3-Amino-2-methyl-5,6,7,8-tetra­hydro-1-benzothieno­[2,3-d]­pyrimidin-4(3H)-one

In the title compound, C₁₁H₁₃N₃OS, the dihedral angle between the fused thio­phene and pyrid­imino­ne moieties is 3.3 (1)°. The crystal structure is stabilized by an intramolecular N—H...O hydrogen bond and weak intermolecular C—H...O interactions.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.007 Å
• R factor = 0.090
• wR factor = 0.234
• Data-to-parameter ratio = 15.2

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT022_ALERT_3_C Ratio Unique / Expected Reflections too Low ....       0.93
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       3.04 Ratio
PLAT230_ALERT_2_C Hirshfeld Test Diff for    C2     -   C3      ..       5.66 su
PLAT241_ALERT_2_C Check High   U(eq) as Compared to Neighbors ....         C2
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          7
PLAT360_ALERT_2_C Short  C(sp3)-C(sp3) Bond  C2     -   C3     ...       1.42 Ang.
PLAT420_ALERT_2_C D-H Without Acceptor       N2     -   HN2A   ...          ?
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          2

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   8 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   5 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

Data collection: SMART (Bruker, 1998); cell refinement: SMART; data reduction: SAINT (Bruker, 1998); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and CAMERON (Watkin et al., 1993); software used to prepare material for publication: PLATON (Spek, 2003).

3-amino-2-methyl-5,6,7,8-tetrahydro-1-benzothieno[2,3-d]pyrimidin-4(3H)-one

Crystal data

C11H13N3OS	F(000) = 496
Mr = 235.31	Dx = 1.441 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 660 reflections
a = 10.001 (3) Å	θ = 1.4–25.8°
b = 11.929 (3) Å	µ = 0.28 mm^−1
c = 9.544 (3) Å	T = 293 K
β = 107.656 (4)°	Block, yellow
V = 1085.0 (5) Å^3	0.35 × 0.25 × 0.20 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer	2252 independent reflections
Radiation source: fine-focus sealed tube	1972 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.028
φ and ω scans	θmax = 27.2°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Sheldrick, 1997)	h = −12→12
Tmin = 0.899, Tmax = 0.946	k = −15→15
8148 measured reflections	l = −11→12

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)] = 0.090	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.234	H-atom parameters constrained
S = 1.01	w = 1/[σ^2(Fo^2) + (0.121P)^2 + 2.7775P] where P = (Fo^2 + 2Fc^2)/3
2252 reflections	(Δ/σ)max < 0.001
148 parameters	Δρmax = 0.87 e Å^−3
0 restraints	Δρmin = −0.46 e Å^−3

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 (Ų)

	x	y	z	Uiso*/Ueq
S1	0.81865 (12)	0.94992 (9)	0.01825 (13)	0.0431 (4)
N1	0.4389 (3)	1.1354 (3)	−0.2031 (4)	0.0353 (8)
N2	0.3204 (4)	1.1996 (3)	−0.2808 (4)	0.0480 (10)
N3	0.5790 (4)	0.9767 (3)	−0.2047 (4)	0.0375 (8)
O1	0.4788 (4)	1.2576 (3)	−0.0132 (4)	0.0496 (8)
C1	0.9901 (5)	1.0513 (5)	0.2800 (5)	0.0532 (13)
C2	1.0165 (8)	1.1654 (6)	0.3467 (9)	0.093 (2)
C3	0.8975 (7)	1.2213 (7)	0.3658 (8)	0.086 (2)
C4	0.7654 (6)	1.2313 (4)	0.2306 (5)	0.0507 (12)
C5	0.7551 (4)	1.1308 (3)	0.1318 (4)	0.0349 (9)
C6	0.8558 (5)	1.0521 (4)	0.1553 (5)	0.0395 (10)
C7	0.6436 (4)	1.1098 (3)	0.0005 (4)	0.0307 (8)
C8	0.6617 (4)	1.0166 (3)	−0.0762 (5)	0.0332 (9)
C9	0.5189 (4)	1.1755 (3)	−0.0644 (5)	0.0363 (9)
C10	0.4672 (4)	1.0385 (3)	−0.2676 (5)	0.0355 (9)
C11	0.3687 (5)	1.0049 (4)	−0.4097 (5)	0.0442 (11)
H1A	0.9837	0.9973	0.3537	0.064*
H1B	1.0673	1.0295	0.2441	0.064*
HN2A	0.2684	1.1778	−0.3658	0.058*
HN2B	0.3004	1.2604	−0.2430	0.058*
H2A	1.0870	1.1591	0.4420	0.112*
H2B	1.0555	1.2118	0.2854	0.112*
H3A	0.9262	1.2965	0.4011	0.103*
H3B	0.8708	1.1828	0.4428	0.103*
H4A	0.6824	1.2356	0.2628	0.061*
H4B	0.7707	1.2992	0.1767	0.061*
H11A	0.3926	0.9313	−0.4350	0.066*
H11B	0.3742	1.0572	−0.4842	0.066*
H11C	0.2749	1.0043	−0.4027	0.066*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0423 (6)	0.0416 (6)	0.0429 (7)	0.0112 (5)	0.0094 (5)	−0.0026 (5)
N1	0.0353 (18)	0.0347 (17)	0.0333 (18)	0.0018 (14)	0.0068 (14)	0.0068 (14)
N2	0.045 (2)	0.047 (2)	0.046 (2)	0.0116 (17)	0.0057 (17)	0.0047 (18)
N3	0.043 (2)	0.0350 (18)	0.0356 (19)	−0.0012 (15)	0.0143 (16)	−0.0036 (14)
O1	0.057 (2)	0.0381 (17)	0.055 (2)	0.0128 (15)	0.0198 (16)	−0.0036 (15)
C1	0.046 (3)	0.071 (3)	0.038 (3)	0.002 (2)	0.007 (2)	0.003 (2)
C2	0.079 (5)	0.082 (5)	0.086 (5)	−0.003 (4)	−0.023 (4)	−0.024 (4)
C3	0.062 (4)	0.109 (5)	0.077 (4)	−0.008 (4)	0.007 (3)	−0.050 (4)
C4	0.064 (3)	0.050 (3)	0.039 (2)	−0.009 (2)	0.019 (2)	−0.016 (2)
C5	0.037 (2)	0.039 (2)	0.030 (2)	−0.0060 (17)	0.0127 (17)	−0.0002 (16)
C6	0.042 (2)	0.046 (2)	0.032 (2)	−0.0085 (19)	0.0134 (18)	−0.0032 (18)
C7	0.036 (2)	0.0289 (19)	0.0309 (19)	−0.0022 (15)	0.0163 (16)	0.0000 (15)
C8	0.0318 (19)	0.033 (2)	0.038 (2)	−0.0008 (16)	0.0141 (17)	0.0006 (16)
C9	0.044 (2)	0.0294 (19)	0.039 (2)	−0.0023 (17)	0.0174 (19)	0.0027 (17)
C10	0.039 (2)	0.033 (2)	0.039 (2)	−0.0045 (17)	0.0179 (18)	0.0059 (17)
C11	0.046 (3)	0.044 (2)	0.042 (2)	−0.004 (2)	0.012 (2)	0.006 (2)

Geometric parameters (Å, º)

S1—C6	1.743 (4)	C6—C1	1.501 (7)
S1—C8	1.747 (4)	C11—H11A	0.9600
N1—C10	1.378 (5)	C11—H11B	0.9600
N1—C9	1.407 (5)	C11—H11C	0.9600
N1—N2	1.418 (5)	C4—C3	1.545 (8)
N3—C10	1.322 (6)	C4—H4A	0.9700
N3—C8	1.341 (5)	C4—H4B	0.9700
O1—C9	1.216 (5)	C1—C2	1.491 (8)
C7—C8	1.373 (6)	C1—H1A	0.9700
C7—C5	1.425 (6)	C1—H1B	0.9700
C7—C9	1.443 (6)	C3—C2	1.424 (10)
C10—C11	1.470 (6)	C3—H3A	0.9700
N2—HN2A	0.8600	C3—H3B	0.9700
N2—HN2B	0.8600	C2—H2A	0.9700
C5—C6	1.345 (6)	C2—H2B	0.9700
C5—C4	1.509 (6)
C6—S1—C8	91.3 (2)	H11A—C11—H11B	109.5
C10—N1—C9	124.8 (3)	C10—C11—H11C	109.5
C10—N1—N2	118.2 (3)	H11A—C11—H11C	109.5
C9—N1—N2	117.1 (3)	H11B—C11—H11C	109.5
C10—N3—C8	114.8 (4)	C5—C4—C3	109.9 (5)
C8—C7—C5	114.6 (4)	C5—C4—H4A	109.7
C8—C7—C9	116.6 (4)	C3—C4—H4A	109.7
C5—C7—C9	128.7 (4)	C5—C4—H4B	109.7
O1—C9—N1	119.3 (4)	C3—C4—H4B	109.7
O1—C9—C7	127.8 (4)	H4A—C4—H4B	108.2
N1—C9—C7	112.9 (3)	C2—C1—C6	109.5 (5)
N3—C10—N1	121.7 (4)	C2—C1—H1A	109.8
N3—C10—C11	120.3 (4)	C6—C1—H1A	109.8
N1—C10—C11	118.0 (4)	C2—C1—H1B	109.8
N3—C8—C7	129.1 (4)	C6—C1—H1B	109.8
N3—C8—S1	121.2 (3)	H1A—C1—H1B	108.2
C7—C8—S1	109.7 (3)	C2—C3—C4	117.7 (5)
N1—N2—HN2A	120.0	C2—C3—H3A	107.9
N1—N2—HN2B	120.0	C4—C3—H3A	107.9
HN2A—N2—HN2B	120.0	C2—C3—H3B	107.9
C6—C5—C7	111.7 (4)	C4—C3—H3B	107.9
C6—C5—C4	123.0 (4)	H3A—C3—H3B	107.2
C7—C5—C4	125.2 (4)	C3—C2—C1	115.8 (6)
C5—C6—C1	125.5 (4)	C3—C2—H2A	108.3
C5—C6—S1	112.6 (3)	C1—C2—H2A	108.3
C1—C6—S1	121.8 (4)	C3—C2—H2B	108.3
C10—C11—H11A	109.5	C1—C2—H2B	108.3
C10—C11—H11B	109.5	H2A—C2—H2B	107.4
C10—N1—C9—O1	−174.7 (4)	C6—S1—C8—N3	178.1 (4)
N2—N1—C9—O1	4.9 (5)	C6—S1—C8—C7	−1.3 (3)
C10—N1—C9—C7	5.3 (5)	C8—C7—C5—C6	−1.2 (5)
N2—N1—C9—C7	−175.1 (3)	C9—C7—C5—C6	−178.4 (4)
C8—C7—C9—O1	176.5 (4)	C8—C7—C5—C4	175.9 (4)
C5—C7—C9—O1	−6.4 (7)	C9—C7—C5—C4	−1.3 (7)
C8—C7—C9—N1	−3.5 (5)	C7—C5—C6—C1	177.5 (4)
C5—C7—C9—N1	173.6 (4)	C4—C5—C6—C1	0.3 (7)
C8—N3—C10—N1	−0.8 (6)	C7—C5—C6—S1	0.1 (4)
C8—N3—C10—C11	179.3 (4)	C4—C5—C6—S1	−177.0 (3)
C9—N1—C10—N3	−3.3 (6)	C8—S1—C6—C5	0.7 (3)
N2—N1—C10—N3	177.1 (3)	C8—S1—C6—C1	−176.8 (4)
C9—N1—C10—C11	176.7 (4)	C6—C5—C4—C3	−5.9 (7)
N2—N1—C10—C11	−3.0 (5)	C7—C5—C4—C3	177.3 (5)
C10—N3—C8—C7	2.4 (6)	C5—C6—C1—C2	−17.2 (7)
C10—N3—C8—S1	−176.8 (3)	S1—C6—C1—C2	159.9 (5)
C5—C7—C8—N3	−177.7 (4)	C5—C4—C3—C2	31.6 (9)
C9—C7—C8—N3	−0.1 (6)	C4—C3—C2—C1	−52.5 (10)
C5—C7—C8—S1	1.7 (4)	C6—C1—C2—C3	42.2 (9)
C9—C7—C8—S1	179.2 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—HN2B···O1	0.86	2.37	2.657 (5)	100
C11—H11A···O1^i	0.96	2.57	3.500 (6)	165

Symmetry code: (i) −x+1, y−1/2, −z−1/2.