# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:42:20 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: methyl alpha-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
 M8C  M8C  'methyl alpha-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 GRAND
;

data_comp_M8C
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
 M8C  C1    C  CH1   0   0.217  28.0855  -1.2204   0.1031
 M8C  C2    C  CH1   0  -0.008  27.7167   0.2385  -0.1819
 M8C  C3    C  CH1   0   0.005  26.4099   0.5955   0.5140
 M8C  O4    O  OH1   0  -0.666  24.9663  -0.2701  -1.2447
 M8C  C5    C  CH1   0  -0.082  25.8064  -1.8087   0.3486
 M8C  C6    C  C     0   0.557  24.8022  -2.8082  -0.1961
 M8C  O6A   O  O     0  -0.423  25.0019  -3.5615  -1.1091
 M8C  O6B   O  O2    0  -0.453  23.6684  -2.7326   0.4831
 M8C  CH3   C  CH3   0  -0.421  22.6002  -3.5931   0.0866
 M8C  O5    O  O2    0  -0.495  27.0276  -2.0600  -0.2983
 M8C  C4    C  CH1   0  -0.006  25.3106  -0.3832   0.1124
 M8C  O3    O  OH1   0  -0.671  25.9677   1.8846   0.1667
 M8C  O2    O  OH1   0  -0.666  28.6935   1.1447   0.2655
 M8C  O1    O  OH1   0  -0.656  28.3911  -1.3529   1.4498
 M8C  H1    H  HCH1  0   0.237  28.9274  -1.5243  -0.5303
 M8C  H2    H  HCH1  0   0.230  27.5666   0.3227  -1.2658
 M8C  H3    H  HCH1  0   0.221  26.5516   0.5098   1.6013
 M8C  HO4   H  HOH1  0   0.454  24.7789   0.6569  -1.4303
 M8C  H5    H  HCH1  0   0.274  25.8873  -1.9622   1.4330
 M8C  HH31  H  HCH3  0   0.253  21.7807  -3.3831   0.7673
 M8C  HH32  H  HCH3  0   0.240  22.2835  -3.3878  -0.9355
 M8C  HH33  H  HCH3  0   0.240  22.8827  -4.6419   0.1727
 M8C  H4    H  HCH1  0   0.246  24.4421  -0.2099   0.7622
 M8C  HO3   H  HOH1  0   0.453  26.7134   2.4900   0.2430
 M8C  HO2   H  HOH1  0   0.458  29.4156   1.1699  -0.3697
 M8C  HO1   H  HOH1  0   0.462  28.8265  -2.2002   1.5938

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
 M8C  C1   O5    single  1.409  0.020  1.409
 M8C  C1   C2    single  1.532  0.020  1.532
 M8C  C1   O1    single  1.387  0.020  1.387
 M8C  C1   H1    single  0.970  0.020  1.090
 M8C  C2   O2    single  1.406  0.020  1.406
 M8C  C2   C3    single  1.523  0.020  1.523
 M8C  C2   H2    single  0.970  0.020  1.090
 M8C  C3   O3    single  1.406  0.020  1.406
 M8C  C3   C4    single  1.526  0.020  1.526
 M8C  C3   H3    single  0.970  0.020  1.090
 M8C  O4   C4    single  1.405  0.020  1.405
 M8C  O4   HO4   single  0.850  0.020  0.980
 M8C  C5   O5    single  1.405  0.020  1.405
 M8C  C5   C6    single  1.518  0.020  1.518
 M8C  C5   C4    single  1.528  0.020  1.528
 M8C  C5   H5    single  0.970  0.020  1.090
 M8C  C6   O6A   double  1.200  0.020  1.200
 M8C  C6   O6B   single  1.324  0.020  1.324
 M8C  O6B  CH3   single  1.428  0.020  1.428
 M8C  CH3  HH31  single  0.970  0.020  1.090
 M8C  CH3  HH32  single  0.970  0.020  1.090
 M8C  CH3  HH33  single  0.970  0.020  1.090
 M8C  C4   H4    single  0.970  0.020  1.090
 M8C  O3   HO3   single  0.850  0.020  0.980
 M8C  O2   HO2   single  0.850  0.020  0.980
 M8C  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
 M8C  H1    C1   O1    111.42  3.000
 M8C  H1    C1   O5    104.29  3.000
 M8C  O1    C1   O5    112.65  3.000
 M8C  H1    C1   C2    109.96  3.000
 M8C  O1    C1   C2    108.95  3.000
 M8C  O5    C1   C2    109.50  3.000
 M8C  H2    C2   O2    111.10  3.000
 M8C  H2    C2   C3    108.41  3.000
 M8C  O2    C2   C3    107.44  3.000
 M8C  H2    C2   C1    106.85  3.000
 M8C  C3    C2   C1    110.17  3.000
 M8C  O2    C2   C1    112.81  3.000
 M8C  H3    C3   O3    110.86  3.000
 M8C  H3    C3   C4    107.64  3.000
 M8C  O3    C3   C4    107.24  3.000
 M8C  H3    C3   C2    108.84  3.000
 M8C  C4    C3   C2    110.34  3.000
 M8C  O3    C3   C2    111.83  3.000
 M8C  HO4   O4   C4    108.13  3.000
 M8C  H5    C5   C4    107.88  3.000
 M8C  H5    C5   O5    111.45  3.000
 M8C  C4    C5   O5    112.20  3.000
 M8C  H5    C5   C6    108.12  3.000
 M8C  C4    C5   C6    110.14  3.000
 M8C  O5    C5   C6    106.98  3.000
 M8C  O6B   C6   O6A   124.65  3.000
 M8C  O6B   C6   C5    110.17  3.000
 M8C  O6A   C6   C5    125.18  3.000
 M8C  CH3   O6B  C6    117.64  3.000
 M8C  HH33  CH3  HH32  109.32  3.000
 M8C  HH33  CH3  HH31  109.41  3.000
 M8C  HH32  CH3  HH31  109.41  3.000
 M8C  HH33  CH3  O6B   111.36  3.000
 M8C  HH32  CH3  O6B   111.37  3.000
 M8C  HH31  CH3  O6B   105.90  3.000
 M8C  C5    O5   C1    114.52  3.000
 M8C  H4    C4   C5    108.20  3.000
 M8C  H4    C4   O4    111.42  3.000
 M8C  C5    C4   O4    107.71  3.000
 M8C  H4    C4   C3    108.22  3.000
 M8C  C5    C4   C3    108.91  3.000
 M8C  O4    C4   C3    112.29  3.000
 M8C  HO3   O3   C3    108.24  3.000
 M8C  HO2   O2   C2    109.16  3.000
 M8C  HO1   O1   C1    109.19  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
 M8C  Var_01  HH31  CH3  O6B  C6  179.41  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
 M8C  chir_01  C1  O5  C2  O1  negativ
 M8C  chir_02  C2  O2  C1  C3  negativ
 M8C  chir_03  C3  O3  C2  C4  positiv
 M8C  chir_04  C5  O5  C4  C6  negativ
 M8C  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
 M8C  plan-1  C5   0.020
 M8C  plan-1  C6   0.020
 M8C  plan-1  O6A  0.020
 M8C  plan-1  O6B  0.020

