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|
global_
_lib_name ?
_lib_version ?
_lib_update ?
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
CXY CXY 'CYTIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE ' non-polymer 55 34 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CXY
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
CXY O2 O O 0.000 0.000 0.000 0.000
CXY C2 C CR6 0.000 0.499 0.515 -0.986
CXY N3 N NRD6 0.000 1.370 1.512 -0.835
CXY C4 C CR6 0.000 1.927 2.090 -1.891
CXY N4 N NH2 0.000 2.825 3.118 -1.723
CXY HN42 H H 0.000 3.252 3.562 -2.528
CXY HN41 H H 0.000 3.067 3.440 -0.793
CXY C5 C CR16 0.000 1.589 1.648 -3.187
CXY H5 H H 0.000 2.029 2.116 -4.059
CXY C6 C CR16 0.000 0.707 0.631 -3.323
CXY H6 H H 0.000 0.438 0.268 -4.308
CXY N1 N NR6 0.000 0.160 0.069 -2.209
CXY C1D C CH1 0.000 -0.801 -1.029 -2.344
CXY H1D H H 0.000 -1.041 -1.200 -3.403
CXY O4D O O2 0.000 -2.003 -0.739 -1.597
CXY C2D C CH1 0.000 -0.238 -2.318 -1.705
CXY H2D H H 0.000 0.512 -2.073 -0.941
CXY O2D O OH1 0.000 0.325 -3.174 -2.701
CXY H7 H H 0.000 0.616 -3.999 -2.289
CXY C3D C CH1 0.000 -1.475 -2.984 -1.055
CXY H3D H H 0.000 -1.339 -3.070 0.032
CXY O3D O OH1 0.000 -1.713 -4.269 -1.633
CXY H4 H H 0.000 -0.977 -4.859 -1.419
CXY C4D C CH1 0.000 -2.636 -2.020 -1.382
CXY H4D H H 0.000 -3.159 -2.345 -2.292
CXY C5D C CH2 0.000 -3.613 -1.941 -0.206
CXY "H5'1" H H 0.000 -3.095 -1.546 0.670
CXY "H5'2" H H 0.000 -3.995 -2.939 0.017
CXY O5D O O2 0.000 -4.699 -1.079 -0.548
CXY PA P P 0.000 -5.682 -1.042 0.727
CXY O1A O OP -0.500 -6.263 -2.389 0.942
CXY O2A O OP -0.500 -4.917 -0.635 1.930
CXY O3A O O2 0.000 -6.867 0.017 0.461
CXY PB P P 0.000 -7.477 0.402 1.900
CXY O1B O OP -0.500 -7.553 -0.813 2.748
CXY O2B O OP -0.500 -6.604 1.407 2.554
CXY "O1'" O O2 0.000 -8.953 1.017 1.709
CXY "C1'" C CH1 0.000 -9.484 1.227 3.020
CXY "H1'" H H 0.000 -9.060 0.485 3.710
CXY "O5'" O O2 0.000 -9.143 2.539 3.464
CXY "C5'" C CH2 0.000 -9.553 3.458 2.455
CXY H5D H H 0.000 -9.140 3.145 1.493
CXY H5B H H 0.000 -9.182 4.455 2.702
CXY "C4'" C CH1 0.000 -11.080 3.487 2.371
CXY "H4'" H H 0.000 -11.497 3.778 3.346
CXY "O4'" O OH1 0.000 -11.487 4.430 1.377
CXY H1 H H 0.000 -11.161 5.309 1.615
CXY "C3'" C CH1 0.000 -11.587 2.091 1.991
CXY "H3'" H H 0.000 -11.257 1.843 0.973
CXY "O3'" O OH1 0.000 -13.014 2.065 2.054
CXY H2 H H 0.000 -13.375 2.715 1.437
CXY "C2'" C CH1 0.000 -11.006 1.075 2.981
CXY "H2'" H H 0.000 -11.420 1.260 3.983
CXY "O2'" O OH1 0.000 -11.345 -0.247 2.561
CXY H3 H H 0.000 -10.978 -0.887 3.186
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
CXY O2 n/a C2 START
CXY C2 O2 N1 .
CXY N3 C2 C4 .
CXY C4 N3 C5 .
CXY N4 C4 HN41 .
CXY HN42 N4 . .
CXY HN41 N4 . .
CXY C5 C4 C6 .
CXY H5 C5 . .
CXY C6 C5 H6 .
CXY H6 C6 . .
CXY N1 C2 C1D .
CXY C1D N1 C2D .
CXY H1D C1D . .
CXY O4D C1D . .
CXY C2D C1D C3D .
CXY H2D C2D . .
CXY O2D C2D H7 .
CXY H7 O2D . .
CXY C3D C2D C4D .
CXY H3D C3D . .
CXY O3D C3D H4 .
CXY H4 O3D . .
CXY C4D C3D C5D .
CXY H4D C4D . .
CXY C5D C4D O5D .
CXY "H5'1" C5D . .
CXY "H5'2" C5D . .
CXY O5D C5D PA .
CXY PA O5D O3A .
CXY O1A PA . .
CXY O2A PA . .
CXY O3A PA PB .
CXY PB O3A "O1'" .
CXY O1B PB . .
CXY O2B PB . .
CXY "O1'" PB "C1'" .
CXY "C1'" "O1'" "O5'" .
CXY "H1'" "C1'" . .
CXY "O5'" "C1'" "C5'" .
CXY "C5'" "O5'" "C4'" .
CXY H5D "C5'" . .
CXY H5B "C5'" . .
CXY "C4'" "C5'" "C3'" .
CXY "H4'" "C4'" . .
CXY "O4'" "C4'" H1 .
CXY H1 "O4'" . .
CXY "C3'" "C4'" "C2'" .
CXY "H3'" "C3'" . .
CXY "O3'" "C3'" H2 .
CXY H2 "O3'" . .
CXY "C2'" "C3'" "O2'" .
CXY "H2'" "C2'" . .
CXY "O2'" "C2'" H3 .
CXY H3 "O2'" . END
CXY C4D O4D . ADD
CXY N1 C6 . ADD
CXY "C1'" "C2'" . ADD
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
CXY O1B PB deloc 1.510 0.020
CXY O2B PB deloc 1.510 0.020
CXY "O1'" PB single 1.610 0.020
CXY PB O3A single 1.610 0.020
CXY "C1'" "O1'" single 1.426 0.020
CXY O3A PA single 1.610 0.020
CXY O1A PA deloc 1.510 0.020
CXY O2A PA deloc 1.510 0.020
CXY PA O5D single 1.610 0.020
CXY O5D C5D single 1.426 0.020
CXY C5D C4D single 1.524 0.020
CXY "H5'1" C5D single 1.092 0.020
CXY "H5'2" C5D single 1.092 0.020
CXY C4D O4D single 1.426 0.020
CXY C4D C3D single 1.524 0.020
CXY H4D C4D single 1.099 0.020
CXY O4D C1D single 1.426 0.020
CXY O3D C3D single 1.432 0.020
CXY C3D C2D single 1.524 0.020
CXY H3D C3D single 1.099 0.020
CXY H4 O3D single 0.967 0.020
CXY O2D C2D single 1.432 0.020
CXY C2D C1D single 1.524 0.020
CXY H2D C2D single 1.099 0.020
CXY H7 O2D single 0.967 0.020
CXY C1D N1 single 1.465 0.020
CXY H1D C1D single 1.099 0.020
CXY N1 C6 single 1.337 0.020
CXY N1 C2 single 1.410 0.020
CXY C6 C5 double 1.390 0.020
CXY H6 C6 single 1.083 0.020
CXY C5 C4 single 1.390 0.020
CXY H5 C5 single 1.083 0.020
CXY C4 N3 double 1.350 0.020
CXY N4 C4 single 1.355 0.020
CXY N3 C2 single 1.350 0.020
CXY C2 O2 double 1.250 0.020
CXY HN41 N4 single 1.010 0.020
CXY HN42 N4 single 1.010 0.020
CXY "C1'" "C2'" single 1.524 0.020
CXY "O5'" "C1'" single 1.426 0.020
CXY "H1'" "C1'" single 1.099 0.020
CXY "C2'" "C3'" single 1.524 0.020
CXY "O2'" "C2'" single 1.432 0.020
CXY "H2'" "C2'" single 1.099 0.020
CXY "C3'" "C4'" single 1.524 0.020
CXY "O3'" "C3'" single 1.432 0.020
CXY "H3'" "C3'" single 1.099 0.020
CXY "C4'" "C5'" single 1.524 0.020
CXY "O4'" "C4'" single 1.432 0.020
CXY "H4'" "C4'" single 1.099 0.020
CXY "C5'" "O5'" single 1.426 0.020
CXY H5D "C5'" single 1.092 0.020
CXY H5B "C5'" single 1.092 0.020
CXY H3 "O2'" single 0.967 0.020
CXY H2 "O3'" single 0.967 0.020
CXY H1 "O4'" single 0.967 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
CXY O2 C2 N3 120.000 3.000
CXY O2 C2 N1 120.000 3.000
CXY N3 C2 N1 120.000 3.000
CXY C2 N3 C4 120.000 3.000
CXY N3 C4 N4 120.000 3.000
CXY N3 C4 C5 120.000 3.000
CXY N4 C4 C5 120.000 3.000
CXY C4 N4 HN42 120.000 3.000
CXY C4 N4 HN41 120.000 3.000
CXY HN42 N4 HN41 120.000 3.000
CXY C4 C5 H5 120.000 3.000
CXY C4 C5 C6 120.000 3.000
CXY H5 C5 C6 120.000 3.000
CXY C5 C6 H6 120.000 3.000
CXY C5 C6 N1 120.000 3.000
CXY H6 C6 N1 120.000 3.000
CXY C2 N1 C1D 120.000 3.000
CXY C2 N1 C6 120.000 3.000
CXY C1D N1 C6 120.000 3.000
CXY N1 C1D H1D 109.470 3.000
CXY N1 C1D O4D 109.470 3.000
CXY N1 C1D C2D 109.470 3.000
CXY H1D C1D O4D 109.470 3.000
CXY H1D C1D C2D 108.340 3.000
CXY O4D C1D C2D 109.470 3.000
CXY C1D O4D C4D 111.800 3.000
CXY C1D C2D H2D 108.340 3.000
CXY C1D C2D O2D 109.470 3.000
CXY C1D C2D C3D 111.000 3.000
CXY H2D C2D O2D 109.470 3.000
CXY H2D C2D C3D 108.340 3.000
CXY O2D C2D C3D 109.470 3.000
CXY C2D O2D H7 109.470 3.000
CXY C2D C3D H3D 108.340 3.000
CXY C2D C3D O3D 109.470 3.000
CXY C2D C3D C4D 111.000 3.000
CXY H3D C3D O3D 109.470 3.000
CXY H3D C3D C4D 108.340 3.000
CXY O3D C3D C4D 109.470 3.000
CXY C3D O3D H4 109.470 3.000
CXY C3D C4D H4D 108.340 3.000
CXY C3D C4D C5D 111.000 3.000
CXY C3D C4D O4D 109.470 3.000
CXY H4D C4D C5D 108.340 3.000
CXY H4D C4D O4D 109.470 3.000
CXY C5D C4D O4D 109.470 3.000
CXY C4D C5D "H5'1" 109.470 3.000
CXY C4D C5D "H5'2" 109.470 3.000
CXY C4D C5D O5D 109.470 3.000
CXY "H5'1" C5D "H5'2" 107.900 3.000
CXY "H5'1" C5D O5D 109.470 3.000
CXY "H5'2" C5D O5D 109.470 3.000
CXY C5D O5D PA 120.500 3.000
CXY O5D PA O1A 108.200 3.000
CXY O5D PA O2A 108.200 3.000
CXY O5D PA O3A 102.600 3.000
CXY O1A PA O2A 119.900 3.000
CXY O1A PA O3A 108.200 3.000
CXY O2A PA O3A 108.200 3.000
CXY PA O3A PB 120.500 3.000
CXY O3A PB O1B 108.200 3.000
CXY O3A PB O2B 108.200 3.000
CXY O3A PB "O1'" 102.600 3.000
CXY O1B PB O2B 119.900 3.000
CXY O1B PB "O1'" 108.200 3.000
CXY O2B PB "O1'" 108.200 3.000
CXY PB "O1'" "C1'" 120.500 3.000
CXY "O1'" "C1'" "H1'" 109.470 3.000
CXY "O1'" "C1'" "O5'" 109.470 3.000
CXY "O1'" "C1'" "C2'" 109.470 3.000
CXY "H1'" "C1'" "O5'" 109.470 3.000
CXY "H1'" "C1'" "C2'" 108.340 3.000
CXY "O5'" "C1'" "C2'" 109.470 3.000
CXY "C1'" "O5'" "C5'" 111.800 3.000
CXY "O5'" "C5'" H5D 109.470 3.000
CXY "O5'" "C5'" H5B 109.470 3.000
CXY "O5'" "C5'" "C4'" 109.470 3.000
CXY H5D "C5'" H5B 107.900 3.000
CXY H5D "C5'" "C4'" 109.470 3.000
CXY H5B "C5'" "C4'" 109.470 3.000
CXY "C5'" "C4'" "H4'" 108.340 3.000
CXY "C5'" "C4'" "O4'" 109.470 3.000
CXY "C5'" "C4'" "C3'" 111.000 3.000
CXY "H4'" "C4'" "O4'" 109.470 3.000
CXY "H4'" "C4'" "C3'" 108.340 3.000
CXY "O4'" "C4'" "C3'" 109.470 3.000
CXY "C4'" "O4'" H1 109.470 3.000
CXY "C4'" "C3'" "H3'" 108.340 3.000
CXY "C4'" "C3'" "O3'" 109.470 3.000
CXY "C4'" "C3'" "C2'" 111.000 3.000
CXY "H3'" "C3'" "O3'" 109.470 3.000
CXY "H3'" "C3'" "C2'" 108.340 3.000
CXY "O3'" "C3'" "C2'" 109.470 3.000
CXY "C3'" "O3'" H2 109.470 3.000
CXY "C3'" "C2'" "H2'" 108.340 3.000
CXY "C3'" "C2'" "O2'" 109.470 3.000
CXY "C3'" "C2'" "C1'" 111.000 3.000
CXY "H2'" "C2'" "O2'" 109.470 3.000
CXY "H2'" "C2'" "C1'" 108.340 3.000
CXY "O2'" "C2'" "C1'" 109.470 3.000
CXY "C2'" "O2'" H3 109.470 3.000
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
CXY CONST_1 O2 C2 N3 C4 180.000 0.000 0
CXY CONST_2 C2 N3 C4 C5 0.000 0.000 0
CXY CONST_3 N3 C4 N4 HN41 0.058 0.000 0
CXY CONST_4 N3 C4 C5 C6 0.000 0.000 0
CXY CONST_5 C4 C5 C6 N1 0.000 0.000 0
CXY CONST_6 O2 C2 N1 C1D 0.000 0.000 0
CXY CONST_7 C2 N1 C6 C5 0.000 0.000 0
CXY var_1 C2 N1 C1D C2D -63.426 20.000 1
CXY var_2 N1 C1D O4D C4D -150.000 20.000 1
CXY var_3 N1 C1D C2D C3D 150.000 20.000 3
CXY var_4 C1D C2D O2D H7 -176.156 20.000 1
CXY var_5 C1D C2D C3D C4D 0.000 20.000 3
CXY var_6 C2D C3D O3D H4 65.330 20.000 1
CXY var_7 C2D C3D C4D C5D -150.000 20.000 3
CXY var_8 C3D C4D O4D C1D 30.000 20.000 1
CXY var_9 C3D C4D C5D O5D -178.117 20.000 3
CXY var_10 C4D C5D O5D PA 179.992 20.000 1
CXY var_11 C5D O5D PA O3A 175.001 20.000 1
CXY var_12 O5D PA O3A PB -160.010 20.000 1
CXY var_13 PA O3A PB "O1'" -160.033 20.000 1
CXY var_14 O3A PB "O1'" "C1'" 174.984 20.000 1
CXY var_15 PB "O1'" "C1'" "O5'" 89.941 20.000 1
CXY var_16 "O1'" "C1'" "C2'" "C3'" -60.000 20.000 3
CXY var_17 "O1'" "C1'" "O5'" "C5'" 60.000 20.000 1
CXY var_18 "C1'" "O5'" "C5'" "C4'" 60.000 20.000 1
CXY var_19 "O5'" "C5'" "C4'" "C3'" -60.000 20.000 3
CXY var_20 "C5'" "C4'" "O4'" H1 -60.006 20.000 1
CXY var_21 "C5'" "C4'" "C3'" "C2'" 60.000 20.000 3
CXY var_22 "C4'" "C3'" "O3'" H2 60.062 20.000 1
CXY var_23 "C4'" "C3'" "C2'" "O2'" 180.000 20.000 3
CXY var_24 "C3'" "C2'" "O2'" H3 179.985 20.000 1
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
CXY chir_01 C4D C5D O4D C3D negativ
CXY chir_02 C3D C4D O3D C2D negativ
CXY chir_03 C2D C3D O2D C1D negativ
CXY chir_04 C1D O4D C2D N1 positiv
CXY chir_05 "C1'" "O1'" "C2'" "O5'" positiv
CXY chir_06 "C2'" "C1'" "C3'" "O2'" negativ
CXY chir_07 "C3'" "C2'" "C4'" "O3'" positiv
CXY chir_08 "C4'" "C3'" "C5'" "O4'" negativ
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
CXY plan-1 N1 0.020
CXY plan-1 C1D 0.020
CXY plan-1 C6 0.020
CXY plan-1 C2 0.020
CXY plan-1 C5 0.020
CXY plan-1 C4 0.020
CXY plan-1 N3 0.020
CXY plan-1 H6 0.020
CXY plan-1 H5 0.020
CXY plan-1 N4 0.020
CXY plan-1 O2 0.020
CXY plan-1 HN42 0.020
CXY plan-1 HN41 0.020
CXY plan-2 N4 0.020
CXY plan-2 C4 0.020
CXY plan-2 HN41 0.020
CXY plan-2 HN42 0.020
# ------------------------------------------------------
|
