# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 23:51:10 2022
#   Inital geometry file: a 167 line input string
#   Ligand name: (1S,3R,5Z,7E,14beta,17alpha)-9,10-secocholesta-5,7,10-triene-1,3,25-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)C[C@H](O)C3=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
 VDX  VDX  (1S,3R,5Z,7E,14beta,17alpha)-9,10-secocholesta-5,7,10-triene-1,3,25-triol  ligand  74  30  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VDX
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
 VDX  O2    O  OH1   0  -0.674  -0.7265   1.3830  -8.2472
 VDX  O3    O  OH1   0  -0.679  -2.7548   0.3868   7.4641
 VDX  C1    C  CH1   0  -0.028  -2.3285  -0.5872  -5.5071
 VDX  C2    C  CH2   0  -0.488  -2.0915   0.0060  -6.8890
 VDX  C3    C  CH1   0   0.072  -0.8762   0.9214  -6.9206
 VDX  C4    C  CH2   0  -0.533   0.3653   0.1643  -6.4403
 VDX  C5    C  C     0   0.098   0.1416  -0.4371  -5.0788
 VDX  C6    C  C1    0  -0.300   0.9717  -0.1887  -4.0511
 VDX  C7    C  C1    0  -0.359   0.7935  -0.6198  -2.6781
 VDX  C8    C  C     0   0.155   1.6720  -0.4586  -1.6756
 VDX  C9    C  CH2   0  -0.504   3.0483   0.1347  -1.8022
 VDX  C10   C  C     0   0.065  -1.0770  -1.2625  -4.9936
 VDX  C11   C  CH2   0  -0.436   3.2762   1.2720  -0.7993
 VDX  C12   C  CH2   0  -0.417   2.8921   0.8912   0.6309
 VDX  C13   C  CT    0  -0.064   1.4693   0.3302   0.7152
 VDX  C14   C  CH1   0  -0.243   1.3831  -0.8663  -0.2653
 VDX  C15   C  CH2   0  -0.454   0.0773  -1.5541   0.0985
 VDX  C16   C  CH2   0  -0.445  -0.0052  -1.3864   1.6280
 VDX  C17   C  CH1   0  -0.164   1.0957  -0.3733   2.0431
 VDX  C18   C  CH3   0  -0.675   0.4361   1.4007   0.3578
 VDX  C19   C  C2    0  -0.583  -1.1038  -2.5138  -4.5384
 VDX  C20   C  CH1   0  -0.231   0.6721   0.4927   3.2384
 VDX  C21   C  CH3   0  -0.673   1.7161   1.5433   3.6126
 VDX  C22   C  CH2   0  -0.412   0.3639  -0.3925   4.4557
 VDX  C23   C  CH2   0  -0.428  -0.4136   0.3114   5.5644
 VDX  C24   C  CH2   0  -0.429  -0.6412  -0.5984   6.7652
 VDX  C25   C  CT    0   0.202  -1.4610   0.0024   7.9168
 VDX  C26   C  CH3   0  -0.664  -1.5867  -1.0353   9.0324
 VDX  C27   C  CH3   0  -0.668  -0.8165   1.2690   8.4666
 VDX  O1    O  OH1   0  -0.664  -2.7032   0.4715  -4.6451
 VDX  HO2   H  HOH1  0   0.449  -0.0025   2.0165  -8.2651
 VDX  HO3   H  HOH1  0   0.439  -3.1900  -0.3945   7.1062
 VDX  H11   H  HCH1  0   0.225  -3.1307  -1.3342  -5.5760
 VDX  H21   H  HCH2  0   0.250  -2.9857   0.5455  -7.2138
 VDX  H22   H  HCH2  0   0.237  -1.9408  -0.8168  -7.5951
 VDX  H31   H  HCH1  0   0.205  -1.0465   1.7657  -6.2397
 VDX  H41   H  HCH2  0   0.245   1.2317   0.8313  -6.4228
 VDX  H42   H  HCH2  0   0.236   0.5772  -0.6305  -7.1664
 VDX  H61   H  H     0   0.232   1.8326   0.4361  -4.2680
 VDX  H71   H  H     0   0.228  -0.1536  -1.0946  -2.4467
 VDX  H91   H  HCH2  0   0.232   3.7766  -0.6600  -1.5981
 VDX  H92   H  HCH2  0   0.243   3.2597   0.4863  -2.8122
 VDX  H111  H  HCH2  0   0.233   4.3277   1.5672  -0.8266
 VDX  H112  H  HCH2  0   0.222   2.7092   2.1506  -1.1181
 VDX  H121  H  HCH2  0   0.211   3.5871   0.1283   1.0011
 VDX  H122  H  HCH2  0   0.232   3.0184   1.7599   1.2781
 VDX  H141  H  HCH1  0   0.230   2.1994  -1.5458   0.0295
 VDX  H151  H  HCH2  0   0.234   0.0614  -2.6000  -0.2123
 VDX  H152  H  HCH2  0   0.220  -0.7720  -1.0701  -0.3882
 VDX  H161  H  HCH2  0   0.231   0.1340  -2.3405   2.1374
 VDX  H162  H  HCH2  0   0.221  -0.9923  -1.0221   1.9237
 VDX  H171  H  HCH1  0   0.206   1.9846  -0.9393   2.3549
 VDX  H181  H  HCH3  0   0.235   0.5759   1.7774  -0.6556
 VDX  H182  H  HCH3  0   0.231  -0.5857   1.0220   0.4153
 VDX  H183  H  HCH3  0   0.228   0.5006   2.2530   1.0365
 VDX  H191  H  H     0   0.245  -0.2107  -3.0178  -4.1911
 VDX  H192  H  H     0   0.244  -2.0264  -3.0817  -4.5137
 VDX  H201  H  HCH1  0   0.205  -0.2564   1.0101   2.9656
 VDX  H211  H  HCH3  0   0.213   2.7004   1.0866   3.7388
 VDX  H212  H  HCH3  0   0.228   1.8092   2.3277   2.8626
 VDX  H213  H  HCH3  0   0.232   1.4640   2.0368   4.5514
 VDX  H221  H  HCH2  0   0.231  -0.2114  -1.2698   4.1477
 VDX  H222  H  HCH2  0   0.204   1.3076  -0.7817   4.8582
 VDX  H231  H  HCH2  0   0.218   0.1209   1.2097   5.8826
 VDX  H232  H  HCH2  0   0.210  -1.3740   0.6518   5.1662
 VDX  H241  H  HCH2  0   0.216  -1.1414  -1.5174   6.4323
 VDX  H242  H  HCH2  0   0.215   0.3284  -0.9179   7.1614
 VDX  H261  H  HCH3  0   0.229  -2.1762  -0.6477   9.8654
 VDX  H262  H  HCH3  0   0.224  -2.0715  -1.9463   8.6718
 VDX  H263  H  HCH3  0   0.222  -0.6064  -1.3182   9.4184
 VDX  H271  H  HCH3  0   0.223   0.2109   1.0737   8.7751
 VDX  H272  H  HCH3  0   0.233  -0.7964   2.0705   7.7277
 VDX  H273  H  HCH3  0   0.231  -1.3626   1.6324   9.3392
 VDX  HO1   H  HOH1  0   0.449  -2.7891   0.1173  -3.7543

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
 VDX  O2   C3    single  1.413  0.020  1.413
 VDX  O2   HO2   single  0.850  0.020  0.980
 VDX  O3   C25   single  1.424  0.020  1.424
 VDX  O3   HO3   single  0.850  0.020  0.980
 VDX  C1   C2    single  1.522  0.020  1.522
 VDX  C1   C10   single  1.512  0.020  1.512
 VDX  C1   O1    single  1.416  0.020  1.416
 VDX  C1   H11   single  0.970  0.020  1.090
 VDX  C2   C3    single  1.522  0.020  1.522
 VDX  C2   H21   single  0.970  0.020  1.090
 VDX  C2   H22   single  0.970  0.020  1.090
 VDX  C3   C4    single  1.531  0.020  1.531
 VDX  C3   H31   single  0.970  0.020  1.090
 VDX  C4   C5    single  1.505  0.020  1.505
 VDX  C4   H41   single  0.970  0.020  1.090
 VDX  C4   H42   single  0.970  0.020  1.090
 VDX  C5   C6    double  1.344  0.020  1.344
 VDX  C5   C10   single  1.474  0.020  1.474
 VDX  C6   C7    single  1.450  0.020  1.450
 VDX  C6   H61   single  0.930  0.020  1.080
 VDX  C7   C8    double  1.343  0.020  1.343
 VDX  C7   H71   single  0.930  0.020  1.080
 VDX  C8   C9    single  1.504  0.020  1.504
 VDX  C8   C14   single  1.496  0.020  1.496
 VDX  C9   C11   single  1.533  0.020  1.533
 VDX  C9   H91   single  0.970  0.020  1.090
 VDX  C9   H92   single  0.970  0.020  1.090
 VDX  C10  C19   double  1.332  0.020  1.332
 VDX  C11  C12   single  1.529  0.020  1.529
 VDX  C11  H111  single  0.970  0.020  1.090
 VDX  C11  H112  single  0.970  0.020  1.090
 VDX  C12  C13   single  1.532  0.020  1.532
 VDX  C12  H121  single  0.970  0.020  1.090
 VDX  C12  H122  single  0.970  0.020  1.090
 VDX  C13  C14   single  1.549  0.020  1.549
 VDX  C13  C17   single  1.549  0.020  1.549
 VDX  C13  C18   single  1.530  0.020  1.530
 VDX  C14  C15   single  1.520  0.020  1.520
 VDX  C14  H141  single  0.970  0.020  1.090
 VDX  C15  C16   single  1.541  0.020  1.541
 VDX  C15  H151  single  0.970  0.020  1.090
 VDX  C15  H152  single  0.970  0.020  1.090
 VDX  C16  C17   single  1.553  0.020  1.553
 VDX  C16  H161  single  0.970  0.020  1.090
 VDX  C16  H162  single  0.970  0.020  1.090
 VDX  C17  C20   single  1.536  0.020  1.536
 VDX  C17  H171  single  0.970  0.020  1.090
 VDX  C18  H181  single  0.970  0.020  1.090
 VDX  C18  H182  single  0.970  0.020  1.090
 VDX  C18  H183  single  0.970  0.020  1.090
 VDX  C19  H191  single  0.930  0.020  1.080
 VDX  C19  H192  single  0.930  0.020  1.080
 VDX  C20  C21   single  1.528  0.020  1.528
 VDX  C20  C22   single  1.536  0.020  1.536
 VDX  C20  H201  single  0.970  0.020  1.090
 VDX  C21  H211  single  0.970  0.020  1.090
 VDX  C21  H212  single  0.970  0.020  1.090
 VDX  C21  H213  single  0.970  0.020  1.090
 VDX  C22  C23   single  1.526  0.020  1.526
 VDX  C22  H221  single  0.970  0.020  1.090
 VDX  C22  H222  single  0.970  0.020  1.090
 VDX  C23  C24   single  1.524  0.020  1.524
 VDX  C23  H231  single  0.970  0.020  1.090
 VDX  C23  H232  single  0.970  0.020  1.090
 VDX  C24  C25   single  1.536  0.020  1.536
 VDX  C24  H241  single  0.970  0.020  1.090
 VDX  C24  H242  single  0.970  0.020  1.090
 VDX  C25  C26   single  1.529  0.020  1.529
 VDX  C25  C27   single  1.524  0.020  1.524
 VDX  C26  H261  single  0.970  0.020  1.090
 VDX  C26  H262  single  0.970  0.020  1.090
 VDX  C26  H263  single  0.970  0.020  1.090
 VDX  C27  H271  single  0.970  0.020  1.090
 VDX  C27  H272  single  0.970  0.020  1.090
 VDX  C27  H273  single  0.970  0.020  1.090
 VDX  O1   HO1   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
 VDX  HO2   O2   C3    108.20  3.000
 VDX  HO3   O3   C25   108.05  3.000
 VDX  H11   C1   O1    110.70  3.000
 VDX  H11   C1   C10   108.79  3.000
 VDX  O1    C1   C10   110.26  3.000
 VDX  H11   C1   C2    108.77  3.000
 VDX  O1    C1   C2    107.61  3.000
 VDX  C10   C1   C2    110.70  3.000
 VDX  H22   C2   H21   106.96  3.000
 VDX  H22   C2   C3    109.20  3.000
 VDX  H21   C2   C3    110.49  3.000
 VDX  H22   C2   C1    108.31  3.000
 VDX  H21   C2   C1    109.54  3.000
 VDX  C3    C2   C1    112.18  3.000
 VDX  H31   C3   C4    108.14  3.000
 VDX  H31   C3   C2    109.02  3.000
 VDX  C4    C3   C2    110.09  3.000
 VDX  H31   C3   O2    110.34  3.000
 VDX  C4    C3   O2    111.73  3.000
 VDX  C2    C3   O2    107.50  3.000
 VDX  H42   C4   H41   107.42  3.000
 VDX  H42   C4   C5    109.75  3.000
 VDX  H41   C4   C5    110.30  3.000
 VDX  H42   C4   C3    107.89  3.000
 VDX  H41   C4   C3    110.23  3.000
 VDX  C5    C4   C3    111.15  3.000
 VDX  C10   C5   C6    124.73  3.000
 VDX  C10   C5   C4    113.51  3.000
 VDX  C6    C5   C4    121.73  3.000
 VDX  H61   C6   C7    117.25  3.000
 VDX  H61   C6   C5    116.31  3.000
 VDX  C7    C6   C5    126.37  3.000
 VDX  H71   C7   C8    117.69  3.000
 VDX  H71   C7   C6    116.08  3.000
 VDX  C8    C7   C6    126.22  3.000
 VDX  C14   C8   C9    111.32  3.000
 VDX  C14   C8   C7    123.01  3.000
 VDX  C9    C8   C7    125.68  3.000
 VDX  H92   C9   H91   106.10  3.000
 VDX  H92   C9   C11   109.75  3.000
 VDX  H91   C9   C11   108.48  3.000
 VDX  H92   C9   C8    112.50  3.000
 VDX  H91   C9   C8    107.82  3.000
 VDX  C11   C9   C8    111.93  3.000
 VDX  C19   C10  C5    124.22  3.000
 VDX  C19   C10  C1    121.27  3.000
 VDX  C5    C10  C1    114.49  3.000
 VDX  H112  C11  H111  105.95  3.000
 VDX  H112  C11  C12   110.04  3.000
 VDX  H111  C11  C12   109.42  3.000
 VDX  H112  C11  C9    109.16  3.000
 VDX  H111  C11  C9    109.09  3.000
 VDX  C12   C11  C9    112.94  3.000
 VDX  H122  C12  H121  106.29  3.000
 VDX  H122  C12  C13   111.51  3.000
 VDX  H121  C12  C13   108.38  3.000
 VDX  H122  C12  C11   109.12  3.000
 VDX  H121  C12  C11   109.26  3.000
 VDX  C13   C12  C11   112.09  3.000
 VDX  C18   C13  C17   110.81  3.000
 VDX  C18   C13  C14   110.79  3.000
 VDX  C17   C13  C14   100.28  3.000
 VDX  C18   C13  C12   110.99  3.000
 VDX  C17   C13  C12   115.96  3.000
 VDX  C14   C13  C12   107.44  3.000
 VDX  H141  C14  C15   107.05  3.000
 VDX  H141  C14  C13   105.40  3.000
 VDX  C15   C14  C13   104.23  3.000
 VDX  H141  C14  C8    106.09  3.000
 VDX  C15   C14  C8    120.98  3.000
 VDX  C13   C14  C8    112.05  3.000
 VDX  H152  C15  H151  106.65  3.000
 VDX  H152  C15  C16   110.65  3.000
 VDX  H151  C15  C16   112.72  3.000
 VDX  H152  C15  C14   111.15  3.000
 VDX  H151  C15  C14   112.21  3.000
 VDX  C16   C15  C14   103.55  3.000
 VDX  H162  C16  H161  106.30  3.000
 VDX  H162  C16  C17   110.52  3.000
 VDX  H161  C16  C17   110.82  3.000
 VDX  H162  C16  C15   110.68  3.000
 VDX  H161  C16  C15   111.20  3.000
 VDX  C17   C16  C15   107.36  3.000
 VDX  H171  C17  C20   107.02  3.000
 VDX  H171  C17  C16   108.26  3.000
 VDX  C20   C17  C16   112.36  3.000
 VDX  H171  C17  C13   106.39  3.000
 VDX  C20   C17  C13   118.54  3.000
 VDX  C16   C17  C13   103.79  3.000
 VDX  H183  C18  H182  107.07  3.000
 VDX  H183  C18  H181  107.50  3.000
 VDX  H182  C18  H181  106.80  3.000
 VDX  H183  C18  C13   111.18  3.000
 VDX  H182  C18  C13   112.16  3.000
 VDX  H181  C18  C13   111.86  3.000
 VDX  H192  C19  H191  116.81  3.000
 VDX  H192  C19  C10   121.15  3.000
 VDX  H191  C19  C10   122.03  3.000
 VDX  H201  C20  C22   107.39  3.000
 VDX  H201  C20  C21   108.35  3.000
 VDX  C22   C20  C21   109.83  3.000
 VDX  H201  C20  C17   107.81  3.000
 VDX  C22   C20  C17   110.31  3.000
 VDX  C21   C20  C17   112.96  3.000
 VDX  H213  C21  H212  106.66  3.000
 VDX  H213  C21  H211  107.34  3.000
 VDX  H212  C21  H211  107.67  3.000
 VDX  H213  C21  C20   111.36  3.000
 VDX  H212  C21  C20   112.65  3.000
 VDX  H211  C21  C20   110.89  3.000
 VDX  H222  C22  H221  105.74  3.000
 VDX  H222  C22  C23   109.59  3.000
 VDX  H221  C22  C23   107.86  3.000
 VDX  H222  C22  C20   108.81  3.000
 VDX  H221  C22  C20   110.16  3.000
 VDX  C23   C22  C20   114.34  3.000
 VDX  H232  C23  H231  106.24  3.000
 VDX  H232  C23  C24   109.97  3.000
 VDX  H231  C23  C24   109.54  3.000
 VDX  H232  C23  C22   109.05  3.000
 VDX  H231  C23  C22   109.97  3.000
 VDX  C24   C23  C22   111.92  3.000
 VDX  H242  C24  H241  105.60  3.000
 VDX  H242  C24  C25   108.39  3.000
 VDX  H241  C24  C25   108.16  3.000
 VDX  H242  C24  C23   109.09  3.000
 VDX  H241  C24  C23   109.20  3.000
 VDX  C25   C24  C23   115.92  3.000
 VDX  C27   C25  C26   109.62  3.000
 VDX  C27   C25  C24   111.71  3.000
 VDX  C26   C25  C24   108.99  3.000
 VDX  C27   C25  O3    105.94  3.000
 VDX  C26   C25  O3    109.91  3.000
 VDX  C24   C25  O3    110.62  3.000
 VDX  H263  C26  H262  107.41  3.000
 VDX  H263  C26  H261  107.90  3.000
 VDX  H262  C26  H261  107.95  3.000
 VDX  H263  C26  C25   111.12  3.000
 VDX  H262  C26  C25   111.19  3.000
 VDX  H261  C26  C25   111.11  3.000
 VDX  H273  C27  H272  107.84  3.000
 VDX  H273  C27  H271  107.75  3.000
 VDX  H272  C27  H271  107.82  3.000
 VDX  H273  C27  C25   110.71  3.000
 VDX  H272  C27  C25   111.98  3.000
 VDX  H271  C27  C25   110.59  3.000
 VDX  HO1   O1   C1    108.18  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
 VDX  Var_01  C4    C5   C10  C1    -50.75  30.0  1
 VDX  Var_02  C10   C5   C4   C3     52.63  30.0  1
 VDX  Var_03  C12   C11  C9   C8     49.71  30.0  1
 VDX  Var_04  C13   C12  C11  C9    -52.43  30.0  1
 VDX  Var_05  C14   C8   C9   C11   -52.88  30.0  1
 VDX  Var_06  C17   C16  C15  C14    11.16  30.0  1
 VDX  Var_07  C7    C6   C5   C4    174.48  30.0  2
 VDX  Var_08  C8    C7   C6   C5    174.56  30.0  2
 VDX  Var_09  C9    C8   C7   C6     -3.66  30.0  2
 VDX  Var_10  H191  C19  C10  C1    178.43  30.0  2
 VDX  Var_11  C23   C24  C25  O3     59.28  30.0  2
 VDX  Var_12  C24   C23  C22  C20  -177.76  30.0  3
 VDX  Var_13  C25   C24  C23  C22  -177.86  30.0  3
 VDX  Var_14  H261  C26  C25  O3    -57.85  30.0  3
 VDX  Var_15  H271  C27  C25  O3   -176.16  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
 VDX  chir_01  C1   C2   C10  O1   negativ
 VDX  chir_02  C3   O2   C4   C2   positiv
 VDX  chir_03  C13  C14  C17  C12  negativ
 VDX  chir_04  C14  C8   C13  C15  negativ
 VDX  chir_05  C17  C13  C16  C20  positiv
 VDX  chir_06  C20  C22  C21  C17  negativ

