# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 00:03:25 2021
#   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  68  28  .  2022-03-22  2022-11-17
;
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  -0.433  -3.1732   2.6559  -7.4797
 JN3  C2    C  CH2   0  -0.476  -1.7833   2.0707  -7.2743
 JN3  C3    C  CH1   0   0.086  -1.7342   1.3114  -5.9573
 JN3  O3    O  OH1   0  -0.680  -0.4568   0.7672  -5.6871
 JN3  C4    C  CH2   0  -0.449  -2.0987   2.2417  -4.8157
 JN3  C5    C  CH1   0  -0.226  -3.4849   2.8729  -5.0046
 JN3  C6    C  CH2   0  -0.446  -3.8847   3.7731  -3.8325
 JN3  C7    C  CH1   0   0.054  -3.2043   5.1422  -3.8008
 JN3  O7    O  OH1   0  -0.676  -1.8784   5.0825  -3.2995
 JN3  C8    C  CH1   0  -0.297  -3.2981   5.8375  -5.1646
 JN3  C9    C  CH1   0  -0.200  -2.8281   4.9227  -6.3159
 JN3  C10   C  CT    0  -0.052  -3.6428   3.6020  -6.3600
 JN3  C11   C  CH2   0  -0.441  -2.7974   5.6671  -7.6548
 JN3  C12   C  CH2   0  -0.407  -2.0857   7.0214  -7.6057
 JN3  C13   C  CT    0  -0.056  -2.6593   7.9283  -6.5170
 JN3  C14   C  CH1   0  -0.163  -2.5321   7.1517  -5.1940
 JN3  C15   C  CH2   0  -0.447  -2.8373   8.1857  -4.1191
 JN3  C16   C  CH2   0  -0.451  -2.2429   9.4859  -4.6932
 JN3  C17   C  CH1   0  -0.160  -1.8368   9.1946  -6.1632
 JN3  C18   C  CH3   0  -0.688  -4.1065   8.3138  -6.8382
 JN3  C19   C  CH3   0  -0.673  -5.1304   3.8690  -6.6282
 JN3  C20   C  CH1   0  -0.239  -1.9623  10.4429  -7.0496
 JN3  C21   C  CH3   0  -0.674  -1.6373  10.1714  -8.5154
 JN3  C22   C  CH2   0  -0.409  -1.0611  11.5533  -6.4905
 JN3  C23   C  CH2   0  -0.592  -1.2176  12.8914  -7.1976
 JN3  O25   O  O     0  -0.446   0.2678  13.8906  -5.5787
 JN3  C24   C  C     0   0.555  -0.4205  13.9979  -6.5635
 JN3  O26   O  OH1   0  -0.599  -0.5562  15.1449  -7.2252
 JN3  H11   H  HCH2  0   0.235  -3.2331   3.1562  -8.4486
 JN3  H12   H  HCH2  0   0.221  -3.8901   1.8275  -7.5348
 JN3  H21   H  HCH2  0   0.231  -1.5444   1.3993  -8.1057
 JN3  H22   H  HCH2  0   0.217  -1.0207   2.8575  -7.2747
 JN3  H3    H  HCH1  0   0.182  -2.4870   0.5072  -6.0043
 JN3  HO3   H  HOH1  0   0.445  -0.2284   0.1726  -6.4084
 JN3  H41   H  HCH2  0   0.235  -2.0914   1.6926  -3.8689
 JN3  H42   H  HCH2  0   0.200  -1.3068   2.9916  -4.7396
 JN3  H5    H  HCH1  0   0.219  -4.1956   2.0349  -5.0170
 JN3  H61   H  HCH2  0   0.231  -4.9641   3.9455  -3.8724
 JN3  H62   H  HCH2  0   0.230  -3.7009   3.2571  -2.8855
 JN3  H7    H  HCH1  0   0.227  -3.7436   5.7583  -3.0743
 JN3  HO7   H  HOH1  0   0.444  -1.2842   4.8180  -4.0072
 JN3  H8    H  HCH1  0   0.223  -4.3604   6.0642  -5.3079
 JN3  H9    H  HCH1  0   0.200  -1.7801   4.6575  -6.1068
 JN3  H111  H  HCH2  0   0.218  -3.8146   5.8092  -8.0298
 JN3  H112  H  HCH2  0   0.232  -2.2917   5.0481  -8.3996
 JN3  H121  H  HCH2  0   0.208  -1.0188   6.8658  -7.4059
 JN3  H122  H  HCH2  0   0.225  -2.1482   7.4741  -8.5965
 JN3  H14   H  HCH1  0   0.205  -1.4619   6.9134  -5.1042
 JN3  H151  H  HCH2  0   0.214  -3.9154   8.2804  -3.9615
 JN3  H152  H  HCH2  0   0.230  -2.4016   7.9194  -3.1556
 JN3  H161  H  HCH2  0   0.230  -1.3852   9.8208  -4.1084
 JN3  H162  H  HCH2  0   0.219  -2.9716  10.3008  -4.6559
 JN3  H17   H  HCH1  0   0.204  -0.7808   8.8899  -6.1787
 JN3  H181  H  HCH3  0   0.231  -4.5407   8.9626  -6.0754
 JN3  H182  H  HCH3  0   0.230  -4.1572   8.8545  -7.7856
 JN3  H183  H  HCH3  0   0.232  -4.7621   7.4481  -6.9306
 JN3  H191  H  HCH3  0   0.232  -5.5804   4.5951  -5.9526
 JN3  H192  H  HCH3  0   0.229  -5.2921   4.2326  -7.6442
 JN3  H193  H  HCH3  0   0.227  -5.6985   2.9413  -6.5281
 JN3  H20   H  HCH1  0   0.209  -3.0000  10.7962  -6.9861
 JN3  H211  H  HCH3  0   0.234  -1.7030  11.0762  -9.1203
 JN3  H212  H  HCH3  0   0.213  -0.6257   9.7736  -8.6279
 JN3  H213  H  HCH3  0   0.233  -2.3250   9.4555  -8.9603
 JN3  H221  H  HCH2  0   0.244  -1.2798  11.7003  -5.4321
 JN3  H222  H  HCH2  0   0.218  -0.0173  11.2271  -6.5474
 JN3  H231  H  HCH2  0   0.277  -0.9184  12.8343  -8.2468
 JN3  H232  H  HCH2  0   0.274  -2.2689  13.1990  -7.2109
 JN3  HO26  H  HOH1  0   0.477  -0.0256  15.8347  -6.7998

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  1.522  0.020  1.522
 JN3  C1   C10   single  1.539  0.020  1.539
 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  1.415  0.020  1.415
 JN3  C3   C4    single  1.517  0.020  1.517
 JN3  C3   H3    single  0.970  0.020  1.090
 JN3  O3   HO3   single  0.850  0.020  0.980
 JN3  C4   C5    single  1.535  0.020  1.535
 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  1.529  0.020  1.529
 JN3  C6   H61   single  0.970  0.020  1.090
 JN3  C6   H62   single  0.970  0.020  1.090
 JN3  C7   C8    single  1.534  0.020  1.534
 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  1.544  0.020  1.544
 JN3  C8   C14   single  1.521  0.020  1.521
 JN3  C8   H8    single  0.970  0.020  1.090
 JN3  C9   C11   single  1.532  0.020  1.532
 JN3  C9   C10   single  1.552  0.020  1.552
 JN3  C9   H9    single  0.970  0.020  1.090
 JN3  C10  C19   single  1.535  0.020  1.535
 JN3  C11  C12   single  1.531  0.020  1.531
 JN3  C11  H111  single  0.970  0.020  1.090
 JN3  C11  H112  single  0.970  0.020  1.090
 JN3  C12  C13   single  1.529  0.020  1.529
 JN3  C12  H121  single  0.970  0.020  1.090
 JN3  C12  H122  single  0.970  0.020  1.090
 JN3  C13  C18   single  1.532  0.020  1.532
 JN3  C13  C17   single  1.551  0.020  1.551
 JN3  C13  C14   single  1.539  0.020  1.539
 JN3  C14  C15   single  1.522  0.020  1.522
 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  1.536  0.020  1.536
 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  1.526  0.020  1.526
 JN3  C20  C22   single  1.535  0.020  1.535
 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  1.521  0.020  1.521
 JN3  C22  H221  single  0.970  0.020  1.090
 JN3  C22  H222  single  0.970  0.020  1.090
 JN3  C23  C24   single  1.504  0.020  1.504
 JN3  C23  H231  single  0.970  0.020  1.090
 JN3  C23  H232  single  0.970  0.020  1.090
 JN3  O25  C24   double  1.206  0.020  1.206
 JN3  C24  O26   single  1.331  0.020  1.331
 JN3  O26  HO26  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
 JN3  H12   C1   H11   105.40  3.000
 JN3  H12   C1   C10   107.54  3.000
 JN3  H11   C1   C10   110.31  3.000
 JN3  H12   C1   C2    108.26  3.000
 JN3  H11   C1   C2    110.23  3.000
 JN3  C10   C1   C2    114.63  3.000
 JN3  H22   C2   H21   106.75  3.000
 JN3  H22   C2   C3    109.65  3.000
 JN3  H21   C2   C3    110.13  3.000
 JN3  H22   C2   C1    111.07  3.000
 JN3  H21   C2   C1    109.42  3.000
 JN3  C3    C2   C1    109.77  3.000
 JN3  H3    C3   C4    108.38  3.000
 JN3  H3    C3   O3    110.13  3.000
 JN3  C4    C3   O3    108.01  3.000
 JN3  H3    C3   C2    107.77  3.000
 JN3  C4    C3   C2    109.73  3.000
 JN3  O3    C3   C2    112.74  3.000
 JN3  HO3   O3   C3    108.00  3.000
 JN3  H42   C4   H41   106.20  3.000
 JN3  H42   C4   C5    112.37  3.000
 JN3  H41   C4   C5    108.59  3.000
 JN3  H42   C4   C3    107.39  3.000
 JN3  H41   C4   C3    109.98  3.000
 JN3  C5    C4   C3    112.12  3.000
 JN3  H5    C5   C10   106.47  3.000
 JN3  H5    C5   C6    106.75  3.000
 JN3  C10   C5   C6    111.53  3.000
 JN3  H5    C5   C4    105.77  3.000
 JN3  C6    C5   C4    112.55  3.000
 JN3  C10   C5   C4    113.19  3.000
 JN3  H62   C6   H61   105.76  3.000
 JN3  H62   C6   C7    109.24  3.000
 JN3  H61   C6   C7    107.38  3.000
 JN3  H62   C6   C5    109.97  3.000
 JN3  H61   C6   C5    108.81  3.000
 JN3  C7    C6   C5    115.22  3.000
 JN3  H7    C7   C8    107.75  3.000
 JN3  H7    C7   O7    104.46  3.000
 JN3  C8    C7   O7    112.98  3.000
 JN3  H7    C7   C6    107.37  3.000
 JN3  O7    C7   C6    112.67  3.000
 JN3  C8    C7   C6    111.12  3.000
 JN3  HO7   O7   C7    109.21  3.000
 JN3  H8    C8   C14   107.87  3.000
 JN3  H8    C8   C9    108.68  3.000
 JN3  C14   C8   C9    110.13  3.000
 JN3  H8    C8   C7    105.63  3.000
 JN3  C14   C8   C7    112.21  3.000
 JN3  C9    C8   C7    112.08  3.000
 JN3  H9    C9   C11   105.30  3.000
 JN3  H9    C9   C10   107.46  3.000
 JN3  C11   C9   C10   113.51  3.000
 JN3  H9    C9   C8    106.91  3.000
 JN3  C10   C9   C8    111.44  3.000
 JN3  C11   C9   C8    111.71  3.000
 JN3  C19   C10  C9    111.45  3.000
 JN3  C19   C10  C5    109.51  3.000
 JN3  C9    C10  C5    108.81  3.000
 JN3  C19   C10  C1    105.99  3.000
 JN3  C9    C10  C1    112.55  3.000
 JN3  C5    C10  C1    108.45  3.000
 JN3  H112  C11  H111  105.69  3.000
 JN3  H112  C11  C12   107.94  3.000
 JN3  H111  C11  C12   109.18  3.000
 JN3  H112  C11  C9    109.25  3.000
 JN3  H111  C11  C9    110.13  3.000
 JN3  C12   C11  C9    114.27  3.000
 JN3  H122  C12  H121  106.26  3.000
 JN3  H122  C12  C13   112.28  3.000
 JN3  H121  C12  C13   108.64  3.000
 JN3  H122  C12  C11   108.14  3.000
 JN3  H121  C12  C11   109.43  3.000
 JN3  C13   C12  C11   111.92  3.000
 JN3  C18   C13  C17   110.09  3.000
 JN3  C17   C13  C14    99.90  3.000
 JN3  C18   C13  C14   112.66  3.000
 JN3  C14   C13  C12   106.36  3.000
 JN3  C17   C13  C12   116.61  3.000
 JN3  C18   C13  C12   110.76  3.000
 JN3  H14   C14  C15   106.53  3.000
 JN3  H14   C14  C13   105.06  3.000
 JN3  C15   C14  C13   104.33  3.000
 JN3  H14   C14  C8    107.52  3.000
 JN3  C15   C14  C8    118.18  3.000
 JN3  C13   C14  C8    114.26  3.000
 JN3  H152  C15  H151  106.71  3.000
 JN3  H152  C15  C16   112.41  3.000
 JN3  H151  C15  C16   111.16  3.000
 JN3  H152  C15  C14   112.20  3.000
 JN3  H151  C15  C14   110.99  3.000
 JN3  C16   C15  C14   103.46  3.000
 JN3  H162  C16  H161  106.07  3.000
 JN3  H162  C16  C17   110.27  3.000
 JN3  H161  C16  C17   111.07  3.000
 JN3  H162  C16  C15   111.04  3.000
 JN3  H161  C16  C15   111.26  3.000
 JN3  C17   C16  C15   107.18  3.000
 JN3  H17   C17  C20   107.20  3.000
 JN3  H17   C17  C16   108.46  3.000
 JN3  C20   C17  C16   111.87  3.000
 JN3  H17   C17  C13   106.26  3.000
 JN3  C20   C17  C13   119.24  3.000
 JN3  C16   C17  C13   103.33  3.000
 JN3  H183  C18  H182  106.97  3.000
 JN3  H183  C18  H181  106.99  3.000
 JN3  H182  C18  H181  107.07  3.000
 JN3  H183  C18  C13   112.72  3.000
 JN3  H182  C18  C13   110.51  3.000
 JN3  H181  C18  C13   112.26  3.000
 JN3  H193  C19  H192  106.93  3.000
 JN3  H193  C19  H191  107.12  3.000
 JN3  H192  C19  H191  107.11  3.000
 JN3  H193  C19  C10   109.90  3.000
 JN3  H192  C19  C10   111.36  3.000
 JN3  H191  C19  C10   114.08  3.000
 JN3  H20   C20  C22   107.51  3.000
 JN3  H20   C20  C21   108.31  3.000
 JN3  C22   C20  C21   110.70  3.000
 JN3  H20   C20  C17   107.78  3.000
 JN3  C22   C20  C17   109.24  3.000
 JN3  C21   C20  C17   113.10  3.000
 JN3  H213  C21  H212  107.67  3.000
 JN3  H213  C21  H211  106.33  3.000
 JN3  H212  C21  H211  107.50  3.000
 JN3  H213  C21  C20   112.04  3.000
 JN3  H212  C21  C20   111.15  3.000
 JN3  H211  C21  C20   111.87  3.000
 JN3  H222  C22  H221  106.35  3.000
 JN3  H222  C22  C23   109.63  3.000
 JN3  H221  C22  C23   108.17  3.000
 JN3  H222  C22  C20   108.98  3.000
 JN3  H221  C22  C20   109.46  3.000
 JN3  C23   C22  C20   113.98  3.000
 JN3  H232  C23  H231  105.42  3.000
 JN3  H232  C23  C24   107.89  3.000
 JN3  H231  C23  C24   107.35  3.000
 JN3  H232  C23  C22   110.57  3.000
 JN3  H231  C23  C22   111.85  3.000
 JN3  C24   C23  C22   113.37  3.000
 JN3  O26   C24  O25   122.73  3.000
 JN3  O26   C24  C23   111.74  3.000
 JN3  O25   C24  C23   125.54  3.000
 JN3  HO26  O26  C24   109.85  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  CONST_01  HO26  O26  C24  C23  180.00   0.0  0
 JN3  Var_01    C10   C1   C2   C3    57.94  30.0  1
 JN3  Var_02    C13   C12  C11  C9   -54.17  30.0  1
 JN3  Var_03    C17   C16  C15  C14    9.23  30.0  1
 JN3  Var_04    C24   C23  C22  C20  174.92  30.0  3
 JN3  Var_05    O25   C24  C23  C22   -1.35  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
 JN3  plan-1  HO26  0.020

