# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 00:43:21 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  33  18  .  2021-08-07  2021-08-07  
;
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   0.299   0.4691  -0.2512   2.3078
 CDG  C2    C  CH1    0  -0.031  -0.9235   0.2950   2.0021
 CDG  C3    C  CH1    0   0.013  -1.5554  -0.5613   0.9114
 CDG  C4    C  CH1    0  -0.014  -0.6439  -0.6524  -0.2999
 CDG  C5    C  CH1    0   0.010   0.7561  -1.0900   0.1268
 CDG  C6    C  CH2    0  -0.232   1.6797  -0.9689  -1.0680
 CDG  C7    C  CT     0   0.392   0.2852   0.6607  -2.0279
 CDG  C8    C  C      0   0.353  -0.2236  -0.2154  -3.2227
 CDG  C9    C  CH3    0  -0.703   0.3295   2.1103  -2.4764
 CDG  O1    O  O2     0  -0.497   1.0624   0.5669   3.2447
 CDG  O2    O  OH1    0  -0.673  -1.7605   0.2196   3.1312
 CDG  O3    O  OH1    0  -0.667  -2.8094  -0.0765   0.5101
 CDG  O4    O  O2     0  -0.501  -0.5803   0.6081  -0.9215
 CDG  O5    O  O2     0  -0.499   1.2598  -0.2545   1.1496
 CDG  O6    O  O2     0  -0.493   1.5904   0.3140  -1.6397
 CDG  O8A   O  OC    -1  -0.590  -1.4530  -0.3781  -3.3017
 CDG  O8B   O  O      0  -0.595   0.6468  -0.6038  -4.0208
 CDG  C10   C  CH3    0  -0.410   2.2173   0.0291   3.8587
 CDG  H1    H  HCH1   0   0.177   0.3749  -1.2859   2.6953
 CDG  H2    H  HCH1   0   0.224  -0.8233   1.3285   1.6420
 CDG  H3    H  HCH1   0   0.215  -1.6439  -1.5870   1.3074
 CDG  H4    H  HCH1   0   0.239  -1.0495  -1.4092  -0.9848
 CDG  H5    H  HCH1   0   0.233   0.7272  -2.1382   0.4603
 CDG  H6C1  H  HCH2   0   0.248   2.7181  -1.1194  -0.7660
 CDG  H6C2  H  HCH2   0   0.219   1.4318  -1.7549  -1.7911
 CDG  H9C1  H  HCH3   0   0.235   1.0089   2.2254  -3.3203
 CDG  H9C2  H  HCH3   0   0.235  -0.6598   2.4410  -2.7907
 CDG  H9C3  H  HCH3   0   0.235   0.6700   2.7578  -1.6662
 CDG  HA    H  HOH1   0   0.456  -1.4521   0.8547   3.7850
 CDG  HB    H  HOH1   0   0.450  -3.3904  -0.0844   1.2775
 CDG  H101  H  HCH3   0   0.239   2.4853   0.6894   4.6816
 CDG  H102  H  HCH3   0   0.213   2.0279  -0.9706   4.2626
 CDG  H103  H  HCH3   0   0.219   3.0642  -0.0297   3.1713

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  1.378  0.020  1.378
 CDG  C1   O5    single  1.402  0.020  1.402
 CDG  C1   H1    single  0.970  0.020  1.090
 CDG  C2   C3    single  1.524  0.020  1.524
 CDG  C2   O2    single  1.408  0.020  1.408
 CDG  C2   H2    single  0.970  0.020  1.090
 CDG  C3   C4    single  1.519  0.020  1.519
 CDG  C3   O3    single  1.403  0.020  1.403
 CDG  C3   H3    single  0.970  0.020  1.090
 CDG  C4   C5    single  1.528  0.020  1.528
 CDG  C4   O4    single  1.407  0.020  1.407
 CDG  C4   H4    single  0.970  0.020  1.090
 CDG  C5   C6    single  1.515  0.020  1.515
 CDG  C5   O5    single  1.413  0.020  1.413
 CDG  C5   H5    single  0.970  0.020  1.090
 CDG  C6   O6    single  1.407  0.020  1.407
 CDG  C6   H6C1  single  0.970  0.020  1.090
 CDG  C6   H6C2  single  0.970  0.020  1.090
 CDG  C7   C8    single  1.567  0.020  1.567
 CDG  C7   C9    single  1.518  0.020  1.518
 CDG  C7   O4    single  1.406  0.020  1.406
 CDG  C7   O6    single  1.405  0.020  1.405
 CDG  C8   O8A   deloc   1.243  0.020  1.243
 CDG  C8   O8B   deloc   1.243  0.020  1.243
 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  1.414  0.020  1.414
 CDG  O2   HA    single  0.850  0.020  0.980
 CDG  O3   HB    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    109.54  3.000
 CDG  H1    C1   O1    110.66  3.000
 CDG  O5    C1   O1    108.67  3.000
 CDG  H1    C1   C2    109.04  3.000
 CDG  O5    C1   C2    110.47  3.000
 CDG  O1    C1   C2    108.44  3.000
 CDG  H2    C2   O2    111.56  3.000
 CDG  H2    C2   C3    109.38  3.000
 CDG  O2    C2   C3    107.30  3.000
 CDG  H2    C2   C1    108.59  3.000
 CDG  O2    C2   C1    111.26  3.000
 CDG  C3    C2   C1    108.69  3.000
 CDG  H3    C3   O3    110.63  3.000
 CDG  H3    C3   C4    106.19  3.000
 CDG  O3    C3   C4    109.21  3.000
 CDG  H3    C3   C2    107.39  3.000
 CDG  O3    C3   C2    112.40  3.000
 CDG  C4    C3   C2    110.83  3.000
 CDG  H4    C4   O4    111.01  3.000
 CDG  H4    C4   C5    108.37  3.000
 CDG  O4    C4   C5    109.80  3.000
 CDG  H4    C4   C3    108.48  3.000
 CDG  O4    C4   C3    109.02  3.000
 CDG  C5    C4   C3    110.15  3.000
 CDG  H5    C5   O5    110.68  3.000
 CDG  H5    C5   C6    109.34  3.000
 CDG  O5    C5   C6    107.84  3.000
 CDG  H5    C5   C4    109.48  3.000
 CDG  O5    C5   C4    111.06  3.000
 CDG  C6    C5   C4    108.39  3.000
 CDG  H6C2  C6   H6C1  107.38  3.000
 CDG  H6C2  C6   O6    111.79  3.000
 CDG  H6C1  C6   O6    107.36  3.000
 CDG  H6C2  C6   C5    108.97  3.000
 CDG  H6C1  C6   C5    110.52  3.000
 CDG  O6    C6   C5    110.76  3.000
 CDG  O6    C7   O4    110.20  3.000
 CDG  O6    C7   C9    106.86  3.000
 CDG  O4    C7   C9    106.63  3.000
 CDG  O6    C7   C8    111.99  3.000
 CDG  O4    C7   C8    112.30  3.000
 CDG  C9    C7   C8    108.55  3.000
 CDG  O8B   C8   O8A   127.66  3.000
 CDG  O8B   C8   C7    115.91  3.000
 CDG  O8A   C8   C7    116.30  3.000
 CDG  H9C3  C9   H9C2  108.51  3.000
 CDG  H9C3  C9   H9C1  108.53  3.000
 CDG  H9C2  C9   H9C1  108.10  3.000
 CDG  H9C3  C9   C7    110.86  3.000
 CDG  H9C2  C9   C7    110.40  3.000
 CDG  H9C1  C9   C7    110.36  3.000
 CDG  C10   O1   C1    114.89  3.000
 CDG  HA    O2   C2    108.60  3.000
 CDG  HB    O3   C3    107.97  3.000
 CDG  C7    O4   C4    114.15  3.000
 CDG  C5    O5   C1    113.46  3.000
 CDG  C7    O6   C6    113.33  3.000
 CDG  H103  C10  H102  108.50  3.000
 CDG  H103  C10  H101  108.51  3.000
 CDG  H102  C10  H101  108.52  3.000
 CDG  H103  C10  O1    112.36  3.000
 CDG  H102  C10  O1    111.48  3.000
 CDG  H101  C10  O1    107.37  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  Var_01  H6C1  C6   O6  C7  -177.64  30.0  1
 CDG  Var_02  H101  C10  O1  C1  -170.71  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

