# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 21:26:26 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: prop-2-en-1-yl D-glycero-alpha-D-talo-oct-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H]1O[C@](OCC=C)([C@@H](O)[C@@H](O)[C@H]1O)C(O)=O
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 KO2  KO2  'prop-2-en-1-yl D-glycero-alpha-D-talo-oct-2-ulopyranosidonic acid'  D-saccharide  37  20  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KO2
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 KO2  C1    C  C      0   0.369  -1.9273  -0.9047   1.4443
 KO2  O1B   O  OC    -1  -0.579  -1.4408  -0.8257   2.5802
 KO2  C2    C  CT     0   0.386  -1.0952  -0.3539   0.2452
 KO2  O6    O  O2     0  -0.505   0.1418   0.0856   0.7213
 KO2  C6    C  CH1    0  -0.032   1.0178   0.6168  -0.2533
 KO2  C7    C  CH1    0  -0.014   2.3590   0.8751   0.4422
 KO2  C8    C  CH2    0  -0.162   2.9336  -0.4201   0.9966
 KO2  O8    O  OH1    0  -0.671   4.1334  -0.1306   1.6752
 KO2  O7    O  OH1    0  -0.662   3.2583   1.5118  -0.4361
 KO2  C5    C  CH1    0   0.043   0.4230   1.8557  -0.9105
 KO2  O5    O  OH1    0  -0.672   0.3797   2.8989   0.0291
 KO2  C4    C  CH1    0  -0.027  -0.9523   1.4842  -1.4643
 KO2  O4    O  OH1    0  -0.675  -1.5511   2.6727  -1.9432
 KO2  C3    C  CH1    0   0.005  -1.8504   0.7946  -0.4325
 KO2  O3    O  OH1    0  -0.671  -2.2757   1.6720   0.5775
 KO2  O2    O  O2     0  -0.517  -0.9366  -1.3279  -0.7534
 KO2  C11   C  C2     0  -0.525   1.0173  -3.9058  -1.9272
 KO2  C10   C  C1     0  -0.197  -0.1496  -3.3875  -1.5657
 KO2  C9    C  CH2    0  -0.216  -0.3437  -2.5463  -0.3472
 KO2  O1A   O  O      0  -0.607  -3.0277  -1.3818   1.1119
 KO2  H6    H  HCH1   0   0.220   1.1912  -0.1171  -1.0561
 KO2  H7    H  HCH1   0   0.235   2.2030   1.5737   1.2694
 KO2  H8    H  HCH2   0   0.214   2.1977  -0.8863   1.6601
 KO2  H8A   H  HCH2   0   0.182   3.1009  -1.1213   0.1624
 KO2  HO8   H  HOH1   0   0.454   4.4690  -0.9514   2.0458
 KO2  HO7   H  HOH1   0   0.443   3.4811   0.8987  -1.1453
 KO2  H5    H  HCH1   0   0.218   1.0596   2.1246  -1.7656
 KO2  HO5   H  HOH1   0   0.449  -0.0400   3.6604  -0.3828
 KO2  H4    H  HCH1   0   0.230  -0.7861   0.7762  -2.2853
 KO2  HO4   H  HOH1   0   0.460  -2.3292   2.4425  -2.4619
 KO2  H3    H  HCH1   0   0.210  -2.7139   0.3650  -0.9616
 KO2  HO3   H  HOH1   0   0.442  -2.4669   2.5211   0.1654
 KO2  H11   H  H      0   0.238   1.9222  -3.7258  -1.3580
 KO2  H11A  H  H      0   0.243   1.1129  -4.5351  -2.8024
 KO2  H10   H  H      0   0.249  -1.0370  -3.5889  -2.1590
 KO2  H9    H  HCH2   0   0.218   0.6192  -2.3880   0.1517
 KO2  H9A   H  HCH2   0   0.225  -0.9954  -3.0744   0.3609

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
_chem_comp_bond.value_dist_neutron
 KO2  O1A  C1    deloc   1.245  0.020  1.245
 KO2  O1B  C1    deloc   1.238  0.020  1.238
 KO2  C1   C2    single  1.560  0.020  1.560
 KO2  C3   C2    single  1.533  0.020  1.533
 KO2  C2   O6    single  1.396  0.020  1.396
 KO2  C2   O2    single  1.404  0.020  1.404
 KO2  O6   C6    single  1.414  0.020  1.414
 KO2  C5   C6    single  1.523  0.020  1.523
 KO2  C6   C7    single  1.533  0.020  1.533
 KO2  C6   H6    single  0.970  0.020  1.090
 KO2  C7   O7    single  1.409  0.020  1.409
 KO2  C7   C8    single  1.522  0.020  1.522
 KO2  C7   H7    single  0.970  0.020  1.090
 KO2  C8   O8    single  1.408  0.020  1.408
 KO2  C8   H8    single  0.970  0.020  1.090
 KO2  C8   H8A   single  0.970  0.020  1.090
 KO2  O8   HO8   single  0.850  0.020  0.980
 KO2  O7   HO7   single  0.850  0.020  0.980
 KO2  O5   C5    single  1.405  0.020  1.405
 KO2  C4   C5    single  1.529  0.020  1.529
 KO2  C5   H5    single  0.970  0.020  1.090
 KO2  O5   HO5   single  0.850  0.020  0.980
 KO2  O4   C4    single  1.414  0.020  1.414
 KO2  C3   C4    single  1.532  0.020  1.532
 KO2  C4   H4    single  0.970  0.020  1.090
 KO2  O4   HO4   single  0.850  0.020  0.980
 KO2  O3   C3    single  1.404  0.020  1.404
 KO2  C3   H3    single  0.970  0.020  1.090
 KO2  O3   HO3   single  0.850  0.020  0.980
 KO2  O2   C9    single  1.415  0.020  1.415
 KO2  C10  C11   double  1.327  0.020  1.327
 KO2  C11  H11   single  0.930  0.020  1.080
 KO2  C11  H11A  single  0.930  0.020  1.080
 KO2  C9   C10   single  1.493  0.020  1.493
 KO2  C10  H10   single  0.930  0.020  1.080
 KO2  C9   H9    single  0.970  0.020  1.090
 KO2  C9   H9A   single  0.970  0.020  1.090

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
 KO2  O1A   C1   C2   113.68  3.000
 KO2  C2    C1   O1B  118.23  3.000
 KO2  O1A   C1   O1B  128.09  3.000
 KO2  O2    C2   C3   105.13  3.000
 KO2  O2    C2   O6   111.16  3.000
 KO2  C3    C2   O6   110.57  3.000
 KO2  O2    C2   C1   111.23  3.000
 KO2  O6    C2   C1   108.76  3.000
 KO2  C3    C2   C1   109.97  3.000
 KO2  C6    O6   C2   115.59  3.000
 KO2  H6    C6   C5   106.80  3.000
 KO2  H6    C6   C7   107.77  3.000
 KO2  C5    C6   C7   113.60  3.000
 KO2  H6    C6   O6   110.47  3.000
 KO2  C7    C6   O6   107.02  3.000
 KO2  C5    C6   O6   111.16  3.000
 KO2  H7    C7   O7   105.89  3.000
 KO2  H7    C7   C8   108.78  3.000
 KO2  O7    C7   C8   111.77  3.000
 KO2  H7    C7   C6   109.02  3.000
 KO2  C8    C7   C6   110.63  3.000
 KO2  O7    C7   C6   110.60  3.000
 KO2  H8A   C8   H8   106.83  3.000
 KO2  H8A   C8   O8   111.47  3.000
 KO2  H8    C8   O8   111.60  3.000
 KO2  H8A   C8   C7   108.84  3.000
 KO2  H8    C8   C7   109.23  3.000
 KO2  O8    C8   C7   108.80  3.000
 KO2  HO8   O8   C8   107.92  3.000
 KO2  HO7   O7   C7   108.59  3.000
 KO2  H5    C5   C4   107.38  3.000
 KO2  H5    C5   O5   110.89  3.000
 KO2  C4    C5   O5   113.27  3.000
 KO2  H5    C5   C6   107.96  3.000
 KO2  C4    C5   C6   108.05  3.000
 KO2  O5    C5   C6   109.12  3.000
 KO2  HO5   O5   C5   108.35  3.000
 KO2  H4    C4   C3   107.61  3.000
 KO2  H4    C4   O4   110.68  3.000
 KO2  C3    C4   O4   110.99  3.000
 KO2  H4    C4   C5   106.96  3.000
 KO2  C3    C4   C5   113.14  3.000
 KO2  O4    C4   C5   107.42  3.000
 KO2  HO4   O4   C4   108.88  3.000
 KO2  H3    C3   O3   110.63  3.000
 KO2  H3    C3   C4   108.18  3.000
 KO2  O3    C3   C4   112.39  3.000
 KO2  H3    C3   C2   107.87  3.000
 KO2  O3    C3   C2   107.43  3.000
 KO2  C4    C3   C2   110.26  3.000
 KO2  HO3   O3   C3   107.66  3.000
 KO2  C9    O2   C2   116.14  3.000
 KO2  H11A  C11  H11  116.58  3.000
 KO2  H11A  C11  C10  121.68  3.000
 KO2  H11   C11  C10  121.74  3.000
 KO2  H10   C10  C9   116.35  3.000
 KO2  H10   C10  C11  119.81  3.000
 KO2  C9    C10  C11  123.82  3.000
 KO2  H9A   C9   H9   107.31  3.000
 KO2  H9A   C9   C10  109.42  3.000
 KO2  H9    C9   C10  109.79  3.000
 KO2  H9A   C9   O2   110.53  3.000
 KO2  H9    C9   O2   112.00  3.000
 KO2  C10   C9   O2   107.78  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
 KO2  Var_01  C10  C9   O2   C2  -174.81  30.0  3
 KO2  Var_02  C11  C10  C9   O2   125.27  30.0  3
 KO2  Var_03  H11  C11  C10  C9    -1.44   0.0  2

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
 KO2  chir_01  C2  C3  O6  O2  positiv
 KO2  chir_02  C6  O6  C7  C5  positiv
 KO2  chir_03  C7  O7  C6  C8  negativ
 KO2  chir_04  C5  O5  C6  C4  negativ
 KO2  chir_05  C4  O4  C5  C3  negativ
 KO2  chir_06  C3  O3  C4  C2  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
 KO2  plan-1  C1    0.020
 KO2  plan-1  O1B   0.020
 KO2  plan-1  C2    0.020
 KO2  plan-1  O1A   0.020
 KO2  plan-2  C11   0.020
 KO2  plan-2  C10   0.020
 KO2  plan-2  C9    0.020
 KO2  plan-2  H11   0.020
 KO2  plan-2  H11A  0.020
 KO2  plan-2  H10   0.020

