# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 20:02:18 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: methyl 4,6-O-[(1R)-1-carboxyethylidene]-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@@H]2CO[C@](C)(O[C@@H]2[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
 CDG  CDG  'methyl 4,6-O-[(1R)-1-carboxyethylidene]-beta-D-galactopyranoside'  ligand  34  18  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CDG
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
 CDG  C1    C  CH1   0   0.298   0.4673  -0.2442   2.2987
 CDG  C2    C  CH1   0  -0.032  -0.9405   0.2593   1.9864
 CDG  C3    C  CH1   0   0.014  -1.5571  -0.6378   0.9184
 CDG  C4    C  CH1   0  -0.032  -0.6425  -0.7443  -0.2884
 CDG  C5    C  CH1   0   0.008   0.7671  -1.1364   0.1446
 CDG  C6    C  CH2   0  -0.243   1.6797  -1.0461  -1.0583
 CDG  C7    C  CT    0   0.406   0.2697   0.5898  -2.0198
 CDG  C8    C  C     0   0.483  -0.2256  -0.2632  -3.2134
 CDG  C9    C  CH3   0  -0.693   0.3105   2.0417  -2.4696
 CDG  O1    O  O2    0  -0.495   1.0445   0.6104   3.2096
 CDG  O2    O  OH1   0  -0.670  -1.7729   0.1857   3.1174
 CDG  O3    O  OH1   0  -0.665  -2.8165  -0.1884   0.4992
 CDG  O4    O  O2    0  -0.485  -0.6086   0.5102  -0.9415
 CDG  O5    O  O2    0  -0.496   1.2509  -0.2544   1.1320
 CDG  O6    O  O2    0  -0.479   1.5663   0.2186  -1.6841
 CDG  O8A   O  OH1   0  -0.576  -1.5435  -0.2666  -3.3041
 CDG  O8B   O  O     0  -0.420   0.5125  -0.7916  -4.0018
 CDG  C10   C  CH3   0  -0.411   2.2181   0.1184   3.8286
 CDG  H1    H  HCH1  0   0.183   0.4033  -1.2723   2.7077
 CDG  H2    H  HCH1  0   0.229  -0.8677   1.2873   1.6046
 CDG  H3    H  HCH1  0   0.224  -1.6228  -1.6548   1.3389
 CDG  H4    H  HCH1  0   0.255  -1.0353  -1.5261  -0.9549
 CDG  H5    H  HCH1  0   0.250   0.7584  -2.1738   0.5099
 CDG  H6C1  H  HCH2  0   0.268   2.7234  -1.1579  -0.7637
 CDG  H6C2  H  HCH2  0   0.235   1.4443  -1.8636  -1.7490
 CDG  H9C1  H  HCH3  0   0.253   0.9865   2.1635  -3.3148
 CDG  H9C2  H  HCH3  0   0.254  -0.6786   2.3869  -2.7658
 CDG  H9C3  H  HCH3  0   0.263   0.6648   2.6659  -1.6489
 CDG  HA    H  HOH1  0   0.458  -1.4906   0.8520   3.7519
 CDG  HB    H  HOH1  0   0.453  -3.3959  -0.1654   1.2678
 CDG  H8A   H  HOH1  0   0.486  -1.8212  -0.7546  -4.0948
 CDG  H101  H  HCH3  0   0.240   2.4654   0.7974   4.6425
 CDG  H102  H  HCH3  0   0.215   2.0614  -0.8816   4.2449
 CDG  H103  H  HCH3  0   0.221   3.0644   0.0785   3.1392

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
 CDG  C1   C2    single  1.527  0.020  1.527
 CDG  C1   O1    single  1.376  0.020  1.376
 CDG  C1   O5    single  1.406  0.020  1.406
 CDG  C1   H1    single  0.970  0.020  1.090
 CDG  C2   C3    single  1.525  0.020  1.525
 CDG  C2   O2    single  1.406  0.020  1.406
 CDG  C2   H2    single  0.970  0.020  1.090
 CDG  C3   C4    single  1.518  0.020  1.518
 CDG  C3   O3    single  1.401  0.020  1.401
 CDG  C3   H3    single  0.970  0.020  1.090
 CDG  C4   C5    single  1.526  0.020  1.526
 CDG  C4   O4    single  1.415  0.020  1.415
 CDG  C4   H4    single  0.970  0.020  1.090
 CDG  C5   C6    single  1.513  0.020  1.513
 CDG  C5   O5    single  1.410  0.020  1.410
 CDG  C5   H5    single  0.970  0.020  1.090
 CDG  C6   O6    single  1.416  0.020  1.416
 CDG  C6   H6C1  single  0.970  0.020  1.090
 CDG  C6   H6C2  single  0.970  0.020  1.090
 CDG  C7   C8    single  1.548  0.020  1.548
 CDG  C7   C9    single  1.521  0.020  1.521
 CDG  C7   O4    single  1.393  0.020  1.393
 CDG  C7   O6    single  1.390  0.020  1.390
 CDG  C8   O8A   single  1.321  0.020  1.321
 CDG  C8   O8B   double  1.202  0.020  1.202
 CDG  C9   H9C1  single  0.970  0.020  1.090
 CDG  C9   H9C2  single  0.970  0.020  1.090
 CDG  C9   H9C3  single  0.970  0.020  1.090
 CDG  O1   C10   single  1.415  0.020  1.415
 CDG  O2   HA    single  0.850  0.020  0.980
 CDG  O3   HB    single  0.850  0.020  0.980
 CDG  O8A  H8A   single  0.850  0.020  0.980
 CDG  C10  H101  single  0.970  0.020  1.090
 CDG  C10  H102  single  0.970  0.020  1.090
 CDG  C10  H103  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
 CDG  H1    C1   O5    109.38  3.000
 CDG  H1    C1   O1    110.86  3.000
 CDG  O5    C1   O1    108.67  3.000
 CDG  H1    C1   C2    109.15  3.000
 CDG  O5    C1   C2    110.27  3.000
 CDG  O1    C1   C2    108.49  3.000
 CDG  H2    C2   O2    111.56  3.000
 CDG  H2    C2   C3    109.50  3.000
 CDG  O2    C2   C3    107.05  3.000
 CDG  H2    C2   C1    108.57  3.000
 CDG  O2    C2   C1    111.34  3.000
 CDG  C3    C2   C1    108.78  3.000
 CDG  H3    C3   O3    110.87  3.000
 CDG  H3    C3   C4    105.93  3.000
 CDG  O3    C3   C4    109.04  3.000
 CDG  H3    C3   C2    107.44  3.000
 CDG  O3    C3   C2    112.60  3.000
 CDG  C4    C3   C2    110.76  3.000
 CDG  H4    C4   O4    111.04  3.000
 CDG  H4    C4   C5    108.62  3.000
 CDG  O4    C4   C5    109.68  3.000
 CDG  H4    C4   C3    108.45  3.000
 CDG  O4    C4   C3    108.61  3.000
 CDG  C5    C4   C3    110.43  3.000
 CDG  H5    C5   O5    111.11  3.000
 CDG  H5    C5   C6    108.98  3.000
 CDG  O5    C5   C6    108.22  3.000
 CDG  H5    C5   C4    109.22  3.000
 CDG  O5    C5   C4    110.80  3.000
 CDG  C6    C5   C4    108.44  3.000
 CDG  H6C2  C6   H6C1  107.42  3.000
 CDG  H6C2  C6   O6    111.76  3.000
 CDG  H6C1  C6   O6    106.72  3.000
 CDG  H6C2  C6   C5    109.10  3.000
 CDG  H6C1  C6   C5    110.89  3.000
 CDG  O6    C6   C5    110.89  3.000
 CDG  O6    C7   O4    112.70  3.000
 CDG  O6    C7   C9    107.54  3.000
 CDG  O4    C7   C9    107.48  3.000
 CDG  O6    C7   C8    109.72  3.000
 CDG  O4    C7   C8    111.32  3.000
 CDG  C9    C7   C8    107.86  3.000
 CDG  O8B   C8   O8A   124.49  3.000
 CDG  O8B   C8   C7    123.45  3.000
 CDG  O8A   C8   C7    111.93  3.000
 CDG  H9C3  C9   H9C2  108.58  3.000
 CDG  H9C3  C9   H9C1  108.57  3.000
 CDG  H9C2  C9   H9C1  108.50  3.000
 CDG  H9C3  C9   C7    109.43  3.000
 CDG  H9C2  C9   C7    111.03  3.000
 CDG  H9C1  C9   C7    110.66  3.000
 CDG  C10   O1   C1    114.93  3.000
 CDG  HA    O2   C2    108.68  3.000
 CDG  HB    O3   C3    108.04  3.000
 CDG  C7    O4   C4    115.03  3.000
 CDG  C5    O5   C1    113.25  3.000
 CDG  C7    O6   C6    114.84  3.000
 CDG  H8A   O8A  C8    110.05  3.000
 CDG  H103  C10  H102  108.51  3.000
 CDG  H103  C10  H101  108.58  3.000
 CDG  H102  C10  H101  108.55  3.000
 CDG  H103  C10  O1    112.29  3.000
 CDG  H102  C10  O1    111.43  3.000
 CDG  H101  C10  O1    107.38  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
 CDG  CONST_01  H8A   O8A  C8  C7   180.00   0.0  0
 CDG  Var_01    H6C1  C6   O6  C7  -174.35  30.0  1
 CDG  Var_02    H101  C10  O1  C1  -169.87  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
 CDG  chir_01  C1  C2  O1  O5  positiv
 CDG  chir_02  C2  O2  C1  C3  negativ
 CDG  chir_03  C3  O3  C2  C4  positiv
 CDG  chir_04  C4  O4  C5  C3  negativ
 CDG  chir_05  C5  O5  C4  C6  negativ
 CDG  chir_06  C7  O6  O4  C9  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
 CDG  plan-1  C7   0.020
 CDG  plan-1  C8   0.020
 CDG  plan-1  O8A  0.020
 CDG  plan-1  O8B  0.020
 CDG  plan-1  H8A  0.020

