# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:22:17 2021
#   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  28  14  .  2023-02-15  2023-02-16
;
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   0.014  13.3588  47.1808   9.3110
 ZDC  C1M   C  CH3   0  -0.680  14.0098  47.8295  10.5154
 ZDC  C2    C  CH1   0   0.015  14.2878  47.0758   8.1067
 ZDC  C3    C  CH1   0  -0.002  13.5663  46.3408   6.9797
 ZDC  C4    C  CH1   0   0.006  13.0533  44.9981   7.4799
 ZDC  C5    C  CH1   0  -0.028  12.1861  45.1805   8.7340
 ZDC  C6    C  CH2   0  -0.607  10.8188  45.8070   8.4409
 ZDC  C7    C  C     0   0.551  10.0582  45.9823   9.7270
 ZDC  O2    O  OH1   0  -0.672  15.4682  46.4127   8.4865
 ZDC  O3    O  OH1   0  -0.677  14.4697  46.1919   5.9094
 ZDC  O4    O  OH1   0  -0.671  12.3453  44.3882   6.4255
 ZDC  O5    O  O2    0  -0.493  12.8968  45.9017   9.7157
 ZDC  O7A   O  O     0  -0.451   9.7987  45.0809  10.4861
 ZDC  O7B   O  OH1   0  -0.586   9.6996  47.2410   9.9471
 ZDC  H1    H  HCH1  0   0.221  12.5131  47.8096   8.9978
 ZDC  H1M1  H  HCH3  0   0.231  14.3616  48.8285  10.2583
 ZDC  H1M2  H  HCH3  0   0.239  13.2911  47.9299  11.3287
 ZDC  H1M3  H  HCH3  0   0.234  14.8596  47.2503  10.8743
 ZDC  H2    H  HCH1  0   0.226  14.5033  48.1010   7.7679
 ZDC  H2O   H  HOH1  0   0.450  15.9743  46.2314   7.6873
 ZDC  H3    H  HCH1  0   0.216  12.7090  46.9602   6.6726
 ZDC  H3O   H  HOH1  0   0.454  14.0823  45.5853   5.2689
 ZDC  H4    H  HCH1  0   0.240  13.9193  44.3875   7.7681
 ZDC  H4O   H  HOH1  0   0.461  12.2715  43.4458   6.6043
 ZDC  H5    H  HCH1  0   0.260  12.0106  44.1942   9.1730
 ZDC  H61   H  HCH2  0   0.269  10.8958  46.7536   7.9060
 ZDC  H62   H  HCH2  0   0.299  10.2510  45.1272   7.8024
 ZDC  H7OB  H  HOH1  0   0.479   9.2147  47.3049  10.7843

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  1.515  0.020  1.515
 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  1.419  0.020  1.419
 ZDC  C1   C2    single  1.525  0.020  1.525
 ZDC  C2   H2    single  0.970  0.020  1.090
 ZDC  C2   O2    single  1.406  0.020  1.406
 ZDC  O2   H2O   single  0.850  0.020  0.980
 ZDC  C2   C3    single  1.527  0.020  1.527
 ZDC  C3   H3    single  0.970  0.020  1.090
 ZDC  C3   O3    single  1.408  0.020  1.408
 ZDC  O3   H3O   single  0.850  0.020  0.980
 ZDC  C3   C4    single  1.522  0.020  1.522
 ZDC  C4   H4    single  0.970  0.020  1.090
 ZDC  C4   O4    single  1.409  0.020  1.409
 ZDC  O4   H4O   single  0.850  0.020  0.980
 ZDC  C4   C5    single  1.536  0.020  1.536
 ZDC  C5   H5    single  0.970  0.020  1.090
 ZDC  C5   O5    single  1.410  0.020  1.410
 ZDC  C5   C6    single  1.532  0.020  1.532
 ZDC  C6   H61   single  0.970  0.020  1.090
 ZDC  C6   H62   single  0.970  0.020  1.090
 ZDC  C6   C7    single  1.504  0.020  1.504
 ZDC  C7   O7A   double  1.207  0.020  1.207
 ZDC  C7   O7B   single  1.327  0.020  1.327
 ZDC  O7B  H7OB  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
 ZDC  H1    C1   O5    110.27  3.000
 ZDC  O5    C1   C2    111.20  3.000
 ZDC  H1    C1   C2    106.44  3.000
 ZDC  C2    C1   C1M   113.30  3.000
 ZDC  O5    C1   C1M   107.41  3.000
 ZDC  H1    C1   C1M   108.19  3.000
 ZDC  H1M3  C1M  H1M2  108.51  3.000
 ZDC  H1M3  C1M  H1M1  108.26  3.000
 ZDC  H1M2  C1M  H1M1  107.72  3.000
 ZDC  H1M3  C1M  C1    111.68  3.000
 ZDC  H1M2  C1M  C1    110.45  3.000
 ZDC  H1M1  C1M  C1    110.10  3.000
 ZDC  H2    C2   O2    110.97  3.000
 ZDC  O2    C2   C3    111.66  3.000
 ZDC  H2    C2   C3    108.28  3.000
 ZDC  C3    C2   C1    109.16  3.000
 ZDC  O2    C2   C1    109.30  3.000
 ZDC  H2    C2   C1    107.35  3.000
 ZDC  H3    C3   O3    110.30  3.000
 ZDC  O3    C3   C4    111.88  3.000
 ZDC  H3    C3   C4    109.00  3.000
 ZDC  C4    C3   C2    109.97  3.000
 ZDC  O3    C3   C2    107.98  3.000
 ZDC  H3    C3   C2    107.63  3.000
 ZDC  H4    C4   O4    110.61  3.000
 ZDC  O4    C4   C5    112.26  3.000
 ZDC  H4    C4   C5    107.28  3.000
 ZDC  C5    C4   C3    110.73  3.000
 ZDC  O4    C4   C3    107.78  3.000
 ZDC  H4    C4   C3    108.12  3.000
 ZDC  H5    C5   O5    105.22  3.000
 ZDC  O5    C5   C6    111.95  3.000
 ZDC  H5    C5   C6    107.59  3.000
 ZDC  C6    C5   C4    113.35  3.000
 ZDC  O5    C5   C4    110.16  3.000
 ZDC  H5    C5   C4    108.14  3.000
 ZDC  H62   C6   H61   106.89  3.000
 ZDC  H62   C6   C7    108.04  3.000
 ZDC  H61   C6   C7    110.73  3.000
 ZDC  C7    C6   C5    109.59  3.000
 ZDC  H62   C6   C5    108.74  3.000
 ZDC  H61   C6   C5    112.70  3.000
 ZDC  O7B   C7   O7A   123.10  3.000
 ZDC  O7B   C7   C6    112.89  3.000
 ZDC  O7A   C7   C6    124.02  3.000
 ZDC  H2O   O2   C2    107.80  3.000
 ZDC  H3O   O3   C3    108.29  3.000
 ZDC  H4O   O4   C4    108.88  3.000
 ZDC  C5    O5   C1    115.25  3.000
 ZDC  H7OB  O7B  C7    109.93  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  CONST_01  H7OB  O7B  C7  C6  180.00   0.0  0
 ZDC  Var_01    O7A   C7   C6  C5  -57.34  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
 ZDC  plan-1  H7OB  0.020

