# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:03:19 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1OC(=C[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
 GCD  GCD  '4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid'  L-saccharide  19  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GCD
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
 GCD  C1   C  CH1    0   0.272  19.4883  28.0466  50.6033
 GCD  C2   C  CH1    0  -0.021  18.1623  28.0548  49.8578
 GCD  C3   C  CH1    0   0.003  17.5235  29.4248  50.0411
 GCD  C4   C  C1     0  -0.406  17.6225  29.8441  51.4764
 GCD  C5   C  C      0   0.170  18.4415  29.2508  52.3467
 GCD  C6   C  C      0   0.373  18.5402  29.6411  53.8223
 GCD  O1   O  OH1    0  -0.648  20.1070  26.8313  50.4348
 GCD  O2   O  OH1    0  -0.664  18.4129  27.7590  48.5100
 GCD  O3   O  OH1    0  -0.669  16.1848  29.3250  49.5913
 GCD  O5   O  O2     0  -0.483  19.2671  28.2359  51.9917
 GCD  O6A  O  O      0  -0.583  17.7227  30.4933  54.2134
 GCD  O6B  O  OC    -1  -0.589  19.4263  29.0702  54.4787
 GCD  H1   H  HCH1   0   0.200  20.1143  28.8797  50.2430
 GCD  H2   H  HCH1   0   0.215  17.5040  27.3022  50.3223
 GCD  H3   H  HCH1   0   0.219  18.0732  30.1382  49.4084
 GCD  HO1  H  HOH1   0   0.463  21.0365  26.9080  50.6756
 GCD  HO2  H  HOH1   0   0.449  17.5880  27.8713  48.0259
 GCD  HO3  H  HOH1   0   0.454  15.8525  30.2134  49.4310
 GCD  H4   H  H      0   0.246  17.0129  30.6680  51.8214

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
 GCD  C1  C2   single  1.521  0.020  1.521
 GCD  C1  O1   single  1.374  0.020  1.374
 GCD  C1  O5   single  1.419  0.020  1.419
 GCD  C1  H1   single  0.970  0.020  1.090
 GCD  C2  C3   single  1.523  0.020  1.523
 GCD  C2  O2   single  1.402  0.020  1.402
 GCD  C2  H2   single  0.970  0.020  1.090
 GCD  C3  C4   single  1.499  0.020  1.499
 GCD  C3  O3   single  1.416  0.020  1.416
 GCD  C3  H3   single  0.970  0.020  1.090
 GCD  C4  C5   double  1.334  0.020  1.334
 GCD  C5  C6   single  1.530  0.020  1.530
 GCD  C5  O5   single  1.356  0.020  1.356
 GCD  C6  O6A  deloc   1.244  0.020  1.244
 GCD  C6  O6B  deloc   1.242  0.020  1.242
 GCD  O1  HO1  single  0.850  0.020  0.980
 GCD  O2  HO2  single  0.850  0.020  0.980
 GCD  O3  HO3  single  0.850  0.020  0.980
 GCD  C4  H4   single  0.930  0.020  1.080

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
 GCD  H1   C1  O5   107.91  3.000
 GCD  H1   C1  O1   111.87  3.000
 GCD  O5   C1  O1   107.95  3.000
 GCD  H1   C1  C2   109.31  3.000
 GCD  O5   C1  C2   110.06  3.000
 GCD  O1   C1  C2   109.70  3.000
 GCD  H2   C2  O2   111.57  3.000
 GCD  H2   C2  C3   108.24  3.000
 GCD  O2   C2  C3   112.36  3.000
 GCD  H2   C2  C1   108.08  3.000
 GCD  O2   C2  C1   108.31  3.000
 GCD  C3   C2  C1   108.15  3.000
 GCD  H3   C3  O3   109.59  3.000
 GCD  H3   C3  C4   109.64  3.000
 GCD  O3   C3  C4   112.74  3.000
 GCD  H3   C3  C2   107.73  3.000
 GCD  O3   C3  C2   107.16  3.000
 GCD  C4   C3  C2   109.83  3.000
 GCD  H4   C4  C5   118.47  3.000
 GCD  H4   C4  C3   118.78  3.000
 GCD  C5   C4  C3   122.75  3.000
 GCD  O5   C5  C6   113.85  3.000
 GCD  O5   C5  C4   122.41  3.000
 GCD  C6   C5  C4   123.74  3.000
 GCD  O6B  C6  O6A  128.15  3.000
 GCD  O6B  C6  C5   116.02  3.000
 GCD  O6A  C6  C5   115.83  3.000
 GCD  HO1  O1  C1   109.47  3.000
 GCD  HO2  O2  C2   107.79  3.000
 GCD  HO3  O3  C3   108.32  3.000
 GCD  C5   O5  C1   116.82  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
 GCD  Var_01  C4   C5  O5  C1  15.75  30.0  1
 GCD  Var_02  O5   C5  C4  C3   1.24  30.0  1
 GCD  Var_03  O6A  C6  C5  C4   5.57  30.0  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
 GCD  chir_01  C1  C2  O1  O5  positiv
 GCD  chir_02  C2  O2  C1  C3  negativ
 GCD  chir_03  C3  O3  C2  C4  positiv

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
 GCD  plan-1  C5   0.020
 GCD  plan-1  C6   0.020
 GCD  plan-1  O6A  0.020
 GCD  plan-1  O6B  0.020

