# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 09:56:27 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: methyl 9-(beta-D-galactopyranosyloxy)nonanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CCCCCCCCO[C@@H]1O[C@H](CO)[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
 DR4  DR4  'methyl 9-(beta-D-galactopyranosyloxy)nonanoate'  saccharide  54  24  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DR4
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
 DR4  CAA   C  CH3   0  -0.428  15.2400  61.5710  43.2034
 DR4  OAP   O  O2    0  -0.450  15.0016  62.9769  43.2620
 DR4  CAS   C  C     0   0.574  14.4816  63.5527  42.1827
 DR4  OAB   O  O     0  -0.448  14.2319  62.9445  41.1712
 DR4  CAO   C  CH2   0  -0.540  14.2411  65.0240  42.3797
 DR4  CAL   C  CH2   0  -0.432  15.5020  65.8377  42.6854
 DR4  CAJ   C  CH2   0  -0.429  15.2015  67.3316  42.6285
 DR4  CAH   C  CH2   0  -0.428  16.4060  68.2363  42.8723
 DR4  CAG   C  CH2   0  -0.440  16.9844  68.1534  44.2924
 DR4  CAI   C  CH2   0  -0.433  18.2498  67.3066  44.3940
 DR4  CAK   C  CH2   0  -0.451  18.8097  67.1746  45.8067
 DR4  CAM   C  CH2   0  -0.198  17.8580  66.5478  46.8163
 DR4  O1    O  O2    0  -0.497  17.2743  65.3265  46.3854
 DR4  C1    C  CH1   0   0.307  17.9857  64.1770  46.6353
 DR4  O5    O  O2    0  -0.491  19.0093  64.0470  45.6811
 DR4  C5    C  CH1   0  -0.014  19.8145  62.9069  45.8934
 DR4  C6    C  CH2   0  -0.155  20.9865  62.9703  44.9376
 DR4  O6    O  OH1   0  -0.666  21.8059  64.0526  45.3132
 DR4  C4    C  CH1   0  -0.004  18.9949  61.6311  45.7459
 DR4  O4    O  OH1   0  -0.667  18.5830  61.5053  44.4075
 DR4  C3    C  CH1   0   0.011  17.8132  61.6969  46.7125
 DR4  O3    O  OH1   0  -0.669  17.0177  60.5566  46.5029
 DR4  C2    C  CH1   0  -0.038  17.0294  62.9903  46.5269
 DR4  O2    O  OH1   0  -0.667  16.0358  63.0249  47.5217
 DR4  HAA1  H  HCH3  0   0.236  15.9947  61.3252  42.4564
 DR4  HAA2  H  HCH3  0   0.240  15.5984  61.2842  44.1876
 DR4  HAA3  H  HCH3  0   0.238  14.3256  61.0219  42.9804
 DR4  HAO1  H  HCH2  0   0.264  13.5220  65.1561  43.1939
 DR4  HAO2  H  HCH2  0   0.253  13.7665  65.4022  41.4735
 DR4  HAL1  H  HCH2  0   0.225  16.2855  65.6001  41.9594
 DR4  HAL2  H  HCH2  0   0.233  15.8933  65.5667  43.6687
 DR4  HAJ1  H  HCH2  0   0.215  14.4216  67.5682  43.3603
 DR4  HAJ2  H  HCH2  0   0.221  14.7760  67.5656  41.6476
 DR4  HAH1  H  HCH2  0   0.227  16.0989  69.2636  42.6629
 DR4  HAH2  H  HCH2  0   0.214  17.1861  68.0055  42.1387
 DR4  HAG1  H  HCH2  0   0.220  16.2140  67.7635  44.9651
 DR4  HAG2  H  HCH2  0   0.220  17.2112  69.1588  44.6591
 DR4  HAI1  H  HCH2  0   0.221  19.0212  67.7574  43.7622
 DR4  HAI2  H  HCH2  0   0.221  18.0742  66.3133  43.9732
 DR4  HAK1  H  HCH2  0   0.219  19.0676  68.1663  46.1940
 DR4  HAK2  H  HCH2  0   0.227  19.7440  66.6104  45.7749
 DR4  HAM1  H  HCH2  0   0.229  17.0210  67.2208  47.0114
 DR4  HAM2  H  HCH2  0   0.224  18.3757  66.4009  47.7722
 DR4  H1    H  HCH1  0   0.183  18.4296  64.2010  47.6500
 DR4  H5    H  HCH1  0   0.226  20.2105  62.9122  46.9224
 DR4  H61   H  HCH2  0   0.207  20.6209  63.0759  43.9103
 DR4  H62   H  HCH2  0   0.200  21.5264  62.0158  44.9938
 DR4  HO6   H  HOH1  0   0.454  22.4905  64.1570  44.6466
 DR4  H4    H  HCH1  0   0.232  19.6353  60.7873  46.0434
 DR4  HO4   H  HOH1  0   0.455  18.0673  60.6963  44.3282
 DR4  H3    H  HCH1  0   0.214  18.2295  61.7027  47.7330
 DR4  HO3   H  HOH1  0   0.454  16.2247  60.6308  47.0447
 DR4  H2    H  HCH1  0   0.226  16.5903  63.0065  45.5200
 DR4  HO2   H  HOH1  0   0.454  15.4172  63.7327  47.3154

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
 DR4  CAA  OAP   single  1.427  0.020  1.427
 DR4  CAA  HAA1  single  0.970  0.020  1.090
 DR4  CAA  HAA2  single  0.970  0.020  1.090
 DR4  CAA  HAA3  single  0.970  0.020  1.090
 DR4  OAP  CAS   single  1.329  0.020  1.329
 DR4  CAS  OAB   double  1.206  0.020  1.206
 DR4  CAS  CAO   single  1.504  0.020  1.504
 DR4  CAO  CAL   single  1.531  0.020  1.531
 DR4  CAO  HAO1  single  0.970  0.020  1.090
 DR4  CAO  HAO2  single  0.970  0.020  1.090
 DR4  CAL  CAJ   single  1.525  0.020  1.525
 DR4  CAL  HAL1  single  0.970  0.020  1.090
 DR4  CAL  HAL2  single  0.970  0.020  1.090
 DR4  CAJ  CAH   single  1.526  0.020  1.526
 DR4  CAJ  HAJ1  single  0.970  0.020  1.090
 DR4  CAJ  HAJ2  single  0.970  0.020  1.090
 DR4  CAH  CAG   single  1.536  0.020  1.536
 DR4  CAH  HAH1  single  0.970  0.020  1.090
 DR4  CAH  HAH2  single  0.970  0.020  1.090
 DR4  CAG  CAI   single  1.526  0.020  1.526
 DR4  CAG  HAG1  single  0.970  0.020  1.090
 DR4  CAG  HAG2  single  0.970  0.020  1.090
 DR4  CAI  CAK   single  1.525  0.020  1.525
 DR4  CAI  HAI1  single  0.970  0.020  1.090
 DR4  CAI  HAI2  single  0.970  0.020  1.090
 DR4  CAK  CAM   single  1.523  0.020  1.523
 DR4  CAK  HAK1  single  0.970  0.020  1.090
 DR4  CAK  HAK2  single  0.970  0.020  1.090
 DR4  CAM  O1    single  1.421  0.020  1.421
 DR4  CAM  HAM1  single  0.970  0.020  1.090
 DR4  CAM  HAM2  single  0.970  0.020  1.090
 DR4  O1   C1    single  1.375  0.020  1.375
 DR4  C1   O5    single  1.405  0.020  1.405
 DR4  C1   C2    single  1.528  0.020  1.528
 DR4  C1   H1    single  0.970  0.020  1.090
 DR4  O5   C5    single  1.412  0.020  1.412
 DR4  C5   C6    single  1.514  0.020  1.514
 DR4  C5   C4    single  1.524  0.020  1.524
 DR4  C5   H5    single  0.970  0.020  1.090
 DR4  C6   O6    single  1.409  0.020  1.409
 DR4  C6   H61   single  0.970  0.020  1.090
 DR4  C6   H62   single  0.970  0.020  1.090
 DR4  O6   HO6   single  0.850  0.020  0.980
 DR4  C4   O4    single  1.406  0.020  1.406
 DR4  C4   C3    single  1.528  0.020  1.528
 DR4  C4   H4    single  0.970  0.020  1.090
 DR4  O4   HO4   single  0.850  0.020  0.980
 DR4  C3   O3    single  1.406  0.020  1.406
 DR4  C3   C2    single  1.524  0.020  1.524
 DR4  C3   H3    single  0.970  0.020  1.090
 DR4  O3   HO3   single  0.850  0.020  0.980
 DR4  C2   O2    single  1.406  0.020  1.406
 DR4  C2   H2    single  0.970  0.020  1.090
 DR4  O2   HO2   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
 DR4  HAA3  CAA  HAA2  109.23  3.000
 DR4  HAA3  CAA  HAA1  109.10  3.000
 DR4  HAA2  CAA  HAA1  109.46  3.000
 DR4  HAA3  CAA  OAP   111.38  3.000
 DR4  HAA2  CAA  OAP   106.14  3.000
 DR4  HAA1  CAA  OAP   111.47  3.000
 DR4  CAS   OAP  CAA   117.30  3.000
 DR4  CAO   CAS  OAB   124.75  3.000
 DR4  CAO   CAS  OAP   112.33  3.000
 DR4  OAB   CAS  OAP   122.92  3.000
 DR4  HAO2  CAO  HAO1  106.88  3.000
 DR4  HAO2  CAO  CAL   109.87  3.000
 DR4  HAO1  CAO  CAL   109.17  3.000
 DR4  HAO2  CAO  CAS   107.46  3.000
 DR4  HAO1  CAO  CAS   108.71  3.000
 DR4  CAL   CAO  CAS   114.48  3.000
 DR4  HAL2  CAL  HAL1  106.67  3.000
 DR4  HAL2  CAL  CAJ   110.32  3.000
 DR4  HAL1  CAL  CAJ   109.21  3.000
 DR4  HAL2  CAL  CAO   110.04  3.000
 DR4  HAL1  CAL  CAO   109.98  3.000
 DR4  CAJ   CAL  CAO   110.54  3.000
 DR4  HAJ2  CAJ  HAJ1  106.01  3.000
 DR4  HAJ2  CAJ  CAH   108.86  3.000
 DR4  HAJ1  CAJ  CAH   109.10  3.000
 DR4  HAJ2  CAJ  CAL   108.63  3.000
 DR4  HAJ1  CAJ  CAL   109.09  3.000
 DR4  CAH   CAJ  CAL   114.79  3.000
 DR4  HAH2  CAH  HAH1  105.66  3.000
 DR4  HAH2  CAH  CAG   109.86  3.000
 DR4  HAH1  CAH  CAG   109.50  3.000
 DR4  HAH2  CAH  CAJ   109.28  3.000
 DR4  HAH1  CAH  CAJ   107.76  3.000
 DR4  CAG   CAH  CAJ   114.40  3.000
 DR4  HAG2  CAG  HAG1  105.50  3.000
 DR4  HAG2  CAG  CAI   108.41  3.000
 DR4  HAG1  CAG  CAI   110.19  3.000
 DR4  HAG2  CAG  CAH   109.79  3.000
 DR4  HAG1  CAG  CAH   108.81  3.000
 DR4  CAI   CAG  CAH   113.82  3.000
 DR4  HAI2  CAI  HAI1  105.39  3.000
 DR4  HAI2  CAI  CAK   109.68  3.000
 DR4  HAI1  CAI  CAK   108.16  3.000
 DR4  HAI2  CAI  CAG   110.21  3.000
 DR4  HAI1  CAI  CAG   108.51  3.000
 DR4  CAK   CAI  CAG   114.46  3.000
 DR4  HAK2  CAK  HAK1  106.06  3.000
 DR4  HAK2  CAK  CAM   109.96  3.000
 DR4  HAK1  CAK  CAM   106.58  3.000
 DR4  HAK2  CAK  CAI   109.38  3.000
 DR4  HAK1  CAK  CAI   109.60  3.000
 DR4  CAM   CAK  CAI   114.86  3.000
 DR4  HAM2  CAM  HAM1  106.78  3.000
 DR4  HAM2  CAM  O1    110.07  3.000
 DR4  HAM1  CAM  O1    105.62  3.000
 DR4  HAM2  CAM  CAK   109.75  3.000
 DR4  HAM1  CAM  CAK   110.12  3.000
 DR4  O1    CAM  CAK   114.18  3.000
 DR4  C1    O1   CAM   116.81  3.000
 DR4  H1    C1   C2    109.43  3.000
 DR4  H1    C1   O5    109.39  3.000
 DR4  C2    C1   O5    109.63  3.000
 DR4  H1    C1   O1    110.84  3.000
 DR4  C2    C1   O1    108.22  3.000
 DR4  O5    C1   O1    109.32  3.000
 DR4  C5    O5   C1    112.83  3.000
 DR4  H5    C5   C4    106.71  3.000
 DR4  H5    C5   C6    108.12  3.000
 DR4  C4    C5   C6    112.99  3.000
 DR4  H5    C5   O5    109.95  3.000
 DR4  C4    C5   O5    110.78  3.000
 DR4  C6    C5   O5    108.24  3.000
 DR4  H62   C6   H61   107.21  3.000
 DR4  H62   C6   O6    111.61  3.000
 DR4  H61   C6   O6    111.72  3.000
 DR4  H62   C6   C5    108.18  3.000
 DR4  H61   C6   C5    109.74  3.000
 DR4  O6    C6   C5    108.31  3.000
 DR4  HO6   O6   C6    108.24  3.000
 DR4  H4    C4   C3    108.19  3.000
 DR4  H4    C4   O4    111.05  3.000
 DR4  C3    C4   O4    112.29  3.000
 DR4  H4    C4   C5    107.64  3.000
 DR4  C3    C4   C5    108.59  3.000
 DR4  O4    C4   C5    108.95  3.000
 DR4  HO4   O4   C4    108.10  3.000
 DR4  H3    C3   C2    107.61  3.000
 DR4  H3    C3   O3    110.86  3.000
 DR4  C2    C3   O3    112.29  3.000
 DR4  H3    C3   C4    107.08  3.000
 DR4  C2    C3   C4    110.93  3.000
 DR4  O3    C3   C4    107.96  3.000
 DR4  HO3   O3   C3    108.63  3.000
 DR4  H2    C2   O2    111.44  3.000
 DR4  H2    C2   C3    109.26  3.000
 DR4  O2    C2   C3    107.35  3.000
 DR4  H2    C2   C1    107.67  3.000
 DR4  O2    C2   C1    111.89  3.000
 DR4  C3    C2   C1    109.19  3.000
 DR4  HO2   O2   C2    108.70  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
 DR4  Var_01  HAM1  CAM  O1   C1   -151.93  30.0  2
 DR4  Var_02  OAB   CAS  OAP  CAA    -1.29  30.0  3
 DR4  Var_03  CAL   CAO  CAS  OAP    60.74  30.0  3
 DR4  Var_04  CAJ   CAL  CAO  CAS   170.17  30.0  3
 DR4  Var_05  CAH   CAJ  CAL  CAO  -178.01  30.0  3
 DR4  Var_06  CAG   CAH  CAJ  CAL   -66.11  30.0  3
 DR4  Var_07  CAI   CAG  CAH  CAJ   101.73  30.0  3
 DR4  Var_08  CAK   CAI  CAG  CAH  -177.98  30.0  3
 DR4  Var_09  CAM   CAK  CAI  CAG    59.45  30.0  3
 DR4  Var_10  O1    CAM  CAK  CAI    50.22  30.0  3
 DR4  Var_11  HAA1  CAA  OAP  CAS    64.52  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
 DR4  chir_01  C1  O1  O5  C2  positiv
 DR4  chir_02  C5  O5  C6  C4  positiv
 DR4  chir_03  C4  O4  C5  C3  negativ
 DR4  chir_04  C3  O3  C2  C4  positiv
 DR4  chir_05  C2  O2  C1  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
 DR4  plan-1  OAP  0.020
 DR4  plan-1  CAS  0.020
 DR4  plan-1  OAB  0.020
 DR4  plan-1  CAO  0.020

