============ SYMMOL A PROGRAM FOR THE SYMMETRIZATION OF GROUPS OF ATOMS By Tullio Pilati and Alessandra Forni Version November 4th 2002 =================================================== INDWGH=1 ===> WEIGHTS AS ATOMIC MASS INDTOL=1 ===> TOLERANCE=CONSTANT CONSTANTS OF TOLERANCE= 0.500 0.500 CELL 1.00000 1.00000 1.00000 90.000 90.000 90.000 1.00000 ATOM GROUP INPUT COORDINATES AND THEIR S.U. C4 1 -0.29432 -0.13656 -2.61425 0.00000 0.00000 0.00000 C5 1 0.31507 1.07498 -2.29616 0.00000 0.00000 0.00000 C7 1 -1.63152 -0.05253 -2.24644 0.00000 0.00000 0.00000 C3 1 0.22063 -1.32080 -2.09480 0.00000 0.00000 0.00000 C6 1 -0.67231 1.93560 -1.82640 0.00000 0.00000 0.00000 C5 1 1.57313 1.07542 -1.70175 0.00000 0.00000 0.00000 C6 1 -1.83615 1.19111 -1.65653 0.00000 0.00000 0.00000 C7 1 -1.95973 -1.21044 -1.55092 0.00000 0.00000 0.00000 C3 1 1.47891 -1.32036 -1.50028 0.00000 0.00000 0.00000 C4 1 -0.82549 -2.01048 -1.48865 0.00000 0.00000 0.00000 C4 1 2.20651 -0.13569 -1.43265 0.00000 0.00000 0.00000 C7 1 -0.45935 2.65873 -0.65668 0.00000 0.00000 0.00000 C6 1 1.83673 1.93647 -0.64092 0.00000 0.00000 0.00000 C5 1 -2.19524 1.26859 -0.31440 0.00000 0.00000 0.00000 C4 1 1.67534 -2.00961 -0.30705 0.00000 0.00000 0.00000 C6 1 -2.49138 -1.12047 -0.26804 0.00000 0.00000 0.00000 C5 1 -0.68548 -2.45487 -0.17592 0.00000 0.00000 0.00000 C7 1 2.77144 -0.05100 -0.16611 0.00000 0.00000 0.00000 C7 1 0.79746 2.65917 -0.06285 0.00000 0.00000 0.00000 C4 1 -1.38096 2.22474 0.28817 0.00000 0.00000 0.00000 C6 1 2.44496 1.19261 0.36623 0.00000 0.00000 0.00000 C5 1 -2.52378 0.10953 0.38180 0.00000 0.00000 0.00000 C5 1 0.57258 -2.45443 0.41850 0.00000 0.00000 0.00000 C7 1 2.44323 -1.20891 0.52940 0.00000 0.00000 0.00000 C6 1 -1.79031 -2.00861 0.54273 0.00000 0.00000 0.00000 C4 1 0.65303 2.22545 1.24920 0.00000 0.00000 0.00000 C3 1 -0.68547 1.90021 1.44938 0.00000 0.00000 0.00000 C5 1 1.63613 1.26992 1.49586 0.00000 0.00000 0.00000 C4 1 -2.03405 -0.07928 1.67210 0.00000 0.00000 0.00000 C6 1 0.71873 -2.00773 1.72821 0.00000 0.00000 0.00000 C6 1 1.78973 -1.11898 1.75471 0.00000 0.00000 0.00000 C7 1 -1.60917 -1.39773 1.77988 0.00000 0.00000 0.00000 C3 1 -1.01407 0.74096 2.14570 0.00000 0.00000 0.00000 C5 1 1.30759 0.11087 2.19206 0.00000 0.00000 0.00000 C7 1 -0.35236 -1.39729 2.37371 0.00000 0.00000 0.00000 C4 1 -0.00006 -0.07857 2.63313 0.00000 0.00000 0.00000 SYMMETRIZATION OF GROUP NR. 1 PRINCIPAL INERTIA MOMENTS and DEGENERATION DEGREE 2146.08 1982.83 1982.83 3 ********************** WARNING ********************** INCREASING THE TOLERANCE COULD BE USEFUL ***************************************************** Weights are changed PRINCIPAL INERTIA MOMENTS and DEGENERATION DEGREE 1911.44 1656.62 1656.62 2 ORTHOGONALIZATION MATRIX 0.000000 -0.623242 -0.782029 0.000000 0.782029 -0.623242 1.000000 0.000000 0.000000 ATOM ORTHOGONAL COORDINATES VECTORS TO MAKE SYMMETRICAL THE GROUP C4 1.77324 0.18254 -1.93955 0.00001 0.00000 0.00001 C5 1.99011 -1.00624 -1.24664 0.00001 0.00000 0.00000 C7 2.21314 1.23024 -1.14000 0.00000 0.00000 0.00001 C3 0.49202 0.49202 -2.38688 0.00001 0.00001 0.00000 C6 2.65516 -0.69293 -0.06520 0.00000 0.00000 0.00001 C5 1.00624 -1.99013 -1.24664 0.00001 0.00000 0.00000 C6 2.65516 0.69294 0.06517 0.00000 -0.00001 0.00002 C7 1.23023 2.21314 -1.14000 0.00001 0.00000 0.00001 C3 -0.49204 -0.49204 -2.38687 0.00001 0.00001 -0.00001 C4 0.18253 1.77325 -1.93954 0.00001 0.00001 0.00000 C4 -0.18256 -1.77326 -1.93954 0.00001 0.00001 0.00000 C7 2.21315 -1.23023 1.13998 -0.00001 0.00000 0.00001 C6 0.69293 -2.65516 -0.06519 0.00000 0.00000 0.00000 C5 1.99013 1.00625 1.24663 -0.00001 0.00000 0.00001 C4 -1.77327 -0.18256 -1.93953 0.00001 0.00001 -0.00001 C6 0.69293 2.65516 0.06518 0.00000 0.00000 0.00001 C5 -1.00625 1.99012 -1.24664 0.00001 0.00001 0.00000 C7 -1.23024 -2.21315 -1.13998 0.00000 0.00000 -0.00001 C7 1.23025 -2.21314 1.13999 -0.00001 -0.00001 0.00000 C4 1.77326 -0.18254 1.93953 -0.00001 -0.00001 0.00001 C6 -0.69293 -2.65516 0.06520 0.00000 0.00000 -0.00001 C5 1.00625 1.99013 1.24663 -0.00001 -0.00001 0.00001 C5 -1.99013 1.00623 -1.24663 0.00001 0.00001 -0.00001 C7 -2.21315 -1.23024 -1.13998 0.00001 0.00001 -0.00001 C6 -0.69294 2.65516 -0.06520 0.00001 0.00000 0.00001 C4 0.18255 -1.77325 1.93955 -0.00001 -0.00001 -0.00001 C3 0.49203 -0.49202 2.38688 -0.00001 -0.00001 0.00000 C5 -1.00624 -1.99012 1.24665 -0.00001 0.00000 -0.00001 C4 -0.18254 1.77326 1.93953 -0.00001 -0.00001 0.00001 C6 -2.65516 0.69293 -0.06518 0.00000 0.00001 -0.00001 C6 -2.65516 -0.69293 0.06520 0.00000 0.00000 -0.00001 C7 -1.23024 2.21315 1.13998 0.00000 0.00000 0.00000 C3 -0.49201 0.49203 2.38688 -0.00001 -0.00001 0.00000 C5 -1.99011 -1.00624 1.24665 -0.00001 0.00000 -0.00001 C7 -2.21314 1.23024 1.14000 0.00000 0.00000 -0.00001 C4 -1.77324 0.18255 1.93955 -0.00001 -0.00001 -0.00001 SYMMETRIZED ORTHOGONAL COORDINATES ATOMIC R.M.S. C4 1 1.77325 0.18255 -1.93954 0.00001 0.00001 0.00001 * C5 1 1.99012 -1.00624 -1.24664 0.00001 0.00001 0.00001 * C7 1 2.21315 1.23024 -1.13999 0.00000 0.00001 0.00001 * C3 1 0.49203 0.49203 -2.38688 0.00001 0.00001 0.00000 * C6 1 2.65516 -0.69293 -0.06519 0.00000 0.00000 0.00001 * C5 1 1.00624 -1.99012 -1.24664 0.00001 0.00001 0.00001 C6 1 2.65516 0.69293 0.06519 0.00000 0.00000 0.00001 C7 1 1.23024 2.21315 -1.13999 0.00001 0.00000 0.00001 C3 1 -0.49203 -0.49203 -2.38688 0.00001 0.00001 0.00000 C4 1 0.18255 1.77325 -1.93954 0.00001 0.00001 0.00001 C4 1 -0.18255 -1.77325 -1.93954 0.00001 0.00001 0.00001 C7 1 2.21315 -1.23024 1.13999 0.00000 0.00001 0.00001 C6 1 0.69293 -2.65516 -0.06519 0.00000 0.00000 0.00001 C5 1 1.99012 1.00624 1.24664 0.00001 0.00001 0.00001 C4 1 -1.77325 -0.18255 -1.93954 0.00001 0.00001 0.00001 C6 1 0.69293 2.65516 0.06519 0.00000 0.00000 0.00001 C5 1 -1.00624 1.99012 -1.24664 0.00001 0.00001 0.00001 C7 1 -1.23024 -2.21315 -1.13999 0.00001 0.00000 0.00001 C7 1 1.23024 -2.21315 1.13999 0.00001 0.00000 0.00001 C4 1 1.77325 -0.18255 1.93954 0.00001 0.00001 0.00001 C6 1 -0.69293 -2.65516 0.06519 0.00000 0.00000 0.00001 C5 1 1.00624 1.99012 1.24664 0.00001 0.00001 0.00001 C5 1 -1.99012 1.00624 -1.24664 0.00001 0.00001 0.00001 C7 1 -2.21315 -1.23024 -1.13999 0.00000 0.00001 0.00001 C6 1 -0.69293 2.65516 -0.06519 0.00000 0.00000 0.00001 C4 1 0.18255 -1.77325 1.93954 0.00001 0.00001 0.00001 C3 1 0.49203 -0.49203 2.38688 0.00001 0.00001 0.00000 C5 1 -1.00624 -1.99012 1.24664 0.00001 0.00001 0.00001 C4 1 -0.18255 1.77325 1.93954 0.00001 0.00001 0.00001 C6 1 -2.65516 0.69293 -0.06519 0.00000 0.00000 0.00001 C6 1 -2.65516 -0.69293 0.06519 0.00000 0.00000 0.00001 C7 1 -1.23024 2.21315 1.13999 0.00001 0.00000 0.00001 C3 1 -0.49203 0.49203 2.38688 0.00001 0.00001 0.00000 C5 1 -1.99012 -1.00624 1.24664 0.00001 0.00001 0.00001 C7 1 -2.21315 1.23024 1.13999 0.00000 0.00001 0.00001 C4 1 -1.77325 0.18255 1.93954 0.00001 0.00001 0.00001 * Atom defining the asymmetric unit for the found symmetry group. AVERAGE DIFFERENCE ON X,Y,Z,D 0.00001 0.00000 0.00001 0.00001 MAXIMUM DIFFERENCE ON X,Y,Z,D 0.00001 0.00001 0.00002 0.00002 DUE TO THE ATOMS C4 C3 C6 C6 Bond lengths and bond angles after symmetrization C4 -C5 1.3930 C4 -C7 1.3894 C4 -C3 1.3919 C5 -C4 1.3930 C5 -C6 1.3915 C5 -C5 1.3914 C7 -C4 1.3894 C7 -C6 1.3916 C7 -C7 1.3900 C3 -C4 1.3919 C3 -C3 1.3917 C3 -C4 1.3919 C6 -C5 1.3915 C6 -C6 1.3920 C6 -C7 1.3916 C5 -C4 -C7 107.938 C5 -C4 -C3 119.533 C7 -C4 -C3 107.982 C4 -C5 -C6 107.734 C4 -C5 -C5 119.562 C6 -C5 -C5 119.812 C4 -C7 -C6 107.926 C4 -C7 -C7 108.019 C6 -C7 -C7 119.843 C4 -C3 -C3 119.581 C4 -C3 -C4 107.820 C3 -C3 -C4 119.581 C5 -C6 -C6 107.680 C5 -C6 -C7 119.774 C6 -C6 -C7 107.655 Schoenflies symbol = D2d CSM = 0.0000 Molecular RMS = 0.0000 CSM,see: Zabrodsky et al. (1993) JACS, 115, 8278-8298 Symmetry element its CSM and Max.Diff. Symmetry element its CSM and Max.Diff. 1) [E ] x,y,z 0.0000 0.0000 2) [S4 ] y,-x,-z 0.0000 0.0000 3) [C2 ] -x,-y,z 0.0000 0.0000 4) [Cs ] y,x,z 0.0000 0.0000 5) [C2 ] -x,y,-z 0.0000 0.0000 6) [C2 ] x,-y,-z 0.0000 0.0000 7) [S4 ] -y,x,-z 0.0000 0.0000 8) [Cs ] -y,-x,z 0.0000 0.0000