# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  8 15:31:58 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](CC(O)=O)[C@@H](O)[C@H](O)[C@@H]1O
#
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
 ZDC  ZDC  '3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid'  D-saccharide  27  14  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZDC
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
 ZDC  C1    C  CH1    0  -0.019  -1.0490   1.0680   0.7619
 ZDC  C1M   C  CH3    0  -0.689  -1.0661   2.1924  -0.2653
 ZDC  C2    C  CH1    0   0.023  -2.1595   0.0136   0.6182
 ZDC  C3    C  CH1    0  -0.034  -1.9160  -0.9551  -0.5359
 ZDC  C4    C  CH1    0   0.017  -0.4940  -1.5233  -0.4490
 ZDC  C5    C  CH1    0   0.048   0.5201  -0.3971  -0.2893
 ZDC  C6    C  CH2    0  -0.585   1.9429  -0.8801  -0.0972
 ZDC  C7    C  C      0   0.408   2.9691   0.2676  -0.1116
 ZDC  O2    O  OH1    0  -0.674  -3.4340   0.5850   0.4271
 ZDC  O3    O  OH1    0  -0.671  -2.0615  -0.3572  -1.8030
 ZDC  O4    O  OH1    0  -0.675  -0.3834  -2.4006   0.6488
 ZDC  O5    O  O2     0  -0.503   0.1995   0.4062   0.8339
 ZDC  O7A   O  O      0  -0.614   2.8428   1.1231  -1.0105
 ZDC  O7B   O  OC    -1  -0.622   3.8657   0.2349   0.7563
 ZDC  H1    H  HCH1   0   0.230  -1.1699   1.5325   1.7476
 ZDC  H1M1  H  HCH3   0   0.232  -0.9804   1.8430  -1.2912
 ZDC  H1M2  H  HCH3   0   0.226  -1.9897   2.7662  -0.1885
 ZDC  H1M3  H  HCH3   0   0.230  -0.2413   2.8787  -0.0696
 ZDC  H2    H  HCH1   0   0.221  -2.1404  -0.5908   1.5356
 ZDC  H2O   H  HOH1   0   0.456  -3.6325   1.1587   1.1739
 ZDC  H3    H  HCH1   0   0.220  -2.6307  -1.7887  -0.4317
 ZDC  H3O   H  HOH1   0   0.452  -2.8788   0.1520  -1.8046
 ZDC  H4    H  HCH1   0   0.221  -0.2752  -2.0428  -1.3937
 ZDC  H4O   H  HOH1   0   0.451  -0.9619  -3.1534   0.4922
 ZDC  H5    H  HCH1   0   0.214   0.4941   0.1972  -1.2103
 ZDC  H61   H  HCH2   0   0.211   2.0286  -1.4631   0.8212
 ZDC  H62   H  HCH2   0   0.226   2.1836  -1.5630  -0.9203

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
 ZDC  C1   C1M   single  1.523  0.020  1.523
 ZDC  C1M  H1M1  single  0.970  0.020  1.090
 ZDC  C1M  H1M2  single  0.970  0.020  1.090
 ZDC  C1M  H1M3  single  0.970  0.020  1.090
 ZDC  C1   H1    single  0.970  0.020  1.090
 ZDC  C1   O5    single  1.415  0.020  1.415
 ZDC  C1   C2    single  1.538  0.020  1.538
 ZDC  C2   H2    single  0.970  0.020  1.090
 ZDC  C2   O2    single  1.410  0.020  1.410
 ZDC  O2   H2O   single  0.850  0.020  0.980
 ZDC  C2   C3    single  1.526  0.020  1.526
 ZDC  C3   H3    single  0.970  0.020  1.090
 ZDC  C3   O3    single  1.409  0.020  1.409
 ZDC  O3   H3O   single  0.850  0.020  0.980
 ZDC  C3   C4    single  1.534  0.020  1.534
 ZDC  C4   H4    single  0.970  0.020  1.090
 ZDC  C4   O4    single  1.410  0.020  1.410
 ZDC  O4   H4O   single  0.850  0.020  0.980
 ZDC  C4   C5    single  1.524  0.020  1.524
 ZDC  C5   H5    single  0.970  0.020  1.090
 ZDC  C5   O5    single  1.418  0.020  1.418
 ZDC  C5   C6    single  1.515  0.020  1.515
 ZDC  C6   H61   single  0.970  0.020  1.090
 ZDC  C6   H62   single  0.970  0.020  1.090
 ZDC  C6   C7    single  1.540  0.020  1.540
 ZDC  C7   O7A   deloc   1.247  0.020  1.247
 ZDC  C7   O7B   deloc   1.248  0.020  1.248

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
 ZDC  H1    C1   O5    104.46  3.000
 ZDC  O5    C1   C2    108.74  3.000
 ZDC  H1    C1   C2    107.14  3.000
 ZDC  C2    C1   C1M   115.78  3.000
 ZDC  O5    C1   C1M   112.93  3.000
 ZDC  H1    C1   C1M   107.00  3.000
 ZDC  H1M3  C1M  H1M2  107.27  3.000
 ZDC  H1M3  C1M  H1M1  108.18  3.000
 ZDC  H1M2  C1M  H1M1  107.61  3.000
 ZDC  H1M3  C1M  C1    109.57  3.000
 ZDC  H1M2  C1M  C1    110.52  3.000
 ZDC  H1M1  C1M  C1    113.47  3.000
 ZDC  H2    C2   O2    110.61  3.000
 ZDC  O2    C2   C3    107.40  3.000
 ZDC  H2    C2   C3    106.22  3.000
 ZDC  C3    C2   C1    112.99  3.000
 ZDC  O2    C2   C1    112.80  3.000
 ZDC  H2    C2   C1    106.65  3.000
 ZDC  H3    C3   O3    109.81  3.000
 ZDC  O3    C3   C4    107.69  3.000
 ZDC  H3    C3   C4    108.39  3.000
 ZDC  C4    C3   C2    109.89  3.000
 ZDC  O3    C3   C2    113.22  3.000
 ZDC  H3    C3   C2    107.75  3.000
 ZDC  H4    C4   O4    111.06  3.000
 ZDC  O4    C4   C5    109.04  3.000
 ZDC  H4    C4   C5    107.85  3.000
 ZDC  C5    C4   C3    110.43  3.000
 ZDC  O4    C4   C3    110.33  3.000
 ZDC  H4    C4   C3    108.10  3.000
 ZDC  H5    C5   O5    110.67  3.000
 ZDC  O5    C5   C6    107.02  3.000
 ZDC  H5    C5   C6    107.56  3.000
 ZDC  C6    C5   C4    113.75  3.000
 ZDC  O5    C5   C4    110.56  3.000
 ZDC  H5    C5   C4    107.27  3.000
 ZDC  H62   C6   H61   106.37  3.000
 ZDC  H62   C6   C7    108.12  3.000
 ZDC  H61   C6   C7    110.72  3.000
 ZDC  C7    C6   C5    112.78  3.000
 ZDC  H62   C6   C5    108.04  3.000
 ZDC  H61   C6   C5    110.54  3.000
 ZDC  O7B   C7   O7A   126.29  3.000
 ZDC  O7B   C7   C6    116.92  3.000
 ZDC  O7A   C7   C6    116.77  3.000
 ZDC  H2O   O2   C2    108.83  3.000
 ZDC  H3O   O3   C3    108.28  3.000
 ZDC  H4O   O4   C4    108.24  3.000
 ZDC  C5    O5   C1    115.11  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
 ZDC  Var_01  O7A  C7  C6  C5  -45.24  30.0  3

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
 ZDC  chir_01  C1  C1M  O5  C2  positiv
 ZDC  chir_02  C2  O2   C1  C3  positiv
 ZDC  chir_03  C3  O3   C2  C4  positiv
 ZDC  chir_04  C4  O4   C3  C5  negativ
 ZDC  chir_05  C5  O5   C6  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
 ZDC  plan-1  C6   0.020
 ZDC  plan-1  C7   0.020
 ZDC  plan-1  O7A  0.020
 ZDC  plan-1  O7B  0.020

