Cimetidine, C10H16N6S, form C: crystal structure and modelling of polytypes using the superspace approach

Authors:

Arakcheeva, Alla; Pattison, Philip; Bauer-Brandl, Annette; Birkedale, Henrik; Chapuis, Gervais

Journal:

Journal of Applied Crystallography 46 99-107 (2013)

DOI:

https://doi.org/10.1107/S0021889812048133

B-IncStrDB ID: xBFrGHx3RoJ Entry date: 2022-01-20 Last revision: 2022-01-20

Supercell

Chemical data


Full Name: N-Cyano-N'-methyl-N''-[2-((4-methyl-5-imidazolyl)-methylthio)ethyl]guanidine [ Help ]

Common Name: Cimetidine [ Help ]

Formula moiety: C10 H16 N6 S1 [ Help ]

Structural Formula Sum: C10 H16 N6 S1 [ Help ]

Formula weight: 252.36 Da [ Help ]

Crystallographic data and experimental details


Crystal system: monoclinic [ Help ]

Space group name (H-M): C 1 2/c 1 [ Help ]

Space group name (Hall): -C 2yc [ Help ]

Space group nb.: 15 [ Help ]

Symmetry operations of the space group: [ Help ]

Operation code Operation in algebraic form
1 x,y,z
2 -x,y,-z+1/2
3 -x,-y,-z
4 x,-y,z+1/2
5 x+1/2,y+1/2,z
6 -x+1/2,y+1/2,-z+1/2
7 -x+1/2,-y+1/2,-z
8 x+1/2,-y+1/2,z+1/2

a: 82.904(10) Å [ Help ]

b: 4.8500(10) Å [ Help ]

c: 18.760(5) Å [ Help ]

α: 90 ° [ Help ]

β: 74.340(10) ° [ Help ]

γ: 90 ° [ Help ]

Volume: 7263(3) Å3 [ Help ]

Z: 24 [ Help ]

Cell determination reflection Nb.: 15754 [ Help ]

θ(min) for cell determination: 2.75 ° [ Help ]

θ(max) for cell determination: 25.46 ° [ Help ]

Cell measurement temperature: 100 K [ Help ]

μ: 0.341 mm-1 [ Help ]

Absorption correction type: empirical [ Help ]

Refinement details


Total nb. of reflections: 4725 [ Help ]

Nb. of observed reflections: 3822 [ Help ]

Intense reflections threshold: I>3σ(I) [ Help ]

Refinement based on: F [ Help ]

R(obs): 0.0457 [ Help ]

wR(obs): 0.0582 [ Help ]

R(all): 0.0608 [ Help ]

wR(all): 0.0713 [ Help ]

S(all): 4.54 [ Help ]

S(obs): 4.15 [ Help ]

Nb. of reflections: 4668 [ Help ]

Nb. of parameters: 460 [ Help ]

Number of restraints: 0 [ Help ]

Number of constraints: 0 [ Help ]

Weighting scheme: sigma [ Help ]

Weighting scheme remarks: w=1/(σ2(F)+0.0001F2) [ Help ]

Refinement of hydrogen atoms: constr [ Help ]

Δ/σ(max): 0.0046 [ Help ]

Δ/σ(mean): 0.0001 [ Help ]

Δρ(max): 0.40 e_Å-3 [ Help ]

Δρ(min): -0.41 e_Å-3 [ Help ]

Extinction method: none [ Help ]

Structural Information


Average Structure: [ Help ]

Atom site label Atom symbol x y z ADP type Uiso/equiv Symmetry multiplicity Occupancy Coords from (d)iffraction or (c)alculated Coords restraints or constraints Disordered cluster Disordered group
S1a S 0.503019(10) 0.05176(19) 0.61024(5) Uani 0.0138(3) 8 1 d . . .
N1a N 0.45295(3) 0.1772(6) 0.78800(16) Uani 0.0142(10) 8 1 d . . .
C3a C 0.46708(4) 0.3119(7) 0.74755(19) Uani 0.0120(12) 8 1 d . . .
N2a N 0.45888(4) -0.0063(6) 0.67547(16) Uani 0.0143(10) 8 1 d . . .
C5a C 0.48484(4) 0.2673(7) 0.61338(18) Uani 0.0140(11) 8 1 d . . .
C2a C 0.47058(4) 0.1973(7) 0.67842(19) Uani 0.0130(12) 8 1 d . . .
C1a C 0.44866(4) -0.0087(8) 0.74282(20) Uani 0.0164(13) 8 1 d . . .
N5a N 0.55565(4) 0.5129(6) 0.55095(16) Uani 0.0156(10) 8 1 d . . .
N3a N 0.54751(3) 0.2528(6) 0.46456(16) Uani 0.0151(10) 8 1 d . . .
C6a C 0.51809(4) 0.2386(8) 0.53785(18) Uani 0.0133(11) 8 1 d . . .
C10a C 0.56450(4) 0.7213(8) 0.56566(19) Uani 0.0151(12) 8 1 d . . .
C7a C 0.53519(4) 0.1049(8) 0.52267(19) Uani 0.0142(12) 8 1 d . . .
C8a C 0.55690(4) 0.4559(7) 0.47886(19) Uani 0.0124(12) 8 1 d . . .
C4a C 0.47599(4) 0.5288(8) 0.7794(2) Uani 0.0164(13) 8 1 d . . .
N6a N 0.57153(4) 0.9033(7) 0.58504(16) Uani 0.0176(11) 8 1 d . . .
N4a N 0.56680(3) 0.5967(6) 0.42323(16) Uani 0.0148(10) 8 1 d . . .
C9a C 0.56919(4) 0.5228(8) 0.34649(19) Uani 0.0167(13) 8 1 d . . .
H1c1a H 0.43918 -0.129551 0.758089 Uani 0.0197 8 1 d . . .
H1n1a H 0.447748 0.206483 0.834237 Uani 0.017 8 1 d . . .
H1c4a H 0.483689 0.442399 0.802554 Uani 0.0197 8 1 d . . .
H2c4a H 0.482034 0.64831 0.7405 Uani 0.0197 8 1 d . . .
H3c4a H 0.467961 0.634615 0.815462 Uani 0.0197 8 1 d . . .
H1c5a H 0.481477 0.242764 0.568676 Uani 0.0168 8 1 d . . .
H2c5a H 0.487794 0.457715 0.616048 Uani 0.0168 8 1 d . . .
H1c6a H 0.514449 0.238117 0.493416 Uani 0.016 8 1 d . . .
H2c6a H 0.518782 0.426166 0.553137 Uani 0.016 8 1 d . . .
H1c7a H 0.53448 -0.083029 0.507754 Uani 0.0171 8 1 d . . .
H2c7a H 0.538781 0.103749 0.567232 Uani 0.0171 8 1 d . . .
H1n3a H 0.548721 0.205472 0.418681 Uani 0.0182 8 1 d . . .
H1n4a H 0.572091 0.739837 0.433514 Uani 0.0178 8 1 d . . .
H2c9a H 0.573574 0.338888 0.338335 Uani 0.02 8 1 d . . .
H1c9a H 0.576925 0.649002 0.315576 Uani 0.02 8 1 d . . .
H3c9a H 0.558641 0.531512 0.334567 Uani 0.02 8 1 d . . .
S1b S 0.338982(11) 0.09204(19) 0.61518(5) Uani 0.0163(3) 8 1 d . . .
N1b N 0.29041(4) 0.1555(6) 0.79823(16) Uani 0.0168(11) 8 1 d . . .
C3b C 0.30389(4) 0.3079(7) 0.75956(19) Uani 0.0152(12) 8 1 d . . .
N2b N 0.29538(4) 0.0224(6) 0.68163(16) Uani 0.0169(11) 8 1 d . . .
C5b C 0.32082(4) 0.3171(7) 0.62429(19) Uani 0.0155(12) 8 1 d . . .
C2b C 0.30688(4) 0.2243(7) 0.68787(19) Uani 0.0140(12) 8 1 d . . .
C1b C 0.28580(5) -0.0114(8) 0.7498(2) Uani 0.0195(13) 8 1 d . . .
N5b N 0.39189(4) 0.5630(6) 0.56047(16) Uani 0.0160(11) 8 1 d . . .
N3b N 0.38369(4) 0.3006(6) 0.47484(16) Uani 0.0154(10) 8 1 d . . .
C6b C 0.35421(4) 0.2883(8) 0.54696(19) Uani 0.0159(12) 8 1 d . . .
C10b C 0.40095(4) 0.7682(8) 0.57503(19) Uani 0.0150(12) 8 1 d . . .
C7b C 0.37128(4) 0.1538(8) 0.53229(19) Uani 0.0161(12) 8 1 d . . .
C8b C 0.39318(4) 0.5036(7) 0.4890(2) Uani 0.0144(13) 8 1 d . . .
C4b C 0.31248(5) 0.5144(8) 0.7953(2) Uani 0.0193(14) 8 1 d . . .
N6b N 0.40831(4) 0.9462(7) 0.59387(16) Uani 0.0183(11) 8 1 d . . .
N4b N 0.40329(3) 0.6413(7) 0.43255(15) Uani 0.0156(11) 8 1 d . . .
C9b C 0.40568(4) 0.5657(8) 0.3558(2) Uani 0.0206(14) 8 1 d . . .
H1c1b H 0.276653 -0.139546 0.763192 Uani 0.0234 8 1 d . . .
H1n1b H 0.285693 0.164873 0.845589 Uani 0.0202 8 1 d . . .
H1c4b H 0.304474 0.597884 0.836381 Uani 0.0231 8 1 d . . .
H2c4b H 0.321019 0.424433 0.812688 Uani 0.0231 8 1 d . . .
H3c4b H 0.317495 0.653968 0.759998 Uani 0.0231 8 1 d . . .
H1c5b H 0.323818 0.503202 0.632574 Uani 0.0186 8 1 d . . .
H2c5b H 0.317279 0.309519 0.579642 Uani 0.0186 8 1 d . . .
H1c6b H 0.350883 0.295957 0.501798 Uani 0.0191 8 1 d . . .
H2c6b H 0.354772 0.472504 0.564841 Uani 0.0191 8 1 d . . .
H1c7b H 0.374764 0.15146 0.577104 Uani 0.0194 8 1 d . . .
H2c7b H 0.370563 -0.03403 0.517267 Uani 0.0194 8 1 d . . .
H1n3b H 0.384959 0.252935 0.428952 Uani 0.0185 8 1 d . . .
H1n4b H 0.4087 0.783463 0.442517 Uani 0.0187 8 1 d . . .
H2c9b H 0.413219 0.693851 0.324606 Uani 0.0247 8 1 d . . .
H1c9b H 0.410303 0.383253 0.347611 Uani 0.0247 8 1 d . . .
H3c9b H 0.395092 0.569772 0.344113 Uani 0.0247 8 1 d . . .
S1c S 0.667026(11) -0.01787(19) 0.60291(5) Uani 0.0166(3) 8 1 d . . .
N1c N 0.61657(4) 0.1521(6) 0.77287(17) Uani 0.0191(11) 8 1 d . . .
C3c C 0.63107(4) 0.2794(7) 0.73266(19) Uani 0.0153(12) 8 1 d . . .
N2c N 0.62296(4) -0.0478(6) 0.66253(17) Uani 0.0176(11) 8 1 d . . .
C5c C 0.64958(4) 0.2117(8) 0.60153(19) Uani 0.0157(12) 8 1 d . . .
C2c C 0.63485(4) 0.1540(8) 0.66499(19) Uani 0.0159(12) 8 1 d . . .
C1c C 0.61237(5) -0.0409(8) 0.7290(2) Uani 0.0190(13) 8 1 d . . .
N5c N 0.72165(4) 0.3496(7) 0.54827(16) Uani 0.0192(11) 8 1 d . . .
N3c N 0.71249(4) 0.1272(6) 0.45911(16) Uani 0.0159(10) 8 1 d . . .
C6c C 0.68308(4) 0.1477(8) 0.53083(19) Uani 0.0155(12) 8 1 d . . .
C10c C 0.73124(5) 0.5373(9) 0.5676(2) Uani 0.0227(14) 8 1 d . . .
C7c C 0.69950(4) -0.0129(8) 0.51493(19) Uani 0.0154(12) 8 1 d . . .
C8c C 0.72277(4) 0.3112(8) 0.47635(19) Uani 0.0142(12) 8 1 d . . .
C4c C 0.63974(5) 0.4965(8) 0.7645(2) Uani 0.0203(14) 8 1 d . . .
N6c N 0.73844(5) 0.6945(9) 0.59302(19) Uani 0.0387(14) 8 1 d . . .
N4c N 0.73337(4) 0.4505(7) 0.42261(16) Uani 0.0208(11) 8 1 d . . .
C9c C 0.73508(5) 0.4086(9) 0.3445(2) Uani 0.0288(15) 8 1 d . . .
H1c1c H 0.602783 -0.159349 0.744529 Uani 0.0228 8 1 d . . .
H1n1c H 0.611102 0.189419 0.818334 Uani 0.0229 8 1 d . . .
H1c4c H 0.64505 0.62468 0.726406 Uani 0.0243 8 1 d . . .
H2c4c H 0.648052 0.412579 0.784577 Uani 0.0243 8 1 d . . .
H3c4c H 0.631724 0.592151 0.803104 Uani 0.0243 8 1 d . . .
H1c5c H 0.653005 0.399902 0.603763 Uani 0.0188 8 1 d . . .
H2c5c H 0.646548 0.186818 0.556042 Uani 0.0188 8 1 d . . .
H1c6c H 0.67943 0.159227 0.486504 Uani 0.0186 8 1 d . . .
H2c6c H 0.684846 0.331887 0.545858 Uani 0.0186 8 1 d . . .
H1c7c H 0.697843 -0.194532 0.497825 Uani 0.0185 8 1 d . . .
H2c7c H 0.702936 -0.030075 0.559655 Uani 0.0185 8 1 d . . .
H1n3c H 0.713596 0.089634 0.41269 Uani 0.019 8 1 d . . .
H1n4c H 0.739673 0.57452 0.435147 Uani 0.025 8 1 d . . .
H2c9c H 0.743924 0.523382 0.316036 Uani 0.0346 8 1 d . . .
H1c9c H 0.724757 0.456032 0.333579 Uani 0.0346 8 1 d . . .
H3c9c H 0.737681 0.218749 0.332141 Uani 0.0346 8 1 d . . .

ADP components: [ Help ]

Atom site label Atom site symbol U11 U22 U33 U12 U13 U23
S1a S 0.0105(5) 0.0156(5) 0.0144(5) -0.0018(4) -0.0019(4) 0.0031(4)
N1a N 0.0121(16) 0.0182(17) 0.0114(16) 0.0007(13) -0.0016(14) 0.0043(14)
C3a C 0.0078(17) 0.0133(19) 0.0156(19) 0.0046(15) -0.0043(15) 0.0012(16)
N2a N 0.0133(15) 0.0161(17) 0.0138(17) -0.0017(13) -0.0039(14) 0.0027(13)
C5a C 0.0151(18) 0.0137(19) 0.0131(18) -0.0011(16) -0.0036(15) 0.0030(17)
C2a C 0.0123(18) 0.0130(19) 0.0150(19) 0.0038(16) -0.0059(16) 0.0034(16)
C1a C 0.014(2) 0.018(2) 0.017(2) -0.0019(16) -0.0032(18) 0.0059(17)
N5a N 0.0141(15) 0.0173(17) 0.0144(17) -0.0056(14) -0.0023(14) 0.0006(13)
N3a N 0.0113(14) 0.0214(17) 0.0128(16) -0.0035(14) -0.0033(14) -0.0017(14)
C6a C 0.0120(17) 0.0152(19) 0.0126(19) -0.0018(16) -0.0032(15) 0.0005(17)
C10a C 0.0145(18) 0.020(2) 0.0096(18) 0.0047(19) -0.0005(16) 0.0041(17)
C7a C 0.0136(17) 0.0161(19) 0.0143(19) -0.0007(16) -0.0059(16) -0.0017(17)
C8a C 0.0068(17) 0.016(2) 0.014(2) 0.0032(16) -0.0018(16) -0.0007(16)
C4a C 0.016(2) 0.018(2) 0.016(2) 0.0003(16) -0.0051(17) -0.0009(16)
N6a N 0.0174(16) 0.0182(18) 0.0170(17) 0.0015(15) -0.0043(14) -0.0023(14)
N4a N 0.0134(16) 0.0144(17) 0.0164(17) -0.0040(13) -0.0034(14) -0.0016(14)
C9a C 0.014(2) 0.023(2) 0.0124(19) -0.0030(17) -0.0037(16) 0.0036(17)
H1c1a H 0.017219 0.021162 0.02011 -0.002245 -0.003893 0.007118
H1n1a H 0.014503 0.021784 0.013621 0.000809 -0.001957 0.005109
H1c4a H 0.019172 0.0213 0.019159 0.000414 -0.006083 -0.001079
H2c4a H 0.019172 0.0213 0.019159 0.000414 -0.006083 -0.001079
H3c4a H 0.019172 0.0213 0.019159 0.000414 -0.006083 -0.001079
H1c5a H 0.01807 0.016443 0.015703 -0.001352 -0.004328 0.003608
H2c5a H 0.01807 0.016443 0.015703 -0.001352 -0.004328 0.003608
H1c6a H 0.014429 0.018251 0.015086 -0.002204 -0.003828 0.000639
H2c6a H 0.014429 0.018251 0.015086 -0.002204 -0.003828 0.000639
H1c7a H 0.0163 0.019297 0.017124 -0.000893 -0.007109 -0.002067
H2c7a H 0.0163 0.019297 0.017124 -0.000893 -0.007109 -0.002067
H1n3a H 0.013531 0.025676 0.015311 -0.004213 -0.003965 -0.002052
H1n4a H 0.016114 0.017274 0.019657 -0.004774 -0.004137 -0.001929
H2c9a H 0.017119 0.027998 0.014898 -0.003639 -0.004405 0.004321
H1c9a H 0.017119 0.027998 0.014898 -0.003639 -0.004405 0.004321
H3c9a H 0.017119 0.027998 0.014898 -0.003639 -0.004405 0.004321
S1b S 0.0156(5) 0.0153(5) 0.0171(5) -0.0032(4) -0.0030(4) 0.0026(4)
N1b N 0.0171(17) 0.0244(18) 0.0084(16) 0.0015(14) -0.0024(15) -0.0012(15)
C3b C 0.0149(18) 0.015(2) 0.016(2) 0.0013(16) -0.0057(16) 0.0018(16)
N2b N 0.0164(16) 0.0209(18) 0.0126(17) -0.0048(14) -0.0024(14) 0.0016(13)
C5b C 0.0176(18) 0.014(2) 0.0153(19) -0.0019(16) -0.0049(16) 0.0008(16)
C2b C 0.0131(18) 0.015(2) 0.0135(19) 0.0021(16) -0.0033(15) -0.0018(16)
C1b C 0.018(2) 0.025(2) 0.017(2) -0.0031(17) -0.0064(18) -0.0009(18)
N5b N 0.0136(15) 0.0163(17) 0.0171(18) -0.0039(14) -0.0027(14) -0.0002(14)
N3b N 0.0133(15) 0.0166(17) 0.0150(16) -0.0042(14) -0.0015(14) -0.0013(14)
C6b C 0.0163(18) 0.014(2) 0.0176(19) -0.0025(16) -0.0056(16) 0.0017(17)
C10b C 0.0127(18) 0.019(2) 0.0108(18) 0.0056(18) 0.0013(16) 0.0006(17)
C7b C 0.0174(18) 0.016(2) 0.017(2) -0.0043(17) -0.0064(16) 0.0017(17)
C8b C 0.0102(18) 0.015(2) 0.018(2) 0.0031(16) -0.0039(17) -0.0005(17)
C4b C 0.023(2) 0.021(2) 0.016(2) 0.0008(17) -0.0080(18) -0.0048(16)
N6b N 0.0210(17) 0.0194(18) 0.0147(17) 0.0007(15) -0.0050(14) -0.0021(14)
N4b N 0.0139(16) 0.0171(18) 0.0163(17) -0.0017(14) -0.0049(14) -0.0020(15)
C9b C 0.019(2) 0.026(2) 0.018(2) -0.0030(18) -0.0057(17) 0.0052(18)
H1c1b H 0.021803 0.029486 0.019997 -0.003678 -0.007641 -0.00107
H1n1b H 0.020504 0.029306 0.010115 0.001836 -0.002931 -0.001401
H1c4b H 0.027288 0.02518 0.018867 0.000929 -0.009561 -0.005798
H2c4b H 0.027288 0.02518 0.018867 0.000929 -0.009561 -0.005798
H3c4b H 0.027288 0.02518 0.018867 0.000929 -0.009561 -0.005798
H1c5b H 0.021143 0.016548 0.018403 -0.00232 -0.005833 0.000976
H2c5b H 0.021143 0.016548 0.018403 -0.00232 -0.005833 0.000976
H1c6b H 0.019502 0.017312 0.021117 -0.002991 -0.006678 0.002031
H2c6b H 0.019502 0.017312 0.021117 -0.002991 -0.006678 0.002031
H1c7b H 0.020893 0.018653 0.01984 -0.005207 -0.007717 0.002056
H2c7b H 0.020893 0.018653 0.01984 -0.005207 -0.007717 0.002056
H1n3b H 0.015986 0.019906 0.017961 -0.005034 -0.001845 -0.001523
H1n4b H 0.016738 0.020573 0.019537 -0.002038 -0.005934 -0.002412
H2c9b H 0.022323 0.031243 0.021038 -0.003586 -0.006882 0.006198
H1c9b H 0.022323 0.031243 0.021038 -0.003586 -0.006882 0.006198
H3c9b H 0.022323 0.031243 0.021038 -0.003586 -0.006882 0.006198
S1c S 0.0148(5) 0.0164(5) 0.0173(5) -0.0025(4) -0.0021(4) 0.0051(4)
N1c N 0.0183(17) 0.0255(18) 0.0119(17) 0.0014(15) -0.0015(14) 0.0032(15)
C3c C 0.0143(18) 0.015(2) 0.016(2) 0.0027(16) -0.0040(16) 0.0049(17)
N2c N 0.0163(16) 0.0177(17) 0.0185(18) -0.0012(14) -0.0041(15) 0.0057(14)
C5c C 0.0186(18) 0.015(2) 0.0129(18) -0.0021(16) -0.0037(15) 0.0001(17)
C2c C 0.0182(19) 0.015(2) 0.015(2) -0.0003(16) -0.0058(17) 0.0064(16)
C1c C 0.016(2) 0.019(2) 0.022(2) -0.0015(17) -0.0043(19) 0.0095(18)
N5c N 0.0223(17) 0.0226(18) 0.0120(17) -0.0096(15) -0.0036(14) -0.0015(14)
N3c N 0.0151(15) 0.0230(18) 0.0085(16) -0.0064(14) -0.0016(14) -0.0025(14)
C6c C 0.0177(18) 0.0140(19) 0.0141(19) -0.0048(16) -0.0029(16) 0.0008(17)
C10c C 0.020(2) 0.034(3) 0.010(2) -0.007(2) 0.0029(18) -0.0019(19)
C7c C 0.0166(18) 0.016(2) 0.014(2) -0.0106(16) -0.0060(16) 0.0028(17)
C8c C 0.0109(18) 0.020(2) 0.0094(19) -0.0012(17) 0.0021(15) -0.0016(16)
C4c C 0.019(2) 0.026(2) 0.017(2) 0.0030(17) -0.0079(18) 0.0016(17)
N6c N 0.041(2) 0.055(3) 0.0173(18) -0.030(2) -0.0021(17) -0.0047(19)
N4c N 0.0219(18) 0.0263(19) 0.0133(17) -0.0138(15) -0.0031(15) -0.0022(15)
C9c C 0.028(2) 0.040(3) 0.015(2) -0.021(2) -0.0021(18) -0.0027(19)
H1c1c H 0.01865 0.023201 0.02613 -0.001812 -0.005106 0.011348
H1n1c H 0.021921 0.030654 0.014293 0.001706 -0.001772 0.003843
H1c4c H 0.023323 0.03155 0.020154 0.00365 -0.009498 0.001905
H2c4c H 0.023323 0.03155 0.020154 0.00365 -0.009498 0.001905
H3c4c H 0.023323 0.03155 0.020154 0.00365 -0.009498 0.001905
H1c5c H 0.022328 0.018324 0.015469 -0.002469 -0.004429 0.000077
H2c5c H 0.022328 0.018324 0.015469 -0.002469 -0.004429 0.000077
H1c6c H 0.021237 0.016756 0.016893 -0.005703 -0.003456 0.001003
H2c6c H 0.021237 0.016756 0.016893 -0.005703 -0.003456 0.001003
H1c7c H 0.019933 0.01958 0.017128 -0.012759 -0.007146 0.003412
H2c7c H 0.019933 0.01958 0.017128 -0.012759 -0.007146 0.003412
H1n3c H 0.018155 0.027638 0.01017 -0.007644 -0.001922 -0.003026
H1n4c H 0.026331 0.031598 0.015901 -0.016518 -0.003716 -0.002622
H2c9c H 0.034186 0.048428 0.018444 -0.025573 -0.002507 -0.003286
H1c9c H 0.034186 0.048428 0.018444 -0.025573 -0.002507 -0.003286
H3c9c H 0.034186 0.048428 0.018444 -0.025573 -0.002507 -0.003286

Superspace

Chemical data


Full Name: N-Cyano-N'-methyl-N''-[2-((4-methyl-5-imidazolyl)-methylthio)ethyl]guanidine [ Help ]

Common Name: Cimetidine [ Help ]

Formula moiety: C10 H16 N6 S1 [ Help ]

Structural Formula Sum: C10 H16 N6 S1 [ Help ]

Formula weight: 252.36 Da [ Help ]

Crystallographic data and experimental details


Crystal system: monoclinic [ Help ]

Superspace group name: X2/c(α0γ)00 [ Help ]

Symmetry operations of the superspace group: [ Help ]

Operation code Operation in algebraic form
1 x1,x2,x3,x4
2 -x1,x2,-x3+1/2,-x4
3 -x1,-x2,-x3,-x4
4 x1,-x2,x3+1/2,x4
5 x1,x2+1/2,x3,x4+1/2
6 -x1,x2+1/2,-x3+1/2,-x4+1/2
7 -x1,-x2+1/2,-x3,-x4+1/2
8 x1,-x2+1/2,x3+1/2,x4+1/2

a: 13.817(1) Å [ Help ]

b: 4.850(1) Å [ Help ]

c: 18.760(5) Å [ Help ]

α: 90 ° [ Help ]

β: 74.340(19) ° [ Help ]

γ: 90 ° [ Help ]

Volume: 1210.521 Å3 [ Help ]

Modulation dimension: 1 [ Help ]

Measured independent wave vectors: [ Help ]

Wave vector id q_x q_y q_z
1 0.166667 0.000000 0.000000

Z: 4 [ Help ]

Cell measurement temperature: 100 K [ Help ]

μ: 0.253 mm-1 [ Help ]

Absorption correction type: empirical [ Help ]

Refinement details


Total nb. of reflections: 4668 [ Help ]

Nb. of observed reflections: 3823 [ Help ]

Intense reflections threshold: I>5σ(I) [ Help ]

Refinement based on: F [ Help ]

R(obs): 0.0458 [ Help ]

wR(obs): 0.0582 [ Help ]

R(all): 0.0609 [ Help ]

wR(all): 0.0712 [ Help ]

S(all): 4.56 [ Help ]

S(obs): 4.16 [ Help ]

Nb. of reflections: 4668 [ Help ]

Nb. of parameters: 460 [ Help ]

Number of restraints: 0 [ Help ]

Number of constraints: 0 [ Help ]

Weighting scheme: sigma [ Help ]

Weighting scheme remarks: w=1/(σ2(F)+0.0001F2) [ Help ]

Refinement of hydrogen atoms: constr [ Help ]

Δ/σ(max): 0.0030 [ Help ]

Δ/σ(mean): 0.0009 [ Help ]

Δρ(max): 0.41 e_Å-3 [ Help ]

Δρ(min): -0.40 e_Å-3 [ Help ]

Extinction method: none [ Help ]

Structural Information


Average Structure: [ Help ]

Atom site label Atom symbol x y z ADP type Uiso/equiv Symmetry multiplicity Occupancy Coords from (d)iffraction or (c)alculated Coords restraints or constraints Disordered cluster Disordered group
S1a S 0.01833(4) 0.45700(11) -0.89044(3) Uani 0.0155(2) 8 0.5 d . . .
N1a N -0.27971(13) 0.3385(4) -0.71337(10) Uani 0.0166(6) 8 0.5 d . . .
C3a C -0.19560(15) 0.2000(5) -0.75318(12) Uani 0.0143(7) 8 0.5 d . . .
N2a N -0.24536(14) 0.5099(4) -0.82655(10) Uani 0.0165(6) 8 0.5 d . . .
C5a C -0.08943(16) 0.2337(5) -0.88666(12) Uani 0.0153(7) 8 0.5 d . . .
C2a C -0.17504(15) 0.3076(5) -0.82268(12) Uani 0.0144(7) 8 0.5 d . . .
C1a C -0.30601(16) 0.5201(5) -0.75933(12) Uani 0.0182(8) 8 0.5 d . . .
N5a N 0.33860(13) 0.0227(4) -0.94663(10) Uani 0.0172(6) 8 0.5 d . . .
N3a N 0.28760(13) 0.2715(4) -1.03364(10) Uani 0.0155(6) 8 0.5 d . . .
C6a C 0.11114(15) 0.2734(5) -0.96135(12) Uani 0.0149(7) 8 0.5 d . . .
C10a C 0.39346(16) -0.1776(5) -0.93054(12) Uani 0.0172(7) 8 0.5 d . . .
C7a C 0.21218(16) 0.4166(5) -0.97658(12) Uani 0.0156(7) 8 0.5 d . . .
C8a C 0.34592(15) 0.0745(5) -1.01851(12) Uani 0.0138(7) 8 0.5 d . . .
C4a C -0.14330(18) -0.0133(5) -0.71998(13) Uani 0.0188(8) 8 0.5 d . . .
N6a N 0.43681(15) -0.3502(5) -0.90934(11) Uani 0.0247(7) 8 0.5 d . . .
N4a N 0.40708(13) -0.0647(4) -1.07377(10) Uani 0.0170(6) 8 0.5 d . . .
C9a C 0.42004(19) -0.0006(6) -1.15098(13) Uani 0.0219(8) 8 0.5 d . . .
H1c1a H -0.362481 0.64237 -0.744587 Uani 0.0219 8 0.5 d . . .
H1n1a H -0.31044 0.313726 -0.666966 Uani 0.02 8 0.5 d . . .
H1c4a H -0.093781 0.073357 -0.700253 Uani 0.0225 8 0.5 d . . .
H2c4a H -0.191373 -0.106829 -0.681018 Uani 0.0225 8 0.5 d . . .
H3c4a H -0.111137 -0.143654 -0.757334 Uani 0.0225 8 0.5 d . . .
H1c5a H -0.109338 0.252573 -0.931567 Uani 0.0184 8 0.5 d . . .
H2c5a H -0.070743 0.045417 -0.882234 Uani 0.0184 8 0.5 d . . .
H1c6a H 0.117259 0.088038 -0.945176 Uani 0.0179 8 0.5 d . . .
H2c6a H 0.089886 0.267089 -1.005992 Uani 0.0179 8 0.5 d . . .
H1c7a H 0.205916 0.602429 -0.99232 Uani 0.0187 8 0.5 d . . .
H2c7a H 0.23328 0.423661 -0.931883 Uani 0.0187 8 0.5 d . . .
H1n3a H 0.294774 0.31596 -1.079686 Uani 0.0187 8 0.5 d . . .
H1n4a H 0.441083 -0.201539 -1.062835 Uani 0.0204 8 0.5 d . . .
H2c9a H 0.357128 -0.020488 -1.162469 Uani 0.0263 8 0.5 d . . .
H1c9a H 0.468232 -0.123659 -1.18115 Uani 0.0263 8 0.5 d . . .
H3c9a H 0.443372 0.184783 -1.160555 Uani 0.0263 8 0.5 d . . .

ADP components: [ Help ]

Atom site label Atom site symbol U11 U22 U33 U12 U13 U23
S1a S 0.0136(3) 0.0157(3) 0.0164(3) 0.0026(2) -0.0024(2) -0.0036(2)
N1a N 0.0153(9) 0.0230(10) 0.0106(9) -0.0011(8) -0.0017(8) -0.0022(8)
C3a C 0.0128(10) 0.0146(11) 0.0162(11) -0.0033(9) -0.0049(9) -0.0027(9)
N2a N 0.0153(9) 0.0185(10) 0.0151(10) 0.0029(8) -0.0032(8) -0.0033(8)
C5a C 0.0170(11) 0.0150(12) 0.0142(11) 0.0020(9) -0.0044(9) -0.0014(10)
C2a C 0.0147(10) 0.0143(11) 0.0150(11) -0.0020(9) -0.0055(9) -0.0026(9)
C1a C 0.0159(12) 0.0204(13) 0.0184(12) 0.0021(9) -0.0046(10) -0.0041(10)
N5a N 0.0166(9) 0.0192(10) 0.0149(10) 0.0065(8) -0.0028(8) 0.0000(8)
N3a N 0.0132(9) 0.0201(10) 0.0122(9) 0.0047(8) -0.0015(8) 0.0017(8)
C6a C 0.0156(10) 0.0153(11) 0.0139(11) 0.0032(9) -0.0041(9) -0.0009(10)
C10a C 0.0154(11) 0.0236(13) 0.0101(11) -0.0011(11) 0.0009(9) -0.0004(10)
C7a C 0.0168(11) 0.0162(12) 0.0152(12) 0.0040(10) -0.0065(9) -0.0010(10)
C8a C 0.0096(10) 0.0169(12) 0.0139(12) -0.0012(9) -0.0016(9) 0.0003(9)
C4a C 0.0197(13) 0.0214(14) 0.0167(13) -0.0006(10) -0.0075(11) 0.0023(10)
N6a N 0.0261(11) 0.0304(12) 0.0160(10) 0.0088(10) -0.0032(9) 0.0029(9)
N4a N 0.0158(9) 0.0195(10) 0.0153(10) 0.0065(8) -0.0034(8) 0.0015(8)
C9a C 0.0214(13) 0.0289(15) 0.0153(12) 0.0089(11) -0.0046(10) -0.0019(11)
H1c1a H 0.019068 0.024535 0.022062 0.002575 -0.005557 -0.004975
H1n1a H 0.018385 0.027553 0.01268 -0.00135 -0.001991 -0.002602
H1c4a H 0.023682 0.025711 0.020007 -0.000734 -0.008977 0.002739
H2c4a H 0.023682 0.025711 0.020007 -0.000734 -0.008977 0.002739
H3c4a H 0.023682 0.025711 0.020007 -0.000734 -0.008977 0.002739
H1c5a H 0.02036 0.018002 0.017031 0.002391 -0.005331 -0.001707
H2c5a H 0.02036 0.018002 0.017031 0.002391 -0.005331 -0.001707
H1c6a H 0.018752 0.018411 0.016723 0.003874 -0.004905 -0.001096
H2c6a H 0.018752 0.018411 0.016723 0.003874 -0.004905 -0.001096
H1c7a H 0.020106 0.019428 0.018186 0.004842 -0.007821 -0.001197
H2c7a H 0.020106 0.019428 0.018186 0.004842 -0.007821 -0.001197
H1n3a H 0.015831 0.024167 0.014651 0.005587 -0.00183 0.002027
H1n4a H 0.018965 0.023421 0.018315 0.007834 -0.004115 0.001847
H2c9a H 0.025685 0.034647 0.018418 0.01067 -0.005569 -0.002239
H1c9a H 0.025685 0.034647 0.018418 0.01067 -0.005569 -0.002239
H3c9a H 0.025685 0.034647 0.018418 0.01067 -0.005569 -0.002239

Fourier Wave Vectors (explicit: q_x,q_y,q_z or coefficients: q_1,q_2,...): [ Help ]

Wave vector code q_1
1 1

Occupation crenel coefficients: [ Help ]

Atom site label Center (x0) Width
S1a 0 0.5
N1a 0 0.5
C3a 0 0.5
N2a 0 0.5
C5a 0 0.5
C2a 0 0.5
C1a 0 0.5
N5a 0 0.5
N3a 0 0.5
C6a 0 0.5
C10a 0 0.5
C7a 0 0.5
C8a 0 0.5
C4a 0 0.5
N6a 0 0.5
N4a 0 0.5
C9a 0 0.5
H1c1a 0 0.5
H1n1a 0 0.5
H1c4a 0 0.5
H2c4a 0 0.5
H3c4a 0 0.5
H1c5a 0 0.5
H2c5a 0 0.5
H1c6a 0 0.5
H2c6a 0 0.5
H1c7a 0 0.5
H2c7a 0 0.5
H1n3a 0 0.5
H1n4a 0 0.5
H2c9a 0 0.5
H1c9a 0 0.5
H3c9a 0 0.5

Displacive (translational) Legendre coefficients: [ Help ]

Atom site label Displacement axis Polynomial order Polynomial coeff.
S1a x 1 -0.0195
S1a y 1 0.0668
S1a z 1 -0.0075
S1a x 2 0
S1a y 2 -0.0097
S1a z 2 0.0008
N1a x 1 -0.026(7)
N1a y 1 0.001(16)
N1a z 1 -0.016(6)
N1a x 2 -0.002(7)
N1a y 2 -0.016(16)
N1a z 2 0.002(6)
C3a x 1 -0.023(5)
C3a y 1 0.017(12)
C3a z 1 -0.017(5)
C3a x 2 -0.001(5)
C3a y 2 -0.012(12)
C3a z 2 0.001(5)
N2a x 1 -0.021(3)
N2a y 1 0.043(12)
N2a z 1 -0.012(6)
N2a x 2 -0.001(3)
N2a y 2 -0.004(12)
N2a z 2 0.002(6)
C5a x 1 -0.0169(18)
C5a y 1 0.064(5)
C5a z 1 -0.014(3)
C5a x 2 -0.0014(18)
C5a y 2 -0.002(5)
C5a z 2 0.000(3)
C2a x 1 -0.020(3)
C2a y 1 0.043(9)
C2a z 1 -0.014(4)
C2a x 2 -0.001(3)
C2a y 2 -0.005(9)
C2a z 2 0.001(4)
C1a x 1 -0.025(5)
C1a y 1 0.017(16)
C1a z 1 -0.013(7)
C1a x 2 -0.002(5)
C1a y 2 -0.012(16)
C1a z 2 0.002(7)
N5a x 1 -0.013(4)
N5a y 1 0.129(15)
N5a z 1 -0.008(8)
N5a x 2 -0.005(4)
N5a y 2 -0.038(15)
N5a z 2 -0.002(8)
N3a x 1 -0.017(6)
N3a y 1 0.105(14)
N3a z 1 -0.010(6)
N3a x 2 -0.002(6)
N3a y 2 -0.026(14)
N3a z 2 -0.002(6)
C6a x 1 -0.017(3)
C6a y 1 0.086(6)
C6a z 1 -0.010(2)
C6a x 2 -0.002(3)
C6a y 2 -0.014(6)
C6a z 2 -0.001(2)
C10a x 1 -0.012(5)
C10a y 1 0.140(18)
C10a z 1 -0.005(10)
C10a x 2 -0.006(5)
C10a y 2 -0.046(17)
C10a z 2 -0.004(10)
C7a x 1 -0.019(3)
C7a y 1 0.101(10)
C7a z 1 -0.011(4)
C7a x 2 -0.001(3)
C7a y 2 -0.023(10)
C7a z 2 -0.001(4)
C8a x 1 -0.014(6)
C8a y 1 0.116(16)
C8a z 1 -0.008(8)
C8a x 2 -0.004(6)
C8a y 2 -0.032(16)
C8a z 2 -0.002(8)
C4a x 1 -0.022(7)
C4a y 1 0.010(12)
C4a z 1 -0.019(4)
C4a x 2 0.000(7)
C4a y 2 -0.016(12)
C4a z 2 0.000(4)
N6a x 1 -0.012(6)
N6a y 1 0.15(2)
N6a z 1 -0.001(11)
N6a x 2 -0.007(6)
N6a y 2 -0.06(2)
N6a z 2 -0.006(11)
N4a x 1 -0.012(8)
N4a y 1 0.12(2)
N4a z 1 -0.006(9)
N4a x 2 -0.006(8)
N4a y 2 -0.034(19)
N4a z 2 -0.003(9)
C9a x 1 -0.015(11)
C9a y 1 0.10(2)
C9a z 1 -0.007(9)
C9a x 2 -0.005(11)
C9a y 2 -0.03(2)
C9a z 2 -0.003(9)
H1c1a x 1 -0.02(10)
H1c1a y 1 0.02(10)
H1c1a z 1 -0.01(10)
H1c1a x 2 0.00(10)
H1c1a y 2 -0.01(10)
H1c1a z 2 0.00(10)
H1n1a x 1 -0.03(10)
H1n1a y 1 0.00(10)
H1n1a z 1 -0.02(10)
H1n1a x 2 -0.01(10)
H1n1a y 2 -0.03(10)
H1n1a z 2 0.00(10)
H1c4a x 1 -0.02(10)
H1c4a y 1 0.01(10)
H1c4a z 1 -0.02(10)
H1c4a x 2 0.00(10)
H1c4a y 2 -0.02(10)
H1c4a z 2 0.00(10)
H2c4a x 1 -0.02(10)
H2c4a y 1 0.01(10)
H2c4a z 1 -0.02(10)
H2c4a x 2 0.00(10)
H2c4a y 2 -0.03(10)
H2c4a z 2 0.00(10)
H3c4a x 1 -0.02(10)
H3c4a y 1 0.02(10)
H3c4a z 1 -0.02(10)
H3c4a x 2 0.00(10)
H3c4a y 2 -0.01(10)
H3c4a z 2 0.00(10)
H1c5a x 1 -0.02(10)
H1c5a y 1 0.08(10)
H1c5a z 1 -0.01(10)
H1c5a x 2 0.00(10)
H1c5a y 2 0.01(10)
H1c5a z 2 0.00(10)
H2c5a x 1 -0.02(10)
H2c5a y 1 0.06(10)
H2c5a z 1 -0.02(10)
H2c5a x 2 0.00(10)
H2c5a y 2 0.00(10)
H2c5a z 2 0.00(10)
H1c6a x 1 -0.01(10)
H1c6a y 1 0.09(10)
H1c6a z 1 -0.01(10)
H1c6a x 2 0.00(10)
H1c6a y 2 -0.02(10)
H1c6a z 2 0.00(10)
H2c6a x 1 -0.02(10)
H2c6a y 1 0.08(10)
H2c6a z 1 -0.01(10)
H2c6a x 2 0.00(10)
H2c6a y 2 -0.01(10)
H2c6a z 2 0.00(10)
H1c7a x 1 -0.02(10)
H1c7a y 1 0.10(10)
H1c7a z 1 -0.01(10)
H1c7a x 2 0.00(10)
H1c7a y 2 -0.02(10)
H1c7a z 2 0.00(10)
H2c7a x 1 -0.02(10)
H2c7a y 1 0.11(10)
H2c7a z 1 -0.01(10)
H2c7a x 2 0.00(10)
H2c7a y 2 -0.03(10)
H2c7a z 2 0.00(10)
H1n3a x 1 -0.02(10)
H1n3a y 1 0.10(10)
H1n3a z 1 -0.01(10)
H1n3a x 2 0.00(10)
H1n3a y 2 -0.02(10)
H1n3a z 2 0.00(10)
H1n4a x 1 -0.01(10)
H1n4a y 1 0.13(10)
H1n4a z 1 -0.01(10)
H1n4a x 2 -0.01(10)
H1n4a y 2 -0.04(10)
H1n4a z 2 -0.01(10)
H2c9a x 1 -0.01(10)
H2c9a y 1 0.07(10)
H2c9a z 1 -0.01(10)
H2c9a x 2 0.00(10)
H2c9a y 2 0.00(10)
H2c9a z 2 0.00(10)
H1c9a x 1 -0.01(10)
H1c9a y 1 0.11(10)
H1c9a z 1 -0.01(10)
H1c9a x 2 -0.01(10)
H1c9a y 2 -0.02(10)
H1c9a z 2 -0.01(10)
H3c9a x 1 -0.02(10)
H3c9a y 1 0.11(10)
H3c9a z 1 -0.01(10)
H3c9a x 2 0.00(10)
H3c9a y 2 -0.02(10)
H3c9a z 2 0.00(10)