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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
GMB GMB '1,7-di-O-phosphono-L-glycero-beta-D-' non-polymer 34 22 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_GMB
#
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
GMB OP6 O OP -0.666 0.000 0.000 0.000
GMB P2 P P 0.000 -1.378 -0.579 -0.236
GMB OP4 O OP -0.666 -1.636 -1.690 0.758
GMB OP5 O OP -0.666 -1.458 -1.133 -1.642
GMB O7 O O2 0.000 -2.484 0.575 -0.050
GMB C7 C CH2 0.000 -3.875 0.369 -0.308
GMB H7 H H 0.000 -4.252 -0.424 0.342
GMB H7A H H 0.000 -4.013 0.079 -1.351
GMB C6 C CH1 0.000 -4.642 1.663 -0.032
GMB H6 H H 0.000 -4.204 2.482 -0.620
GMB O6 O OH1 0.000 -4.559 1.979 1.359
GMB HO6 H H 0.000 -4.945 1.258 1.876
GMB C5 C CH1 0.000 -6.110 1.480 -0.427
GMB H5 H H 0.000 -6.181 1.326 -1.512
GMB C4 C CH1 0.000 -6.902 2.731 -0.035
GMB H4 H H 0.000 -6.798 2.909 1.044
GMB O4 O OH1 0.000 -6.403 3.859 -0.757
GMB HO4 H H 0.000 -6.909 4.646 -0.512
GMB C3 C CH1 0.000 -8.380 2.516 -0.379
GMB H3 H H 0.000 -8.491 2.389 -1.465
GMB O3 O OH1 0.000 -9.139 3.648 0.051
GMB HO3 H H 0.000 -10.072 3.509 -0.161
GMB C2 C CH1 0.000 -8.882 1.260 0.340
GMB H2 H H 0.000 -9.926 1.067 0.056
GMB O2 O OH1 0.000 -8.799 1.453 1.753
GMB HO2 H H 0.000 -9.113 0.658 2.206
GMB O5 O O2 0.000 -6.648 0.345 0.253
GMB C1 C CH1 0.000 -8.013 0.067 -0.066
GMB H1 H H 0.000 -8.109 -0.106 -1.147
GMB O1 O O2 0.000 -8.440 -1.097 0.644
GMB P1 P P 0.000 -8.305 -2.586 0.046
GMB OP1 O OP -0.666 -6.841 -2.935 -0.110
GMB OP2 O OP -0.666 -8.960 -3.570 0.991
GMB OP3 O OP -0.666 -8.986 -2.653 -1.303
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
GMB OP6 n/a P2 START
GMB P2 OP6 O7 .
GMB OP4 P2 . .
GMB OP5 P2 . .
GMB O7 P2 C7 .
GMB C7 O7 C6 .
GMB H7 C7 . .
GMB H7A C7 . .
GMB C6 C7 C5 .
GMB H6 C6 . .
GMB O6 C6 HO6 .
GMB HO6 O6 . .
GMB C5 C6 O5 .
GMB H5 C5 . .
GMB C4 C5 C3 .
GMB H4 C4 . .
GMB O4 C4 HO4 .
GMB HO4 O4 . .
GMB C3 C4 C2 .
GMB H3 C3 . .
GMB O3 C3 HO3 .
GMB HO3 O3 . .
GMB C2 C3 O2 .
GMB H2 C2 . .
GMB O2 C2 HO2 .
GMB HO2 O2 . .
GMB O5 C5 C1 .
GMB C1 O5 O1 .
GMB H1 C1 . .
GMB O1 C1 P1 .
GMB P1 O1 OP3 .
GMB OP1 P1 . .
GMB OP2 P1 . .
GMB OP3 P1 . END
GMB 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
GMB O1 C1 single 1.426 0.020
GMB C1 C2 single 1.524 0.020
GMB C1 O5 single 1.426 0.020
GMB H1 C1 single 1.099 0.020
GMB P1 O1 single 1.610 0.020
GMB OP3 P1 deloc 1.510 0.020
GMB OP1 P1 deloc 1.510 0.020
GMB OP2 P1 deloc 1.510 0.020
GMB C2 C3 single 1.524 0.020
GMB O2 C2 single 1.432 0.020
GMB H2 C2 single 1.099 0.020
GMB HO2 O2 single 0.967 0.020
GMB O7 P2 single 1.610 0.020
GMB OP5 P2 deloc 1.510 0.020
GMB P2 OP6 deloc 1.510 0.020
GMB OP4 P2 deloc 1.510 0.020
GMB O3 C3 single 1.432 0.020
GMB C3 C4 single 1.524 0.020
GMB H3 C3 single 1.099 0.020
GMB HO3 O3 single 0.967 0.020
GMB C4 C5 single 1.524 0.020
GMB O4 C4 single 1.432 0.020
GMB H4 C4 single 1.099 0.020
GMB HO4 O4 single 0.967 0.020
GMB O5 C5 single 1.426 0.020
GMB C5 C6 single 1.524 0.020
GMB H5 C5 single 1.099 0.020
GMB C6 C7 single 1.524 0.020
GMB O6 C6 single 1.432 0.020
GMB H6 C6 single 1.099 0.020
GMB HO6 O6 single 0.967 0.020
GMB C7 O7 single 1.426 0.020
GMB H7 C7 single 1.092 0.020
GMB H7A C7 single 1.092 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
GMB OP6 P2 OP4 119.900 3.000
GMB OP6 P2 OP5 119.900 3.000
GMB OP6 P2 O7 108.200 3.000
GMB OP4 P2 OP5 119.900 3.000
GMB OP4 P2 O7 108.200 3.000
GMB OP5 P2 O7 108.200 3.000
GMB P2 O7 C7 120.500 3.000
GMB O7 C7 H7 109.470 3.000
GMB O7 C7 H7A 109.470 3.000
GMB O7 C7 C6 109.470 3.000
GMB H7 C7 H7A 107.900 3.000
GMB H7 C7 C6 109.470 3.000
GMB H7A C7 C6 109.470 3.000
GMB C7 C6 H6 108.340 3.000
GMB C7 C6 O6 109.470 3.000
GMB C7 C6 C5 111.000 3.000
GMB H6 C6 O6 109.470 3.000
GMB H6 C6 C5 108.340 3.000
GMB O6 C6 C5 109.470 3.000
GMB C6 O6 HO6 109.470 3.000
GMB C6 C5 H5 108.340 3.000
GMB C6 C5 C4 111.000 3.000
GMB C6 C5 O5 109.470 3.000
GMB H5 C5 C4 108.340 3.000
GMB H5 C5 O5 109.470 3.000
GMB C4 C5 O5 109.470 3.000
GMB C5 C4 H4 108.340 3.000
GMB C5 C4 O4 109.470 3.000
GMB C5 C4 C3 111.000 3.000
GMB H4 C4 O4 109.470 3.000
GMB H4 C4 C3 108.340 3.000
GMB O4 C4 C3 109.470 3.000
GMB C4 O4 HO4 109.470 3.000
GMB C4 C3 H3 108.340 3.000
GMB C4 C3 O3 109.470 3.000
GMB C4 C3 C2 111.000 3.000
GMB H3 C3 O3 109.470 3.000
GMB H3 C3 C2 108.340 3.000
GMB O3 C3 C2 109.470 3.000
GMB C3 O3 HO3 109.470 3.000
GMB C3 C2 H2 108.340 3.000
GMB C3 C2 O2 109.470 3.000
GMB C3 C2 C1 111.000 3.000
GMB H2 C2 O2 109.470 3.000
GMB H2 C2 C1 108.340 3.000
GMB O2 C2 C1 109.470 3.000
GMB C2 O2 HO2 109.470 3.000
GMB C5 O5 C1 111.800 3.000
GMB O5 C1 H1 109.470 3.000
GMB O5 C1 O1 109.470 3.000
GMB O5 C1 C2 109.470 3.000
GMB H1 C1 O1 109.470 3.000
GMB H1 C1 C2 108.340 3.000
GMB O1 C1 C2 109.470 3.000
GMB C1 O1 P1 120.500 3.000
GMB O1 P1 OP1 108.200 3.000
GMB O1 P1 OP2 108.200 3.000
GMB O1 P1 OP3 108.200 3.000
GMB OP1 P1 OP2 119.900 3.000
GMB OP1 P1 OP3 119.900 3.000
GMB OP2 P1 OP3 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
GMB var_1 OP6 P2 O7 C7 175.019 20.000 1
GMB var_2 P2 O7 C7 C6 -179.987 20.000 1
GMB var_3 O7 C7 C6 C5 174.979 20.000 3
GMB var_4 C7 C6 O6 HO6 -59.955 20.000 1
GMB var_5 C7 C6 C5 O5 55.054 20.000 3
GMB var_6 C6 C5 C4 C3 180.000 20.000 3
GMB var_7 C5 C4 O4 HO4 179.609 20.000 1
GMB var_8 C5 C4 C3 C2 60.000 20.000 3
GMB var_9 C4 C3 O3 HO3 -179.617 20.000 1
GMB var_10 C4 C3 C2 O2 60.000 20.000 3
GMB var_11 C3 C2 O2 HO2 -179.718 20.000 1
GMB var_12 C6 C5 O5 C1 180.000 20.000 1
GMB var_13 C5 O5 C1 O1 180.000 20.000 1
GMB var_14 O5 C1 C2 C3 60.000 20.000 3
GMB var_15 O5 C1 O1 P1 -90.048 20.000 1
GMB var_16 C1 O1 P1 OP3 -54.946 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
GMB chir_01 C1 O1 C2 O5 negativ
GMB chir_02 C2 C1 O2 C3 negativ
GMB chir_03 C3 C2 O3 C4 negativ
GMB chir_04 C4 C3 O4 C5 positiv
GMB chir_05 C5 C4 O5 C6 positiv
GMB chir_06 C6 C5 O6 C7 negativ
# ------------------------------------------------------
|
