# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun  6 00:46:53 2020
#   Inital geometry file: a 163 line input string
#   Ligand name: (1S,3R,5Z,7E,14beta,17alpha,22E,24S)-26,27-cyclo-9,10-secocholesta-5,7,10,22-tetraene-1,3,24-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](\C=C\[C@@H](O)C1CC1)[C@H]2CC[C@H]3C(/CCC[C@]23C)=C/C=C4/C[C@@H](O)C[C@H](O)C4=C
#
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
 MC9  MC9  (1S,3R,5Z,7E,14beta,17alpha,22E,24S)-26,27-cyclo-9,10-secocholesta-5,7,10,22-tetraene-1,3,24-triol  ligand  70  30  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MC9
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
 MC9  O2    O  OH1   0  -0.670  16.7873  18.5763  34.2047
 MC9  O1    O  OH1   0  -0.665  13.6625  17.7604  36.8801
 MC9  C1    C  CH1   0   0.022  14.3204  18.3728  35.8005
 MC9  C2    C  CH2   0  -0.483  14.9545  17.2736  34.9503
 MC9  C3    C  CH1   0   0.026  15.6798  17.8337  33.7355
 MC9  C4    C  CH2   0  -0.541  14.7359  18.6974  32.8976
 MC9  C5    C  C     0   0.104  14.0842  19.7632  33.7335
 MC9  C6    C  C1    0  -0.305  14.1468  21.0640  33.4038
 MC9  C7    C  C1    0  -0.356  13.6099  22.1698  34.1740
 MC9  C8    C  C     0   0.151  13.5687  23.4562  33.7934
 MC9  C9    C  CH2   0  -0.505  14.0568  24.0007  32.4770
 MC9  C10   C  C     0   0.035  13.4164  19.2294  34.9391
 MC9  C11   C  CH2   0  -0.436  12.9696  24.7950  31.7390
 MC9  C12   C  CH2   0  -0.415  12.3090  25.8490  32.6302
 MC9  C13   C  CT    0  -0.054  11.7971  25.2381  33.9324
 MC9  C14   C  CH1   0  -0.245  12.9816  24.5392  34.6407
 MC9  C15   C  CH2   0  -0.451  12.4495  24.2592  36.0394
 MC9  C16   C  CH2   0  -0.446  11.5948  25.5059  36.3570
 MC9  C17   C  CH1   0  -0.180  11.4189  26.2658  35.0166
 MC9  C18   C  CH3   0  -0.666  10.6681  24.2465  33.6406
 MC9  C19   C  C2    0  -0.584  12.1269  19.4298  35.2031
 MC9  C20   C  CH1   0  -0.305  10.1104  27.0577  34.8613
 MC9  C22   C  C1    0  -0.186   8.8510  26.2648  35.0462
 MC9  C24   C  CH1   0   0.003   6.5417  25.5133  34.4888
 MC9  C21   C  CH3   0  -0.653  10.0985  28.2204  35.8623
 MC9  C25   C  CH1   0  -0.257   6.3633  24.4722  33.4074
 MC9  C26   C  CH2   0  -0.490   5.7777  24.8214  32.0758
 MC9  C27   C  CH2   0  -0.492   5.0164  23.9424  33.0266
 MC9  O3    O  OH1   0  -0.675   5.3999  26.3464  34.5119
 MC9  C23   C  C1    0  -0.253   7.7925  26.3047  34.2455
 MC9  HO2   H  HOH1  0   0.449  17.2207  18.9825  33.4476
 MC9  HO1   H  HOH1  0   0.454  13.4059  18.4453  37.5057
 MC9  H1    H  HCH1  0   0.220  15.1258  19.0264  36.1664
 MC9  H21   H  HCH2  0   0.251  15.6480  16.6883  35.5602
 MC9  H22A  H  HCH2  0   0.238  14.1727  16.5906  34.6055
 MC9  H3    H  HCH1  0   0.226  16.0176  16.9913  33.1162
 MC9  H41   H  HCH2  0   0.253  15.2705  19.1375  32.0511
 MC9  H42   H  HCH2  0   0.244  13.9684  18.0403  32.4731
 MC9  H6    H  H     0   0.232  14.6660  21.3060  32.4816
 MC9  H7    H  H     0   0.232  13.2063  21.9174  35.1481
 MC9  H91   H  HCH2  0   0.230  14.8939  24.6793  32.6816
 MC9  H92   H  HCH2  0   0.243  14.4463  23.2196  31.8242
 MC9  H111  H  HCH2  0   0.233  13.4155  25.2795  30.8672
 MC9  H112  H  HCH2  0   0.223  12.2165  24.1057  31.3488
 MC9  H121  H  HCH2  0   0.212  13.0464  26.6249  32.8689
 MC9  H122  H  HCH2  0   0.226  11.4988  26.3432  32.0848
 MC9  H14   H  HCH1  0   0.229  13.7595  25.3135  34.7411
 MC9  H151  H  HCH2  0   0.222  11.8325  23.3575  36.0512
 MC9  H152  H  HCH2  0   0.234  13.2485  24.1058  36.7665
 MC9  H161  H  HCH2  0   0.228  10.6412  25.2176  36.8023
 MC9  H162  H  HCH2  0   0.234  12.0892  26.1431  37.0916
 MC9  H17   H  HCH1  0   0.218  12.2104  27.0267  34.9763
 MC9  H181  H  HCH3  0   0.227  10.1764  23.8910  34.5466
 MC9  H182  H  HCH3  0   0.235   9.8987  24.7081  33.0218
 MC9  H183  H  HCH3  0   0.234  11.0322  23.3652  33.1101
 MC9  H191  H  H     0   0.235  11.6375  18.9964  36.0658
 MC9  H192  H  H     0   0.240  11.5107  20.0330  34.5492
 MC9  H20   H  HCH1  0   0.233  10.0981  27.4865  33.8523
 MC9  H22   H  H     0   0.232   8.7924  25.6483  35.9413
 MC9  H24   H  HCH1  0   0.210   6.6504  24.9831  35.4481
 MC9  H211  H  HCH3  0   0.231   9.2272  28.8590  35.7136
 MC9  H212  H  HCH3  0   0.224  10.0680  27.8550  36.8909
 MC9  H213  H  HCH3  0   0.226  10.9929  28.8376  35.7566
 MC9  H25   H  HCH1  0   0.262   7.1768  23.7540  33.3944
 MC9  H261  H  HCH2  0   0.243   5.4168  25.8306  31.9227
 MC9  H262  H  HCH2  0   0.243   6.2121  24.3690  31.1936
 MC9  H271  H  HCH2  0   0.245   4.9342  22.8879  32.7947
 MC9  H272  H  HCH2  0   0.244   4.1425  24.3590  33.5101
 MC9  HO3   H  HOH1  0   0.450   5.5615  27.0497  35.1483
 MC9  H23   H  H     0   0.231   7.8093  26.9086  33.3396

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
 MC9  O2   C3    single  1.414  0.020  1.414
 MC9  O2   HO2   single  0.850  0.020  0.980
 MC9  O1   C1    single  1.405  0.020  1.405
 MC9  O1   HO1   single  0.850  0.020  0.980
 MC9  C1   C2    single  1.527  0.020  1.527
 MC9  C1   C10   single  1.514  0.020  1.514
 MC9  C1   H1    single  0.970  0.020  1.090
 MC9  C2   C3    single  1.522  0.020  1.522
 MC9  C2   H21   single  0.970  0.020  1.090
 MC9  C2   H22A  single  0.970  0.020  1.090
 MC9  C3   C4    single  1.529  0.020  1.529
 MC9  C3   H3    single  0.970  0.020  1.090
 MC9  C4   C5    single  1.503  0.020  1.503
 MC9  C4   H41   single  0.970  0.020  1.090
 MC9  C4   H42   single  0.970  0.020  1.090
 MC9  C5   C6    double  1.343  0.020  1.343
 MC9  C5   C10   single  1.478  0.020  1.478
 MC9  C6   C7    single  1.451  0.020  1.451
 MC9  C6   H6    single  0.930  0.020  1.080
 MC9  C7   C8    double  1.342  0.020  1.342
 MC9  C7   H7    single  0.930  0.020  1.080
 MC9  C8   C9    single  1.506  0.020  1.506
 MC9  C8   C14   single  1.495  0.020  1.495
 MC9  C9   C11   single  1.535  0.020  1.535
 MC9  C9   H91   single  0.970  0.020  1.090
 MC9  C9   H92   single  0.970  0.020  1.090
 MC9  C10  C19   double  1.331  0.020  1.331
 MC9  C11  C12   single  1.530  0.020  1.530
 MC9  C11  H111  single  0.970  0.020  1.090
 MC9  C11  H112  single  0.970  0.020  1.090
 MC9  C12  C13   single  1.527  0.020  1.527
 MC9  C12  H121  single  0.970  0.020  1.090
 MC9  C12  H122  single  0.970  0.020  1.090
 MC9  C13  C14   single  1.547  0.020  1.547
 MC9  C13  C17   single  1.541  0.020  1.541
 MC9  C13  C18   single  1.531  0.020  1.531
 MC9  C14  C15   single  1.522  0.020  1.522
 MC9  C14  H14   single  0.970  0.020  1.090
 MC9  C15  C16   single  1.545  0.020  1.545
 MC9  C15  H151  single  0.970  0.020  1.090
 MC9  C15  H152  single  0.970  0.020  1.090
 MC9  C16  C17   single  1.551  0.020  1.551
 MC9  C16  H161  single  0.970  0.020  1.090
 MC9  C16  H162  single  0.970  0.020  1.090
 MC9  C17  C20   single  1.537  0.020  1.537
 MC9  C17  H17   single  0.970  0.020  1.090
 MC9  C18  H181  single  0.970  0.020  1.090
 MC9  C18  H182  single  0.970  0.020  1.090
 MC9  C18  H183  single  0.970  0.020  1.090
 MC9  C19  H191  single  0.930  0.020  1.080
 MC9  C19  H192  single  0.930  0.020  1.080
 MC9  C20  C22   single  1.500  0.020  1.500
 MC9  C20  C21   single  1.534  0.020  1.534
 MC9  C20  H20   single  0.970  0.020  1.090
 MC9  C22  C23   double  1.328  0.020  1.328
 MC9  C22  H22   single  0.930  0.020  1.080
 MC9  C24  C25   single  1.512  0.020  1.512
 MC9  C24  O3    single  1.414  0.020  1.414
 MC9  C24  C23   single  1.500  0.020  1.500
 MC9  C24  H24   single  0.970  0.020  1.090
 MC9  C21  H211  single  0.970  0.020  1.090
 MC9  C21  H212  single  0.970  0.020  1.090
 MC9  C21  H213  single  0.970  0.020  1.090
 MC9  C25  C26   single  1.496  0.020  1.496
 MC9  C25  C27   single  1.497  0.020  1.497
 MC9  C25  H25   single  0.970  0.020  1.090
 MC9  C26  C27   single  1.502  0.020  1.502
 MC9  C26  H261  single  0.970  0.020  1.090
 MC9  C26  H262  single  0.970  0.020  1.090
 MC9  C27  H271  single  0.970  0.020  1.090
 MC9  C27  H272  single  0.970  0.020  1.090
 MC9  O3   HO3   single  0.850  0.020  0.980
 MC9  C23  H23   single  0.930  0.020  1.080

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
 MC9  HO2   O2   C3    108.27  3.000
 MC9  HO1   O1   C1    108.31  3.000
 MC9  H1    C1   C10   106.87  3.000
 MC9  H1    C1   C2    107.99  3.000
 MC9  C10   C1   C2    109.77  3.000
 MC9  H1    C1   O1    110.26  3.000
 MC9  C10   C1   O1    113.84  3.000
 MC9  C2    C1   O1    107.96  3.000
 MC9  H22A  C2   H21   107.15  3.000
 MC9  H22A  C2   C3    108.59  3.000
 MC9  H21   C2   C3    109.88  3.000
 MC9  H22A  C2   C1    109.15  3.000
 MC9  H21   C2   C1    109.76  3.000
 MC9  C3    C2   C1    112.17  3.000
 MC9  H3    C3   C4    108.29  3.000
 MC9  H3    C3   C2    108.32  3.000
 MC9  C4    C3   C2    110.55  3.000
 MC9  H3    C3   O2    110.43  3.000
 MC9  C4    C3   O2    111.63  3.000
 MC9  C2    C3   O2    107.57  3.000
 MC9  H42   C4   H41   106.48  3.000
 MC9  H42   C4   C5    109.69  3.000
 MC9  H41   C4   C5    110.92  3.000
 MC9  H42   C4   C3    107.81  3.000
 MC9  H41   C4   C3    110.47  3.000
 MC9  C5    C4   C3    111.31  3.000
 MC9  C10   C5   C6    124.82  3.000
 MC9  C10   C5   C4    113.17  3.000
 MC9  C6    C5   C4    122.00  3.000
 MC9  H6    C6   C7    117.26  3.000
 MC9  H6    C6   C5    116.53  3.000
 MC9  C7    C6   C5    126.20  3.000
 MC9  H7    C7   C8    117.80  3.000
 MC9  H7    C7   C6    115.94  3.000
 MC9  C8    C7   C6    126.26  3.000
 MC9  C14   C8   C9    111.15  3.000
 MC9  C14   C8   C7    123.07  3.000
 MC9  C9    C8   C7    125.77  3.000
 MC9  H92   C9   H91   106.40  3.000
 MC9  H92   C9   C11   109.63  3.000
 MC9  H91   C9   C11   108.06  3.000
 MC9  H92   C9   C8    112.35  3.000
 MC9  H91   C9   C8    107.94  3.000
 MC9  C11   C9   C8    112.19  3.000
 MC9  C19   C10  C5    123.03  3.000
 MC9  C19   C10  C1    123.40  3.000
 MC9  C5    C10  C1    113.49  3.000
 MC9  H112  C11  H111  106.03  3.000
 MC9  H112  C11  C12   110.17  3.000
 MC9  H111  C11  C12   109.61  3.000
 MC9  H112  C11  C9    109.46  3.000
 MC9  H111  C11  C9    108.90  3.000
 MC9  C12   C11  C9    112.46  3.000
 MC9  H122  C12  H121  106.66  3.000
 MC9  H122  C12  C13   110.95  3.000
 MC9  H121  C12  C13   108.84  3.000
 MC9  H122  C12  C11   109.90  3.000
 MC9  H121  C12  C11   108.89  3.000
 MC9  C13   C12  C11   111.46  3.000
 MC9  C18   C13  C17   112.65  3.000
 MC9  C18   C13  C14   111.06  3.000
 MC9  C17   C13  C14    99.62  3.000
 MC9  C18   C13  C12   110.11  3.000
 MC9  C17   C13  C12   114.55  3.000
 MC9  C14   C13  C12   108.34  3.000
 MC9  H14   C14  C15   106.99  3.000
 MC9  H14   C14  C13   105.35  3.000
 MC9  C15   C14  C13   103.66  3.000
 MC9  H14   C14  C8    106.46  3.000
 MC9  C15   C14  C8    121.64  3.000
 MC9  C13   C14  C8    111.62  3.000
 MC9  H152  C15  H151  106.88  3.000
 MC9  H152  C15  C16   112.43  3.000
 MC9  H151  C15  C16   110.57  3.000
 MC9  H152  C15  C14   112.47  3.000
 MC9  H151  C15  C14   111.05  3.000
 MC9  C16   C15  C14   103.52  3.000
 MC9  H162  C16  H161  106.00  3.000
 MC9  H162  C16  C17   110.32  3.000
 MC9  H161  C16  C17   112.52  3.000
 MC9  H162  C16  C15   111.05  3.000
 MC9  H161  C16  C15   110.74  3.000
 MC9  C17   C16  C15   106.29  3.000
 MC9  H17   C17  C20   104.64  3.000
 MC9  H17   C17  C16   106.82  3.000
 MC9  C20   C17  C16   115.87  3.000
 MC9  H17   C17  C13   105.02  3.000
 MC9  C20   C17  C13   118.77  3.000
 MC9  C16   C17  C13   104.69  3.000
 MC9  H183  C18  H182  107.55  3.000
 MC9  H183  C18  H181  106.92  3.000
 MC9  H182  C18  H181  106.94  3.000
 MC9  H183  C18  C13   111.71  3.000
 MC9  H182  C18  C13   110.76  3.000
 MC9  H181  C18  C13   112.67  3.000
 MC9  H192  C19  H191  116.57  3.000
 MC9  H192  C19  C10   121.03  3.000
 MC9  H191  C19  C10   122.39  3.000
 MC9  H20   C20  C21   107.69  3.000
 MC9  H20   C20  C22   108.11  3.000
 MC9  C21   C20  C22   108.28  3.000
 MC9  H20   C20  C17   107.70  3.000
 MC9  C21   C20  C17   109.33  3.000
 MC9  C22   C20  C17   115.47  3.000
 MC9  H22   C22  C23   118.03  3.000
 MC9  H22   C22  C20   116.49  3.000
 MC9  C23   C22  C20   125.40  3.000
 MC9  H24   C24  C23   108.24  3.000
 MC9  H24   C24  O3    110.44  3.000
 MC9  C23   C24  O3    111.42  3.000
 MC9  H24   C24  C25   107.65  3.000
 MC9  C23   C24  C25   110.23  3.000
 MC9  O3    C24  C25   108.80  3.000
 MC9  H213  C21  H212  107.65  3.000
 MC9  H213  C21  H211  108.08  3.000
 MC9  H212  C21  H211  107.58  3.000
 MC9  H213  C21  C20   111.03  3.000
 MC9  H212  C21  C20   111.17  3.000
 MC9  H211  C21  C20   111.16  3.000
 MC9  H25   C25  C27   115.93  3.000
 MC9  H25   C25  C26   115.93  3.000
 MC9  C27   C25  C26    60.26  3.000
 MC9  H25   C25  C24   112.08  3.000
 MC9  C27   C25  C24   122.14  3.000
 MC9  C26   C25  C24   121.48  3.000
 MC9  H262  C26  H261  114.09  3.000
 MC9  H262  C26  C27   118.34  3.000
 MC9  H261  C26  C27   117.78  3.000
 MC9  H262  C26  C25   118.08  3.000
 MC9  H261  C26  C25   118.29  3.000
 MC9  C27   C26  C25    59.89  3.000
 MC9  H272  C27  H271  114.16  3.000
 MC9  H272  C27  C26   117.82  3.000
 MC9  H271  C27  C26   118.22  3.000
 MC9  H272  C27  C25   118.48  3.000
 MC9  H271  C27  C25   117.88  3.000
 MC9  C26   C27  C25    59.85  3.000
 MC9  HO3   O3   C24   107.82  3.000
 MC9  H23   C23  C24   116.14  3.000
 MC9  H23   C23  C22   120.40  3.000
 MC9  C24   C23  C22   123.44  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
 MC9  Var_01  C4    C5   C10  C1     53.59  30.0  1
 MC9  Var_02  C10   C5   C4   C3    -53.04  30.0  1
 MC9  Var_03  C12   C11  C9   C8     50.49  30.0  1
 MC9  Var_04  C13   C12  C11  C9    -52.85  30.0  1
 MC9  Var_05  C14   C8   C9   C11   -53.25  30.0  1
 MC9  Var_06  C17   C16  C15  C14    12.78  30.0  1
 MC9  Var_07  C27   C26  C25  C24  -111.63  30.0  1
 MC9  Var_08  H271  C27  C26  C25  -107.58  30.0  1
 MC9  Var_09  C7    C6   C5   C4   -176.81  30.0  2
 MC9  Var_10  C8    C7   C6   C5   -173.84  30.0  2
 MC9  Var_11  C9    C8   C7   C6      0.94  30.0  2
 MC9  Var_12  H191  C19  C10  C1      0.62  30.0  2
 MC9  Var_13  C24   C23  C22  C20  -178.64   0.0  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
 MC9  chir_01  C1   O1   C2   C10  negativ
 MC9  chir_02  C3   O2   C4   C2   positiv
 MC9  chir_03  C13  C14  C17  C12  negativ
 MC9  chir_04  C14  C8   C13  C15  negativ
 MC9  chir_05  C17  C13  C16  C20  positiv
 MC9  chir_06  C20  C17  C22  C21  negativ
 MC9  chir_07  C24  O3   C23  C25  positiv
 MC9  chir_08  C25  C24  C26  C27  both

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
 MC9  plan-1  C20  0.020
 MC9  plan-1  C22  0.020
 MC9  plan-1  C24  0.020
 MC9  plan-1  C23  0.020
 MC9  plan-1  H22  0.020
 MC9  plan-1  H23  0.020

