# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 22:32:45 2021
#   Inital geometry file: a 161 line input string
#   Ligand name: (5beta,14beta,17alpha,25S)-3-oxocholest-7-en-26-oic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCC[C@H](C)C(O)=O)[C@H]1CC[C@H]2C3=CC[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
 D7S  D7S  '(5beta,14beta,17alpha,25S)-3-oxocholest-7-en-26-oic acid'  ligand  72  30  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D7S
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
 D7S  O3   O  OH1   0  -0.588  -0.2592  -17.7845  36.4662
 D7S  C27  C  C     0   0.547  -0.2953  -18.6443  35.4539
 D7S  O2   O  O     0  -0.449  -1.2584  -18.7705  34.7363
 D7S  C25  C  CH1   0  -0.359   0.9714  -19.4572  35.3202
 D7S  C26  C  CH3   0  -0.656   0.6779  -20.8939  35.7597
 D7S  C24  C  CH2   0  -0.411   1.4840  -19.4113  33.8806
 D7S  C23  C  CH2   0  -0.449   1.8844  -18.0144  33.4208
 D7S  C22  C  CH2   0  -0.410   2.4972  -17.9760  32.0233
 D7S  C20  C  CH1   0  -0.242   1.6255  -18.5193  30.8798
 D7S  C21  C  CH3   0  -0.674   0.2511  -17.8568  30.8797
 D7S  C17  C  CH1   0  -0.161   2.3839  -18.3441  29.5559
 D7S  C16  C  CH2   0  -0.444   3.7412  -19.0969  29.5559
 D7S  C15  C  CH2   0  -0.453   4.0237  -19.5342  28.1053
 D7S  C14  C  CH1   0  -0.255   2.9461  -18.8212  27.3036
 D7S  C8   C  C     0   0.196   2.6465  -19.2514  25.9019
 D7S  C7   C  C1    0  -0.346   3.3842  -20.1436  25.2416
 D7S  C6   C  CH2   0  -0.448   3.2192  -20.4417  23.7856
 D7S  C13  C  CT    0  -0.060   1.7193  -18.8016  28.2350
 D7S  C18  C  CH3   0  -0.682   1.1175  -20.1996  28.3873
 D7S  C12  C  CH2   0  -0.415   0.7171  -17.8319  27.6083
 D7S  C11  C  CH2   0  -0.448   0.3287  -18.2627  26.1944
 D7S  C9   C  CH1   0  -0.251   1.5217  -18.4745  25.2450
 D7S  C10  C  CT    0  -0.055   1.1009  -19.0695  23.8771
 D7S  C1   C  CH2   0  -0.440   0.2962  -18.0194  23.1003
 D7S  C19  C  CH3   0  -0.702   0.2745  -20.3491  24.0615
 D7S  C5   C  CH1   0  -0.237   2.3898  -19.3722  23.0881
 D7S  C4   C  CH2   0  -0.558   2.1349  -19.7540  21.6245
 D7S  C3   C  C     0   0.419   1.2301  -18.7863  20.9117
 D7S  O1   O  O     0  -0.410   1.4884  -18.3351  19.8162
 D7S  C2   C  CH2   0  -0.561  -0.0247  -18.4380  21.6634
 D7S  H1   H  HOH1  0   0.476  -1.1024  -17.3094  36.5251
 D7S  H2   H  HCH1  0   0.255   1.7328  -19.0359  35.9821
 D7S  H3   H  HCH3  0   0.241   0.3203  -20.9410  36.7888
 D7S  H4   H  HCH3  0   0.231  -0.0733  -21.3534  35.1166
 D7S  H5   H  HCH3  0   0.243   1.5866  -21.4921  35.6965
 D7S  H6   H  HCH2  0   0.226   0.7192  -19.8315  33.2223
 D7S  H7   H  HCH2  0   0.232   2.3488  -20.0775  33.8084
 D7S  H8   H  HCH2  0   0.227   2.6176  -17.6077  34.1245
 D7S  H9   H  HCH2  0   0.220   1.0237  -17.3411  33.4692
 D7S  H10  H  HCH2  0   0.228   3.4377  -18.5330  32.0502
 D7S  H11  H  HCH2  0   0.213   2.7648  -16.9391  31.7897
 D7S  H12  H  HCH1  0   0.210   1.4806  -19.5944  31.0411
 D7S  H13  H  HCH3  0   0.232  -0.2492  -17.9679  31.8427
 D7S  H14  H  HCH3  0   0.211   0.3263  -16.7878  30.6644
 D7S  H15  H  HCH3  0   0.231  -0.4114  -18.2988  30.1374
 D7S  H16  H  HCH1  0   0.204   2.5870  -17.2694  29.4418
 D7S  H17  H  HCH2  0   0.219   3.6938  -19.9665  30.2170
 D7S  H18  H  HCH2  0   0.231   4.5407  -18.4656  29.9450
 D7S  H19  H  HCH2  0   0.220   3.9367  -20.6181  28.0011
 D7S  H20  H  HCH2  0   0.231   5.0288  -19.2670  27.7753
 D7S  H21  H  HCH1  0   0.226   3.2602  -17.7671  27.2240
 D7S  H22  H  H     0   0.226   4.1909  -20.6574  25.7552
 D7S  H23  H  HCH2  0   0.228   2.7716  -21.4326  23.6369
 D7S  H24  H  HCH2  0   0.241   4.2063  -20.5031  23.3166
 D7S  H25  H  HCH3  0   0.229   0.2049  -20.1715  28.9866
 D7S  H26  H  HCH3  0   0.235   0.8618  -20.6425  27.4240
 D7S  H27  H  HCH3  0   0.231   1.8026  -20.8905  28.8814
 D7S  H28  H  HCH2  0   0.210   1.1681  -16.8328  27.5782
 D7S  H29  H  HCH2  0   0.231  -0.1920  -17.7409  28.2045
 D7S  H30  H  HCH2  0   0.235  -0.3317  -17.5062  25.7656
 D7S  H31  H  HCH2  0   0.228  -0.2661  -19.1757  26.2532
 D7S  H32  H  HCH1  0   0.228   1.9308  -17.4716  25.0424
 D7S  H33  H  HCH2  0   0.233   0.8636  -17.0828  23.0768
 D7S  H34  H  HCH2  0   0.249  -0.6411  -17.7964  23.6141
 D7S  H35  H  HCH3  0   0.243   0.7155  -21.0010  24.8171
 D7S  H36  H  HCH3  0   0.236  -0.7473  -20.1280  24.3726
 D7S  H37  H  HCH3  0   0.237   0.2072  -20.9291  23.1404
 D7S  H38  H  HCH1  0   0.234   2.9822  -18.4475  23.0849
 D7S  H39  H  HCH2  0   0.257   1.6527  -20.7379  21.5791
 D7S  H40  H  HCH2  0   0.261   3.0797  -19.8428  21.0846
 D7S  H41  H  HCH2  0   0.261  -0.5688  -17.6510  21.1394
 D7S  H42  H  HCH2  0   0.264  -0.6670  -19.3255  21.6728

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
 D7S  O1   C3   double  1.213  0.020  1.213
 D7S  C3   C2   single  1.504  0.020  1.504
 D7S  C3   C4   single  1.504  0.020  1.504
 D7S  C2   C1   single  1.531  0.020  1.531
 D7S  C4   C5   single  1.534  0.020  1.534
 D7S  C1   C10  single  1.534  0.020  1.534
 D7S  C5   C10  single  1.541  0.020  1.541
 D7S  C5   C6   single  1.522  0.020  1.522
 D7S  C10  C19  single  1.534  0.020  1.534
 D7S  C10  C9   single  1.550  0.020  1.550
 D7S  C6   C7   single  1.495  0.020  1.495
 D7S  C9   C8   single  1.517  0.020  1.517
 D7S  C9   C11  single  1.539  0.020  1.539
 D7S  C7   C8   double  1.333  0.020  1.333
 D7S  C8   C14  single  1.496  0.020  1.496
 D7S  C11  C12  single  1.528  0.020  1.528
 D7S  C14  C15  single  1.521  0.020  1.521
 D7S  C14  C13  single  1.541  0.020  1.541
 D7S  C12  C13  single  1.529  0.020  1.529
 D7S  C15  C16  single  1.541  0.020  1.541
 D7S  C13  C18  single  1.530  0.020  1.530
 D7S  C13  C17  single  1.548  0.020  1.548
 D7S  C17  C16  single  1.552  0.020  1.552
 D7S  C17  C20  single  1.536  0.020  1.536
 D7S  C21  C20  single  1.526  0.020  1.526
 D7S  C20  C22  single  1.537  0.020  1.537
 D7S  C22  C23  single  1.526  0.020  1.526
 D7S  C23  C24  single  1.524  0.020  1.524
 D7S  C24  C25  single  1.529  0.020  1.529
 D7S  O2   C27  double  1.208  0.020  1.208
 D7S  C25  C27  single  1.511  0.020  1.511
 D7S  C25  C26  single  1.531  0.020  1.531
 D7S  C27  O3   single  1.329  0.020  1.329
 D7S  O3   H1   single  0.850  0.020  0.980
 D7S  C25  H2   single  0.970  0.020  1.090
 D7S  C26  H3   single  0.970  0.020  1.090
 D7S  C26  H4   single  0.970  0.020  1.090
 D7S  C26  H5   single  0.970  0.020  1.090
 D7S  C24  H6   single  0.970  0.020  1.090
 D7S  C24  H7   single  0.970  0.020  1.090
 D7S  C23  H8   single  0.970  0.020  1.090
 D7S  C23  H9   single  0.970  0.020  1.090
 D7S  C22  H10  single  0.970  0.020  1.090
 D7S  C22  H11  single  0.970  0.020  1.090
 D7S  C20  H12  single  0.970  0.020  1.090
 D7S  C21  H13  single  0.970  0.020  1.090
 D7S  C21  H14  single  0.970  0.020  1.090
 D7S  C21  H15  single  0.970  0.020  1.090
 D7S  C17  H16  single  0.970  0.020  1.090
 D7S  C16  H17  single  0.970  0.020  1.090
 D7S  C16  H18  single  0.970  0.020  1.090
 D7S  C15  H19  single  0.970  0.020  1.090
 D7S  C15  H20  single  0.970  0.020  1.090
 D7S  C14  H21  single  0.970  0.020  1.090
 D7S  C7   H22  single  0.930  0.020  1.080
 D7S  C6   H23  single  0.970  0.020  1.090
 D7S  C6   H24  single  0.970  0.020  1.090
 D7S  C18  H25  single  0.970  0.020  1.090
 D7S  C18  H26  single  0.970  0.020  1.090
 D7S  C18  H27  single  0.970  0.020  1.090
 D7S  C12  H28  single  0.970  0.020  1.090
 D7S  C12  H29  single  0.970  0.020  1.090
 D7S  C11  H30  single  0.970  0.020  1.090
 D7S  C11  H31  single  0.970  0.020  1.090
 D7S  C9   H32  single  0.970  0.020  1.090
 D7S  C1   H33  single  0.970  0.020  1.090
 D7S  C1   H34  single  0.970  0.020  1.090
 D7S  C19  H35  single  0.970  0.020  1.090
 D7S  C19  H36  single  0.970  0.020  1.090
 D7S  C19  H37  single  0.970  0.020  1.090
 D7S  C5   H38  single  0.970  0.020  1.090
 D7S  C4   H39  single  0.970  0.020  1.090
 D7S  C4   H40  single  0.970  0.020  1.090
 D7S  C2   H41  single  0.970  0.020  1.090
 D7S  C2   H42  single  0.970  0.020  1.090

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
 D7S  H1   O3   C27  109.86  3.000
 D7S  C25  C27  O2   124.04  3.000
 D7S  C25  C27  O3   113.13  3.000
 D7S  O2   C27  O3   122.82  3.000
 D7S  H2   C25  C24  108.97  3.000
 D7S  H2   C25  C26  108.74  3.000
 D7S  C24  C25  C26  111.27  3.000
 D7S  H2   C25  C27  108.84  3.000
 D7S  C26  C25  C27  108.59  3.000
 D7S  C24  C25  C27  110.38  3.000
 D7S  H5   C26  H4   107.99  3.000
 D7S  H5   C26  H3   107.73  3.000
 D7S  H4   C26  H3   108.21  3.000
 D7S  H5   C26  C25  109.79  3.000
 D7S  H4   C26  C25  110.99  3.000
 D7S  H3   C26  C25  111.99  3.000
 D7S  H7   C24  H6   106.21  3.000
 D7S  H7   C24  C23  109.30  3.000
 D7S  H6   C24  C23  110.76  3.000
 D7S  H7   C24  C25  107.99  3.000
 D7S  H6   C24  C25  108.72  3.000
 D7S  C23  C24  C25  113.56  3.000
 D7S  H9   C23  H8   105.66  3.000
 D7S  H9   C23  C22  109.93  3.000
 D7S  H8   C23  C22  108.08  3.000
 D7S  H9   C23  C24  110.13  3.000
 D7S  H8   C23  C24  108.82  3.000
 D7S  C22  C23  C24  113.87  3.000
 D7S  H11  C22  H10  106.09  3.000
 D7S  H11  C22  C20  108.32  3.000
 D7S  H10  C22  C20  109.03  3.000
 D7S  H11  C22  C23  108.48  3.000
 D7S  H10  C22  C23  108.06  3.000
 D7S  C20  C22  C23  116.39  3.000
 D7S  H12  C20  C17  107.69  3.000
 D7S  H12  C20  C21  107.86  3.000
 D7S  C17  C20  C21  113.28  3.000
 D7S  H12  C20  C22  108.18  3.000
 D7S  C21  C20  C22  110.94  3.000
 D7S  C17  C20  C22  108.72  3.000
 D7S  H15  C21  H14  107.73  3.000
 D7S  H15  C21  H13  106.34  3.000
 D7S  H14  C21  H13  107.77  3.000
 D7S  H15  C21  C20  111.83  3.000
 D7S  H14  C21  C20  111.27  3.000
 D7S  H13  C21  C20  111.65  3.000
 D7S  H16  C17  C13  106.24  3.000
 D7S  H16  C17  C16  108.21  3.000
 D7S  C13  C17  C16  103.42  3.000
 D7S  H16  C17  C20  106.98  3.000
 D7S  C16  C17  C20  112.11  3.000
 D7S  C13  C17  C20  119.34  3.000
 D7S  H18  C16  H17  106.04  3.000
 D7S  H18  C16  C15  111.45  3.000
 D7S  H17  C16  C15  110.58  3.000
 D7S  H18  C16  C17  111.12  3.000
 D7S  H17  C16  C17  110.36  3.000
 D7S  C15  C16  C17  107.33  3.000
 D7S  H20  C15  H19  106.71  3.000
 D7S  H20  C15  C14  112.24  3.000
 D7S  H19  C15  C14  111.01  3.000
 D7S  H20  C15  C16  112.58  3.000
 D7S  H19  C15  C16  110.90  3.000
 D7S  C14  C15  C16  103.49  3.000
 D7S  H21  C14  C13  104.97  3.000
 D7S  H21  C14  C8   105.33  3.000
 D7S  C13  C14  C8   114.24  3.000
 D7S  H21  C14  C15  106.52  3.000
 D7S  C13  C14  C15  104.57  3.000
 D7S  C8   C14  C15  120.06  3.000
 D7S  C9   C8   C7   122.60  3.000
 D7S  C7   C8   C14  123.07  3.000
 D7S  C9   C8   C14  114.01  3.000
 D7S  H22  C7   C6   116.64  3.000
 D7S  H22  C7   C8   119.59  3.000
 D7S  C6   C7   C8   123.69  3.000
 D7S  H24  C6   H23  105.01  3.000
 D7S  H24  C6   C5   109.54  3.000
 D7S  H23  C6   C5   110.49  3.000
 D7S  H24  C6   C7   109.20  3.000
 D7S  H23  C6   C7   110.91  3.000
 D7S  C5   C6   C7   111.48  3.000
 D7S  C12  C13  C18  111.26  3.000
 D7S  C18  C13  C14  111.21  3.000
 D7S  C12  C13  C14  106.39  3.000
 D7S  C18  C13  C17  110.74  3.000
 D7S  C12  C13  C17  116.35  3.000
 D7S  C14  C13  C17  100.24  3.000
 D7S  H27  C18  H26  106.86  3.000
 D7S  H27  C18  H25  107.00  3.000
 D7S  H26  C18  H25  107.41  3.000
 D7S  H27  C18  C13  112.13  3.000
 D7S  H26  C18  C13  112.06  3.000
 D7S  H25  C18  C13  111.09  3.000
 D7S  H29  C12  H28  106.36  3.000
 D7S  H29  C12  C11  108.50  3.000
 D7S  H28  C12  C11  109.63  3.000
 D7S  H29  C12  C13  112.02  3.000
 D7S  H28  C12  C13  108.64  3.000
 D7S  C11  C12  C13  111.53  3.000
 D7S  H31  C11  H30  105.73  3.000
 D7S  H31  C11  C9   109.91  3.000
 D7S  H30  C11  C9   108.78  3.000
 D7S  H31  C11  C12  108.94  3.000
 D7S  H30  C11  C12  108.77  3.000
 D7S  C9   C11  C12  114.36  3.000
 D7S  H32  C9   C10  106.74  3.000
 D7S  H32  C9   C11  106.01  3.000
 D7S  C10  C9   C11  112.75  3.000
 D7S  H32  C9   C8   105.69  3.000
 D7S  C11  C9   C8   112.22  3.000
 D7S  C10  C9   C8   112.77  3.000
 D7S  C5   C10  C19  110.38  3.000
 D7S  C19  C10  C1   110.44  3.000
 D7S  C5   C10  C1   108.30  3.000
 D7S  C19  C10  C9   111.12  3.000
 D7S  C5   C10  C9   107.46  3.000
 D7S  C1   C10  C9   109.05  3.000
 D7S  H34  C1   H33  106.27  3.000
 D7S  H34  C1   C2   108.52  3.000
 D7S  H33  C1   C2   108.80  3.000
 D7S  H34  C1   C10  110.60  3.000
 D7S  H33  C1   C10  108.93  3.000
 D7S  C2   C1   C10  113.46  3.000
 D7S  H37  C19  H36  106.91  3.000
 D7S  H37  C19  H35  106.98  3.000
 D7S  H36  C19  H35  107.59  3.000
 D7S  H37  C19  C10  112.04  3.000
 D7S  H36  C19  C10  111.71  3.000
 D7S  H35  C19  C10  111.34  3.000
 D7S  H38  C5   C4   107.24  3.000
 D7S  H38  C5   C10  106.69  3.000
 D7S  C4   C5   C10  113.47  3.000
 D7S  H38  C5   C6   107.40  3.000
 D7S  C10  C5   C6   111.04  3.000
 D7S  C4   C5   C6   110.66  3.000
 D7S  H40  C4   H39  106.68  3.000
 D7S  H40  C4   C3   109.78  3.000
 D7S  H39  C4   C3   107.04  3.000
 D7S  H40  C4   C5   110.38  3.000
 D7S  H39  C4   C5   109.63  3.000
 D7S  C3   C4   C5   113.07  3.000
 D7S  C2   C3   O1   122.90  3.000
 D7S  C2   C3   C4   114.46  3.000
 D7S  O1   C3   C4   122.63  3.000
 D7S  H42  C2   H41  107.22  3.000
 D7S  H42  C2   C3   107.81  3.000
 D7S  H41  C2   C3   110.07  3.000
 D7S  H42  C2   C1   109.66  3.000
 D7S  H41  C2   C1   110.99  3.000
 D7S  C3   C2   C1   110.96  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
 D7S  CONST_01  H1   O3   C27  O2      0.00   0.0  0
 D7S  Var_01    C6   C7   C8   C14  -171.02   0.0  0
 D7S  Var_02    C14  C15  C16  C17     9.07  30.0  1
 D7S  Var_03    C5   C6   C7   C8     14.98  30.0  1
 D7S  Var_04    C9   C11  C12  C13   -54.36  30.0  1
 D7S  Var_05    C3   C2   C1   C10   -55.47  30.0  1
 D7S  Var_06    C4   C3   C2   C1     50.29  30.0  1
 D7S  Var_07    C2   C3   C4   C5    -48.19  30.0  1
 D7S  Var_08    C22  C23  C24  C25   175.55  30.0  2
 D7S  Var_09    C20  C22  C23  C24    58.46  30.0  1

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
 D7S  chir_01  C25  C24  C27  C26  negativ
 D7S  chir_02  C20  C17  C21  C22  positiv
 D7S  chir_03  C17  C20  C16  C13  negativ
 D7S  chir_04  C14  C13  C15  C8   negativ
 D7S  chir_05  C13  C17  C12  C14  negativ
 D7S  chir_06  C9   C11  C8   C10  negativ
 D7S  chir_07  C10  C9   C5   C1   positiv
 D7S  chir_08  C5   C4   C10  C6   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
 D7S  plan-1  C4   0.020
 D7S  plan-1  C3   0.020
 D7S  plan-1  O1   0.020
 D7S  plan-1  C2   0.020
 D7S  plan-2  O3   0.020
 D7S  plan-2  C27  0.020
 D7S  plan-2  O2   0.020
 D7S  plan-2  C25  0.020
 D7S  plan-2  H1   0.020
 D7S  plan-3  C14  0.020
 D7S  plan-3  C8   0.020
 D7S  plan-3  C7   0.020
 D7S  plan-3  C6   0.020
 D7S  plan-3  C9   0.020
 D7S  plan-3  H22  0.020

