@ccp-nc/crystvis-js 0.4.13

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Files changed (100) hide show
  1. package/.eslintrc.json +16 -0
  2. package/.github/workflows/test-mocha.yml +30 -0
  3. package/.vscode/settings.json +4 -0
  4. package/LICENSE +21 -0
  5. package/README.html +1127 -0
  6. package/README.md +76 -0
  7. package/demo/demo.css +30 -0
  8. package/demo/index.html +76 -0
  9. package/demo/main.js +143 -0
  10. package/docs/.nojekyll +0 -0
  11. package/docs-tutorials/Events.md +57 -0
  12. package/docs-tutorials/Queries.md +50 -0
  13. package/fonts/Rubik/OFL.txt +93 -0
  14. package/fonts/Rubik/README.txt +77 -0
  15. package/fonts/Rubik/Rubik-Italic-VariableFont_wght.ttf +0 -0
  16. package/fonts/Rubik/Rubik-VariableFont_wght.ttf +0 -0
  17. package/fonts/Rubik/static/Rubik-Black.ttf +0 -0
  18. package/fonts/Rubik/static/Rubik-BlackItalic.ttf +0 -0
  19. package/fonts/Rubik/static/Rubik-Bold.ttf +0 -0
  20. package/fonts/Rubik/static/Rubik-BoldItalic.ttf +0 -0
  21. package/fonts/Rubik/static/Rubik-ExtraBold.ttf +0 -0
  22. package/fonts/Rubik/static/Rubik-ExtraBoldItalic.ttf +0 -0
  23. package/fonts/Rubik/static/Rubik-Italic.ttf +0 -0
  24. package/fonts/Rubik/static/Rubik-Light.ttf +0 -0
  25. package/fonts/Rubik/static/Rubik-LightItalic.ttf +0 -0
  26. package/fonts/Rubik/static/Rubik-Medium.ttf +0 -0
  27. package/fonts/Rubik/static/Rubik-MediumItalic.ttf +0 -0
  28. package/fonts/Rubik/static/Rubik-Regular.ttf +0 -0
  29. package/fonts/Rubik/static/Rubik-SemiBold.ttf +0 -0
  30. package/fonts/Rubik/static/Rubik-SemiBoldItalic.ttf +0 -0
  31. package/index.html +25 -0
  32. package/index.js +11 -0
  33. package/jsconf.json +14 -0
  34. package/lib/assets/fonts/Rubik-Medium.fnt +297 -0
  35. package/lib/assets/fonts/Rubik-Medium.png +0 -0
  36. package/lib/assets/fonts/bmpfonts.in.js +16 -0
  37. package/lib/assets/fonts/bmpfonts.js +9 -0
  38. package/lib/assets/fonts/font.js +82 -0
  39. package/lib/assets/fonts/index.js +14 -0
  40. package/lib/assets/fonts/threebmfont.js +28 -0
  41. package/lib/data.js +125 -0
  42. package/lib/formats/cell.js +114 -0
  43. package/lib/formats/cif.js +22 -0
  44. package/lib/formats/magres.js +337 -0
  45. package/lib/formats/xyz.js +124 -0
  46. package/lib/loader.js +87 -0
  47. package/lib/model.js +2076 -0
  48. package/lib/modelview.js +382 -0
  49. package/lib/nmrdata.js +2898 -0
  50. package/lib/orbit.js +1233 -0
  51. package/lib/primitives/atoms.js +261 -0
  52. package/lib/primitives/cell.js +160 -0
  53. package/lib/primitives/dither.js +156 -0
  54. package/lib/primitives/ellipsoid.js +183 -0
  55. package/lib/primitives/geometries.js +20 -0
  56. package/lib/primitives/index.js +48 -0
  57. package/lib/primitives/isosurface.js +171 -0
  58. package/lib/primitives/shapes.js +100 -0
  59. package/lib/primitives/sprites.js +172 -0
  60. package/lib/query.js +158 -0
  61. package/lib/render.js +440 -0
  62. package/lib/selbox.js +361 -0
  63. package/lib/shaders/aura.frag +26 -0
  64. package/lib/shaders/aura.vert +37 -0
  65. package/lib/shaders/dither.frag +42 -0
  66. package/lib/shaders/dither.vert +8 -0
  67. package/lib/shaders/index.in.js +17 -0
  68. package/lib/shaders/index.js +25 -0
  69. package/lib/shaders/msdf300.frag +25 -0
  70. package/lib/shaders/msdf300.vert +45 -0
  71. package/lib/tensor.js +227 -0
  72. package/lib/utils.js +168 -0
  73. package/lib/visualizer.js +480 -0
  74. package/package.json +106 -0
  75. package/scripts/build-bundle.js +17 -0
  76. package/scripts/build-fonts.js +43 -0
  77. package/scripts/build-resources.js +46 -0
  78. package/scripts/plugins-shim.js +10 -0
  79. package/test/chemdata.js +69 -0
  80. package/test/data/CHA.cif +74 -0
  81. package/test/data/H2O.xyz +8 -0
  82. package/test/data/H2_bound.xyz +4 -0
  83. package/test/data/ethanol.cell +25 -0
  84. package/test/data/ethanol.magres +238 -0
  85. package/test/data/example_single.cif +789 -0
  86. package/test/data/frac.cell +8 -0
  87. package/test/data/org.cif +427 -0
  88. package/test/data/pyridine.xyz +13 -0
  89. package/test/data/si8.xyz +10 -0
  90. package/test/loader.js +107 -0
  91. package/test/model.js +368 -0
  92. package/test/query.js +135 -0
  93. package/test/tensor.js +133 -0
  94. package/test/test-html/examples.js +1485 -0
  95. package/test/test-html/index.html +33 -0
  96. package/test/test-html/index.js +279 -0
  97. package/tools/compile_colors.py +120 -0
  98. package/tools/compile_periodic.py +96 -0
  99. package/tools/ptable.json +497 -0
  100. package/tools/test +5844 -0
@@ -0,0 +1,789 @@
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+ #########################################################################
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+ # #
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+ # THIS IS AN EXAMPLE OF A CIF REPORTING A SINGLE #
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+ # STRUCTURE AND INCLUDING USER-DEFINABLE TEXT #
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+ # SECTIONS #
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+ # #
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+ #########################################################################
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+
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+ data_global
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+
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+ loop_
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+ _publ_body_element
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+ _publ_body_title
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+ _publ_body_contents
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+
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+ section .
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+ ;
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+ ?
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+ ;
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+ section
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+ ;
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+ Introduction
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+ ;
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+ ;\
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+ INTRODUCTION TEXT HERE
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+ ;
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+ section Experimental
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+ ;
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+ ?
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+ ;
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+ subsection 'Synthesis and crystallization'
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+ ;
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+ TEXT HERE
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+ ;
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+
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+ subsection Refinement
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+ ;
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+ TEXT HERE
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+ ;
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+
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+ section 'Results and discussion'
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+ ;
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+ TEXT HERE
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+ ;
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+
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+ #=============================================================
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+
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+ _audit_creation_date 'June 17, 2013'
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+ _audit_creation_method 'from SHELXL-97'
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+ _audit_update_record
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+ ;
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+ ;
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+
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+ #===================================================================
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+ # 1. SUBMISSION DETAILS
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+
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+ _publ_contact_author_name 'NAME'
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+ _publ_contact_author_address
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+ ;
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+ ADDRESS
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+ ;
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+
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+ _publ_contact_author_phone ?
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+ _publ_contact_author_fax ?
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+ _publ_contact_author_email ?
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+
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+ _publ_requested_journal 'Acta Crystallographica C'
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+ _publ_requested_category FA
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+ _publ_requested_coeditor_name ?
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+
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+ _publ_contact_letter
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+ ;
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+ ;
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+
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+ #=====================================================================
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+ # 2. PROCESSING SUMMARY (IUCr Office Use Only)
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+
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+ _journal_date_recd_electronic ?
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+ _journal_date_to_coeditor ?
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+ _journal_date_from_coeditor ?
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+ _journal_date_accepted ?
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+ _journal_date_printers_first ?
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+ _journal_date_printers_final ?
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+ _journal_date_proofs_out ?
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+ _journal_date_proofs_in ?
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+ _journal_coeditor_name ?
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+ _journal_coeditor_code ?
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+ _journal_paper_doi ?
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+ _journal_paper_category FA
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+ _journal_coeditor_notes ?
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+ _journal_techeditor_code ?
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+ _iucr_compatibility_tag ACTA95
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+ _journal_techeditor_notes ?
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+ _journal_coden_ASTM ACSCGG
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+ _journal_name_full 'Acta Crystallographica, Section C'
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+ _journal_year ?
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+ _journal_volume ?
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+ _journal_issue ?
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+ _journal_page_first ?
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+ _journal_page_last ?
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+ _journal_suppl_publ_number ?
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+ _journal_suppl_publ_pages ?
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+
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+ #=====================================================================
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+ # 3. TITLE AND AUTHOR LIST
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+
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+ _publ_section_title
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+ ;
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+ TITLE
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+ ;
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+
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+ loop_
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+ _publ_author_name
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+ _publ_author_address
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+ _publ_author_email
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+ _publ_author_footnote
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+ 'NAME'
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+ ;
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+ ADDRESS
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+ ;
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+ ? ?
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+
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+ #======================================================================
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+ # 4. TEXT
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+
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+ _publ_section_synopsis
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+ ;
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+ TEXT HERE
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+ ;
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+
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+ _publ_section_keywords
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+ ;
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+ TEXT HERE
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+ ;
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+
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+ _publ_section_abstract
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+ ;
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+ TEXT HERE
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+ ;
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+
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+ _publ_section_references
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+ ;
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+ REFERENCES HERE
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+ ;
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+
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+ _publ_section_figure_captions
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+ ;
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+ FIGURE CAPTIONS HERE
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+ ;
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+
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+ _publ_section_table_legends
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+ ;
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+ TABLE CAPTIONS HERE
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+ ;
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+
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+ _publ_section_acknowledgements
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+ ;
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+ ACKNOWLEDGEMENTS HERE
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+ ;
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+
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+ #=====================================================================
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+
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+ data_I
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+
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+ #=====================================================================
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+ # 5. Chemical Data
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+
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+ _chemical_name_systematic
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+ ;\
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+ (6<i>R</i>*,11<i>R</i>*)-5-Acetyl-11-ethyl-6,11-dihydro-5<i>H</i>-\
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+ dibenzo[<i>b</i>,<i>e</i>]azepine-6-carboxylic acid
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+ ;
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+ _chemical_name_common ?
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+ _chemical_melting_point ?
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+ _chemical_formula_moiety 'C19 H19 N O3'
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+ _chemical_formula_sum 'C19 H19 N O3'
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+ _chemical_formula_weight 309.35
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+ _chemical_compound_source 'synthesised by authors, see text'
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+ _chemical_formula_iupac 'C19 H19 N O3'
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+
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+ loop_
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+ _atom_type_symbol
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+ _atom_type_description
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+ _atom_type_scat_dispersion_real
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+ _atom_type_scat_dispersion_imag
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+ _atom_type_scat_source
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+ 'C' 'C' 0.0033 0.0016
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+ 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
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+ 'H' 'H' 0.0000 0.0000
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+ 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
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+ 'N' 'N' 0.0061 0.0033
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+ 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
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+ 'O' 'O' 0.0106 0.0060
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+ 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
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+
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+
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+ _symmetry_cell_setting monoclinic
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+ _symmetry_space_group_name_H-M 'P 21'
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+ _symmetry_space_group_name_Hall 'P 2yb'
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+
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+ loop_
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+ _symmetry_equiv_pos_as_xyz
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+ 'x, y, z'
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+ '-x, y+1/2, -z'
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+
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+ _cell_length_a 8.8053(3)
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+ _cell_length_b 10.9821(4)
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+ _cell_length_c 9.0080(6)
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+ _cell_angle_alpha 90.00
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+ _cell_angle_beta 118.510(3)
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+ _cell_angle_gamma 90.00
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+ _cell_volume 765.45(6)
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+ _cell_formula_units_Z 2
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+ _cell_measurement_temperature 120(2)
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+ _cell_measurement_reflns_used 1853
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+ _cell_measurement_theta_min 3.20
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+ _cell_measurement_theta_max 27.50
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+
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+ _exptl_crystal_description rod
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+ _exptl_crystal_colour colourless
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+ _exptl_crystal_size_max 0.26
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+ _exptl_crystal_size_mid 0.14
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+ _exptl_crystal_size_min 0.10
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+ _exptl_crystal_density_meas ?
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+ _exptl_crystal_density_diffrn 1.342
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+ _exptl_crystal_density_method 'not measured'
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+ _exptl_crystal_F_000 328
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+ _exptl_absorpt_coefficient_mu 0.091
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+ _exptl_absorpt_correction_type multi-scan
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+ _exptl_absorpt_process_details '(SADABS; Sheldrick, 2003)'
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+ _exptl_absorpt_correction_T_min 0.977
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+ _exptl_absorpt_correction_T_max 0.991
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+
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+ _exptl_special_details
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+ ?
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+
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+ _diffrn_ambient_temperature 120(2)
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+ _diffrn_radiation_wavelength 0.71073
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+ _diffrn_radiation_type 'Mo K\a'
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+ _diffrn_radiation_source 'Bruker Nonius FR591 rotating anode'
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+ _diffrn_radiation_monochromator graphite
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+ _diffrn_measurement_device_type 'Bruker Nonius KappaCCD area-detector'
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+ _diffrn_measurement_method '\f and \w'
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+ _diffrn_detector_area_resol_mean 9.091
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+ _diffrn_standards_interval_count 0
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+ _diffrn_standards_interval_time 0
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+ _diffrn_standards_number 0
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+ _diffrn_standards_decay_% 0
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+
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+ _diffrn_reflns_number 13276
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+ _diffrn_reflns_av_R_equivalents 0.0486
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+ _diffrn_reflns_av_sigmaI/netI 0.0321
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+ _diffrn_reflns_limit_h_min -11
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+ _diffrn_reflns_limit_h_max 11
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+ _diffrn_reflns_limit_k_min -14
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+ _diffrn_reflns_limit_k_max 14
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+ _diffrn_reflns_limit_l_min -11
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+ _diffrn_reflns_limit_l_max 11
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+ _diffrn_reflns_theta_min 3.71
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+ _diffrn_reflns_theta_max 27.50
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+ _diffrn_reflns_theta_full 27.50
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+ _diffrn_measured_fraction_theta_max 0.997
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+ _diffrn_measured_fraction_theta_full 0.997
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+ _reflns_number_total 1851
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+ _reflns_number_gt 1638
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+ _reflns_threshold_expression I>2\s(I)
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+
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+ _computing_data_collection 'COLLECT (Nonius, 1998)'
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+ _computing_cell_refinement
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+ 'DIRAX/LSQ (Duisenberg <i>et al.</i>, 2000)'
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+ _computing_data_reduction
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+ 'EVALCCD (Duisenberg <i>et al.</i>, 2003)'
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+ _computing_structure_solution 'SIR2004 (Burla et al., 2005)'
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+ _computing_structure_refinement 'SHELXL97 (Sheldrick, 2008)'
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+ _computing_molecular_graphics 'PLATON (Spek, 2009)'
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+ _computing_publication_material
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+ 'SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009)'
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+
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+ #=========================================================================
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+ # 8. Refinement Data
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+
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+ _refine_ls_structure_factor_coef Fsqd
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+ _refine_ls_matrix_type full
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+ _refine_ls_weighting_scheme calc
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+ _refine_ls_weighting_details
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+ 'w = 1/[\s^2^(Fo^2^)+(0.0351P)^2^+0.1657P] where P=(Fo^2^+2Fc^2^)/3'
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+ _atom_sites_solution_primary direct
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+ _atom_sites_solution_secondary difmap
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+ _atom_sites_solution_hydrogens geom
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+ _refine_ls_hydrogen_treatment constr
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+ _refine_ls_extinction_method none
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+ _refine_ls_extinction_coef ?
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+ _chemical_absolute_configuration unk
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+ _refine_ls_number_reflns 1851
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+ _refine_ls_number_parameters 210
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+ _refine_ls_number_restraints 1
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+ _refine_ls_R_factor_all 0.0455
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+ _refine_ls_R_factor_gt 0.0360
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+ _refine_ls_wR_factor_ref 0.0807
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+ _refine_ls_wR_factor_gt 0.0772
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+ _refine_ls_goodness_of_fit_ref 1.146
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+ _refine_ls_restrained_S_all 1.146
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+ _refine_ls_shift/su_max 0.001
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+ _refine_ls_shift/su_mean 0.000
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+ _refine_diff_density_max 0.209
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+ _refine_diff_density_min -0.240
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+
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+ #=========================================================================
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+ # 9. Atomic Coordinates and Displacement Parameters
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+
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+ loop_
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+ _atom_site_label
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+ _atom_site_type_symbol
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+ _atom_site_fract_x
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+ _atom_site_fract_y
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+ _atom_site_fract_z
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+ _atom_site_U_iso_or_equiv
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+ _atom_site_adp_type
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+ _atom_site_occupancy
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+ _atom_site_symmetry_multiplicity
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+ _atom_site_calc_flag
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+ _atom_site_refinement_flags
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+ _atom_site_disorder_assembly
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+ _atom_site_disorder_group
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+ C1 C 0.6424(3) 0.5942(2) 0.7939(3) 0.0186(5) Uani 1 1 d . . .
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+ H1 H 0.6599 0.6154 0.9031 0.022 Uiso 1 1 calc R . .
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+ C2 C 0.7828(3) 0.5595(2) 0.7731(3) 0.0211(5) Uani 1 1 d . . .
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+ H2 H 0.8953 0.5589 0.8678 0.025 Uiso 1 1 calc R . .
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+ C3 C 0.7604(3) 0.5255(2) 0.6149(3) 0.0202(5) Uani 1 1 d . . .
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+ H3 H 0.8563 0.4993 0.6019 0.024 Uiso 1 1 calc R . .
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+ C4 C 0.5955(3) 0.5306(2) 0.4757(3) 0.0166(5) Uani 1 1 d . . .
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+ H4 H 0.5780 0.5079 0.3669 0.020 Uiso 1 1 calc R . .
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+ C4a C 0.4576(3) 0.5687(2) 0.4973(3) 0.0142(5) Uani 1 1 d . . .
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+ N5 N 0.2883(2) 0.58197(17) 0.3533(2) 0.0132(4) Uani 1 1 d . . .
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+ C6 C 0.1469(3) 0.4966(2) 0.3244(3) 0.0128(4) Uani 1 1 d . . .
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+ H6 H 0.0389 0.5461 0.2831 0.015 Uiso 1 1 calc R . .
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+ C6a C 0.1714(3) 0.4295(2) 0.4842(3) 0.0145(5) Uani 1 1 d . . .
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+ C7 C 0.1243(3) 0.3077(2) 0.4737(3) 0.0174(5) Uani 1 1 d . . .
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+ H7 H 0.0884 0.2652 0.3704 0.021 Uiso 1 1 calc R . .
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+ C8 C 0.1286(3) 0.2465(2) 0.6107(3) 0.0189(5) Uani 1 1 d . . .
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+ H8 H 0.0977 0.1628 0.6008 0.023 Uiso 1 1 calc R . .
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+ C9 C 0.1780(3) 0.3073(2) 0.7616(3) 0.0188(5) Uani 1 1 d . . .
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+ H9 H 0.1759 0.2670 0.8540 0.023 Uiso 1 1 calc R . .
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+ C10 C 0.2305(3) 0.4277(2) 0.7762(3) 0.0185(5) Uani 1 1 d . . .
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+ H10 H 0.2674 0.4685 0.8808 0.022 Uiso 1 1 calc R . .
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+ C10a C 0.2307(3) 0.4909(2) 0.6412(3) 0.0151(5) Uani 1 1 d . . .
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+ C11 C 0.3097(3) 0.6185(2) 0.6677(3) 0.0150(5) Uani 1 1 d . . .
348
+ H11 H 0.2307 0.6694 0.5686 0.018 Uiso 1 1 calc R . .
349
+ C11a C 0.4763(3) 0.5982(2) 0.6566(3) 0.0145(5) Uani 1 1 d . . .
350
+ C51 C 0.2534(3) 0.6720(2) 0.2388(3) 0.0142(5) Uani 1 1 d . . .
351
+ O51 O 0.10670(19) 0.68043(16) 0.11339(19) 0.0180(4) Uani 1 1 d . . .
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+ C52 C 0.3950(3) 0.7609(2) 0.2675(3) 0.0189(5) Uani 1 1 d . . .
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+ H52A H 0.4784 0.7219 0.2397 0.028 Uiso 1 1 calc R . .
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+ H52B H 0.4537 0.7862 0.3862 0.028 Uiso 1 1 calc R . .
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+ H52C H 0.3452 0.8324 0.1952 0.028 Uiso 1 1 calc R . .
356
+ C61 C 0.1208(3) 0.4093(2) 0.1806(3) 0.0145(5) Uani 1 1 d . . .
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+ O61 O -0.0387(2) 0.36474(17) 0.10291(19) 0.0186(4) Uani 1 1 d . . .
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+ H61 H -0.0487 0.3107 0.0297 0.028 Uiso 1 1 d R . .
359
+ O62 O 0.2327(2) 0.38608(17) 0.1438(2) 0.0224(4) Uani 1 1 d . . .
360
+ C111 C 0.3325(3) 0.6837(2) 0.8280(3) 0.0202(5) Uani 1 1 d . . .
361
+ H11A H 0.2247 0.6761 0.8362 0.024 Uiso 1 1 calc R . .
362
+ H11B H 0.4266 0.6440 0.9284 0.024 Uiso 1 1 calc R . .
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+ C112 C 0.3752(3) 0.8181(2) 0.8272(3) 0.0229(5) Uani 1 1 d . . .
364
+ H12A H 0.4821 0.8260 0.8195 0.034 Uiso 1 1 calc R . .
365
+ H12B H 0.3905 0.8565 0.9317 0.034 Uiso 1 1 calc R . .
366
+ H12C H 0.2804 0.8583 0.7300 0.034 Uiso 1 1 calc R . .
367
+
368
+ loop_
369
+ _atom_site_aniso_label
370
+ _atom_site_aniso_U_11
371
+ _atom_site_aniso_U_22
372
+ _atom_site_aniso_U_33
373
+ _atom_site_aniso_U_23
374
+ _atom_site_aniso_U_13
375
+ _atom_site_aniso_U_12
376
+ C1 0.0214(12) 0.0168(12) 0.0133(11) -0.0003(10) 0.0048(10) -0.0021(10)
377
+ C2 0.0163(12) 0.0170(13) 0.0222(13) 0.0035(10) 0.0027(10) -0.0025(9)
378
+ C3 0.0158(11) 0.0198(13) 0.0252(13) 0.0052(10) 0.0101(11) 0.0018(10)
379
+ C4 0.0191(11) 0.0145(12) 0.0168(11) 0.0012(9) 0.0091(10) -0.0002(9)
380
+ C4a 0.0138(11) 0.0128(12) 0.0136(11) 0.0021(9) 0.0045(10) -0.0010(8)
381
+ N5 0.0120(9) 0.0137(10) 0.0117(9) 0.0010(8) 0.0038(8) -0.0010(7)
382
+ C6 0.0117(10) 0.0148(11) 0.0113(10) -0.0002(9) 0.0049(9) -0.0006(8)
383
+ C6a 0.0133(11) 0.0176(12) 0.0136(11) 0.0004(9) 0.0071(9) 0.0010(9)
384
+ C7 0.0156(11) 0.0201(12) 0.0151(11) -0.0019(9) 0.0061(9) -0.0004(9)
385
+ C8 0.0177(12) 0.0162(12) 0.0217(12) 0.0009(10) 0.0085(10) -0.0028(10)
386
+ C9 0.0173(12) 0.0222(13) 0.0183(12) 0.0054(10) 0.0097(10) 0.0008(10)
387
+ C10 0.0172(12) 0.0242(13) 0.0135(11) -0.0006(10) 0.0069(10) 0.0020(10)
388
+ C10a 0.0125(10) 0.0167(11) 0.0162(11) 0.0002(9) 0.0068(9) 0.0006(9)
389
+ C11 0.0152(11) 0.0167(12) 0.0135(11) -0.0015(9) 0.0073(9) -0.0009(9)
390
+ C11a 0.0184(12) 0.0098(10) 0.0156(11) 0.0006(9) 0.0083(10) -0.0010(9)
391
+ C51 0.0168(11) 0.0142(11) 0.0121(11) -0.0020(9) 0.0074(9) 0.0004(9)
392
+ O51 0.0161(8) 0.0186(9) 0.0150(8) 0.0025(7) 0.0040(7) 0.0005(7)
393
+ C52 0.0207(12) 0.0162(12) 0.0194(12) 0.0029(10) 0.0092(10) -0.0010(10)
394
+ C61 0.0176(11) 0.0127(11) 0.0117(10) 0.0022(9) 0.0058(9) 0.0001(9)
395
+ O61 0.0176(8) 0.0213(9) 0.0150(8) -0.0065(7) 0.0062(7) -0.0045(7)
396
+ O62 0.0221(9) 0.0252(10) 0.0241(9) -0.0062(8) 0.0144(8) -0.0024(7)
397
+ C111 0.0243(12) 0.0195(13) 0.0176(12) -0.0036(11) 0.0106(10) -0.0018(11)
398
+ C112 0.0265(13) 0.0208(13) 0.0248(13) -0.0065(10) 0.0151(11) -0.0031(10)
399
+
400
+ #=========================================================================
401
+ # 10. Molecular Geometry
402
+
403
+ loop_
404
+ _geom_bond_atom_site_label_1
405
+ _geom_bond_atom_site_label_2
406
+ _geom_bond_distance
407
+ _geom_bond_site_symmetry_2
408
+ _geom_bond_publ_flag
409
+ C1 C2 1.388(4) . ?
410
+ C1 C11a 1.395(3) . ?
411
+ C1 H1 0.9500 . ?
412
+ C2 C3 1.393(4) . ?
413
+ C2 H2 0.9500 . ?
414
+ C3 C4 1.395(3) . ?
415
+ C3 H3 0.9500 . ?
416
+ C4 C4a 1.383(3) . ?
417
+ C4 H4 0.9500 . ?
418
+ C4a C11a 1.402(3) . ?
419
+ C4a N5 1.442(3) . ?
420
+ N5 C51 1.354(3) . ?
421
+ N5 C6 1.479(3) . ?
422
+ C6 C6a 1.538(3) . ?
423
+ C6 C61 1.538(3) . ?
424
+ C6 H6 1.0000 . ?
425
+ C6a C7 1.390(3) . ?
426
+ C6a C10a 1.423(3) . ?
427
+ C7 C8 1.390(3) . ?
428
+ C7 H7 0.9500 . ?
429
+ C8 C9 1.386(3) . ?
430
+ C8 H8 0.9500 . ?
431
+ C9 C10 1.386(3) . ?
432
+ C9 H9 0.9500 . ?
433
+ C10 C10a 1.401(3) . ?
434
+ C10 H10 0.9500 . ?
435
+ C10a C11 1.532(3) . ?
436
+ C11 C11a 1.533(3) . ?
437
+ C11 C111 1.536(3) . ?
438
+ C11 H11 1.0000 . ?
439
+ C51 O51 1.249(3) . ?
440
+ C51 C52 1.506(3) . ?
441
+ C52 H52A 0.9800 . ?
442
+ C52 H52B 0.9800 . ?
443
+ C52 H52C 0.9800 . ?
444
+ C61 O62 1.207(3) . ?
445
+ C61 O61 1.328(3) . ?
446
+ O61 H61 0.8602 . ?
447
+ C111 C112 1.523(4) . ?
448
+ C111 H11A 0.9900 . ?
449
+ C111 H11B 0.9900 . ?
450
+ C112 H12A 0.9800 . ?
451
+ C112 H12B 0.9800 . ?
452
+ C112 H12C 0.9800 . ?
453
+
454
+ loop_
455
+ _geom_angle_atom_site_label_1
456
+ _geom_angle_atom_site_label_2
457
+ _geom_angle_atom_site_label_3
458
+ _geom_angle
459
+ _geom_angle_site_symmetry_1
460
+ _geom_angle_site_symmetry_3
461
+ _geom_angle_publ_flag
462
+ C2 C1 C11a 120.9(2) . . ?
463
+ C2 C1 H1 119.5 . . ?
464
+ C11a C1 H1 119.5 . . ?
465
+ C1 C2 C3 120.7(2) . . ?
466
+ C1 C2 H2 119.6 . . ?
467
+ C3 C2 H2 119.6 . . ?
468
+ C2 C3 C4 119.1(2) . . ?
469
+ C2 C3 H3 120.4 . . ?
470
+ C4 C3 H3 120.4 . . ?
471
+ C4a C4 C3 119.6(2) . . ?
472
+ C4a C4 H4 120.2 . . ?
473
+ C3 C4 H4 120.2 . . ?
474
+ C4 C4a C11a 122.1(2) . . ?
475
+ C4 C4a N5 120.27(19) . . ?
476
+ C11a C4a N5 117.61(19) . . ?
477
+ C51 N5 C4a 121.36(18) . . ?
478
+ C51 N5 C6 117.57(18) . . ?
479
+ C4a N5 C6 121.06(17) . . ?
480
+ N5 C6 C6a 114.16(18) . . ?
481
+ N5 C6 C61 108.54(17) . . ?
482
+ C6a C6 C61 112.80(19) . . ?
483
+ N5 C6 H6 107.0 . . ?
484
+ C6a C6 H6 107.0 . . ?
485
+ C61 C6 H6 107.0 . . ?
486
+ C7 C6a C10a 118.7(2) . . ?
487
+ C7 C6a C6 119.6(2) . . ?
488
+ C10a C6a C6 121.6(2) . . ?
489
+ C8 C7 C6a 121.6(2) . . ?
490
+ C8 C7 H7 119.2 . . ?
491
+ C6a C7 H7 119.2 . . ?
492
+ C9 C8 C7 120.0(2) . . ?
493
+ C9 C8 H8 120.0 . . ?
494
+ C7 C8 H8 120.0 . . ?
495
+ C8 C9 C10 119.2(2) . . ?
496
+ C8 C9 H9 120.4 . . ?
497
+ C10 C9 H9 120.4 . . ?
498
+ C9 C10 C10a 122.0(2) . . ?
499
+ C9 C10 H10 119.0 . . ?
500
+ C10a C10 H10 119.0 . . ?
501
+ C10 C10a C6a 118.4(2) . . ?
502
+ C10 C10a C11 120.5(2) . . ?
503
+ C6a C10a C11 120.8(2) . . ?
504
+ C10a C11 C11a 103.51(18) . . ?
505
+ C10a C11 C111 114.78(19) . . ?
506
+ C11a C11 C111 115.41(19) . . ?
507
+ C10a C11 H11 107.6 . . ?
508
+ C11a C11 H11 107.6 . . ?
509
+ C111 C11 H11 107.6 . . ?
510
+ C1 C11a C4a 117.4(2) . . ?
511
+ C1 C11a C11 125.3(2) . . ?
512
+ C4a C11a C11 116.87(19) . . ?
513
+ O51 C51 N5 120.3(2) . . ?
514
+ O51 C51 C52 121.4(2) . . ?
515
+ N5 C51 C52 118.30(19) . . ?
516
+ C51 C52 H52A 109.5 . . ?
517
+ C51 C52 H52B 109.5 . . ?
518
+ H52A C52 H52B 109.5 . . ?
519
+ C51 C52 H52C 109.5 . . ?
520
+ H52A C52 H52C 109.5 . . ?
521
+ H52B C52 H52C 109.5 . . ?
522
+ O62 C61 O61 125.0(2) . . ?
523
+ O62 C61 C6 123.3(2) . . ?
524
+ O61 C61 C6 111.64(18) . . ?
525
+ C61 O61 H61 110.7 . . ?
526
+ C112 C111 C11 111.7(2) . . ?
527
+ C112 C111 H11A 109.3 . . ?
528
+ C11 C111 H11A 109.3 . . ?
529
+ C112 C111 H11B 109.3 . . ?
530
+ C11 C111 H11B 109.3 . . ?
531
+ H11A C111 H11B 108.0 . . ?
532
+ C111 C112 H12A 109.5 . . ?
533
+ C111 C112 H12B 109.5 . . ?
534
+ H12A C112 H12B 109.5 . . ?
535
+ C111 C112 H12C 109.5 . . ?
536
+ H12A C112 H12C 109.5 . . ?
537
+ H12B C112 H12C 109.5 . . ?
538
+
539
+ loop_
540
+ _geom_torsion_atom_site_label_1
541
+ _geom_torsion_atom_site_label_2
542
+ _geom_torsion_atom_site_label_3
543
+ _geom_torsion_atom_site_label_4
544
+ _geom_torsion
545
+ _geom_torsion_site_symmetry_1
546
+ _geom_torsion_site_symmetry_2
547
+ _geom_torsion_site_symmetry_3
548
+ _geom_torsion_site_symmetry_4
549
+ _geom_torsion_publ_flag
550
+ C11a C1 C2 C3 -1.3(4) . . . . ?
551
+ C1 C2 C3 C4 2.1(4) . . . . ?
552
+ C2 C3 C4 C4a -0.1(4) . . . . ?
553
+ C3 C4 C4a C11a -2.7(4) . . . . ?
554
+ C3 C4 C4a N5 176.0(2) . . . . ?
555
+ C4 C4a N5 C51 -70.0(3) . . . . ?
556
+ C11a C4a N5 C51 108.7(2) . . . . ?
557
+ C4 C4a N5 C6 109.3(2) . . . . ?
558
+ C11a C4a N5 C6 -72.0(3) . . . . ?
559
+ C51 N5 C6 C6a -158.55(19) . . . . ?
560
+ C4a N5 C6 C6a 22.1(3) . . . . ?
561
+ C51 N5 C6 C61 74.7(2) . . . . ?
562
+ C4a N5 C6 C61 -104.7(2) . . . . ?
563
+ N5 C6 C6a C7 -141.2(2) . . . . ?
564
+ C61 C6 C6a C7 -16.7(3) . . . . ?
565
+ N5 C6 C6a C10a 42.9(3) . . . . ?
566
+ C61 C6 C6a C10a 167.43(19) . . . . ?
567
+ C10a C6a C7 C8 2.2(3) . . . . ?
568
+ C6 C6a C7 C8 -173.8(2) . . . . ?
569
+ C6a C7 C8 C9 1.0(4) . . . . ?
570
+ C7 C8 C9 C10 -3.0(3) . . . . ?
571
+ C8 C9 C10 C10a 1.8(3) . . . . ?
572
+ C9 C10 C10a C6a 1.4(3) . . . . ?
573
+ C9 C10 C10a C11 -172.7(2) . . . . ?
574
+ C7 C6a C10a C10 -3.4(3) . . . . ?
575
+ C6 C6a C10a C10 172.6(2) . . . . ?
576
+ C7 C6a C10a C11 170.7(2) . . . . ?
577
+ C6 C6a C10a C11 -13.4(3) . . . . ?
578
+ C10 C10a C11 C11a 108.4(2) . . . . ?
579
+ C6a C10a C11 C11a -65.6(3) . . . . ?
580
+ C10 C10a C11 C111 -18.3(3) . . . . ?
581
+ C6a C10a C11 C111 167.7(2) . . . . ?
582
+ C2 C1 C11a C4a -1.4(3) . . . . ?
583
+ C2 C1 C11a C11 171.5(2) . . . . ?
584
+ C4 C4a C11a C1 3.4(3) . . . . ?
585
+ N5 C4a C11a C1 -175.3(2) . . . . ?
586
+ C4 C4a C11a C11 -170.1(2) . . . . ?
587
+ N5 C4a C11a C11 11.2(3) . . . . ?
588
+ C10a C11 C11a C1 -103.1(3) . . . . ?
589
+ C111 C11 C11a C1 23.1(4) . . . . ?
590
+ C10a C11 C11a C4a 69.8(2) . . . . ?
591
+ C111 C11 C11a C4a -163.9(2) . . . . ?
592
+ C4a N5 C51 O51 178.7(2) . . . . ?
593
+ C6 N5 C51 O51 -0.7(3) . . . . ?
594
+ C4a N5 C51 C52 -1.5(3) . . . . ?
595
+ C6 N5 C51 C52 179.1(2) . . . . ?
596
+ N5 C6 C61 O62 24.4(3) . . . . ?
597
+ C6a C6 C61 O62 -103.1(3) . . . . ?
598
+ N5 C6 C61 O61 -155.01(18) . . . . ?
599
+ C6a C6 C61 O61 77.5(2) . . . . ?
600
+ C10a C11 C111 C112 -168.0(2) . . . . ?
601
+ C11a C11 C111 C112 71.7(3) . . . . ?
602
+
603
+ loop_
604
+ _geom_hbond_atom_site_label_D
605
+ _geom_hbond_atom_site_label_H
606
+ _geom_hbond_atom_site_label_A
607
+ _geom_hbond_distance_DH
608
+ _geom_hbond_distance_HA
609
+ _geom_hbond_distance_DA
610
+ _geom_hbond_angle_DHA
611
+ _geom_hbond_site_symmetry_A
612
+ _geom_hbond_publ_flag
613
+ #
614
+ # Hydrogen bonding scheme
615
+ # ======== ======= ======
616
+ #
617
+ # D H A D-H H...A D...A D-H...A symm publ
618
+ # - - - --- ----- ----- ------- ---- ----
619
+ O61 H61 O51 0.86 1.83 2.672(2) 167 2_545 no
620
+ C2 H2 O51 0.95 2.49 3.309(3) 144 1_656 no
621
+ C112 H12A O62 0.98 2.46 3.418(4) 165 2_656 no
622
+
623
+ #======================================================================
624
+
625
+
626
+ _iucr_refine_instructions_details
627
+ ;
628
+ TITL CM45F8
629
+ CELL 0.71073 8.8053 10.9821 9.0080 90.000 118.510 90.000
630
+ ZERR 2.00 0.0003 0.0004 0.0006 0.000 0.003 0.000
631
+ LATT -1
632
+ SYMM - X, 1/2 + Y, - Z
633
+ SFAC C H N O
634
+ UNIT 38 38 2 6
635
+ MERG 4
636
+ OMIT -2.00 55.00
637
+ FMAP 2
638
+ PLAN 20
639
+ SIZE 0.10 0.14 0.26
640
+ ACTA
641
+ BOND $H
642
+ CONF
643
+ HTAB
644
+ OMIT 1 1 0
645
+ OMIT -1 1 1
646
+ LIST 4
647
+ L.S. 8
648
+ TEMP -153.00
649
+ WGHT 0.035100 0.165700
650
+ FVAR 1.39751
651
+ C1 1 0.642443 0.594154 0.793875 11.00000 0.02140 0.01683 =
652
+ 0.01327 -0.00034 0.00478 -0.00213
653
+ AFIX 43
654
+ H1 2 0.659873 0.615425 0.903129 11.00000 -1.20000
655
+ AFIX 0
656
+ C2 1 0.782781 0.559463 0.773119 11.00000 0.01629 0.01699 =
657
+ 0.02217 0.00353 0.00273 -0.00253
658
+ AFIX 43
659
+ H2 2 0.895282 0.558863 0.867841 11.00000 -1.20000
660
+ AFIX 0
661
+ C3 1 0.760432 0.525515 0.614880 11.00000 0.01584 0.01980 =
662
+ 0.02524 0.00519 0.01015 0.00176
663
+ AFIX 43
664
+ H3 2 0.856262 0.499287 0.601936 11.00000 -1.20000
665
+ AFIX 0
666
+ C4 1 0.595473 0.530554 0.475729 11.00000 0.01912 0.01446 =
667
+ 0.01678 0.00125 0.00906 -0.00022
668
+ AFIX 43
669
+ H4 2 0.577979 0.507917 0.366895 11.00000 -1.20000
670
+ AFIX 0
671
+ C4a 1 0.457563 0.568724 0.497261 11.00000 0.01382 0.01282 =
672
+ 0.01356 0.00214 0.00450 -0.00103
673
+ N5 3 0.288314 0.581975 0.353266 11.00000 0.01198 0.01373 =
674
+ 0.01166 0.00100 0.00383 -0.00105
675
+ C6 1 0.146917 0.496600 0.324411 11.00000 0.01169 0.01480 =
676
+ 0.01126 -0.00015 0.00490 -0.00064
677
+ AFIX 13
678
+ H6 2 0.038938 0.546079 0.283111 11.00000 -1.20000
679
+ AFIX 0
680
+ C6a 1 0.171355 0.429513 0.484153 11.00000 0.01329 0.01757 =
681
+ 0.01355 0.00044 0.00709 0.00104
682
+ C7 1 0.124326 0.307677 0.473724 11.00000 0.01560 0.02008 =
683
+ 0.01506 -0.00192 0.00609 -0.00038
684
+ AFIX 43
685
+ H7 2 0.088369 0.265234 0.370398 11.00000 -1.20000
686
+ AFIX 0
687
+ C8 1 0.128614 0.246451 0.610695 11.00000 0.01770 0.01619 =
688
+ 0.02174 0.00087 0.00851 -0.00276
689
+ AFIX 43
690
+ H8 2 0.097654 0.162826 0.600826 11.00000 -1.20000
691
+ AFIX 0
692
+ C9 1 0.178015 0.307296 0.761647 11.00000 0.01733 0.02220 =
693
+ 0.01834 0.00538 0.00971 0.00082
694
+ AFIX 43
695
+ H9 2 0.175933 0.267006 0.853983 11.00000 -1.20000
696
+ AFIX 0
697
+ C10 1 0.230502 0.427676 0.776204 11.00000 0.01718 0.02418 =
698
+ 0.01352 -0.00059 0.00685 0.00203
699
+ AFIX 43
700
+ H10 2 0.267411 0.468531 0.880811 11.00000 -1.20000
701
+ AFIX 0
702
+ C10a 1 0.230749 0.490913 0.641243 11.00000 0.01246 0.01667 =
703
+ 0.01623 0.00016 0.00684 0.00056
704
+ C11 1 0.309683 0.618540 0.667747 11.00000 0.01523 0.01672 =
705
+ 0.01353 -0.00154 0.00732 -0.00093
706
+ AFIX 13
707
+ H11 2 0.230748 0.669420 0.568637 11.00000 -1.20000
708
+ AFIX 0
709
+ C11a 1 0.476255 0.598216 0.656614 11.00000 0.01843 0.00976 =
710
+ 0.01565 0.00055 0.00829 -0.00105
711
+
712
+ C51 1 0.253368 0.672019 0.238787 11.00000 0.01680 0.01421 =
713
+ 0.01210 -0.00198 0.00743 0.00042
714
+ O51 4 0.106700 0.680430 0.113386 11.00000 0.01608 0.01859 =
715
+ 0.01499 0.00249 0.00402 0.00048
716
+ C52 1 0.395047 0.760869 0.267480 11.00000 0.02070 0.01620 =
717
+ 0.01940 0.00286 0.00916 -0.00096
718
+ AFIX 137
719
+ H52A 2 0.478434 0.721879 0.239710 11.00000 -1.50000
720
+ H52B 2 0.453745 0.786182 0.386198 11.00000 -1.50000
721
+ H52C 2 0.345169 0.832372 0.195207 11.00000 -1.50000
722
+ AFIX 0
723
+
724
+ C61 1 0.120819 0.409307 0.180594 11.00000 0.01761 0.01275 =
725
+ 0.01168 0.00224 0.00579 0.00012
726
+ O61 4 -0.038667 0.364738 0.102914 11.00000 0.01765 0.02128 =
727
+ 0.01495 -0.00650 0.00617 -0.00452
728
+ AFIX 3
729
+ H61 2 -0.048669 0.310674 0.029683 11.00000 -1.50000
730
+ AFIX 0
731
+ O62 4 0.232707 0.386081 0.143759 11.00000 0.02212 0.02519 =
732
+ 0.02409 -0.00624 0.01436 -0.00241
733
+
734
+ C111 1 0.332488 0.683745 0.827992 11.00000 0.02428 0.01948 =
735
+ 0.01756 -0.00357 0.01064 -0.00184
736
+ AFIX 23
737
+ H11A 2 0.224713 0.676059 0.836195 11.00000 -1.20000
738
+ H11B 2 0.426599 0.644010 0.928445 11.00000 -1.20000
739
+ AFIX 0
740
+ C112 1 0.375182 0.818096 0.827218 11.00000 0.02653 0.02084 =
741
+ 0.02483 -0.00653 0.01506 -0.00313
742
+ AFIX 137
743
+ H12A 2 0.482058 0.825982 0.819501 11.00000 -1.50000
744
+ H12B 2 0.390518 0.856476 0.931702 11.00000 -1.50000
745
+ H12C 2 0.280435 0.858256 0.729953 11.00000 -1.50000
746
+ HKLF 4
747
+
748
+ REM CM45F8
749
+ REM R1 = 0.0360 for 1638 Fo > 4sig(Fo) and 0.0455 for all 1851 data
750
+ REM 210 parameters refined using 1 restraints
751
+
752
+ END
753
+
754
+ WGHT 0.0351 0.1657
755
+ REM Highest difference peak 0.209, deepest hole -0.240, 1-sigma level 0.047
756
+ Q1 1 0.1374 0.4513 0.2451 11.00000 0.05 0.21
757
+ Q2 1 0.5006 0.7306 0.7023 11.00000 0.05 0.18
758
+ Q3 1 0.2063 0.4551 0.5588 11.00000 0.05 0.18
759
+ Q4 1 0.2180 0.5354 0.3391 11.00000 0.05 0.17
760
+ Q5 1 0.6831 0.6851 0.9667 11.00000 0.05 0.17
761
+ Q6 1 0.0732 0.0693 0.6018 11.00000 0.05 0.17
762
+ Q7 1 0.6020 0.8659 0.3678 11.00000 0.05 0.17
763
+ Q8 1 0.5105 0.9084 0.2589 11.00000 0.05 0.16
764
+ Q9 1 0.5204 0.7451 0.5750 11.00000 0.05 0.16
765
+ Q10 1 0.4683 0.5985 0.5722 11.00000 0.05 0.16
766
+ Q11 1 0.6412 0.7835 0.4017 11.00000 0.05 0.15
767
+ Q12 1 0.1569 0.5382 0.0448 11.00000 0.05 0.15
768
+ Q13 1 0.4688 0.7959 0.5012 11.00000 0.05 0.15
769
+ Q14 1 0.7544 0.4002 0.4802 11.00000 0.05 0.15
770
+ Q15 1 0.5796 0.8187 0.5697 11.00000 0.05 0.15
771
+ Q16 1 0.3044 0.2205 0.6197 11.00000 0.05 0.15
772
+ Q17 1 0.1886 0.2243 1.0318 11.00000 0.05 0.15
773
+ Q18 1 0.2287 0.7530 0.4991 11.00000 0.05 0.14
774
+ Q19 1 0.8512 0.4325 0.9053 11.00000 0.05 0.14
775
+ Q20 1 0.5138 0.7749 0.3766 11.00000 0.05 0.14
776
+ ;
777
+
778
+ # start Validation Reply Form
779
+ _vrf_PUBL005_GLOBAL
780
+ ;
781
+ PROBLEM: _publ_contact_author_email, _publ_contact_author_fax and
782
+ RESPONSE: Example CIF
783
+ ;
784
+ # end Validation Reply Form
785
+
786
+ #======================================================================
787
+ # END of CIF
788
+ #======================================================================
789
+