# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:43:55 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: (3alpha,5alpha,7beta,8alpha,17alpha)-3,7-dihydroxycholan-24-oic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCC(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]3CC[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
 JN3  JN3  '(3alpha,5alpha,7beta,8alpha,17alpha)-3,7-dihydroxycholan-24-oic acid'  ligand  67  28  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JN3
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
 JN3  C1    C  CH2    0  -0.413   1.2016  -6.2243   2.6789
 JN3  C2    C  CH2    0  -0.445   1.7484  -5.6419   3.9735
 JN3  C3    C  CH1    0   0.067   0.6041  -5.1533   4.8490
 JN3  O3    O  OH1    0  -0.654   1.0535  -4.6401   6.0912
 JN3  C4    C  CH2    0  -0.444  -0.2412  -4.1410   4.0914
 JN3  C5    C  CH1    0  -0.208  -0.7604  -4.6767   2.7515
 JN3  C6    C  CH2    0  -0.429  -1.6134  -3.6455   2.0088
 JN3  C7    C  CH1    0   0.063  -0.8330  -2.5179   1.3471
 JN3  O7    O  OH1    0  -0.657  -0.4133  -1.6107   2.3541
 JN3  C8    C  CH1    0  -0.245   0.3346  -3.0596   0.5114
 JN3  C9    C  CH1    0  -0.183   1.1995  -4.0721   1.2879
 JN3  C10   C  CT     0  -0.068   0.3559  -5.2472   1.8446
 JN3  C11   C  CH2    0  -0.434   2.3991  -4.5262   0.4499
 JN3  C12   C  CH2    0  -0.400   3.2184  -3.3749  -0.1375
 JN3  C13   C  CT     0  -0.052   2.3522  -2.4184  -0.9552
 JN3  C14   C  CH1    0  -0.217   1.2217  -1.9423  -0.0237
 JN3  C15   C  CH2    0  -0.443   0.5735  -0.7971  -0.7950
 JN3  C16   C  CH2    0  -0.440   1.7658  -0.1178  -1.4963
 JN3  C17   C  CH1    0  -0.161   2.9919  -1.0546  -1.3198
 JN3  C18   C  CH3    0  -0.671   1.8167  -3.1066  -2.2162
 JN3  C19   C  CH3    0  -0.644  -0.2759  -6.0777   0.7194
 JN3  C20   C  CH1    0  -0.232   3.9470  -0.9816  -2.5182
 JN3  C21   C  CH3    0  -0.653   5.1140  -1.9609  -2.4194
 JN3  C22   C  CH2    0  -0.403   4.4729   0.4505  -2.6972
 JN3  C23   C  CH2    0  -0.571   5.1145   0.7234  -4.0513
 JN3  O25   O  O      0  -0.635   2.9519   0.9893  -5.0345
 JN3  C24   C  C      0   0.323   4.1469   0.7022  -5.2499
 JN3  O26   O  OC    -1  -0.579   4.6481   0.4352  -6.3635
 JN3  H11   H  HCH2   0   0.225   2.0155  -6.6312   2.0751
 JN3  H12   H  HCH2   0   0.210   0.5675  -7.0827   2.9326
 JN3  H21   H  HCH2   0   0.229   2.3278  -6.4015   4.5063
 JN3  H22   H  HCH2   0   0.193   2.4363  -4.8128   3.7664
 JN3  H3    H  HCH1   0   0.198  -0.0191  -6.0182   5.1081
 JN3  HO3   H  HOH1   0   0.412   1.5889  -3.8603   5.9095
 JN3  H41   H  HCH2   0   0.215   0.3454  -3.2308   3.9472
 JN3  H42   H  HCH2   0   0.221  -1.1012  -3.8511   4.7042
 JN3  H5    H  HCH1   0   0.203  -1.4248  -5.5184   2.9911
 JN3  H61   H  HCH2   0   0.223  -2.1870  -4.1515   1.2273
 JN3  H62   H  HCH2   0   0.222  -2.3589  -3.2178   2.6870
 JN3  H7    H  HCH1   0   0.193  -1.5185  -1.9994   0.6595
 JN3  HO7   H  HOH1   0   0.432   0.0151  -0.8624   1.9274
 JN3  H8    H  HCH1   0   0.211  -0.1238  -3.5623  -0.3476
 JN3  H9    H  HCH1   0   0.202   1.6106  -3.5286   2.1493
 JN3  H111  H  HCH2   0   0.216   2.0630  -5.1737  -0.3652
 JN3  H112  H  HCH2   0   0.226   3.0678  -5.1367   1.0605
 JN3  H121  H  HCH2   0   0.203   3.6903  -2.8121   0.6766
 JN3  H122  H  HCH2   0   0.226   4.0317  -3.7967  -0.7300
 JN3  H14   H  HCH1   0   0.196   1.7447  -1.4999   0.8388
 JN3  H151  H  HCH2   0   0.210   0.0264  -0.1014  -0.1542
 JN3  H152  H  HCH2   0   0.220  -0.1502  -1.1819  -1.5179
 JN3  H161  H  HCH2   0   0.230   1.5707   0.0511  -2.5581
 JN3  H162  H  HCH2   0   0.225   1.9611   0.8651  -1.0658
 JN3  H17   H  HCH1   0   0.195   3.5489  -0.7268  -0.4302
 JN3  H181  H  HCH3   0   0.224   1.1980  -3.9751  -1.9900
 JN3  H182  H  HCH3   0   0.227   1.2172  -2.4337  -2.8313
 JN3  H183  H  HCH3   0   0.229   2.6385  -3.4611  -2.8412
 JN3  H191  H  HCH3   0   0.216  -0.9567  -6.8185   1.1450
 JN3  H192  H  HCH3   0   0.219  -0.8464  -5.4871   0.0029
 JN3  H193  H  HCH3   0   0.224   0.4788  -6.6268   0.1539
 JN3  H20   H  HCH1   0   0.207   3.3675  -1.2322  -3.4136
 JN3  H211  H  HCH3   0   0.206   5.6500  -1.8514  -1.4733
 JN3  H212  H  HCH3   0   0.217   4.7893  -2.9973  -2.4950
 JN3  H213  H  HCH3   0   0.227   5.8324  -1.8010  -3.2241
 JN3  H221  H  HCH2   0   0.240   3.6616   1.1656  -2.5623
 JN3  H222  H  HCH2   0   0.200   5.1976   0.6557  -1.9000
 JN3  H231  H  HCH2   0   0.241   5.5731   1.7202  -4.0268
 JN3  H232  H  HCH2   0   0.215   5.9422   0.0355  -4.2434

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
 JN3  C1   C2    single  1.521  0.020  1.521
 JN3  C1   C10   single  1.538  0.020  1.538
 JN3  C1   H11   single  0.970  0.020  1.090
 JN3  C1   H12   single  0.970  0.020  1.090
 JN3  C2   C3    single  1.521  0.020  1.521
 JN3  C2   H21   single  0.970  0.020  1.090
 JN3  C2   H22   single  0.970  0.020  1.090
 JN3  C3   O3    single  1.417  0.020  1.417
 JN3  C3   C4    single  1.521  0.020  1.521
 JN3  C3   H3    single  0.970  0.020  1.090
 JN3  O3   HO3   single  0.850  0.020  0.980
 JN3  C4   C5    single  1.534  0.020  1.534
 JN3  C4   H41   single  0.970  0.020  1.090
 JN3  C4   H42   single  0.970  0.020  1.090
 JN3  C5   C10   single  1.547  0.020  1.547
 JN3  C5   C6    single  1.531  0.020  1.531
 JN3  C5   H5    single  0.970  0.020  1.090
 JN3  C6   C7    single  1.523  0.020  1.523
 JN3  C6   H61   single  0.970  0.020  1.090
 JN3  C6   H62   single  0.970  0.020  1.090
 JN3  C7   C8    single  1.535  0.020  1.535
 JN3  C7   O7    single  1.419  0.020  1.419
 JN3  C7   H7    single  0.970  0.020  1.090
 JN3  O7   HO7   single  0.850  0.020  0.980
 JN3  C8   C9    single  1.542  0.020  1.542
 JN3  C8   C14   single  1.524  0.020  1.524
 JN3  C8   H8    single  0.970  0.020  1.090
 JN3  C9   C11   single  1.532  0.020  1.532
 JN3  C9   C10   single  1.550  0.020  1.550
 JN3  C9   H9    single  0.970  0.020  1.090
 JN3  C10  C19   single  1.535  0.020  1.535
 JN3  C11  C12   single  1.530  0.020  1.530
 JN3  C11  H111  single  0.970  0.020  1.090
 JN3  C11  H112  single  0.970  0.020  1.090
 JN3  C12  C13   single  1.528  0.020  1.528
 JN3  C12  H121  single  0.970  0.020  1.090
 JN3  C12  H122  single  0.970  0.020  1.090
 JN3  C13  C18   single  1.533  0.020  1.533
 JN3  C13  C17   single  1.550  0.020  1.550
 JN3  C13  C14   single  1.540  0.020  1.540
 JN3  C14  C15   single  1.525  0.020  1.525
 JN3  C14  H14   single  0.970  0.020  1.090
 JN3  C15  C16   single  1.541  0.020  1.541
 JN3  C15  H151  single  0.970  0.020  1.090
 JN3  C15  H152  single  0.970  0.020  1.090
 JN3  C16  C17   single  1.553  0.020  1.553
 JN3  C16  H161  single  0.970  0.020  1.090
 JN3  C16  H162  single  0.970  0.020  1.090
 JN3  C17  C20   single  1.534  0.020  1.534
 JN3  C17  H17   single  0.970  0.020  1.090
 JN3  C18  H181  single  0.970  0.020  1.090
 JN3  C18  H182  single  0.970  0.020  1.090
 JN3  C18  H183  single  0.970  0.020  1.090
 JN3  C19  H191  single  0.970  0.020  1.090
 JN3  C19  H192  single  0.970  0.020  1.090
 JN3  C19  H193  single  0.970  0.020  1.090
 JN3  C20  C21   single  1.527  0.020  1.527
 JN3  C20  C22   single  1.536  0.020  1.536
 JN3  C20  H20   single  0.970  0.020  1.090
 JN3  C21  H211  single  0.970  0.020  1.090
 JN3  C21  H212  single  0.970  0.020  1.090
 JN3  C21  H213  single  0.970  0.020  1.090
 JN3  C22  C23   single  1.523  0.020  1.523
 JN3  C22  H221  single  0.970  0.020  1.090
 JN3  C22  H222  single  0.970  0.020  1.090
 JN3  C23  C24   single  1.541  0.020  1.541
 JN3  C23  H231  single  0.970  0.020  1.090
 JN3  C23  H232  single  0.970  0.020  1.090
 JN3  O25  C24   deloc   1.248  0.020  1.248
 JN3  C24  O26   deloc   1.250  0.020  1.250

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
 JN3  H12   C1   H11   105.49  3.000
 JN3  H12   C1   C10   107.74  3.000
 JN3  H11   C1   C10   110.28  3.000
 JN3  H12   C1   C2    108.09  3.000
 JN3  H11   C1   C2    110.20  3.000
 JN3  C10   C1   C2    114.58  3.000
 JN3  H22   C2   H21   106.53  3.000
 JN3  H22   C2   C3    109.73  3.000
 JN3  H21   C2   C3    109.94  3.000
 JN3  H22   C2   C1    110.73  3.000
 JN3  H21   C2   C1    109.82  3.000
 JN3  C3    C2   C1    110.02  3.000
 JN3  H3    C3   C4    109.06  3.000
 JN3  H3    C3   O3    104.99  3.000
 JN3  C4    C3   O3    111.83  3.000
 JN3  H3    C3   C2    108.06  3.000
 JN3  C4    C3   C2    110.19  3.000
 JN3  O3    C3   C2    112.47  3.000
 JN3  HO3   O3   C3    107.71  3.000
 JN3  H42   C4   H41   105.96  3.000
 JN3  H42   C4   C5    108.39  3.000
 JN3  H41   C4   C5    110.95  3.000
 JN3  H42   C4   C3    109.51  3.000
 JN3  H41   C4   C3    108.78  3.000
 JN3  C5    C4   C3    113.01  3.000
 JN3  H5    C5   C10   106.35  3.000
 JN3  H5    C5   C6    106.55  3.000
 JN3  C10   C5   C6    111.47  3.000
 JN3  H5    C5   C4    106.37  3.000
 JN3  C6    C5   C4    112.17  3.000
 JN3  C10   C5   C4    113.37  3.000
 JN3  H62   C6   H61   105.45  3.000
 JN3  H62   C6   C7    109.20  3.000
 JN3  H61   C6   C7    107.51  3.000
 JN3  H62   C6   C5    110.00  3.000
 JN3  H61   C6   C5    109.11  3.000
 JN3  C7    C6   C5    115.10  3.000
 JN3  H7    C7   C8    107.45  3.000
 JN3  H7    C7   O7    109.05  3.000
 JN3  C8    C7   O7    112.77  3.000
 JN3  H7    C7   C6    107.53  3.000
 JN3  O7    C7   C6    108.46  3.000
 JN3  C8    C7   C6    111.42  3.000
 JN3  HO7   O7   C7    108.32  3.000
 JN3  H8    C8   C14   107.74  3.000
 JN3  H8    C8   C9    109.17  3.000
 JN3  C14   C8   C9    109.38  3.000
 JN3  H8    C8   C7    105.69  3.000
 JN3  C14   C8   C7    112.05  3.000
 JN3  C9    C8   C7    112.61  3.000
 JN3  H9    C9   C11   106.42  3.000
 JN3  H9    C9   C10   107.29  3.000
 JN3  C11   C9   C10   113.45  3.000
 JN3  H9    C9   C8    106.26  3.000
 JN3  C10   C9   C8    111.93  3.000
 JN3  C11   C9   C8    111.01  3.000
 JN3  C19   C10  C9    111.78  3.000
 JN3  C19   C10  C5    109.41  3.000
 JN3  C9    C10  C5    108.88  3.000
 JN3  C19   C10  C1    106.28  3.000
 JN3  C9    C10  C1    112.15  3.000
 JN3  C5    C10  C1    108.24  3.000
 JN3  H112  C11  H111  105.90  3.000
 JN3  H112  C11  C12   107.90  3.000
 JN3  H111  C11  C12   108.89  3.000
 JN3  H112  C11  C9    109.83  3.000
 JN3  H111  C11  C9    110.03  3.000
 JN3  C12   C11  C9    113.96  3.000
 JN3  H122  C12  H121  106.31  3.000
 JN3  H122  C12  C13   111.96  3.000
 JN3  H121  C12  C13   108.66  3.000
 JN3  H122  C12  C11   108.46  3.000
 JN3  H121  C12  C11   109.37  3.000
 JN3  C13   C12  C11   111.89  3.000
 JN3  C18   C13  C17   110.22  3.000
 JN3  C17   C13  C14    99.98  3.000
 JN3  C18   C13  C14   112.32  3.000
 JN3  C14   C13  C12   106.62  3.000
 JN3  C17   C13  C12   116.28  3.000
 JN3  C18   C13  C12   110.93  3.000
 JN3  H14   C14  C15   107.23  3.000
 JN3  H14   C14  C13   104.43  3.000
 JN3  C15   C14  C13   103.78  3.000
 JN3  H14   C14  C8    107.22  3.000
 JN3  C15   C14  C8    118.74  3.000
 JN3  C13   C14  C8    114.39  3.000
 JN3  H152  C15  H151  106.29  3.000
 JN3  H152  C15  C16   111.50  3.000
 JN3  H151  C15  C16   111.94  3.000
 JN3  H152  C15  C14   110.58  3.000
 JN3  H151  C15  C14   113.22  3.000
 JN3  C16   C15  C14   103.44  3.000
 JN3  H162  C16  H161  106.04  3.000
 JN3  H162  C16  C17   110.94  3.000
 JN3  H161  C16  C17   110.16  3.000
 JN3  H162  C16  C15   110.86  3.000
 JN3  H161  C16  C15   111.85  3.000
 JN3  C17   C16  C15   107.05  3.000
 JN3  H17   C17  C20   107.61  3.000
 JN3  H17   C17  C16   108.18  3.000
 JN3  C20   C17  C16   111.96  3.000
 JN3  H17   C17  C13   106.33  3.000
 JN3  C20   C17  C13   118.86  3.000
 JN3  C16   C17  C13   103.39  3.000
 JN3  H183  C18  H182  106.92  3.000
 JN3  H183  C18  H181  106.70  3.000
 JN3  H182  C18  H181  107.24  3.000
 JN3  H183  C18  C13   110.72  3.000
 JN3  H182  C18  C13   112.26  3.000
 JN3  H181  C18  C13   112.66  3.000
 JN3  H193  C19  H192  107.10  3.000
 JN3  H193  C19  H191  106.96  3.000
 JN3  H192  C19  H191  107.30  3.000
 JN3  H193  C19  C10   111.56  3.000
 JN3  H192  C19  C10   113.85  3.000
 JN3  H191  C19  C10   109.75  3.000
 JN3  H20   C20  C22   107.41  3.000
 JN3  H20   C20  C21   108.09  3.000
 JN3  C22   C20  C21   110.11  3.000
 JN3  H20   C20  C17   107.35  3.000
 JN3  C22   C20  C17   110.40  3.000
 JN3  C21   C20  C17   113.25  3.000
 JN3  H213  C21  H212  106.55  3.000
 JN3  H213  C21  H211  107.52  3.000
 JN3  H212  C21  H211  107.56  3.000
 JN3  H213  C21  C20   111.21  3.000
 JN3  H212  C21  C20   112.22  3.000
 JN3  H211  C21  C20   111.51  3.000
 JN3  H222  C22  H221  106.21  3.000
 JN3  H222  C22  C23   109.54  3.000
 JN3  H221  C22  C23   107.83  3.000
 JN3  H222  C22  C20   108.42  3.000
 JN3  H221  C22  C20   110.02  3.000
 JN3  C23   C22  C20   114.51  3.000
 JN3  H232  C23  H231  105.01  3.000
 JN3  H232  C23  C24   109.28  3.000
 JN3  H231  C23  C24   106.99  3.000
 JN3  H232  C23  C22   111.25  3.000
 JN3  H231  C23  C22   108.60  3.000
 JN3  C24   C23  C22   115.13  3.000
 JN3  O26   C24  O25   125.94  3.000
 JN3  O26   C24  C23   116.38  3.000
 JN3  O25   C24  C23   117.65  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
 JN3  Var_01  C10  C1   C2   C3    58.39  30.0  1
 JN3  Var_02  C13  C12  C11  C9   -54.84  30.0  1
 JN3  Var_03  C17  C16  C15  C14   10.63  30.0  1
 JN3  Var_04  C24  C23  C22  C20   67.64  30.0  3
 JN3  Var_05  O25  C24  C23  C22   27.28  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
 JN3  chir_01  C3   C2   O3   C4   negativ
 JN3  chir_02  C5   C4   C10  C6   positiv
 JN3  chir_03  C7   O7   C8   C6   negativ
 JN3  chir_04  C8   C7   C9   C14  positiv
 JN3  chir_05  C9   C10  C11  C8   negativ
 JN3  chir_06  C10  C9   C5   C1   positiv
 JN3  chir_07  C13  C12  C17  C14  positiv
 JN3  chir_08  C14  C15  C13  C8   positiv
 JN3  chir_09  C17  C20  C16  C13  negativ
 JN3  chir_10  C20  C17  C21  C22  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
 JN3  plan-1  C23  0.020
 JN3  plan-1  O25  0.020
 JN3  plan-1  C24  0.020
 JN3  plan-1  O26  0.020

