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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
APU APU 'ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MO' non-polymer 65 43 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_APU
#
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
APU O3X O OP -0.666 0.000 0.000 0.000
APU PU P P 0.000 -0.777 1.154 -0.596
APU O1X O OP -0.666 -1.812 0.620 -1.561
APU O2X O OP -0.666 0.173 2.073 -1.333
APU O3D O O2 0.000 -1.511 1.970 0.581
APU C3D C CH1 0.000 -2.389 1.052 1.235
APU H3D H H 0.000 -2.339 0.065 0.756
APU C2D C CH1 0.000 -2.034 0.942 2.740
APU H2D H H 0.000 -2.178 -0.085 3.102
APU O2D O OH1 0.000 -0.697 1.386 2.983
APU "HO2'" H H 0.000 -0.530 1.397 3.935
APU C4D C CH1 0.000 -3.836 1.581 1.230
APU H4D H H 0.000 -3.873 2.564 0.740
APU O4D O O2 0.000 -4.255 1.702 2.599
APU C1D C CH1 0.000 -3.062 1.904 3.388
APU H1D H H 0.000 -2.719 2.945 3.311
APU N1U N NR6 0.000 -3.302 1.543 4.787
APU C6U C CR16 0.000 -3.118 2.477 5.769
APU H6U H H 0.000 -2.795 3.479 5.514
APU C5U C CR16 0.000 -3.339 2.143 7.059
APU H5U H H 0.000 -3.196 2.873 7.847
APU C4U C CR6 0.000 -3.761 0.829 7.368
APU O4U O O 0.000 -3.967 0.505 8.524
APU N3U N NR16 0.000 -3.931 -0.063 6.371
APU H3U H H 0.000 -4.236 -1.033 6.589
APU C2U C CR6 0.000 -3.707 0.297 5.093
APU O2U O O 0.000 -3.865 -0.517 4.205
APU C5D C CH2 0.000 -4.748 0.597 0.494
APU H51U H H 0.000 -4.714 -0.373 0.994
APU H52U H H 0.000 -4.404 0.485 -0.537
APU O5D O O2 0.000 -6.087 1.092 0.500
APU PA P P 0.000 -6.986 0.013 -0.287
APU O1A O OP -0.500 -6.484 -0.128 -1.676
APU O2A O OP -0.500 -6.905 -1.296 0.405
APU O3B O O2 0.000 -8.517 0.511 -0.318
APU C3B C CH1 0.000 -9.259 -0.483 -1.027
APU H3B H H 0.000 -8.602 -1.309 -1.333
APU C4B C CH1 0.000 -9.958 0.136 -2.257
APU H4B H H 0.000 -10.103 1.216 -2.110
APU C5B C CH2 0.000 -9.139 -0.122 -3.524
APU H51A H H 0.000 -8.990 -1.197 -3.647
APU H52A H H 0.000 -8.169 0.371 -3.437
APU O5B O OH1 0.000 -9.839 0.397 -4.657
APU HO5A H H 0.000 -9.321 0.233 -5.457
APU C2B C CH1 0.000 -10.426 -1.011 -0.158
APU H2B H H 0.000 -10.349 -2.100 -0.032
APU O2B O OH1 0.000 -10.437 -0.360 1.113
APU HO2A H H 0.000 -11.171 -0.701 1.642
APU C1B C CH1 0.000 -11.689 -0.649 -0.970
APU H1B H H 0.000 -12.103 0.309 -0.625
APU O4B O O2 0.000 -11.233 -0.536 -2.336
APU N9A N NR5 0.000 -12.692 -1.709 -0.853
APU C4A C CR56 0.000 -13.694 -1.782 0.081
APU C5A C CR56 0.000 -14.397 -2.966 -0.194
APU N7A N NRD5 0.000 -13.804 -3.542 -1.267
APU C8A C CR15 0.000 -12.802 -2.807 -1.654
APU H8A H H 0.000 -12.151 -3.034 -2.489
APU N3A N NRD6 0.000 -14.083 -1.020 1.098
APU C2A C CR16 0.000 -15.116 -1.365 1.837
APU H2A H H 0.000 -15.408 -0.722 2.659
APU N1A N NRD6 0.000 -15.811 -2.466 1.614
APU C6A C CR6 0.000 -15.496 -3.288 0.620
APU N6A N NH2 0.000 -16.229 -4.440 0.394
APU H62A H H 0.000 -15.985 -5.066 -0.368
APU H61A H H 0.000 -17.020 -4.672 0.987
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
APU O3X n/a PU START
APU PU O3X O3D .
APU O1X PU . .
APU O2X PU . .
APU O3D PU C3D .
APU C3D O3D C4D .
APU H3D C3D . .
APU C2D C3D O2D .
APU H2D C2D . .
APU O2D C2D "HO2'" .
APU "HO2'" O2D . .
APU C4D C3D C5D .
APU H4D C4D . .
APU O4D C4D C1D .
APU C1D O4D N1U .
APU H1D C1D . .
APU N1U C1D C6U .
APU C6U N1U C5U .
APU H6U C6U . .
APU C5U C6U C4U .
APU H5U C5U . .
APU C4U C5U N3U .
APU O4U C4U . .
APU N3U C4U C2U .
APU H3U N3U . .
APU C2U N3U O2U .
APU O2U C2U . .
APU C5D C4D O5D .
APU H51U C5D . .
APU H52U C5D . .
APU O5D C5D PA .
APU PA O5D O3B .
APU O1A PA . .
APU O2A PA . .
APU O3B PA C3B .
APU C3B O3B C2B .
APU H3B C3B . .
APU C4B C3B C5B .
APU H4B C4B . .
APU C5B C4B O5B .
APU H51A C5B . .
APU H52A C5B . .
APU O5B C5B HO5A .
APU HO5A O5B . .
APU C2B C3B C1B .
APU H2B C2B . .
APU O2B C2B HO2A .
APU HO2A O2B . .
APU C1B C2B N9A .
APU H1B C1B . .
APU O4B C1B . .
APU N9A C1B C4A .
APU C4A N9A N3A .
APU C5A C4A N7A .
APU N7A C5A C8A .
APU C8A N7A H8A .
APU H8A C8A . .
APU N3A C4A C2A .
APU C2A N3A N1A .
APU H2A C2A . .
APU N1A C2A C6A .
APU C6A N1A N6A .
APU N6A C6A H61A .
APU H62A N6A . .
APU H61A N6A . END
APU C4B O4B . ADD
APU N9A C8A . ADD
APU C5A C6A . ADD
APU N1U C2U . ADD
APU C1D C2D . 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
APU O1A PA deloc 1.510 0.020
APU O2A PA deloc 1.510 0.020
APU O3B PA single 1.610 0.020
APU PA O5D single 1.610 0.020
APU O5B C5B single 1.432 0.020
APU HO5A O5B single 0.967 0.020
APU C5B C4B single 1.524 0.020
APU H51A C5B single 1.092 0.020
APU H52A C5B single 1.092 0.020
APU C4B O4B single 1.426 0.020
APU C4B C3B single 1.524 0.020
APU H4B C4B single 1.099 0.020
APU O4B C1B single 1.426 0.020
APU C3B O3B single 1.426 0.020
APU C2B C3B single 1.524 0.020
APU H3B C3B single 1.099 0.020
APU O2B C2B single 1.432 0.020
APU C1B C2B single 1.524 0.020
APU H2B C2B single 1.099 0.020
APU HO2A O2B single 0.967 0.020
APU N9A C1B single 1.485 0.020
APU H1B C1B single 1.099 0.020
APU N9A C8A single 1.337 0.020
APU C4A N9A single 1.337 0.020
APU C8A N7A double 1.350 0.020
APU H8A C8A single 1.083 0.020
APU N7A C5A single 1.350 0.020
APU C5A C6A single 1.490 0.020
APU C5A C4A double 1.490 0.020
APU N6A C6A single 1.355 0.020
APU C6A N1A double 1.350 0.020
APU H61A N6A single 1.010 0.020
APU H62A N6A single 1.010 0.020
APU N1A C2A single 1.337 0.020
APU C2A N3A double 1.337 0.020
APU H2A C2A single 1.083 0.020
APU N3A C4A single 1.355 0.020
APU N1U C2U single 1.410 0.020
APU C6U N1U single 1.337 0.020
APU N1U C1D single 1.465 0.020
APU O2U C2U double 1.250 0.020
APU C2U N3U single 1.337 0.020
APU N3U C4U single 1.337 0.020
APU H3U N3U single 1.040 0.020
APU O4U C4U double 1.250 0.020
APU C4U C5U single 1.390 0.020
APU C5U C6U double 1.390 0.020
APU H5U C5U single 1.083 0.020
APU H6U C6U single 1.083 0.020
APU C1D C2D single 1.524 0.020
APU C1D O4D single 1.426 0.020
APU H1D C1D single 1.099 0.020
APU O2D C2D single 1.432 0.020
APU C2D C3D single 1.524 0.020
APU H2D C2D single 1.099 0.020
APU "HO2'" O2D single 0.967 0.020
APU C3D O3D single 1.426 0.020
APU C4D C3D single 1.524 0.020
APU H3D C3D single 1.099 0.020
APU O3D PU single 1.610 0.020
APU O4D C4D single 1.426 0.020
APU C5D C4D single 1.524 0.020
APU H4D C4D single 1.099 0.020
APU O5D C5D single 1.426 0.020
APU H51U C5D single 1.092 0.020
APU H52U C5D single 1.092 0.020
APU O1X PU deloc 1.510 0.020
APU O2X PU deloc 1.510 0.020
APU PU O3X deloc 1.510 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
APU O3X PU O1X 119.900 3.000
APU O3X PU O2X 119.900 3.000
APU O3X PU O3D 108.200 3.000
APU O1X PU O2X 119.900 3.000
APU O1X PU O3D 108.200 3.000
APU O2X PU O3D 108.200 3.000
APU PU O3D C3D 120.500 3.000
APU O3D C3D H3D 109.470 3.000
APU O3D C3D C2D 109.470 3.000
APU O3D C3D C4D 109.470 3.000
APU H3D C3D C2D 108.340 3.000
APU H3D C3D C4D 108.340 3.000
APU C2D C3D C4D 111.000 3.000
APU C3D C2D H2D 108.340 3.000
APU C3D C2D O2D 109.470 3.000
APU C3D C2D C1D 111.000 3.000
APU H2D C2D O2D 109.470 3.000
APU H2D C2D C1D 108.340 3.000
APU O2D C2D C1D 109.470 3.000
APU C2D O2D "HO2'" 109.470 3.000
APU C3D C4D H4D 108.340 3.000
APU C3D C4D O4D 109.470 3.000
APU C3D C4D C5D 111.000 3.000
APU H4D C4D O4D 109.470 3.000
APU H4D C4D C5D 108.340 3.000
APU O4D C4D C5D 109.470 3.000
APU C4D O4D C1D 111.800 3.000
APU O4D C1D H1D 109.470 3.000
APU O4D C1D N1U 109.470 3.000
APU O4D C1D C2D 109.470 3.000
APU H1D C1D N1U 109.470 3.000
APU H1D C1D C2D 108.340 3.000
APU N1U C1D C2D 109.470 3.000
APU C1D N1U C6U 120.000 3.000
APU C1D N1U C2U 120.000 3.000
APU C6U N1U C2U 120.000 3.000
APU N1U C6U H6U 120.000 3.000
APU N1U C6U C5U 120.000 3.000
APU H6U C6U C5U 120.000 3.000
APU C6U C5U H5U 120.000 3.000
APU C6U C5U C4U 120.000 3.000
APU H5U C5U C4U 120.000 3.000
APU C5U C4U O4U 120.000 3.000
APU C5U C4U N3U 120.000 3.000
APU O4U C4U N3U 120.000 3.000
APU C4U N3U H3U 120.000 3.000
APU C4U N3U C2U 120.000 3.000
APU H3U N3U C2U 120.000 3.000
APU N3U C2U O2U 120.000 3.000
APU N3U C2U N1U 120.000 3.000
APU O2U C2U N1U 120.000 3.000
APU C4D C5D H51U 109.470 3.000
APU C4D C5D H52U 109.470 3.000
APU C4D C5D O5D 109.470 3.000
APU H51U C5D H52U 107.900 3.000
APU H51U C5D O5D 109.470 3.000
APU H52U C5D O5D 109.470 3.000
APU C5D O5D PA 120.500 3.000
APU O5D PA O1A 108.200 3.000
APU O5D PA O2A 108.200 3.000
APU O5D PA O3B 102.600 3.000
APU O1A PA O2A 119.900 3.000
APU O1A PA O3B 108.200 3.000
APU O2A PA O3B 108.200 3.000
APU PA O3B C3B 120.500 3.000
APU O3B C3B H3B 109.470 3.000
APU O3B C3B C4B 109.470 3.000
APU O3B C3B C2B 109.470 3.000
APU H3B C3B C4B 108.340 3.000
APU H3B C3B C2B 108.340 3.000
APU C4B C3B C2B 111.000 3.000
APU C3B C4B H4B 108.340 3.000
APU C3B C4B C5B 111.000 3.000
APU C3B C4B O4B 109.470 3.000
APU H4B C4B C5B 108.340 3.000
APU H4B C4B O4B 109.470 3.000
APU C5B C4B O4B 109.470 3.000
APU C4B C5B H51A 109.470 3.000
APU C4B C5B H52A 109.470 3.000
APU C4B C5B O5B 109.470 3.000
APU H51A C5B H52A 107.900 3.000
APU H51A C5B O5B 109.470 3.000
APU H52A C5B O5B 109.470 3.000
APU C5B O5B HO5A 109.470 3.000
APU C3B C2B H2B 108.340 3.000
APU C3B C2B O2B 109.470 3.000
APU C3B C2B C1B 111.000 3.000
APU H2B C2B O2B 109.470 3.000
APU H2B C2B C1B 108.340 3.000
APU O2B C2B C1B 109.470 3.000
APU C2B O2B HO2A 109.470 3.000
APU C2B C1B H1B 108.340 3.000
APU C2B C1B O4B 109.470 3.000
APU C2B C1B N9A 109.470 3.000
APU H1B C1B O4B 109.470 3.000
APU H1B C1B N9A 109.470 3.000
APU O4B C1B N9A 109.470 3.000
APU C1B O4B C4B 111.800 3.000
APU C1B N9A C4A 126.000 3.000
APU C1B N9A C8A 126.000 3.000
APU C4A N9A C8A 108.000 3.000
APU N9A C4A C5A 108.000 3.000
APU N9A C4A N3A 132.000 3.000
APU C5A C4A N3A 120.000 3.000
APU C4A C5A N7A 108.000 3.000
APU C4A C5A C6A 120.000 3.000
APU N7A C5A C6A 132.000 3.000
APU C5A N7A C8A 108.000 3.000
APU N7A C8A H8A 126.000 3.000
APU N7A C8A N9A 108.000 3.000
APU H8A C8A N9A 126.000 3.000
APU C4A N3A C2A 120.000 3.000
APU N3A C2A H2A 120.000 3.000
APU N3A C2A N1A 120.000 3.000
APU H2A C2A N1A 120.000 3.000
APU C2A N1A C6A 120.000 3.000
APU N1A C6A N6A 120.000 3.000
APU N1A C6A C5A 120.000 3.000
APU N6A C6A C5A 120.000 3.000
APU C6A N6A H62A 120.000 3.000
APU C6A N6A H61A 120.000 3.000
APU H62A N6A H61A 120.000 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
APU var_1 O3X PU O3D C3D -60.011 20.000 1
APU var_2 PU O3D C3D C4D -123.785 20.000 1
APU var_3 O3D C3D C2D O2D -30.000 20.000 3
APU var_4 C3D C2D O2D "HO2'" 174.115 20.000 1
APU var_5 O3D C3D C4D C5D 120.000 20.000 3
APU var_6 C3D C4D O4D C1D 30.000 20.000 1
APU var_7 C4D O4D C1D N1U -150.000 20.000 1
APU var_8 O4D C1D C2D C3D 30.000 20.000 3
APU var_9 O4D C1D N1U C6U -121.474 20.000 1
APU CONST_1 C1D N1U C2U N3U 180.000 0.000 0
APU CONST_2 C1D N1U C6U C5U 180.000 0.000 0
APU CONST_3 N1U C6U C5U C4U 0.000 0.000 0
APU CONST_4 C6U C5U C4U N3U 0.000 0.000 0
APU CONST_5 C5U C4U N3U C2U 0.000 0.000 0
APU CONST_6 C4U N3U C2U O2U 180.000 0.000 0
APU var_10 C3D C4D C5D O5D 179.713 20.000 3
APU var_11 C4D C5D O5D PA 179.974 20.000 1
APU var_12 C5D O5D PA O3B 179.962 20.000 1
APU var_13 O5D PA O3B C3B 179.967 20.000 1
APU var_14 PA O3B C3B C2B 123.887 20.000 1
APU var_15 O3B C3B C4B C5B 90.000 20.000 3
APU var_16 C3B C4B O4B C1B 30.000 20.000 1
APU var_17 C3B C4B C5B O5B 176.914 20.000 3
APU var_18 C4B C5B O5B HO5A -179.994 20.000 1
APU var_19 O3B C3B C2B C1B 120.000 20.000 3
APU var_20 C3B C2B O2B HO2A 179.974 20.000 1
APU var_21 C3B C2B C1B N9A 150.000 20.000 3
APU var_22 C2B C1B O4B C4B -30.000 20.000 1
APU var_23 C2B C1B N9A C4A 91.488 20.000 1
APU CONST_7 C1B N9A C8A N7A 180.000 0.000 0
APU CONST_8 C1B N9A C4A N3A 0.000 0.000 0
APU CONST_9 N9A C4A C5A N7A 0.000 0.000 0
APU CONST_10 C4A C5A C6A N1A 0.000 0.000 0
APU CONST_11 C4A C5A N7A C8A 0.000 0.000 0
APU CONST_12 C5A N7A C8A N9A 0.000 0.000 0
APU CONST_13 N9A C4A N3A C2A 180.000 0.000 0
APU CONST_14 C4A N3A C2A N1A 0.000 0.000 0
APU CONST_15 N3A C2A N1A C6A 0.000 0.000 0
APU CONST_16 C2A N1A C6A N6A 180.000 0.000 0
APU CONST_17 N1A C6A N6A H61A -0.030 0.000 0
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
APU chir_01 C4B C5B O4B C3B negativ
APU chir_02 C3B C4B O3B C2B negativ
APU chir_03 C2B C3B O2B C1B negativ
APU chir_04 C1B O4B C2B N9A positiv
APU chir_05 C1D N1U C2D O4D negativ
APU chir_06 C2D C1D O2D C3D positiv
APU chir_07 C3D C2D O3D C4D positiv
APU chir_08 C4D C3D O4D C5D positiv
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
APU plan-1 N9A 0.020
APU plan-1 C1B 0.020
APU plan-1 C8A 0.020
APU plan-1 C4A 0.020
APU plan-1 N7A 0.020
APU plan-1 H8A 0.020
APU plan-1 C5A 0.020
APU plan-1 C6A 0.020
APU plan-1 N1A 0.020
APU plan-1 C2A 0.020
APU plan-1 N3A 0.020
APU plan-1 N6A 0.020
APU plan-1 H2A 0.020
APU plan-1 H62A 0.020
APU plan-1 H61A 0.020
APU plan-2 N6A 0.020
APU plan-2 C6A 0.020
APU plan-2 H61A 0.020
APU plan-2 H62A 0.020
APU plan-3 N1U 0.020
APU plan-3 C2U 0.020
APU plan-3 C6U 0.020
APU plan-3 C1D 0.020
APU plan-3 N3U 0.020
APU plan-3 C4U 0.020
APU plan-3 C5U 0.020
APU plan-3 O2U 0.020
APU plan-3 H3U 0.020
APU plan-3 O4U 0.020
APU plan-3 H5U 0.020
APU plan-3 H6U 0.020
# ------------------------------------------------------
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