# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:15:25 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 6-deoxy-2-O-methyl-beta-L-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@@H](O)O[C@@H](C)[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
 MXY  MXY  6-deoxy-2-O-methyl-beta-L-galactopyranose  L-saccharide  26  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 (reasonable std)
;

data_comp_MXY
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
 MXY  C1    C  CH1   0   0.277  36.3165  4.2651  38.3255
 MXY  C2    C  CH1   0   0.008  35.6974  4.4479  39.7135
 MXY  C3    C  CH1   0   0.019  35.6852  3.1025  40.4337
 MXY  C4    C  CH1   0  -0.015  37.0828  2.4805  40.4399
 MXY  C5    C  CH1   0   0.018  37.5869  2.3975  38.9970
 MXY  O2    O  O2    0  -0.493  34.3729  4.9026  39.5886
 MXY  O3    O  OH1   0  -0.662  35.1645  3.2977  41.7221
 MXY  O4    O  OH1   0  -0.668  37.9160  3.2653  41.2573
 MXY  O5    O  O2    0  -0.492  37.5947  3.6880  38.4185
 MXY  CM    C  CH3   0  -0.403  34.1759  6.2667  39.8699
 MXY  C6    C  CH3   0  -0.697  38.9812  1.8170  38.8777
 MXY  O1    O  OH1   0  -0.653  36.4410  5.4999  37.7233
 MXY  H1    H  HCH1  0   0.179  35.6598  3.5952  37.7405
 MXY  H2    H  HCH1  0   0.225  36.3109  5.1601  40.2839
 MXY  H3    H  HCH1  0   0.211  35.0439  2.4220  39.8506
 MXY  H4    H  HCH1  0   0.226  36.9995  1.4531  40.8268
 MXY  H5    H  HCH1  0   0.209  36.8909  1.7433  38.4466
 MXY  HO3   H  HOH1  0   0.449  35.0366  2.4360  42.1314
 MXY  HO4   H  HOH1  0   0.454  38.7102  2.7642  41.4637
 MXY  HCM1  H  HCH3  0   0.227  33.1044  6.4595  39.8161
 MXY  HCM2  H  HCH3  0   0.205  34.5187  6.5306  40.8766
 MXY  HCM3  H  HCH3  0   0.207  34.6780  6.9255  39.1562
 MXY  H61   H  HCH3  0   0.246  39.2707  1.7178  37.8318
 MXY  H62   H  HCH3  0   0.228  39.7259  2.4410  39.3738
 MXY  H63   H  HCH3  0   0.235  39.0140  0.8237  39.3259
 MXY  HO1   H  HOH1  0   0.460  36.5348  5.3835  36.7719

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
 MXY  C1  C2    single  1.531  0.020  1.531
 MXY  C1  O5    single  1.406  0.020  1.406
 MXY  C1  O1    single  1.379  0.020  1.379
 MXY  C1  H1    single  0.970  0.020  1.090
 MXY  C2  C3    single  1.526  0.020  1.526
 MXY  C2  O2    single  1.406  0.020  1.406
 MXY  C2  H2    single  0.970  0.020  1.090
 MXY  C3  C4    single  1.530  0.020  1.530
 MXY  C3  O3    single  1.403  0.020  1.403
 MXY  C3  H3    single  0.970  0.020  1.090
 MXY  C4  C5    single  1.531  0.020  1.531
 MXY  C4  O4    single  1.407  0.020  1.407
 MXY  C4  H4    single  0.970  0.020  1.090
 MXY  C5  O5    single  1.414  0.020  1.414
 MXY  C5  C6    single  1.515  0.020  1.515
 MXY  C5  H5    single  0.970  0.020  1.090
 MXY  O2  CM    single  1.407  0.020  1.407
 MXY  O3  HO3   single  0.850  0.020  0.980
 MXY  O4  HO4   single  0.850  0.020  0.980
 MXY  CM  HCM1  single  0.970  0.020  1.090
 MXY  CM  HCM2  single  0.970  0.020  1.090
 MXY  CM  HCM3  single  0.970  0.020  1.090
 MXY  C6  H61   single  0.970  0.020  1.090
 MXY  C6  H62   single  0.970  0.020  1.090
 MXY  C6  H63   single  0.970  0.020  1.090
 MXY  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
 MXY  H1    C1  O1    111.41  3.000
 MXY  H1    C1  O5    109.05  3.000
 MXY  O1    C1  O5    108.32  3.000
 MXY  H1    C1  C2    108.17  3.000
 MXY  O1    C1  C2    108.99  3.000
 MXY  O5    C1  C2    110.91  3.000
 MXY  H2    C2  O2    111.24  3.000
 MXY  H2    C2  C3    109.31  3.000
 MXY  O2    C2  C3    108.64  3.000
 MXY  H2    C2  C1    108.78  3.000
 MXY  O2    C2  C1    109.82  3.000
 MXY  C3    C2  C1    109.02  3.000
 MXY  H3    C3  O3    110.84  3.000
 MXY  H3    C3  C4    106.42  3.000
 MXY  O3    C3  C4    113.07  3.000
 MXY  H3    C3  C2    107.42  3.000
 MXY  O3    C3  C2    108.28  3.000
 MXY  C4    C3  C2    110.68  3.000
 MXY  H4    C4  O4    111.18  3.000
 MXY  H4    C4  C5    107.79  3.000
 MXY  O4    C4  C5    112.52  3.000
 MXY  H4    C4  C3    108.16  3.000
 MXY  O4    C4  C3    108.46  3.000
 MXY  C5    C4  C3    108.61  3.000
 MXY  H5    C5  C6    108.32  3.000
 MXY  H5    C5  O5    109.92  3.000
 MXY  C6    C5  O5    108.20  3.000
 MXY  H5    C5  C4    107.15  3.000
 MXY  C6    C5  C4    113.46  3.000
 MXY  O5    C5  C4    109.75  3.000
 MXY  CM    O2  C2    115.33  3.000
 MXY  HO3   O3  C3    108.38  3.000
 MXY  HO4   O4  C4    108.86  3.000
 MXY  C5    O5  C1    113.37  3.000
 MXY  HCM3  CM  HCM2  108.11  3.000
 MXY  HCM3  CM  HCM1  108.22  3.000
 MXY  HCM2  CM  HCM1  108.08  3.000
 MXY  HCM3  CM  O2    112.92  3.000
 MXY  HCM2  CM  O2    111.92  3.000
 MXY  HCM1  CM  O2    107.42  3.000
 MXY  H63   C6  H62   108.29  3.000
 MXY  H63   C6  H61   107.68  3.000
 MXY  H62   C6  H61   107.89  3.000
 MXY  H63   C6  C5    110.14  3.000
 MXY  H62   C6  C5    111.91  3.000
 MXY  H61   C6  C5    110.79  3.000
 MXY  HO1   O1  C1    109.38  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
 MXY  Var_01  HCM1  CM  O2  C2  -175.35  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
 MXY  chir_01  C1  C2  O5  O1  positiv
 MXY  chir_02  C2  O2  C3  C1  negativ
 MXY  chir_03  C3  O3  C2  C4  negativ
 MXY  chir_04  C4  O4  C3  C5  negativ
 MXY  chir_05  C5  O5  C4  C6  positiv

