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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
GUD GUD 'GLUCOSE-URIDINE-C1,5'-DIPHOSPHATE ' non-polymer 58 36 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_GUD
#
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
GUD O2B O OP -0.500 0.000 0.000 0.000
GUD PB P P 0.000 -0.668 -1.043 -0.815
GUD O1B O OP -0.500 -0.653 -0.639 -2.242
GUD O3B O O2 0.000 0.114 -2.439 -0.644
GUD "C1'" C CH1 0.000 1.452 -2.223 -1.096
GUD "H1'" H H 0.000 1.453 -1.447 -1.875
GUD "O5'" O O2 0.000 2.258 -1.795 0.000
GUD "C5'" C CH1 0.000 2.086 -2.738 1.055
GUD "H5'" H H 0.000 1.014 -2.871 1.256
GUD "C6'" C CH2 0.000 2.780 -2.221 2.317
GUD "H6'1" H H 0.000 3.846 -2.091 2.117
GUD "H6'2" H H 0.000 2.648 -2.943 3.126
GUD "O6'" O OH1 0.000 2.207 -0.968 2.696
GUD "HO6'" H H 0.000 2.646 -0.641 3.493
GUD "C4'" C CH1 0.000 2.698 -4.082 0.653
GUD "H4'" H H 0.000 3.765 -3.948 0.427
GUD "O4'" O OH1 0.000 2.548 -5.015 1.725
GUD "HO4'" H H 0.000 2.928 -5.866 1.466
GUD "C3'" C CH1 0.000 1.972 -4.608 -0.591
GUD "H3'" H H 0.000 0.928 -4.841 -0.338
GUD "O3'" O OH1 0.000 2.626 -5.786 -1.068
GUD HO3A H H 0.000 2.172 -6.108 -1.859
GUD "C2'" C CH1 0.000 2.010 -3.525 -1.674
GUD "H2'" H H 0.000 3.048 -3.367 -2.000
GUD "O2'" O OH1 0.000 1.215 -3.933 -2.788
GUD HO2A H H 0.000 1.236 -3.245 -3.467
GUD O3A O O2 0.000 -2.191 -1.215 -0.323
GUD PA P P 0.000 -2.909 0.212 -0.521
GUD O1A O OP -0.500 -2.860 0.595 -1.953
GUD O2A O OP -0.500 -2.206 1.235 0.290
GUD O5D O O2 0.000 -4.443 0.111 -0.046
GUD C5D C CH2 0.000 -5.023 1.401 -0.246
GUD "H5'1" H H 0.000 -4.960 1.667 -1.303
GUD "H5'2" H H 0.000 -4.479 2.139 0.347
GUD C4D C CH1 0.000 -6.490 1.375 0.189
GUD H4D H H 0.000 -7.039 0.625 -0.397
GUD C3D C CH1 0.000 -7.122 2.764 -0.015
GUD H3D H H 0.000 -6.370 3.479 -0.377
GUD O3D O OH1 0.000 -8.222 2.693 -0.924
GUD "HO3'" H H 0.000 -8.641 3.562 -0.991
GUD C2D C CH1 0.000 -7.614 3.165 1.401
GUD H2D H H 0.000 -6.881 3.816 1.900
GUD O2D O OH1 0.000 -8.894 3.797 1.336
GUD "HO2'" H H 0.000 -8.809 4.650 0.888
GUD O4D O O2 0.000 -6.579 1.062 1.589
GUD C1D C CH1 0.000 -7.709 1.793 2.113
GUD H1D H H 0.000 -8.650 1.287 1.854
GUD N1 N NR6 0.000 -7.593 1.952 3.564
GUD C6 C CR16 0.000 -8.577 1.464 4.379
GUD H6 H H 0.000 -9.438 0.963 3.954
GUD C5 C CR16 0.000 -8.470 1.609 5.717
GUD H5 H H 0.000 -9.241 1.227 6.374
GUD C4 C CR6 0.000 -7.336 2.268 6.250
GUD O4 O O 0.000 -7.216 2.411 7.454
GUD N3 N NR16 0.000 -6.388 2.734 5.412
GUD HN3 H H 0.000 -5.553 3.222 5.795
GUD C2 C CR6 0.000 -6.518 2.570 4.083
GUD O2 O O 0.000 -5.656 2.996 3.339
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
GUD O2B n/a PB START
GUD PB O2B O3A .
GUD O1B PB . .
GUD O3B PB "C1'" .
GUD "C1'" O3B "O5'" .
GUD "H1'" "C1'" . .
GUD "O5'" "C1'" "C5'" .
GUD "C5'" "O5'" "C4'" .
GUD "H5'" "C5'" . .
GUD "C6'" "C5'" "O6'" .
GUD "H6'1" "C6'" . .
GUD "H6'2" "C6'" . .
GUD "O6'" "C6'" "HO6'" .
GUD "HO6'" "O6'" . .
GUD "C4'" "C5'" "C3'" .
GUD "H4'" "C4'" . .
GUD "O4'" "C4'" "HO4'" .
GUD "HO4'" "O4'" . .
GUD "C3'" "C4'" "C2'" .
GUD "H3'" "C3'" . .
GUD "O3'" "C3'" HO3A .
GUD HO3A "O3'" . .
GUD "C2'" "C3'" "O2'" .
GUD "H2'" "C2'" . .
GUD "O2'" "C2'" HO2A .
GUD HO2A "O2'" . .
GUD O3A PB PA .
GUD PA O3A O5D .
GUD O1A PA . .
GUD O2A PA . .
GUD O5D PA C5D .
GUD C5D O5D C4D .
GUD "H5'1" C5D . .
GUD "H5'2" C5D . .
GUD C4D C5D O4D .
GUD H4D C4D . .
GUD C3D C4D C2D .
GUD H3D C3D . .
GUD O3D C3D "HO3'" .
GUD "HO3'" O3D . .
GUD C2D C3D O2D .
GUD H2D C2D . .
GUD O2D C2D "HO2'" .
GUD "HO2'" O2D . .
GUD O4D C4D C1D .
GUD C1D O4D N1 .
GUD H1D C1D . .
GUD N1 C1D C6 .
GUD C6 N1 C5 .
GUD H6 C6 . .
GUD C5 C6 C4 .
GUD H5 C5 . .
GUD C4 C5 N3 .
GUD O4 C4 . .
GUD N3 C4 C2 .
GUD HN3 N3 . .
GUD C2 N3 O2 .
GUD O2 C2 . END
GUD N1 C2 . ADD
GUD C1D C2D . ADD
GUD "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
GUD N1 C2 single 1.410 0.020
GUD C6 N1 single 1.337 0.020
GUD N1 C1D single 1.465 0.020
GUD C2 N3 single 1.337 0.020
GUD O2 C2 double 1.250 0.020
GUD N3 C4 single 1.337 0.020
GUD HN3 N3 single 1.040 0.020
GUD C4 C5 single 1.390 0.020
GUD O4 C4 double 1.250 0.020
GUD C5 C6 double 1.390 0.020
GUD H5 C5 single 1.083 0.020
GUD H6 C6 single 1.083 0.020
GUD C1D C2D single 1.524 0.020
GUD C1D O4D single 1.426 0.020
GUD H1D C1D single 1.099 0.020
GUD O2D C2D single 1.432 0.020
GUD C2D C3D single 1.524 0.020
GUD H2D C2D single 1.099 0.020
GUD "HO2'" O2D single 0.967 0.020
GUD C3D C4D single 1.524 0.020
GUD O3D C3D single 1.432 0.020
GUD H3D C3D single 1.099 0.020
GUD O4D C4D single 1.426 0.020
GUD C4D C5D single 1.524 0.020
GUD H4D C4D single 1.099 0.020
GUD "HO3'" O3D single 0.967 0.020
GUD C5D O5D single 1.426 0.020
GUD "H5'1" C5D single 1.092 0.020
GUD "H5'2" C5D single 1.092 0.020
GUD O5D PA single 1.610 0.020
GUD O1A PA deloc 1.510 0.020
GUD O2A PA deloc 1.510 0.020
GUD PA O3A single 1.610 0.020
GUD O3A PB single 1.610 0.020
GUD O1B PB deloc 1.510 0.020
GUD PB O2B deloc 1.510 0.020
GUD O3B PB single 1.610 0.020
GUD "C1'" O3B single 1.426 0.020
GUD "C1'" "C2'" single 1.524 0.020
GUD "O5'" "C1'" single 1.426 0.020
GUD "H1'" "C1'" single 1.099 0.020
GUD "C2'" "C3'" single 1.524 0.020
GUD "O2'" "C2'" single 1.432 0.020
GUD "H2'" "C2'" single 1.099 0.020
GUD "C3'" "C4'" single 1.524 0.020
GUD "O3'" "C3'" single 1.432 0.020
GUD "H3'" "C3'" single 1.099 0.020
GUD "C4'" "C5'" single 1.524 0.020
GUD "O4'" "C4'" single 1.432 0.020
GUD "H4'" "C4'" single 1.099 0.020
GUD "C6'" "C5'" single 1.524 0.020
GUD "C5'" "O5'" single 1.426 0.020
GUD "H5'" "C5'" single 1.099 0.020
GUD "O6'" "C6'" single 1.432 0.020
GUD "H6'1" "C6'" single 1.092 0.020
GUD "H6'2" "C6'" single 1.092 0.020
GUD HO2A "O2'" single 0.967 0.020
GUD HO3A "O3'" single 0.967 0.020
GUD "HO4'" "O4'" single 0.967 0.020
GUD "HO6'" "O6'" 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
GUD O2B PB O1B 119.900 3.000
GUD O2B PB O3B 108.200 3.000
GUD O2B PB O3A 108.200 3.000
GUD O1B PB O3B 108.200 3.000
GUD O1B PB O3A 108.200 3.000
GUD O3B PB O3A 102.600 3.000
GUD PB O3B "C1'" 120.500 3.000
GUD O3B "C1'" "H1'" 109.470 3.000
GUD O3B "C1'" "O5'" 109.470 3.000
GUD O3B "C1'" "C2'" 109.470 3.000
GUD "H1'" "C1'" "O5'" 109.470 3.000
GUD "H1'" "C1'" "C2'" 108.340 3.000
GUD "O5'" "C1'" "C2'" 109.470 3.000
GUD "C1'" "O5'" "C5'" 111.800 3.000
GUD "O5'" "C5'" "H5'" 109.470 3.000
GUD "O5'" "C5'" "C6'" 109.470 3.000
GUD "O5'" "C5'" "C4'" 109.470 3.000
GUD "H5'" "C5'" "C6'" 108.340 3.000
GUD "H5'" "C5'" "C4'" 108.340 3.000
GUD "C6'" "C5'" "C4'" 111.000 3.000
GUD "C5'" "C6'" "H6'1" 109.470 3.000
GUD "C5'" "C6'" "H6'2" 109.470 3.000
GUD "C5'" "C6'" "O6'" 109.470 3.000
GUD "H6'1" "C6'" "H6'2" 107.900 3.000
GUD "H6'1" "C6'" "O6'" 109.470 3.000
GUD "H6'2" "C6'" "O6'" 109.470 3.000
GUD "C6'" "O6'" "HO6'" 109.470 3.000
GUD "C5'" "C4'" "H4'" 108.340 3.000
GUD "C5'" "C4'" "O4'" 109.470 3.000
GUD "C5'" "C4'" "C3'" 111.000 3.000
GUD "H4'" "C4'" "O4'" 109.470 3.000
GUD "H4'" "C4'" "C3'" 108.340 3.000
GUD "O4'" "C4'" "C3'" 109.470 3.000
GUD "C4'" "O4'" "HO4'" 109.470 3.000
GUD "C4'" "C3'" "H3'" 108.340 3.000
GUD "C4'" "C3'" "O3'" 109.470 3.000
GUD "C4'" "C3'" "C2'" 111.000 3.000
GUD "H3'" "C3'" "O3'" 109.470 3.000
GUD "H3'" "C3'" "C2'" 108.340 3.000
GUD "O3'" "C3'" "C2'" 109.470 3.000
GUD "C3'" "O3'" HO3A 109.470 3.000
GUD "C3'" "C2'" "H2'" 108.340 3.000
GUD "C3'" "C2'" "O2'" 109.470 3.000
GUD "C3'" "C2'" "C1'" 111.000 3.000
GUD "H2'" "C2'" "O2'" 109.470 3.000
GUD "H2'" "C2'" "C1'" 108.340 3.000
GUD "O2'" "C2'" "C1'" 109.470 3.000
GUD "C2'" "O2'" HO2A 109.470 3.000
GUD PB O3A PA 120.500 3.000
GUD O3A PA O1A 108.200 3.000
GUD O3A PA O2A 108.200 3.000
GUD O3A PA O5D 102.600 3.000
GUD O1A PA O2A 119.900 3.000
GUD O1A PA O5D 108.200 3.000
GUD O2A PA O5D 108.200 3.000
GUD PA O5D C5D 120.500 3.000
GUD O5D C5D "H5'1" 109.470 3.000
GUD O5D C5D "H5'2" 109.470 3.000
GUD O5D C5D C4D 109.470 3.000
GUD "H5'1" C5D "H5'2" 107.900 3.000
GUD "H5'1" C5D C4D 109.470 3.000
GUD "H5'2" C5D C4D 109.470 3.000
GUD C5D C4D H4D 108.340 3.000
GUD C5D C4D C3D 111.000 3.000
GUD C5D C4D O4D 109.470 3.000
GUD H4D C4D C3D 108.340 3.000
GUD H4D C4D O4D 109.470 3.000
GUD C3D C4D O4D 109.470 3.000
GUD C4D C3D H3D 108.340 3.000
GUD C4D C3D O3D 109.470 3.000
GUD C4D C3D C2D 111.000 3.000
GUD H3D C3D O3D 109.470 3.000
GUD H3D C3D C2D 108.340 3.000
GUD O3D C3D C2D 109.470 3.000
GUD C3D O3D "HO3'" 109.470 3.000
GUD C3D C2D H2D 108.340 3.000
GUD C3D C2D O2D 109.470 3.000
GUD C3D C2D C1D 111.000 3.000
GUD H2D C2D O2D 109.470 3.000
GUD H2D C2D C1D 108.340 3.000
GUD O2D C2D C1D 109.470 3.000
GUD C2D O2D "HO2'" 109.470 3.000
GUD C4D O4D C1D 111.800 3.000
GUD O4D C1D H1D 109.470 3.000
GUD O4D C1D N1 109.470 3.000
GUD O4D C1D C2D 109.470 3.000
GUD H1D C1D N1 109.470 3.000
GUD H1D C1D C2D 108.340 3.000
GUD N1 C1D C2D 109.470 3.000
GUD C1D N1 C6 120.000 3.000
GUD C1D N1 C2 120.000 3.000
GUD C6 N1 C2 120.000 3.000
GUD N1 C6 H6 120.000 3.000
GUD N1 C6 C5 120.000 3.000
GUD H6 C6 C5 120.000 3.000
GUD C6 C5 H5 120.000 3.000
GUD C6 C5 C4 120.000 3.000
GUD H5 C5 C4 120.000 3.000
GUD C5 C4 O4 120.000 3.000
GUD C5 C4 N3 120.000 3.000
GUD O4 C4 N3 120.000 3.000
GUD C4 N3 HN3 120.000 3.000
GUD C4 N3 C2 120.000 3.000
GUD HN3 N3 C2 120.000 3.000
GUD N3 C2 O2 120.000 3.000
GUD N3 C2 N1 120.000 3.000
GUD O2 C2 N1 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
GUD var_1 O2B PB O3B "C1'" -60.025 20.000 1
GUD var_2 PB O3B "C1'" "O5'" 90.012 20.000 1
GUD var_3 O3B "C1'" "C2'" "C3'" -60.000 20.000 3
GUD var_4 O3B "C1'" "O5'" "C5'" 60.000 20.000 1
GUD var_5 "C1'" "O5'" "C5'" "C4'" 60.000 20.000 1
GUD var_6 "O5'" "C5'" "C6'" "O6'" 59.864 20.000 3
GUD var_7 "C5'" "C6'" "O6'" "HO6'" 179.997 20.000 1
GUD var_8 "O5'" "C5'" "C4'" "C3'" -60.000 20.000 3
GUD var_9 "C5'" "C4'" "O4'" "HO4'" 179.534 20.000 1
GUD var_10 "C5'" "C4'" "C3'" "C2'" 60.000 20.000 3
GUD var_11 "C4'" "C3'" "O3'" HO3A -179.253 20.000 1
GUD var_12 "C4'" "C3'" "C2'" "O2'" 180.000 20.000 3
GUD var_13 "C3'" "C2'" "O2'" HO2A 179.585 20.000 1
GUD var_14 O2B PB O3A PA 59.994 20.000 1
GUD var_15 PB O3A PA O5D -179.987 20.000 1
GUD var_16 O3A PA O5D C5D -179.975 20.000 1
GUD var_17 PA O5D C5D C4D -179.992 20.000 1
GUD var_18 O5D C5D C4D O4D 61.604 20.000 3
GUD var_19 C5D C4D C3D C2D -120.000 20.000 3
GUD var_20 C4D C3D O3D "HO3'" 176.183 20.000 1
GUD var_21 C4D C3D C2D O2D -150.000 20.000 3
GUD var_22 C3D C2D O2D "HO2'" -67.272 20.000 1
GUD var_23 C5D C4D O4D C1D 150.000 20.000 1
GUD var_24 C4D O4D C1D N1 -150.000 20.000 1
GUD var_25 O4D C1D C2D C3D 30.000 20.000 3
GUD var_26 O4D C1D N1 C6 -121.464 20.000 1
GUD CONST_1 C1D N1 C2 N3 180.000 0.000 0
GUD CONST_2 C1D N1 C6 C5 180.000 0.000 0
GUD CONST_3 N1 C6 C5 C4 0.000 0.000 0
GUD CONST_4 C6 C5 C4 N3 0.000 0.000 0
GUD CONST_5 C5 C4 N3 C2 0.000 0.000 0
GUD CONST_6 C4 N3 C2 O2 180.000 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
GUD chir_01 C1D N1 C2D O4D negativ
GUD chir_02 C2D C1D O2D C3D positiv
GUD chir_03 C3D C2D C4D O3D negativ
GUD chir_04 C4D C3D O4D C5D positiv
GUD chir_05 "C1'" O3B "C2'" "O5'" positiv
GUD chir_06 "C2'" "C1'" "C3'" "O2'" negativ
GUD chir_07 "C3'" "C2'" "C4'" "O3'" positiv
GUD chir_08 "C4'" "C3'" "C5'" "O4'" negativ
GUD chir_09 "C5'" "C4'" "C6'" "O5'" 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
GUD plan-1 N1 0.020
GUD plan-1 C2 0.020
GUD plan-1 C6 0.020
GUD plan-1 C1D 0.020
GUD plan-1 N3 0.020
GUD plan-1 C4 0.020
GUD plan-1 C5 0.020
GUD plan-1 O2 0.020
GUD plan-1 HN3 0.020
GUD plan-1 O4 0.020
GUD plan-1 H5 0.020
GUD plan-1 H6 0.020
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