# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 16:05:45 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: methyl beta-D-galactopyranuronate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H]1O[C@@H](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
 SHB  SHB  'methyl beta-D-galactopyranuronate'  D-saccharide  26  14  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SHB
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
 SHB  C1    C  CH1   0   0.256  15.6294  -34.8143  57.3176
 SHB  C2    C  CH1   0  -0.029  15.9842  -34.9222  58.8076
 SHB  C3    C  CH1   0  -0.033  15.1998  -36.0728  59.4320
 SHB  O4    O  OH1   0  -0.664  13.1358  -34.8318  59.7914
 SHB  C5    C  CH1   0  -0.090  13.5016  -35.7459  57.6428
 SHB  C6    C  C     0   0.571  12.0242  -35.5617  57.3487
 SHB  O6A   O  O     0  -0.448  11.2082  -36.3868  57.6722
 SHB  O6    O  O2    0  -0.432  11.7475  -34.4429  56.7149
 SHB  CH3   C  CH3   0  -0.424  10.3752  -34.1878  56.4065
 SHB  O5    O  O2    0  -0.486  14.2353  -34.6555  57.1635
 SHB  C4    C  CH1   0  -0.001  13.7025  -35.9390  59.1415
 SHB  O3    O  OH1   0  -0.657  15.4427  -36.0772  60.8176
 SHB  O2    O  OH1   0  -0.653  17.3682  -35.0483  58.9964
 SHB  O1    O  OH1   0  -0.641  16.2561  -33.7691  56.6810
 SHB  H1    H  HCH1  0   0.207  15.9536  -35.7328  56.8000
 SHB  H2    H  HCH1  0   0.245  15.6927  -33.9849  59.2970
 SHB  H3    H  HCH1  0   0.225  15.5420  -37.0104  58.9650
 SHB  HO4   H  HOH1  0   0.451  13.3830  -34.8752  60.7221
 SHB  H5    H  HCH1  0   0.274  13.8097  -36.6782  57.1413
 SHB  HH3   H  HCH3  0   0.242   9.7695  -34.1385  57.3107
 SHB  HH3A  H  HCH3  0   0.253  10.3579  -33.2248  55.9053
 SHB  HH3B  H  HCH3  0   0.241   9.9695  -34.9505  55.7426
 SHB  H4    H  HCH1  0   0.238  13.2084  -36.8762  59.4346
 SHB  HO3   H  HOH1  0   0.457  15.1680  -36.9283  61.1756
 SHB  HO2   H  HOH1  0   0.445  17.6653  -35.8774  58.6041
 SHB  HO1   H  HOH1  0   0.454  16.1638  -32.9629  57.2037

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
 SHB  C1   C2    single  1.536  0.020  1.536
 SHB  C1   O5    single  1.412  0.020  1.412
 SHB  C1   O1    single  1.375  0.020  1.375
 SHB  C1   H1    single  0.970  0.020  1.090
 SHB  C2   C3    single  1.526  0.020  1.526
 SHB  C2   O2    single  1.403  0.020  1.403
 SHB  C2   H2    single  0.970  0.020  1.090
 SHB  C3   C4    single  1.531  0.020  1.531
 SHB  C3   O3    single  1.407  0.020  1.407
 SHB  C3   H3    single  0.970  0.020  1.090
 SHB  O4   C4    single  1.403  0.020  1.403
 SHB  O4   HO4   single  0.850  0.020  0.980
 SHB  C5   C6    single  1.518  0.020  1.518
 SHB  C5   O5    single  1.399  0.020  1.399
 SHB  C5   C4    single  1.524  0.020  1.524
 SHB  C5   H5    single  0.970  0.020  1.090
 SHB  C6   O6A   double  1.205  0.020  1.205
 SHB  C6   O6    single  1.315  0.020  1.315
 SHB  O6   CH3   single  1.430  0.020  1.430
 SHB  CH3  HH3   single  0.970  0.020  1.090
 SHB  CH3  HH3A  single  0.970  0.020  1.090
 SHB  CH3  HH3B  single  0.970  0.020  1.090
 SHB  C4   H4    single  0.970  0.020  1.090
 SHB  O3   HO3   single  0.850  0.020  0.980
 SHB  O2   HO2   single  0.850  0.020  0.980
 SHB  O1   HO1   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
 SHB  H1    C1   O1    106.37  3.000
 SHB  H1    C1   O5    109.44  3.000
 SHB  O1    C1   O5    108.31  3.000
 SHB  H1    C1   C2    109.20  3.000
 SHB  O1    C1   C2    113.42  3.000
 SHB  O5    C1   C2    110.00  3.000
 SHB  H2    C2   O2    106.20  3.000
 SHB  H2    C2   C3    108.98  3.000
 SHB  O2    C2   C3    112.60  3.000
 SHB  H2    C2   C1    108.15  3.000
 SHB  O2    C2   C1    111.40  3.000
 SHB  C3    C2   C1    109.35  3.000
 SHB  H3    C3   O3    111.17  3.000
 SHB  H3    C3   C4    107.32  3.000
 SHB  O3    C3   C4    110.86  3.000
 SHB  H3    C3   C2    107.97  3.000
 SHB  O3    C3   C2    108.46  3.000
 SHB  C4    C3   C2    111.04  3.000
 SHB  HO4   O4   C4    107.94  3.000
 SHB  H5    C5   C4    107.65  3.000
 SHB  H5    C5   O5    110.90  3.000
 SHB  C4    C5   O5    111.50  3.000
 SHB  H5    C5   C6    106.65  3.000
 SHB  C4    C5   C6    109.53  3.000
 SHB  O5    C5   C6    110.46  3.000
 SHB  O6    C6   O6A   124.72  3.000
 SHB  O6    C6   C5    113.67  3.000
 SHB  O6A   C6   C5    121.62  3.000
 SHB  CH3   O6   C6    117.24  3.000
 SHB  HH3B  CH3  HH3A  109.49  3.000
 SHB  HH3B  CH3  HH3   109.29  3.000
 SHB  HH3A  CH3  HH3   109.52  3.000
 SHB  HH3B  CH3  O6    111.35  3.000
 SHB  HH3A  CH3  O6    105.85  3.000
 SHB  HH3   CH3  O6    111.26  3.000
 SHB  C5    O5   C1    113.14  3.000
 SHB  H4    C4   C5    108.11  3.000
 SHB  H4    C4   O4    111.57  3.000
 SHB  C5    C4   O4    107.59  3.000
 SHB  H4    C4   C3    108.33  3.000
 SHB  C5    C4   C3    109.06  3.000
 SHB  O4    C4   C3    112.09  3.000
 SHB  HO3   O3   C3    108.63  3.000
 SHB  HO2   O2   C2    109.07  3.000
 SHB  HO1   O1   C1    109.91  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
 SHB  Var_01  HH3  CH3  O6  C6  60.30  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
 SHB  chir_01  C1  C2  O5  O1  negativ
 SHB  chir_02  C2  O2  C1  C3  negativ
 SHB  chir_03  C3  O3  C2  C4  positiv
 SHB  chir_04  C5  O5  C4  C6  negativ
 SHB  chir_05  C4  O4  C5  C3  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
 SHB  plan-1  C5   0.020
 SHB  plan-1  C6   0.020
 SHB  plan-1  O6A  0.020
 SHB  plan-1  O6   0.020

