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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
RUB RUB 'RIBULOSE-1,5-DIPHOSPHATE ' non-polymer 26 18 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_RUB
#
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
RUB O6P O OP -0.666 0.000 0.000 0.000
RUB P2 P P 0.000 -0.511 0.054 -1.423
RUB O4P O OP -0.666 -0.572 -1.347 -1.990
RUB O5P O OP -0.666 0.424 0.897 -2.263
RUB O5 O O2 0.000 -1.983 0.704 -1.441
RUB C5 C CH2 0.000 -2.815 -0.132 -0.637
RUB H51 H H 0.000 -2.418 -0.168 0.380
RUB H52 H H 0.000 -2.830 -1.141 -1.056
RUB C4 C CH1 0.000 -4.237 0.432 -0.612
RUB H4 H H 0.000 -4.220 1.447 -0.190
RUB O4 O OH1 0.000 -4.754 0.479 -1.942
RUB HO4 H H 0.000 -4.768 -0.414 -2.313
RUB C3 C CH1 0.000 -5.127 -0.463 0.251
RUB H3 H H 0.000 -5.144 -1.478 -0.171
RUB O3 O OH1 0.000 -4.610 -0.510 1.582
RUB HO3 H H 0.000 -4.595 0.383 1.952
RUB C2 C C 0.000 -6.526 0.093 0.275
RUB O2 O O 0.000 -6.846 0.886 1.127
RUB C1 C CH2 0.000 -7.528 -0.340 -0.764
RUB H11 H H 0.000 -7.671 -1.421 -0.702
RUB H12 H H 0.000 -7.157 -0.080 -1.757
RUB O1 O O2 0.000 -8.773 0.321 -0.531
RUB P1 P P 0.000 -9.790 -0.185 -1.671
RUB O1P O OP -0.666 -9.953 -1.685 -1.570
RUB O2P O OP -0.666 -11.135 0.481 -1.480
RUB O3P O OP -0.666 -9.238 0.172 -3.034
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
RUB O6P n/a P2 START
RUB P2 O6P O5 .
RUB O4P P2 . .
RUB O5P P2 . .
RUB O5 P2 C5 .
RUB C5 O5 C4 .
RUB H51 C5 . .
RUB H52 C5 . .
RUB C4 C5 C3 .
RUB H4 C4 . .
RUB O4 C4 HO4 .
RUB HO4 O4 . .
RUB C3 C4 C2 .
RUB H3 C3 . .
RUB O3 C3 HO3 .
RUB HO3 O3 . .
RUB C2 C3 C1 .
RUB O2 C2 . .
RUB C1 C2 O1 .
RUB H11 C1 . .
RUB H12 C1 . .
RUB O1 C1 P1 .
RUB P1 O1 O3P .
RUB O1P P1 . .
RUB O2P P1 . .
RUB O3P P1 . END
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
RUB C1 C2 single 1.510 0.020
RUB O1 C1 single 1.426 0.020
RUB H11 C1 single 1.092 0.020
RUB H12 C1 single 1.092 0.020
RUB C2 C3 single 1.500 0.020
RUB O2 C2 double 1.220 0.020
RUB C3 C4 single 1.524 0.020
RUB O3 C3 single 1.432 0.020
RUB H3 C3 single 1.099 0.020
RUB C4 C5 single 1.524 0.020
RUB O4 C4 single 1.432 0.020
RUB H4 C4 single 1.099 0.020
RUB C5 O5 single 1.426 0.020
RUB H51 C5 single 1.092 0.020
RUB H52 C5 single 1.092 0.020
RUB P1 O1 single 1.610 0.020
RUB HO3 O3 single 0.967 0.020
RUB HO4 O4 single 0.967 0.020
RUB O5 P2 single 1.610 0.020
RUB O1P P1 deloc 1.510 0.020
RUB O2P P1 deloc 1.510 0.020
RUB O3P P1 deloc 1.510 0.020
RUB O4P P2 deloc 1.510 0.020
RUB O5P P2 deloc 1.510 0.020
RUB P2 O6P 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
RUB O6P P2 O4P 119.900 3.000
RUB O6P P2 O5P 119.900 3.000
RUB O6P P2 O5 108.200 3.000
RUB O4P P2 O5P 119.900 3.000
RUB O4P P2 O5 108.200 3.000
RUB O5P P2 O5 108.200 3.000
RUB P2 O5 C5 120.500 3.000
RUB O5 C5 H51 109.470 3.000
RUB O5 C5 H52 109.470 3.000
RUB O5 C5 C4 109.470 3.000
RUB H51 C5 H52 107.900 3.000
RUB H51 C5 C4 109.470 3.000
RUB H52 C5 C4 109.470 3.000
RUB C5 C4 H4 108.340 3.000
RUB C5 C4 O4 109.470 3.000
RUB C5 C4 C3 111.000 3.000
RUB H4 C4 O4 109.470 3.000
RUB H4 C4 C3 108.340 3.000
RUB O4 C4 C3 109.470 3.000
RUB C4 O4 HO4 109.470 3.000
RUB C4 C3 H3 108.340 3.000
RUB C4 C3 O3 109.470 3.000
RUB C4 C3 C2 109.470 3.000
RUB H3 C3 O3 109.470 3.000
RUB H3 C3 C2 108.810 3.000
RUB O3 C3 C2 109.470 3.000
RUB C3 O3 HO3 109.470 3.000
RUB C3 C2 O2 120.500 3.000
RUB C3 C2 C1 120.000 3.000
RUB O2 C2 C1 120.500 3.000
RUB C2 C1 H11 109.470 3.000
RUB C2 C1 H12 109.470 3.000
RUB C2 C1 O1 109.470 3.000
RUB H11 C1 H12 107.900 3.000
RUB H11 C1 O1 109.470 3.000
RUB H12 C1 O1 109.470 3.000
RUB C1 O1 P1 120.500 3.000
RUB O1 P1 O1P 108.200 3.000
RUB O1 P1 O2P 108.200 3.000
RUB O1 P1 O3P 108.200 3.000
RUB O1P P1 O2P 119.900 3.000
RUB O1P P1 O3P 119.900 3.000
RUB O2P P1 O3P 119.900 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
RUB var_1 O6P P2 O5 C5 -59.967 20.000 1
RUB var_2 P2 O5 C5 C4 180.000 20.000 1
RUB var_3 O5 C5 C4 C3 -179.973 20.000 3
RUB var_4 C5 C4 O4 HO4 60.014 20.000 1
RUB var_5 C5 C4 C3 C2 179.990 20.000 3
RUB var_6 C4 C3 O3 HO3 60.019 20.000 1
RUB var_7 C4 C3 C2 C1 89.974 20.000 3
RUB var_8 C3 C2 C1 O1 179.990 20.000 3
RUB var_9 C2 C1 O1 P1 179.976 20.000 1
RUB var_10 C1 O1 P1 O3P -59.937 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
RUB chir_01 C3 C2 C4 O3 negativ
RUB chir_02 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
RUB plan-1 C2 0.020
RUB plan-1 C1 0.000
RUB plan-1 C3 0.000
RUB plan-1 O2 0.000
# ------------------------------------------------------
|
