# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri May 22 07:30:03 2020
#   Inital geometry file: a 165 line input string
#   Ligand name: N-[(3beta,5beta,7beta,9beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCC(=O)NCC(O)=O)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C
#
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
 GCH  GCH  N-[(3beta,5beta,7beta,9beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]glycine  ligand  75  33  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GCH
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
 GCH  C    C  CH1    0   0.086   0.6230  -1.5863  -6.5936
 GCH  O    O  OH1    0  -0.681   0.4286  -2.9709  -6.8152
 GCH  C1   C  CH2    0  -0.455  -0.6421  -1.0321  -5.9670
 GCH  C2   C  CH1    0  -0.207  -0.5434   0.4737  -5.6898
 GCH  C3   C  CT     0  -0.060   0.6907   0.8569  -4.8395
 GCH  C4   C  CH2    0  -0.428   1.9344   0.2013  -5.4682
 GCH  C5   C  CH2    0  -0.477   1.8156  -1.2982  -5.6960
 GCH  C6   C  CH3    0  -0.675   0.9175   2.3727  -4.9176
 GCH  C7   C  CH2    0  -0.480  -1.8313   1.0382  -5.0872
 GCH  C8   C  CH1    0   0.070  -2.0724   0.6621  -3.6273
 GCH  O1   O  OH1    0  -0.670  -2.4290  -0.7004  -3.4697
 GCH  C9   C  CH1    0  -0.261  -0.8404   0.9536  -2.7711
 GCH  C10  C  CH1    0  -0.185   0.4642   0.3977  -3.3760
 GCH  C11  C  CH2    0  -0.494   1.6405   0.7392  -2.4579
 GCH  C12  C  CH1    0   0.096   1.4817   0.2643  -1.0111
 GCH  C13  C  CT     0  -0.089   0.1764   0.7978  -0.4059
 GCH  C14  C  CH1    0  -0.171  -0.9862   0.4256  -1.3485
 GCH  C15  C  CH2    0  -0.449  -2.2262   0.8095  -0.5511
 GCH  C16  C  CH2    0  -0.449  -1.8433   0.4672   0.9027
 GCH  C17  C  CH1    0  -0.167  -0.3234   0.1488   0.9134
 GCH  C18  C  CH1    0  -0.236   0.3488   0.5451   2.2364
 GCH  C19  C  CH3    0  -0.674   1.8546   0.2893   2.2339
 GCH  C20  C  CH2    0  -0.411  -0.3224  -0.2038   3.3963
 GCH  C21  C  CH2    0  -0.589   0.1393   0.2462   4.7775
 GCH  C22  C  C      0   0.561  -0.6406  -0.4051   5.9025
 GCH  N    N  NH1    0  -0.633   0.0778  -0.7076   6.9877
 GCH  CA   C  CH2    0  -0.411  -0.4719  -1.2633   8.1963
 GCH  O2   O  O      0  -0.519  -1.8477  -0.6172   5.8275
 GCH  C23  C  CH3    0  -0.694   0.3010   2.3133  -0.2079
 GCH  O3   O  OH1    0  -0.673   1.4878  -1.1478  -0.9305
 GCH  C24  C  C      0   0.397   0.6066  -1.3875   9.2925
 GCH  O4   O  OC    -1  -0.611   0.2059  -1.8341  10.3811
 GCH  O5   O  O      0  -0.600   1.7651  -1.0381   8.9946
 GCH  H12  H  HCH1   0   0.175   0.7950  -1.0696  -7.5527
 GCH  H1   H  HOH1   0   0.443   1.2473  -3.3350  -7.1664
 GCH  H10  H  HCH2   0   0.229  -0.8520  -1.5867  -5.0508
 GCH  H11  H  HCH2   0   0.223  -1.4890  -1.2059  -6.6395
 GCH  H9   H  HCH1   0   0.213  -0.4100   0.9570  -6.6676
 GCH  H4   H  HCH2   0   0.231   2.8257   0.4256  -4.8784
 GCH  H5   H  HCH2   0   0.218   2.1060   0.6785  -6.4412
 GCH  H2   H  HCH2   0   0.216   1.7004  -1.8379  -4.7501
 GCH  H3   H  HCH2   0   0.230   2.7359  -1.6706  -6.1581
 GCH  H6   H  HCH3   0   0.226   0.9483   2.6941  -5.9612
 GCH  H7   H  HCH3   0   0.230   0.1427   2.9579  -4.4222
 GCH  H8   H  HCH3   0   0.229   1.8714   2.6527  -4.4682
 GCH  H17  H  HCH2   0   0.231  -2.6933   0.7298  -5.6912
 GCH  H18  H  HCH2   0   0.234  -1.8133   2.1300  -5.1497
 GCH  H16  H  HCH1   0   0.205  -2.8934   1.2939  -3.2548
 GCH  H13  H  HOH1   0   0.444  -3.1288  -0.8978  -4.0996
 GCH  H15  H  HCH1   0   0.215  -0.7677   2.0471  -2.7311
 GCH  H14  H  HCH1   0   0.217   0.3671  -0.6936  -3.3799
 GCH  H41  H  HCH2   0   0.235   2.5700   0.3127  -2.8478
 GCH  H42  H  HCH2   0   0.229   1.8045   1.8195  -2.4473
 GCH  H40  H  HCH1   0   0.199   2.3363   0.6714  -0.4543
 GCH  H35  H  HCH1   0   0.220  -0.9791  -0.6685  -1.4148
 GCH  H33  H  HCH2   0   0.229  -3.1158   0.2738  -0.8848
 GCH  H34  H  HCH2   0   0.213  -2.4441   1.8757  -0.6595
 GCH  H31  H  HCH2   0   0.229  -2.4190  -0.3830   1.2707
 GCH  H32  H  HCH2   0   0.217  -2.0673   1.2986   1.5770
 GCH  H30  H  HCH1   0   0.216  -0.2079  -0.9352   0.8069
 GCH  H29  H  HCH1   0   0.205   0.1819   1.6193   2.3945
 GCH  H19  H  HCH3   0   0.214   2.0723  -0.7518   1.9866
 GCH  H20  H  HCH3   0   0.229   2.3750   0.9148   1.5114
 GCH  H21  H  HCH3   0   0.233   2.3041   0.5024   3.2044
 GCH  H27  H  HCH2   0   0.241  -1.4033  -0.0693   3.3420
 GCH  H28  H  HCH2   0   0.214  -0.1408  -1.2785   3.2794
 GCH  H25  H  HCH2   0   0.247   1.2062   0.0636   4.9155
 GCH  H26  H  HCH2   0   0.257   0.0011   1.3298   4.8676
 GCH  H24  H  HNH1   0   0.384   1.0687  -0.5163   7.0195
 GCH  H22  H  HCH2   0   0.238  -1.2910  -0.6425   8.5723
 GCH  H23  H  HCH2   0   0.238  -0.8996  -2.2546   8.0125
 GCH  H36  H  HCH3   0   0.234   0.4186   2.8615  -1.1421
 GCH  H37  H  HCH3   0   0.238  -0.5740   2.7290   0.2931
 GCH  H38  H  HCH3   0   0.231   1.1656   2.5577   0.4127
 GCH  H39  H  HOH1   0   0.443   2.2659  -1.4678  -1.3971

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
 GCH  C    O    single  1.416  0.020  1.416
 GCH  C    C1   single  1.517  0.020  1.517
 GCH  C    C5   single  1.520  0.020  1.520
 GCH  C    H12  single  0.970  0.020  1.090
 GCH  O    H1   single  0.850  0.020  0.980
 GCH  C1   C2   single  1.534  0.020  1.534
 GCH  C1   H10  single  0.970  0.020  1.090
 GCH  C1   H11  single  0.970  0.020  1.090
 GCH  C2   C3   single  1.547  0.020  1.547
 GCH  C2   C7   single  1.530  0.020  1.530
 GCH  C2   H9   single  0.970  0.020  1.090
 GCH  C3   C4   single  1.540  0.020  1.540
 GCH  C3   C6   single  1.535  0.020  1.535
 GCH  C3   C10  single  1.550  0.020  1.550
 GCH  C4   C5   single  1.521  0.020  1.521
 GCH  C4   H4   single  0.970  0.020  1.090
 GCH  C4   H5   single  0.970  0.020  1.090
 GCH  C5   H2   single  0.970  0.020  1.090
 GCH  C5   H3   single  0.970  0.020  1.090
 GCH  C6   H6   single  0.970  0.020  1.090
 GCH  C6   H7   single  0.970  0.020  1.090
 GCH  C6   H8   single  0.970  0.020  1.090
 GCH  C7   C8   single  1.527  0.020  1.527
 GCH  C7   H17  single  0.970  0.020  1.090
 GCH  C7   H18  single  0.970  0.020  1.090
 GCH  C8   O1   single  1.417  0.020  1.417
 GCH  C8   C9   single  1.528  0.020  1.528
 GCH  C8   H16  single  0.970  0.020  1.090
 GCH  O1   H13  single  0.850  0.020  0.980
 GCH  C9   C10  single  1.542  0.020  1.542
 GCH  C9   C14  single  1.524  0.020  1.524
 GCH  C9   H15  single  0.970  0.020  1.090
 GCH  C10  C11  single  1.531  0.020  1.531
 GCH  C10  H14  single  0.970  0.020  1.090
 GCH  C11  C12  single  1.531  0.020  1.531
 GCH  C11  H41  single  0.970  0.020  1.090
 GCH  C11  H42  single  0.970  0.020  1.090
 GCH  C12  C13  single  1.534  0.020  1.534
 GCH  C12  O3   single  1.414  0.020  1.414
 GCH  C12  H40  single  0.970  0.020  1.090
 GCH  C13  C14  single  1.542  0.020  1.542
 GCH  C13  C17  single  1.553  0.020  1.553
 GCH  C13  C23  single  1.533  0.020  1.533
 GCH  C14  C15  single  1.523  0.020  1.523
 GCH  C14  H35  single  0.970  0.020  1.090
 GCH  C15  C16  single  1.542  0.020  1.542
 GCH  C15  H33  single  0.970  0.020  1.090
 GCH  C15  H34  single  0.970  0.020  1.090
 GCH  C16  C17  single  1.553  0.020  1.553
 GCH  C16  H31  single  0.970  0.020  1.090
 GCH  C16  H32  single  0.970  0.020  1.090
 GCH  C17  C18  single  1.536  0.020  1.536
 GCH  C17  H30  single  0.970  0.020  1.090
 GCH  C18  C19  single  1.527  0.020  1.527
 GCH  C18  C20  single  1.535  0.020  1.535
 GCH  C18  H29  single  0.970  0.020  1.090
 GCH  C19  H19  single  0.970  0.020  1.090
 GCH  C19  H20  single  0.970  0.020  1.090
 GCH  C19  H21  single  0.970  0.020  1.090
 GCH  C20  C21  single  1.524  0.020  1.524
 GCH  C20  H27  single  0.970  0.020  1.090
 GCH  C20  H28  single  0.970  0.020  1.090
 GCH  C21  C22  single  1.516  0.020  1.516
 GCH  C21  H25  single  0.970  0.020  1.090
 GCH  C21  H26  single  0.970  0.020  1.090
 GCH  C22  N    single  1.336  0.020  1.336
 GCH  C22  O2   double  1.228  0.020  1.228
 GCH  N    CA   single  1.439  0.020  1.439
 GCH  N    H24  single  0.860  0.020  1.020
 GCH  CA   C24  single  1.543  0.020  1.543
 GCH  CA   H22  single  0.970  0.020  1.090
 GCH  CA   H23  single  0.970  0.020  1.090
 GCH  C23  H36  single  0.970  0.020  1.090
 GCH  C23  H37  single  0.970  0.020  1.090
 GCH  C23  H38  single  0.970  0.020  1.090
 GCH  O3   H39  single  0.850  0.020  0.980
 GCH  C24  O4   deloc   1.243  0.020  1.243
 GCH  C24  O5   deloc   1.246  0.020  1.246

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
 GCH  H12  C    C5   107.59  3.000
 GCH  H12  C    C1   108.56  3.000
 GCH  C5   C    C1   109.95  3.000
 GCH  H12  C    O    110.09  3.000
 GCH  C5   C    O    112.67  3.000
 GCH  C1   C    O    107.91  3.000
 GCH  H1   O    C    108.08  3.000
 GCH  H11  C1   H10  106.63  3.000
 GCH  H11  C1   C2   108.44  3.000
 GCH  H10  C1   C2   111.06  3.000
 GCH  H11  C1   C    109.47  3.000
 GCH  H10  C1   C    108.76  3.000
 GCH  C2   C1   C    112.31  3.000
 GCH  H9   C2   C7   106.88  3.000
 GCH  H9   C2   C3   106.46  3.000
 GCH  C7   C2   C3   111.33  3.000
 GCH  H9   C2   C1   106.18  3.000
 GCH  C7   C2   C1   112.28  3.000
 GCH  C3   C2   C1   113.19  3.000
 GCH  C10  C3   C6   111.24  3.000
 GCH  C10  C3   C4   112.16  3.000
 GCH  C6   C3   C4   106.27  3.000
 GCH  C10  C3   C2   109.21  3.000
 GCH  C6   C3   C2   109.55  3.000
 GCH  C4   C3   C2   108.33  3.000
 GCH  H5   C4   H4   105.19  3.000
 GCH  H5   C4   C5   107.94  3.000
 GCH  H4   C4   C5   110.30  3.000
 GCH  H5   C4   C3   107.66  3.000
 GCH  H4   C4   C3   110.56  3.000
 GCH  C5   C4   C3   114.68  3.000
 GCH  H3   C5   H2   106.58  3.000
 GCH  H3   C5   C4   109.44  3.000
 GCH  H2   C5   C4   111.38  3.000
 GCH  H3   C5   C    110.23  3.000
 GCH  H2   C5   C    109.52  3.000
 GCH  C4   C5   C    109.66  3.000
 GCH  H8   C6   H7   107.24  3.000
 GCH  H8   C6   H6   107.06  3.000
 GCH  H7   C6   H6   107.24  3.000
 GCH  H8   C6   C3   111.21  3.000
 GCH  H7   C6   C3   113.71  3.000
 GCH  H6   C6   C3   110.09  3.000
 GCH  H18  C7   H17  105.21  3.000
 GCH  H18  C7   C8   107.65  3.000
 GCH  H17  C7   C8   109.46  3.000
 GCH  H18  C7   C2   109.39  3.000
 GCH  H17  C7   C2   109.93  3.000
 GCH  C8   C7   C2   114.75  3.000
 GCH  H16  C8   C9   107.59  3.000
 GCH  H16  C8   O1   109.06  3.000
 GCH  C9   C8   O1   108.90  3.000
 GCH  H16  C8   C7   107.45  3.000
 GCH  C9   C8   C7   111.19  3.000
 GCH  O1   C8   C7   112.51  3.000
 GCH  H13  O1   C8   107.92  3.000
 GCH  H15  C9   C14  108.53  3.000
 GCH  H15  C9   C10  108.52  3.000
 GCH  C14  C9   C10  108.80  3.000
 GCH  H15  C9   C8   105.31  3.000
 GCH  C14  C9   C8   112.31  3.000
 GCH  C10  C9   C8   113.17  3.000
 GCH  H14  C10  C11  107.01  3.000
 GCH  H14  C10  C9   106.59  3.000
 GCH  C11  C10  C9   109.54  3.000
 GCH  H14  C10  C3   107.73  3.000
 GCH  C11  C10  C3   112.82  3.000
 GCH  C9   C10  C3   112.78  3.000
 GCH  H42  C11  H41  105.14  3.000
 GCH  H42  C11  C12  108.25  3.000
 GCH  H41  C11  C12  107.69  3.000
 GCH  H42  C11  C10  109.98  3.000
 GCH  H41  C11  C10  110.61  3.000
 GCH  C12  C11  C10  114.70  3.000
 GCH  H40  C12  O3   109.74  3.000
 GCH  H40  C12  C13  109.46  3.000
 GCH  O3   C12  C13  109.17  3.000
 GCH  H40  C12  C11  106.46  3.000
 GCH  O3   C12  C11  111.29  3.000
 GCH  C13  C12  C11  110.68  3.000
 GCH  C23  C13  C17  109.24  3.000
 GCH  C23  C13  C14  112.25  3.000
 GCH  C17  C13  C14  100.12  3.000
 GCH  C23  C13  C12  108.99  3.000
 GCH  C17  C13  C12  117.62  3.000
 GCH  C14  C13  C12  108.44  3.000
 GCH  H35  C14  C15  106.77  3.000
 GCH  H35  C14  C13  105.84  3.000
 GCH  C15  C14  C13  103.47  3.000
 GCH  H35  C14  C9   106.78  3.000
 GCH  C15  C14  C9   118.62  3.000
 GCH  C13  C14  C9   114.49  3.000
 GCH  H34  C15  H33  106.62  3.000
 GCH  H34  C15  C16  111.06  3.000
 GCH  H33  C15  C16  112.46  3.000
 GCH  H34  C15  C14  110.86  3.000
 GCH  H33  C15  C14  112.33  3.000
 GCH  C16  C15  C14  103.62  3.000
 GCH  H32  C16  H31  106.05  3.000
 GCH  H32  C16  C17  110.61  3.000
 GCH  H31  C16  C17  110.76  3.000
 GCH  H32  C16  C15  111.21  3.000
 GCH  H31  C16  C15  111.11  3.000
 GCH  C17  C16  C15  107.16  3.000
 GCH  H30  C17  C18  107.03  3.000
 GCH  H30  C17  C16  107.79  3.000
 GCH  C18  C17  C16  112.42  3.000
 GCH  H30  C17  C13  107.28  3.000
 GCH  C18  C17  C13  118.89  3.000
 GCH  C16  C17  C13  102.91  3.000
 GCH  H29  C18  C20  107.57  3.000
 GCH  H29  C18  C19  108.29  3.000
 GCH  C20  C18  C19  110.52  3.000
 GCH  H29  C18  C17  108.04  3.000
 GCH  C20  C18  C17  109.49  3.000
 GCH  C19  C18  C17  112.76  3.000
 GCH  H21  C19  H20  106.34  3.000
 GCH  H21  C19  H19  107.80  3.000
 GCH  H20  C19  H19  107.60  3.000
 GCH  H21  C19  C18  111.85  3.000
 GCH  H20  C19  C18  112.10  3.000
 GCH  H19  C19  C18  110.89  3.000
 GCH  H28  C20  H27  106.25  3.000
 GCH  H28  C20  C21  109.62  3.000
 GCH  H27  C20  C21  108.00  3.000
 GCH  H28  C20  C18  108.98  3.000
 GCH  H27  C20  C18  109.61  3.000
 GCH  C21  C20  C18  114.09  3.000
 GCH  H26  C21  H25  106.16  3.000
 GCH  H26  C21  C22  107.38  3.000
 GCH  H25  C21  C22  109.71  3.000
 GCH  H26  C21  C20  109.16  3.000
 GCH  H25  C21  C20  111.19  3.000
 GCH  C22  C21  C20  112.94  3.000
 GCH  O2   C22  N    122.62  3.000
 GCH  O2   C22  C21  122.32  3.000
 GCH  N    C22  C21  115.05  3.000
 GCH  H24  N    CA   114.93  3.000
 GCH  H24  N    C22  120.69  3.000
 GCH  CA   N    C22  124.34  3.000
 GCH  H23  CA   H22  106.20  3.000
 GCH  H23  CA   C24  108.63  3.000
 GCH  H22  CA   C24  108.95  3.000
 GCH  H23  CA   N    110.95  3.000
 GCH  H22  CA   N    110.82  3.000
 GCH  C24  CA   N    111.14  3.000
 GCH  H38  C23  H37  106.79  3.000
 GCH  H38  C23  H36  106.82  3.000
 GCH  H37  C23  H36  106.78  3.000
 GCH  H38  C23  C13  111.03  3.000
 GCH  H37  C23  C13  111.76  3.000
 GCH  H36  C23  C13  113.28  3.000
 GCH  H39  O3   C12  107.93  3.000
 GCH  O5   C24  O4   127.57  3.000
 GCH  O5   C24  CA   117.23  3.000
 GCH  O4   C24  CA   115.21  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
 GCH  CONST_01  CA   N    C22  C21   180.00   0.0  0
 GCH  CONST_02  O2   C22  N    CA      0.00   0.0  0
 GCH  CONST_03  H24  N    C22  C21     0.00   0.0  0
 GCH  Var_01    C3   C4   C5   C      58.09  30.0  1
 GCH  Var_02    C17  C16  C15  C14    10.12  30.0  1
 GCH  Var_03    C22  C21  C20  C18   174.02  30.0  3
 GCH  Var_04    N    C22  C21  C20   143.08  30.0  3
 GCH  Var_05    C24  CA   N    C22  -175.43  30.0  3
 GCH  Var_06    O4   C24  CA   N     178.54  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
 GCH  chir_01  C    O    C1   C5   negativ
 GCH  chir_02  C2   C7   C3   C1   negativ
 GCH  chir_03  C3   C10  C4   C2   negativ
 GCH  chir_04  C8   O1   C7   C9   positiv
 GCH  chir_05  C9   C8   C10  C14  positiv
 GCH  chir_06  C10  C11  C9   C3   negativ
 GCH  chir_07  C12  O3   C13  C11  positiv
 GCH  chir_08  C13  C17  C14  C12  positiv
 GCH  chir_09  C14  C15  C13  C9   positiv
 GCH  chir_10  C17  C18  C16  C13  negativ
 GCH  chir_11  C18  C17  C19  C20  positiv

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
 GCH  plan-1  C21  0.020
 GCH  plan-1  C22  0.020
 GCH  plan-1  N    0.020
 GCH  plan-1  CA   0.020
 GCH  plan-1  O2   0.020
 GCH  plan-1  H24  0.020
 GCH  plan-2  CA   0.020
 GCH  plan-2  C24  0.020
 GCH  plan-2  O4   0.020
 GCH  plan-2  O5   0.020

