============ 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= 0.600 0.800 CELL 17.31400 6.89800 14.11000 90.000 126.940 90.000 1346.90998 ATOM GROUP INPUT COORDINATES AND THEIR S.U. MN01 1 0.06894 0.73632 0.22326 0.00000 0.00000 0.00000 MN01a 1 -0.06894 0.73632 0.27674 0.00000 0.00000 0.00000 C01 1 0.16145 0.74496 0.19989 0.00000 0.00000 0.00000 C01a 1 -0.16145 0.74496 0.30011 0.00000 0.00000 0.00000 O01 1 0.22114 0.75172 0.18793 0.00000 0.00000 0.00000 O01a 1 -0.22114 0.75172 0.31207 0.00000 0.00000 0.00000 C02 1 0.14901 0.61916 0.37068 0.00000 0.00000 0.00000 C03 1 0.02443 0.49571 0.15178 0.00000 0.00000 0.00000 C04 1 -0.02877 0.84373 0.07844 0.00000 0.00000 0.00000 C05 1 0.10136 0.98120 0.29166 0.00000 0.00000 0.00000 C02a 1 -0.14901 0.61916 0.12932 0.00000 0.00000 0.00000 C03a 1 -0.02443 0.49571 0.34822 0.00000 0.00000 0.00000 C04a 1 0.02877 0.84373 0.42156 0.00000 0.00000 0.00000 C05a 1 -0.10136 0.98120 0.20834 0.00000 0.00000 0.00000 O02 -1 0.19930 0.54679 0.46111 0.00000 0.00000 0.00000 O03 -1 -0.00293 0.35176 0.10241 0.00000 0.00000 0.00000 O04 -1 -0.08929 0.90554 -0.01172 0.00000 0.00000 0.00000 O05 -1 0.12107 1.13294 0.33149 0.00000 0.00000 0.00000 O02a -1 -0.19930 0.54679 0.03889 0.00000 0.00000 0.00000 O03a -1 0.00293 0.35176 0.39759 0.00000 0.00000 0.00000 O04a -1 0.08929 0.90554 0.51172 0.00000 0.00000 0.00000 O05a -1 -0.12107 1.13294 0.16851 0.00000 0.00000 0.00000 SYMMETRIZATION OF GROUP NR. 1 PRINCIPAL INERTIA MOMENTS and DEGENERATION DEGREE 1445.50 1443.89 329.58 2 ORTHOGONALIZATION MATRIX 0.918901 -6.598451 2.782299 3.015552 2.010684 9.130658 -17.024590 0.000000 10.391438 ATOM ORTHOGONAL COORDINATES VECTORS TO MAKE SYMMETRICAL THE GROUP MN01 0.00327 -0.04063 -1.45154 -0.00327 0.04063 -0.00057 MN01a 0.02537 0.03190 1.45154 -0.02537 -0.03190 0.00057 C01 -0.03375 0.04233 -3.26934 0.03375 -0.04233 -0.00045 C01a -0.05162 -0.01632 3.26934 0.05162 0.01632 0.00045 O01 -0.05678 0.12672 -4.40981 0.05678 -0.12672 -0.00219 O01a -0.11780 -0.07352 4.40981 0.11780 0.07352 0.00219 C02 1.26009 1.31130 -1.28280 0.04499 -0.00621 -0.04921 C03 1.35115 -1.31130 -1.43656 -0.04606 0.00621 0.10456 C04 -1.19818 -1.44161 -1.29296 -0.10690 0.13653 -0.03904 C05 -1.39245 1.17405 -1.29271 0.08737 0.13103 -0.03930 C02a 0.31471 -1.79117 1.28280 -0.31471 -0.05450 0.04921 C03a 1.85281 0.33499 1.43656 -0.00714 -0.33499 -0.10456 C04a -0.19065 1.86482 1.29296 0.19065 -0.01915 0.03904 C05a -1.81055 -0.19803 1.29271 -0.03511 0.19803 0.03930 O02 2.03544 2.14312 -1.19926 0.06220 -0.04548 -0.07497 O03 2.13849 -2.13402 -1.48379 -0.04085 0.03638 0.20955 O04 -1.91250 -2.32305 -1.19952 -0.18514 0.22541 -0.07471 O05 -2.26477 1.90226 -1.21437 0.16713 0.19538 -0.05987 O02a 0.49442 -2.91402 1.19926 -0.49442 -0.05249 0.07497 O03a 2.96516 0.57884 1.48379 0.00135 -0.57884 -0.20955 O04a -0.29203 2.99482 1.19952 0.29203 -0.02831 0.07471 O05a -2.94073 -0.31604 1.21437 -0.02577 0.31604 0.05987 SYMMETRIZED ORTHOGONAL COORDINATES ATOMIC R.M.S. MN01 1 0.00000 0.00000 -1.45211 0.02882 0.02882 0.00057 * MN01a 1 0.00000 0.00000 1.45211 0.02882 0.02882 0.00057 C01 1 0.00000 0.00000 -3.26978 0.03828 0.03828 0.00045 * C01a 1 0.00000 0.00000 3.26978 0.03828 0.03828 0.00045 O01 1 0.00000 0.00000 -4.41200 0.09819 0.09819 0.00219 * O01a 1 0.00000 0.00000 4.41200 0.09819 0.09819 0.00219 C02 1 1.30508 1.30508 -1.33200 0.14801 0.14801 0.06407 * C03 1 1.30508 -1.30508 -1.33200 0.14801 0.14801 0.06407 C04 1 -1.30508 -1.30508 -1.33200 0.14801 0.14801 0.06407 C05 1 -1.30508 1.30508 -1.33200 0.14801 0.14801 0.06407 C02a 1 0.00000 -1.84567 1.33200 0.20688 0.03188 0.06407 C03a 1 1.84567 0.00000 1.33200 0.03188 0.20688 0.06407 C04a 1 0.00000 1.84567 1.33200 0.20688 0.03188 0.06407 C05a 1 -1.84567 0.00000 1.33200 0.03188 0.20688 0.06407 O02 -1 2.09764 2.09764 -1.27424 # * O03 -1 2.09764 -2.09764 -1.27424 # O04 -1 -2.09764 -2.09764 -1.27424 # O05 -1 -2.09764 2.09764 -1.27424 # O02a -1 0.00000 -2.96651 1.27424 # O03a -1 2.96651 0.00000 1.27424 # O04a -1 0.00000 2.96651 1.27424 # O05a -1 -2.96651 0.00000 1.27424 # * Atom defining the asymmetric unit for the found symmetry group. # This atom was symmetrized but NOT used to find the symmetry group and to calculate CMS, RMS and so on. AVERAGE DIFFERENCE ON X,Y,Z,D 0.08011 0.08700 0.03362 0.14740 MAXIMUM DIFFERENCE ON X,Y,Z,D 0.31471 0.33499 0.10456 0.35100 DUE TO THE ATOMS C02a C03a C03 C03a Bond lengths and bond angles after symmetrization MN01 -C01 1.8177 MN01 -C02 1.8496 MN01 -C03 1.8496 MN01 -C04 1.8496 MN01 -C05 1.8496 C01 -MN01 1.8177 C01 -O01 1.1422 O01 -C01 1.1422 C02 -MN01 1.8496 C02 -O02 1.1223 C01 -MN01 -C02 93.723 C01 -MN01 -C03 93.723 C01 -MN01 -C04 93.723 C01 -MN01 -C05 93.723 C02 -MN01 -C03 89.758 C02 -MN01 -C04 172.553 C02 -MN01 -C05 89.758 C03 -MN01 -C04 89.758 C03 -MN01 -C05 172.553 C04 -MN01 -C05 89.758 MN01 -C01 -O01 180.000 MN01 -C02 -O02 179.227 SYMMETRIZED FRACTIONAL COORDINATES MN01 1 0.07099 0.73849 0.22656 0.00000 0.00000 0.00000 MN01a 1 -0.07099 0.73849 0.27344 0.00000 0.00000 0.00000 C01 1 0.15984 0.73849 0.19721 0.00000 0.00000 0.00000 C01a 1 -0.15984 0.73849 0.30279 0.00000 0.00000 0.00000 O01 1 0.21568 0.73849 0.17877 0.00000 0.00000 0.00000 O01a 1 -0.21568 0.73849 0.32123 0.00000 0.00000 0.00000 C02 1 0.15180 0.61266 0.37051 0.00000 0.00000 0.00000 C03 1 0.01892 0.50236 0.15282 0.00000 0.00000 0.00000 C04 1 -0.02157 0.86432 0.08648 0.00000 0.00000 0.00000 C05 1 0.11131 0.97462 0.30417 0.00000 0.00000 0.00000 C02a 1 -0.15907 0.66050 0.11757 0.00000 0.00000 0.00000 C03a 1 -0.03648 0.48254 0.31841 0.00000 0.00000 0.00000 C04a 1 0.02884 0.81648 0.42544 0.00000 0.00000 0.00000 C05a 1 -0.09374 0.99444 0.22460 0.00000 0.00000 0.00000 O02 -1 0.20161 0.53624 0.45769 0.00000 0.00000 0.00000 O03 -1 -0.01196 0.35896 0.10779 0.00000 0.00000 0.00000 O04 -1 -0.07703 0.94074 0.00117 0.00000 0.00000 0.00000 O05 -1 0.13654 1.11802 0.35107 0.00000 0.00000 0.00000 O02a -1 -0.21331 0.61314 0.02316 0.00000 0.00000 0.00000 O03a -1 -0.01627 0.32711 0.34596 0.00000 0.00000 0.00000 O04a -1 0.08873 0.86385 0.51799 0.00000 0.00000 0.00000 O05a -1 -0.10831 1.14987 0.19518 0.00000 0.00000 0.00000 Schoenflies symbol = D4d CSM = 3.0795 Molecular RMS = 0.1755 CSM,see: Zabrodsky et al. (1993) JACS, 115, 8278-8298 SYMMETRY GROUP MATRICES 1 CSM = 0.00 MAX. DIFF. (Angstrom)=0.0000 TYPE E 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2 CSM = 1.25 MAX. DIFF. (Angstrom)=0.1906 TYPE S8 -0.7071067812 0.7071067812 0.0000000000 -0.7071067812 -0.7071067812 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 3 CSM = 0.79 MAX. DIFF. (Angstrom)=0.1389 TYPE C2 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4 CSM = 2.60 MAX. DIFF. (Angstrom)=0.2756 TYPE Cs 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 5 CSM = 0.87 MAX. DIFF. (Angstrom)=0.1389 TYPE C4 0.0000000000 -1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 6 CSM = 1.25 MAX. DIFF. (Angstrom)=0.1906 TYPE S8 0.7071067812 -0.7071067812 0.0000000000 0.7071067812 0.7071067812 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7 CSM = 1.84 MAX. DIFF. (Angstrom)=0.1823 TYPE C2 0.7071067812 -0.7071067812 0.0000000000 -0.7071067812 -0.7071067812 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 8 CSM = 1.25 MAX. DIFF. (Angstrom)=0.1906 TYPE S8 0.7071067812 0.7071067812 0.0000000000 -0.7071067812 0.7071067812 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 9 CSM = 0.87 MAX. DIFF. (Angstrom)=0.1389 TYPE C4 0.0000000000 1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 10 CSM = 2.57 MAX. DIFF. (Angstrom)=0.3155 TYPE Cs -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 11 CSM = 1.25 MAX. DIFF. (Angstrom)=0.1906 TYPE S8 -0.7071067812 -0.7071067812 0.0000000000 0.7071067812 -0.7071067812 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 12 CSM = 2.26 MAX. DIFF. (Angstrom)=0.2355 TYPE C2 0.7071067812 0.7071067812 0.0000000000 0.7071067812 -0.7071067812 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 13 CSM = 2.69 MAX. DIFF. (Angstrom)=0.3411 TYPE Cs 0.0000000000 -1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 14 CSM = 2.61 MAX. DIFF. (Angstrom)=0.2596 TYPE C2 -0.7071067812 0.7071067812 0.0000000000 0.7071067812 0.7071067812 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 15 CSM = 2.71 MAX. DIFF. (Angstrom)=0.3358 TYPE Cs 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 16 CSM = 2.37 MAX. DIFF. (Angstrom)=0.2665 TYPE C2 -0.7071067812 -0.7071067812 0.0000000000 -0.7071067812 0.7071067812 0.0000000000 0.0000000000 0.0000000000 -1.0000000000