# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 22:05:39 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: D-galactonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)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
 J0M  J0M  'D-galactonic acid        '  ligand  24  13  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J0M
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
 J0M  C4   C  CH1    0  -0.128   1.6381   0.6437  -0.2817
 J0M  C5   C  CH2    0  -0.164  -3.4046   0.5245   0.0409
 J0M  C6   C  C      0   0.407   2.9353  -0.1788  -0.1102
 J0M  C3   C  CH1    0  -0.010  -2.1288  -0.2747   0.2431
 J0M  C1   C  CH1    0  -0.016  -0.9040   0.5308  -0.2055
 J0M  C2   C  CH1    0  -0.001   0.4174  -0.2052   0.0723
 J0M  O1   O  OH1    0  -0.671  -0.9914   0.9012  -1.5681
 J0M  O2   O  OH1    0  -0.673   0.4898  -0.6250   1.4165
 J0M  O3   O  OH1    0  -0.671  -2.1909  -1.5427  -0.3784
 J0M  O4   O  OH1    0  -0.699   1.6966   1.7755   0.5531
 J0M  O6   O  O      0  -0.608   3.7557   0.3061   0.7026
 J0M  O7   O  OC    -1  -0.593   3.0563  -1.2141  -0.7807
 J0M  H1   H  HCH1   0   0.214   1.5691   0.9446  -1.3354
 J0M  H3   H  HCH2   0   0.196  -3.5744   0.6840  -1.0324
 J0M  H4   H  HCH1   0   0.230  -2.0198  -0.4673   1.3142
 J0M  H5   H  HCH1   0   0.228  -0.9076   1.4686   0.3616
 J0M  H6   H  HCH1   0   0.228   0.4436  -1.1112  -0.5417
 J0M  H7   H  HOH1   0   0.442  -0.8083   0.1272  -2.1116
 J0M  H8   H  HOH1   0   0.435   0.6642   0.1601   1.9491
 J0M  H9   H  HOH1   0   0.442  -2.5391  -1.4400  -1.2701
 J0M  H10  H  HOH1   0   0.432   2.5671   1.6610   0.9838
 J0M  H11  H  HOH1   0   0.454  -5.2828   0.3299   0.4624
 J0M  O5   O  OH1    0  -0.672  -4.4792  -0.1682   0.6344
 J0M  H2   H  HCH2   0   0.198  -3.2676   1.5178   0.4893

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
 J0M  O6  C6   deloc   1.252  0.020  1.252
 J0M  O2  C2   single  1.410  0.020  1.410
 J0M  C6  O7   deloc   1.239  0.020  1.239
 J0M  C6  C4   single  1.545  0.020  1.545
 J0M  O3  C3   single  1.414  0.020  1.414
 J0M  C4  C2   single  1.528  0.020  1.528
 J0M  C4  O4   single  1.408  0.020  1.408
 J0M  C2  C1   single  1.538  0.020  1.538
 J0M  C1  C3   single  1.533  0.020  1.533
 J0M  C1  O1   single  1.415  0.020  1.415
 J0M  C3  C5   single  1.519  0.020  1.519
 J0M  C5  O5   single  1.410  0.020  1.410
 J0M  C4  H1   single  0.970  0.020  1.090
 J0M  C5  H2   single  0.970  0.020  1.090
 J0M  C5  H3   single  0.970  0.020  1.090
 J0M  C3  H4   single  0.970  0.020  1.090
 J0M  C1  H5   single  0.970  0.020  1.090
 J0M  C2  H6   single  0.970  0.020  1.090
 J0M  O1  H7   single  0.850  0.020  0.980
 J0M  O2  H8   single  0.850  0.020  0.980
 J0M  O3  H9   single  0.850  0.020  0.980
 J0M  O4  H10  single  0.850  0.020  0.980
 J0M  O5  H11  single  0.850  0.020  0.980

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
 J0M  H1   C4  O4  110.57  3.000
 J0M  H1   C4  C2  108.92  3.000
 J0M  O4   C4  C2  110.02  3.000
 J0M  H1   C4  C6  107.76  3.000
 J0M  O4   C4  C6  109.09  3.000
 J0M  C2   C4  C6  110.43  3.000
 J0M  H3   C5  H2  106.67  3.000
 J0M  H3   C5  O5  111.40  3.000
 J0M  H2   C5  O5  111.57  3.000
 J0M  H3   C5  C3  109.66  3.000
 J0M  H2   C5  C3  108.47  3.000
 J0M  O5   C5  C3  109.01  3.000
 J0M  O7   C6  O6  127.62  3.000
 J0M  O7   C6  C4  117.80  3.000
 J0M  O6   C6  C4  114.57  3.000
 J0M  H4   C3  O3  106.08  3.000
 J0M  H4   C3  C1  107.43  3.000
 J0M  O3   C3  C1  112.19  3.000
 J0M  H4   C3  C5  107.86  3.000
 J0M  C1   C3  C5  110.84  3.000
 J0M  O3   C3  C5  112.12  3.000
 J0M  H5   C1  O1  105.91  3.000
 J0M  H5   C1  C2  108.60  3.000
 J0M  O1   C1  C2  110.63  3.000
 J0M  H5   C1  C3  107.19  3.000
 J0M  O1   C1  C3  111.72  3.000
 J0M  C2   C1  C3  112.47  3.000
 J0M  H6   C2  O2  106.68  3.000
 J0M  H6   C2  C1  108.38  3.000
 J0M  O2   C2  C1  111.03  3.000
 J0M  H6   C2  C4  108.10  3.000
 J0M  C1   C2  C4  112.25  3.000
 J0M  O2   C2  C4  110.19  3.000
 J0M  H7   O1  C1  108.74  3.000
 J0M  H8   O2  C2  107.06  3.000
 J0M  H9   O3  C3  109.12  3.000
 J0M  H10  O4  C4  101.78  3.000
 J0M  H11  O5  C5  107.91  3.000

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
 J0M  chir_01  C4  C6  C2  O4  negativ
 J0M  chir_02  C3  O3  C1  C5  negativ
 J0M  chir_03  C1  O1  C3  C2  negativ
 J0M  chir_04  C2  O2  C1  C4  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
 J0M  plan-1  C4  0.020
 J0M  plan-1  C6  0.020
 J0M  plan-1  O6  0.020
 J0M  plan-1  O7  0.020

