1'	108.82 (15)
C4—N3—C31	117.62 (17)	O3'—C2'—H2'	109.6
N3—C31—H31A	109.5	C3'—C2'—H2'	109.6
N3—C31—H31B	109.5	C1'—C2'—H2'	109.6
H31A—C31—H31B	109.5	C3'—O2'—H2'A	109.5
N3—C31—H31C	109.5	O2'—C3'—C2'	110.09 (15)
H31A—C31—H31C	109.5	O2'—C3'—C4'	109.71 (15)
H31B—C31—H31C	109.5	C2'—C3'—C4'	109.77 (15)
O4—C4—N3	118.57 (17)	O2'—C3'—H3'	109.1
O4—C4—C5	125.08 (17)	C2'—C3'—H3'	109.1
N3—C4—C5	116.34 (17)	C4'—C3'—H3'	109.1
C6—C5—C4	121.30 (17)	C2'—O3'—H3'A	109.5
C6—C5—N5	120.55 (16)	O4'—C4'—C3'	110.92 (15)
C4—C5—N5	118.05 (16)	O4'—C4'—C5'	111.33 (15)
C51—N5—C5	120.62 (15)	C3'—C4'—C5'	109.89 (15)
C51—N5—C1'	120.79 (15)	O4'—C4'—H4'	108.2
C5—N5—C1'	118.59 (14)	C3'—C4'—H4'	108.2
O51—C51—N5	121.30 (17)	C5'—C4'—H4'	108.2
O51—C51—C52	121.52 (18)	C4'—O4'—H4'A	109.5
N5—C51—C52	117.18 (16)	O1'—C5'—C51'	107.06 (15)
C51—C52—H52A	109.5	O1'—C5'—C4'	109.97 (15)
C51—C52—H52B	109.5	C51'—C5'—C4'	111.78 (15)
H52A—C52—H52B	109.5	O1'—C5'—H5'	109.3
C51—C52—H52C	109.5	C51'—C5'—H5'	109.3
H52A—C52—H52C	109.5	C4'—C5'—H5'	109.3
H52B—C52—H52C	109.5	O5'—C51'—C5'	113.71 (16)
N6—C6—N1	117.69 (17)	O5'—C51'—H51A	108.8
N6—C6—C5	124.36 (17)	C5'—C51'—H51A	108.8
N1—C6—C5	117.86 (17)	O5'—C51'—H51B	108.8
C6—N6—H6A	120.0	C5'—C51'—H51B	108.8
C6—N6—H6B	120.0	H51A—C51'—H51B	107.7
H6A—N6—H6B	120.0	C51'—O5'—H5'A	109.5
O1'—C1'—N5	105.46 (14)	H6WA—O6—H6WB	113.0
O1'—C1'—C2'	111.36 (14)	H7A—O7—H7B	94.0
C6—N1—C2—O2	173.96 (19)	N5—C5—C6—N1	178.06 (16)
C6—N1—C2—N3	−7.5 (3)	C51—N5—C1'—O1'	112.87 (17)
O2—C2—N3—C4	−175.41 (19)	C5—N5—C1'—O1'	−67.23 (19)
N1—C2—N3—C4	6.1 (3)	C51—N5—C1'—C2'	−125.72 (17)
O2—C2—N3—C31	4.5 (3)	C5—N5—C1'—C2'	54.2 (2)
N1—C2—N3—C31	−173.97 (19)	N5—C1'—O1'—C5'	−179.34 (14)
C2—N3—C4—O4	178.96 (18)	C2'—C1'—O1'—C5'	58.68 (19)
C31—N3—C4—O4	−1.0 (3)	O1'—C1'—C2'—O3'	−175.74 (13)
C2—N3—C4—C5	−1.2 (3)	N5—C1'—C2'—O3'	66.29 (19)
C31—N3—C4—C5	178.92 (18)	O1'—C1'—C2'—C3'	−56.40 (18)
O4—C4—C5—C6	176.88 (19)	N5—C1'—C2'—C3'	−174.37 (14)
N3—C4—C5—C6	−3.0 (3)	O3'—C2'—C3'—O2'	−62.83 (19)
O4—C4—C5—N5	0.6 (3)	C1'—C2'—C3'—O2'	177.00 (15)
N3—C4—C5—N5	−179.30 (16)	O3'—C2'—C3'—C4'	176.30 (14)
C6—C5—N5—C51	−88.2 (2)	C1'—C2'—C3'—C4'	56.13 (19)
C4—C5—N5—C51	88.2 (2)	O2'—C3'—C4'—O4'	58.44 (19)
C6—C5—N5—C1'	91.9 (2)	C2'—C3'—C4'—O4'	179.53 (15)
C4—C5—N5—C1'	−91.7 (2)	O2'—C3'—C4'—C5'	−178.03 (14)
C5—N5—C51—O51	−175.57 (17)	C2'—C3'—C4'—C5'	−56.94 (19)
C1'—N5—C51—O51	4.3 (3)	C1'—O1'—C5'—C51'	−179.70 (14)
C5—N5—C51—C52	5.4 (3)	C1'—O1'—C5'—C4'	−58.08 (18)
C1'—N5—C51—C52	−174.66 (16)	O4'—C4'—C5'—O1'	179.65 (14)
C2—N1—C6—N6	−179.68 (18)	C3'—C4'—C5'—O1'	56.36 (18)
C2—N1—C6—C5	3.7 (3)	O4'—C4'—C5'—C51'	−61.59 (19)
C4—C5—C6—N6	−174.52 (18)	C3'—C4'—C5'—C51'	175.12 (15)
N5—C5—C6—N6	1.7 (3)	O1'—C5'—C51'—O5'	−80.28 (18)
C4—C5—C6—N1	1.8 (3)	C4'—C5'—C51'—O5'	159.24 (15)