# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:19:03 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 4-O-acetyl-2,6-dideoxy-beta-D-lyxo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](O)C[C@@H](O)[C@H]1OC(C)=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
 2GL  2GL  4-O-acetyl-2,6-dideoxy-beta-D-lyxo-hexopyranose  D-saccharide  27  13  .  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_2GL
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
 2GL  O5    O  O2    0  -0.481   -7.7319  3.5403   0.8985
 2GL  C1    C  CH1   0   0.298   -7.7210  3.6972  -0.4905
 2GL  C2    C  CH2   0  -0.529   -9.1340  3.8906  -1.0293
 2GL  C3    C  CH1   0   0.044   -9.8002  5.0712  -0.3407
 2GL  O3    O  OH1   0  -0.654  -11.1233  5.1654  -0.8011
 2GL  C4    C  CH1   0  -0.039   -9.7082  4.9118   1.1777
 2GL  O4    O  O2    0  -0.460  -10.4877  3.7872   1.5819
 2GL  CME   C  CH3   0  -0.771  -12.3718  2.6451   2.3499
 2GL  CO4   C  C     0   0.564  -11.7251  3.9635   2.0418
 2GL  OC4   O  O     0  -0.447  -12.2448  5.0389   2.1954
 2GL  C5    C  CH1   0   0.015   -8.2594  4.6566   1.5841
 2GL  O1    O  OH1   0  -0.654   -7.1216  2.5315  -0.9566
 2GL  C6    C  CH3   0  -0.683   -8.0847  4.4280   3.0711
 2GL  HO1   H  HOH1  0   0.457   -6.9852  2.6144  -1.9060
 2GL  H1    H  HCH1  0   0.173   -7.1157  4.5856  -0.7532
 2GL  H2    H  HCH2  0   0.250   -9.0899  4.0691  -2.1071
 2GL  H22   H  HCH2  0   0.241   -9.7139  2.9778  -0.8659
 2GL  H3    H  HCH1  0   0.218   -9.2336  5.9825  -0.5860
 2GL  HO3   H  HOH1  0   0.450  -11.5122  5.9787  -0.4617
 2GL  H4    H  HCH1  0   0.269  -10.0543  5.8205   1.6786
 2GL  HM41  H  HCH3  0   0.259  -13.3450  2.7960   2.8080
 2GL  HM42  H  HCH3  0   0.272  -12.4989  2.0679   1.4329
 2GL  HM43  H  HCH3  0   0.269  -11.7464  2.0537   3.0185
 2GL  H5    H  HCH1  0   0.224   -7.7022  5.5643   1.3021
 2GL  H61   H  HCH3  0   0.244   -7.0281  4.3418   3.3235
 2GL  H62   H  HCH3  0   0.235   -8.4909  5.2720   3.6284
 2GL  H63   H  HCH3  0   0.235   -8.5911  3.5229   3.4047

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
 2GL  O5   C1    single  1.398  0.020  1.398
 2GL  O1   HO1   single  0.850  0.020  0.980
 2GL  C1   C2    single  1.525  0.020  1.525
 2GL  C1   O1    single  1.391  0.020  1.391
 2GL  C1   H1    single  0.970  0.020  1.090
 2GL  C2   C3    single  1.520  0.020  1.520
 2GL  C2   H2    single  0.970  0.020  1.090
 2GL  C2   H22   single  0.970  0.020  1.090
 2GL  C3   O3    single  1.404  0.020  1.404
 2GL  C3   C4    single  1.529  0.020  1.529
 2GL  C3   H3    single  0.970  0.020  1.090
 2GL  O3   HO3   single  0.850  0.020  0.980
 2GL  C4   O4    single  1.427  0.020  1.427
 2GL  C4   C5    single  1.526  0.020  1.526
 2GL  C4   H4    single  0.970  0.020  1.090
 2GL  O4   CO4   single  1.332  0.020  1.332
 2GL  CME  CO4   single  1.500  0.020  1.500
 2GL  CME  HM41  single  0.970  0.020  1.090
 2GL  CME  HM42  single  0.970  0.020  1.090
 2GL  CME  HM43  single  0.970  0.020  1.090
 2GL  CO4  OC4   double  1.204  0.020  1.204
 2GL  C5   O5    single  1.412  0.020  1.412
 2GL  C5   C6    single  1.514  0.020  1.514
 2GL  C5   H5    single  0.970  0.020  1.090
 2GL  C6   H61   single  0.970  0.020  1.090
 2GL  C6   H62   single  0.970  0.020  1.090
 2GL  C6   H63   single  0.970  0.020  1.090

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
 2GL  C5    O5   C1    113.37  3.000
 2GL  H1    C1   O1    110.94  3.000
 2GL  H1    C1   C2    108.74  3.000
 2GL  O1    C1   C2    112.78  3.000
 2GL  H1    C1   O5    109.28  3.000
 2GL  O1    C1   O5    104.02  3.000
 2GL  C2    C1   O5    110.99  3.000
 2GL  H22   C2   H2    107.75  3.000
 2GL  H22   C2   C3    110.37  3.000
 2GL  H2    C2   C3    109.72  3.000
 2GL  H22   C2   C1    109.43  3.000
 2GL  H2    C2   C1    109.37  3.000
 2GL  C3    C2   C1    110.15  3.000
 2GL  H3    C3   C4    106.05  3.000
 2GL  H3    C3   O3    110.88  3.000
 2GL  C4    C3   O3    112.91  3.000
 2GL  H3    C3   C2    108.44  3.000
 2GL  C4    C3   C2    110.02  3.000
 2GL  O3    C3   C2    108.45  3.000
 2GL  HO3   O3   C3    108.76  3.000
 2GL  H4    C4   C5    108.50  3.000
 2GL  H4    C4   O4    110.62  3.000
 2GL  C5    C4   O4    108.14  3.000
 2GL  H4    C4   C3    110.43  3.000
 2GL  C5    C4   C3    109.81  3.000
 2GL  O4    C4   C3    109.30  3.000
 2GL  CO4   O4   C4    120.07  3.000
 2GL  HM43  CME  HM42  107.18  3.000
 2GL  HM43  CME  HM41  109.31  3.000
 2GL  HM42  CME  HM41  108.88  3.000
 2GL  HM43  CME  CO4   110.82  3.000
 2GL  HM42  CME  CO4   110.04  3.000
 2GL  HM41  CME  CO4   110.53  3.000
 2GL  OC4   CO4  CME   124.93  3.000
 2GL  OC4   CO4  O4    124.27  3.000
 2GL  CME   CO4  O4    110.80  3.000
 2GL  H5    C5   C6    108.50  3.000
 2GL  H5    C5   C4    105.91  3.000
 2GL  C6    C5   C4    113.34  3.000
 2GL  H5    C5   O5    109.76  3.000
 2GL  C6    C5   O5    108.32  3.000
 2GL  C4    C5   O5    110.94  3.000
 2GL  HO1   O1   C1    108.62  3.000
 2GL  H63   C6   H62   108.27  3.000
 2GL  H63   C6   H61   108.30  3.000
 2GL  H62   C6   H61   107.70  3.000
 2GL  H63   C6   C5    111.87  3.000
 2GL  H62   C6   C5    110.01  3.000
 2GL  H61   C6   C5    110.56  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
 2GL  Var_01  CME   CO4  O4   C4  177.61  30.0  3
 2GL  Var_02  HM41  CME  CO4  O4  174.89  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
 2GL  chir_01  C1  O5  C2  O1  positiv
 2GL  chir_02  C3  O3  C4  C2  negativ
 2GL  chir_03  C4  O4  C5  C3  negativ
 2GL  chir_04  C5  O5  C4  C6  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
 2GL  plan-1  O4   0.020
 2GL  plan-1  CME  0.020
 2GL  plan-1  CO4  0.020
 2GL  plan-1  OC4  0.020

