# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 00:27:43 2021
#   Inital geometry file: a 143 line input string
#   Ligand name: (5beta,9beta)-3-oxocholan-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]3CC[C@@H]4CC(=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
 3KL  3KL  '(5beta,9beta)-3-oxocholan-24-oic acid'  ligand  65  27  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3KL
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
 3KL  C2   C  CH2   0  -0.562   9.1118   1.7636  27.2420
 3KL  C3   C  C     0   0.420   9.4122   0.3023  27.0622
 3KL  O3   O  O     0  -0.412   8.5552  -0.5556  27.0946
 3KL  C4   C  CH2   0  -0.562  10.8640  -0.0094  26.8267
 3KL  C5   C  CH1   0  -0.219  11.8150   0.6731  27.8280
 3KL  C6   C  CH2   0  -0.431  13.2669   0.3825  27.4490
 3KL  C1   C  CH2   0  -0.437  10.0506   2.3723  28.2835
 3KL  C7   C  CH2   0  -0.433  13.6976   1.1343  26.1955
 3KL  C8   C  CH1   0  -0.217  13.4447   2.6357  26.3125
 3KL  C9   C  CH1   0  -0.195  11.9782   2.9231  26.6877
 3KL  C10  C  CT    0  -0.071  11.5462   2.1874  27.9813
 3KL  C11  C  CH2   0  -0.440  11.6971   4.4291  26.7157
 3KL  C12  C  CH2   0  -0.408  12.1082   5.1500  25.4296
 3KL  C13  C  CT    0  -0.057  13.5731   4.8891  25.0738
 3KL  C14  C  CH1   0  -0.173  13.7546   3.3610  25.0122
 3KL  C15  C  CH2   0  -0.448  15.1261   3.1767  24.3760
 3KL  C16  C  CH2   0  -0.448  15.2038   4.3264  23.3524
 3KL  C17  C  CH1   0  -0.160  14.0065   5.2749  23.6378
 3KL  C18  C  CH3   0  -0.688  14.5073   5.5447  26.0960
 3KL  C19  C  CH3   0  -0.666  12.3037   2.7185  29.2051
 3KL  C20  C  CH1   0  -0.240  14.3340   6.7429  23.3222
 3KL  C21  C  CH3   0  -0.675  13.1909   7.6973  23.6599
 3KL  C22  C  CH2   0  -0.410  14.7244   6.8655  21.8423
 3KL  C23  C  CH2   0  -0.595  15.2067   8.2534  21.4495
 3KL  C24  C  C     0   0.555  15.7430   8.3317  20.0474
 3KL  OT1  O  OH1   0  -0.599  16.1783   9.5554  19.7545
 3KL  OT2  O  O     0  -0.446  15.7839   7.4195  19.2594
 3KL  H1   H  HCH2  0   0.259   9.2463   2.2609  26.2752
 3KL  H2   H  HCH2  0   0.261   8.0683   1.9001  27.5296
 3KL  H3   H  HCH2  0   0.259  11.0154  -1.0907  26.8493
 3KL  H4   H  HCH2  0   0.260  11.0869   0.3169  25.8049
 3KL  H5   H  HCH1  0   0.231  11.6194   0.2146  28.8052
 3KL  H6   H  HCH2  0   0.229  13.3980  -0.6943  27.3061
 3KL  H7   H  HCH2  0   0.229  13.9234   0.6572  28.2798
 3KL  H8   H  HCH2  0   0.246   9.8096   3.4293  28.4108
 3KL  H9   H  HCH2  0   0.236   9.8405   1.9042  29.2514
 3KL  H10  H  HCH2  0   0.209  13.1658   0.7490  25.3178
 3KL  H11  H  HCH2  0   0.236  14.7582   0.9501  26.0057
 3KL  H12  H  HCH1  0   0.208  14.1029   3.0224  27.1006
 3KL  H13  H  HCH1  0   0.207  11.3821   2.5176  25.8565
 3KL  H14  H  HCH2  0   0.218  12.2097   4.8868  27.5659
 3KL  H15  H  HCH2  0   0.230  10.6311   4.6016  26.8830
 3KL  H16  H  HCH2  0   0.225  11.9000   6.2144  25.5490
 3KL  H17  H  HCH2  0   0.208  11.4787   4.8032  24.6012
 3KL  H18  H  HCH1  0   0.203  13.0172   2.9997  24.2772
 3KL  H19  H  HCH2  0   0.229  15.2410   2.1978  23.9083
 3KL  H20  H  HCH2  0   0.215  15.9161   3.2614  25.1270
 3KL  H21  H  HCH2  0   0.229  15.1614   3.9459  22.3310
 3KL  H22  H  HCH2  0   0.220  16.1516   4.8657  23.4346
 3KL  H23  H  HCH1  0   0.205  13.1762   4.9859  22.9765
 3KL  H24  H  HCH3  0   0.232  14.3152   5.2148  27.1165
 3KL  H25  H  HCH3  0   0.232  15.5591   5.3414  25.8890
 3KL  H26  H  HCH3  0   0.230  14.3844   6.6288  26.0906
 3KL  H27  H  HCH3  0   0.227  12.0663   2.1162  30.0852
 3KL  H28  H  HCH3  0   0.233  13.3859   2.7045  29.0822
 3KL  H29  H  HCH3  0   0.231  12.0153   3.7462  29.4308
 3KL  H30  H  HCH1  0   0.209  15.2103   7.0350  23.9163
 3KL  H31  H  HCH3  0   0.232  12.9928   7.7388  24.7294
 3KL  H32  H  HCH3  0   0.235  13.4115   8.7191  23.3501
 3KL  H33  H  HCH3  0   0.214  12.2668   7.3929  23.1624
 3KL  H34  H  HCH2  0   0.219  13.8684   6.5782  21.2228
 3KL  H35  H  HCH2  0   0.245  15.5164   6.1482  21.6215
 3KL  H36  H  HCH2  0   0.273  15.9936   8.5932  22.1317
 3KL  H37  H  HCH2  0   0.278  14.4097   8.9970  21.5328
 3KL  H38  H  HOH1  0   0.477  16.5162   9.5762  18.8469

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
 3KL  OT2  C24  double  1.206  0.020  1.206
 3KL  OT1  C24  single  1.331  0.020  1.331
 3KL  C24  C23  single  1.503  0.020  1.503
 3KL  C23  C22  single  1.521  0.020  1.521
 3KL  C22  C20  single  1.535  0.020  1.535
 3KL  C20  C21  single  1.527  0.020  1.527
 3KL  C20  C17  single  1.537  0.020  1.537
 3KL  C16  C17  single  1.554  0.020  1.554
 3KL  C16  C15  single  1.541  0.020  1.541
 3KL  C17  C13  single  1.549  0.020  1.549
 3KL  C15  C14  single  1.523  0.020  1.523
 3KL  C14  C13  single  1.540  0.020  1.540
 3KL  C14  C8   single  1.521  0.020  1.521
 3KL  C13  C12  single  1.530  0.020  1.530
 3KL  C13  C18  single  1.532  0.020  1.532
 3KL  C12  C11  single  1.531  0.020  1.531
 3KL  C7   C8   single  1.527  0.020  1.527
 3KL  C7   C6   single  1.524  0.020  1.524
 3KL  C8   C9   single  1.541  0.020  1.541
 3KL  C4   C3   single  1.503  0.020  1.503
 3KL  C4   C5   single  1.540  0.020  1.540
 3KL  O3   C3   double  1.213  0.020  1.213
 3KL  C3   C2   single  1.503  0.020  1.503
 3KL  C9   C11  single  1.532  0.020  1.532
 3KL  C9   C10  single  1.550  0.020  1.550
 3KL  C2   C1   single  1.529  0.020  1.529
 3KL  C6   C5   single  1.528  0.020  1.528
 3KL  C5   C10  single  1.546  0.020  1.546
 3KL  C10  C1   single  1.537  0.020  1.537
 3KL  C10  C19  single  1.534  0.020  1.534
 3KL  C2   H1   single  0.970  0.020  1.090
 3KL  C2   H2   single  0.970  0.020  1.090
 3KL  C4   H3   single  0.970  0.020  1.090
 3KL  C4   H4   single  0.970  0.020  1.090
 3KL  C5   H5   single  0.970  0.020  1.090
 3KL  C6   H6   single  0.970  0.020  1.090
 3KL  C6   H7   single  0.970  0.020  1.090
 3KL  C1   H8   single  0.970  0.020  1.090
 3KL  C1   H9   single  0.970  0.020  1.090
 3KL  C7   H10  single  0.970  0.020  1.090
 3KL  C7   H11  single  0.970  0.020  1.090
 3KL  C8   H12  single  0.970  0.020  1.090
 3KL  C9   H13  single  0.970  0.020  1.090
 3KL  C11  H14  single  0.970  0.020  1.090
 3KL  C11  H15  single  0.970  0.020  1.090
 3KL  C12  H16  single  0.970  0.020  1.090
 3KL  C12  H17  single  0.970  0.020  1.090
 3KL  C14  H18  single  0.970  0.020  1.090
 3KL  C15  H19  single  0.970  0.020  1.090
 3KL  C15  H20  single  0.970  0.020  1.090
 3KL  C16  H21  single  0.970  0.020  1.090
 3KL  C16  H22  single  0.970  0.020  1.090
 3KL  C17  H23  single  0.970  0.020  1.090
 3KL  C18  H24  single  0.970  0.020  1.090
 3KL  C18  H25  single  0.970  0.020  1.090
 3KL  C18  H26  single  0.970  0.020  1.090
 3KL  C19  H27  single  0.970  0.020  1.090
 3KL  C19  H28  single  0.970  0.020  1.090
 3KL  C19  H29  single  0.970  0.020  1.090
 3KL  C20  H30  single  0.970  0.020  1.090
 3KL  C21  H31  single  0.970  0.020  1.090
 3KL  C21  H32  single  0.970  0.020  1.090
 3KL  C21  H33  single  0.970  0.020  1.090
 3KL  C22  H34  single  0.970  0.020  1.090
 3KL  C22  H35  single  0.970  0.020  1.090
 3KL  C23  H36  single  0.970  0.020  1.090
 3KL  C23  H37  single  0.970  0.020  1.090
 3KL  OT1  H38  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
 3KL  H2   C2   H1   107.05  3.000
 3KL  H2   C2   C1   110.98  3.000
 3KL  H1   C2   C1   110.19  3.000
 3KL  H2   C2   C3   110.15  3.000
 3KL  H1   C2   C3   108.14  3.000
 3KL  C1   C2   C3   110.24  3.000
 3KL  C4   C3   O3   122.67  3.000
 3KL  O3   C3   C2   122.91  3.000
 3KL  C4   C3   C2   114.42  3.000
 3KL  H4   C4   H3   106.62  3.000
 3KL  H4   C4   C5   110.40  3.000
 3KL  H3   C4   C5   109.85  3.000
 3KL  H4   C4   C3   106.31  3.000
 3KL  H3   C4   C3   109.63  3.000
 3KL  C5   C4   C3   113.73  3.000
 3KL  H5   C5   C10  106.87  3.000
 3KL  H5   C5   C6   108.11  3.000
 3KL  C10  C5   C6   112.09  3.000
 3KL  H5   C5   C4   106.48  3.000
 3KL  C10  C5   C4   113.03  3.000
 3KL  C6   C5   C4   109.94  3.000
 3KL  H7   C6   H6   105.93  3.000
 3KL  H7   C6   C7   109.34  3.000
 3KL  H6   C6   C7   110.13  3.000
 3KL  H7   C6   C5   109.51  3.000
 3KL  H6   C6   C5   109.48  3.000
 3KL  C7   C6   C5   112.25  3.000
 3KL  H9   C1   H8   105.57  3.000
 3KL  H9   C1   C10  107.99  3.000
 3KL  H8   C1   C10  110.74  3.000
 3KL  H9   C1   C2   108.31  3.000
 3KL  H8   C1   C2   109.24  3.000
 3KL  C10  C1   C2   114.57  3.000
 3KL  H11  C7   H10  105.81  3.000
 3KL  H11  C7   C8   109.86  3.000
 3KL  H10  C7   C8   109.06  3.000
 3KL  H11  C7   C6   109.51  3.000
 3KL  H10  C7   C6   110.37  3.000
 3KL  C8   C7   C6   112.04  3.000
 3KL  H12  C8   C14  108.89  3.000
 3KL  H12  C8   C9   109.28  3.000
 3KL  C14  C8   C9   108.25  3.000
 3KL  H12  C8   C7   107.59  3.000
 3KL  C9   C8   C7   111.08  3.000
 3KL  C14  C8   C7   111.70  3.000
 3KL  H13  C9   C11  106.06  3.000
 3KL  H13  C9   C10  107.73  3.000
 3KL  C11  C9   C10  113.59  3.000
 3KL  H13  C9   C8   105.24  3.000
 3KL  C10  C9   C8   112.33  3.000
 3KL  C11  C9   C8   111.25  3.000
 3KL  C19  C10  C9   111.34  3.000
 3KL  C19  C10  C1   106.38  3.000
 3KL  C9   C10  C1   112.23  3.000
 3KL  C19  C10  C5   109.42  3.000
 3KL  C1   C10  C5   107.85  3.000
 3KL  C9   C10  C5   109.50  3.000
 3KL  H15  C11  H14  105.80  3.000
 3KL  H15  C11  C12  108.44  3.000
 3KL  H14  C11  C12  109.29  3.000
 3KL  H15  C11  C9   109.69  3.000
 3KL  H14  C11  C9   109.86  3.000
 3KL  C12  C11  C9   113.47  3.000
 3KL  H17  C12  H16  106.36  3.000
 3KL  H17  C12  C13  108.66  3.000
 3KL  H16  C12  C13  111.99  3.000
 3KL  H17  C12  C11  109.37  3.000
 3KL  H16  C12  C11  108.44  3.000
 3KL  C13  C12  C11  111.86  3.000
 3KL  C18  C13  C17  109.96  3.000
 3KL  C18  C13  C14  112.30  3.000
 3KL  C17  C13  C14  100.20  3.000
 3KL  C18  C13  C12  110.84  3.000
 3KL  C14  C13  C12  106.94  3.000
 3KL  C17  C13  C12  116.17  3.000
 3KL  H18  C14  C15  106.52  3.000
 3KL  H18  C14  C13  105.85  3.000
 3KL  C15  C14  C13  104.06  3.000
 3KL  H18  C14  C8   106.11  3.000
 3KL  C13  C14  C8   114.52  3.000
 3KL  C15  C14  C8   118.88  3.000
 3KL  H20  C15  H19  106.73  3.000
 3KL  H20  C15  C16  111.22  3.000
 3KL  H19  C15  C16  112.29  3.000
 3KL  H20  C15  C14  110.76  3.000
 3KL  H19  C15  C14  112.49  3.000
 3KL  C16  C15  C14  103.45  3.000
 3KL  H22  C16  H21  106.03  3.000
 3KL  H22  C16  C17  110.67  3.000
 3KL  H21  C16  C17  110.79  3.000
 3KL  H22  C16  C15  111.20  3.000
 3KL  H21  C16  C15  111.08  3.000
 3KL  C17  C16  C15  107.13  3.000
 3KL  H23  C17  C20  106.76  3.000
 3KL  H23  C17  C16  108.10  3.000
 3KL  C20  C17  C16  112.41  3.000
 3KL  H23  C17  C13  106.30  3.000
 3KL  C16  C17  C13  103.52  3.000
 3KL  C20  C17  C13  119.21  3.000
 3KL  H26  C18  H25  107.03  3.000
 3KL  H26  C18  H24  106.60  3.000
 3KL  H25  C18  H24  106.94  3.000
 3KL  H26  C18  C13  110.68  3.000
 3KL  H25  C18  C13  112.42  3.000
 3KL  H24  C18  C13  112.81  3.000
 3KL  H29  C19  H28  107.34  3.000
 3KL  H29  C19  H27  107.18  3.000
 3KL  H28  C19  H27  107.44  3.000
 3KL  H29  C19  C10  111.14  3.000
 3KL  H28  C19  C10  113.33  3.000
 3KL  H27  C19  C10  110.15  3.000
 3KL  H30  C20  C22  107.29  3.000
 3KL  H30  C20  C21  108.15  3.000
 3KL  C22  C20  C21  110.71  3.000
 3KL  H30  C20  C17  108.24  3.000
 3KL  C21  C20  C17  113.09  3.000
 3KL  C22  C20  C17  109.17  3.000
 3KL  H33  C21  H32  107.63  3.000
 3KL  H33  C21  H31  107.70  3.000
 3KL  H32  C21  H31  106.28  3.000
 3KL  H33  C21  C20  110.99  3.000
 3KL  H32  C21  C20  111.80  3.000
 3KL  H31  C21  C20  112.17  3.000
 3KL  H35  C22  H34  106.29  3.000
 3KL  H35  C22  C23  108.51  3.000
 3KL  H34  C22  C23  109.95  3.000
 3KL  H35  C22  C20  109.10  3.000
 3KL  H34  C22  C20  109.00  3.000
 3KL  C23  C22  C20  113.73  3.000
 3KL  H37  C23  H36  105.38  3.000
 3KL  H37  C23  C24  107.21  3.000
 3KL  H36  C23  C24  107.97  3.000
 3KL  H37  C23  C22  111.70  3.000
 3KL  H36  C23  C22  110.48  3.000
 3KL  C24  C23  C22  113.68  3.000
 3KL  OT2  C24  OT1  122.71  3.000
 3KL  OT1  C24  C23  111.70  3.000
 3KL  OT2  C24  C23  125.59  3.000
 3KL  H38  OT1  C24  109.87  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
 3KL  CONST_01  H38  OT1  C24  C23  180.00   0.0  0
 3KL  Var_01    C5   C4   C3   C2    48.57  30.0  1
 3KL  Var_02    C10  C1   C2   C3    55.86  30.0  1
 3KL  Var_03    C1   C2   C3   C4   -50.21  30.0  1
 3KL  Var_04    C8   C7   C6   C5    53.90  30.0  1
 3KL  Var_05    C13  C12  C11  C9   -54.38  30.0  1
 3KL  Var_06    C17  C16  C15  C14   10.83  30.0  1
 3KL  Var_07    C24  C23  C22  C20  173.08  30.0  2
 3KL  Var_08    OT2  C24  C23  C22    1.50  30.0  2

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
 3KL  chir_01  C5   C4   C6   C10  negativ
 3KL  chir_02  C8   C14  C7   C9   positiv
 3KL  chir_03  C9   C10  C11  C8   negativ
 3KL  chir_04  C10  C5   C1   C9   positiv
 3KL  chir_05  C13  C14  C12  C17  positiv
 3KL  chir_06  C14  C15  C13  C8   positiv
 3KL  chir_07  C17  C20  C16  C13  negativ
 3KL  chir_08  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
 3KL  plan-1  C2   0.020
 3KL  plan-1  C3   0.020
 3KL  plan-1  O3   0.020
 3KL  plan-1  C4   0.020
 3KL  plan-2  C23  0.020
 3KL  plan-2  C24  0.020
 3KL  plan-2  OT1  0.020
 3KL  plan-2  OT2  0.020
 3KL  plan-2  H38  0.020

