# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 22:46:48 2020
#   Inital geometry file: a 167 line input string
#   Ligand name: "(1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{S},3~{a}~{S},7~{a}~{S})-7~{a}-methyl-1-[(2~{S})-6-methyl-2-oxidanyl-heptan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol"
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCC[C@](C)(O)[C@H]1CC[C@H]2/C(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
 D3V  D3V  "1a,20S-dihydroxyvitamin D3"  ligand  74  30  .  2022-07-24  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D3V
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
 D3V  C4   C  CT    0   0.211   -3.3788   0.1836  -0.6711
 D3V  C5   C  CH3   0  -0.681   -3.7253   1.2278  -1.7262
 D3V  C6   C  CH2   0  -0.448   -4.5952  -0.0314   0.2576
 D3V  C7   C  CH2   0  -0.426   -5.8214  -0.6745  -0.3824
 D3V  C8   C  CH2   0  -0.394   -6.9826  -0.7664   0.6024
 D3V  C9   C  CH1   0  -0.230   -8.2141  -1.5101   0.0805
 D3V  C10  C  CH3   0  -0.652   -9.2663  -1.6249   1.1791
 D3V  C11  C  CH3   0  -0.660   -8.8116  -0.8483  -1.1576
 D3V  C12  C  CT    0  -0.069   -0.8582   1.1227  -0.4209
 D3V  C13  C  CH3   0  -0.653   -0.3166   0.1470  -1.4678
 D3V  C14  C  CH2   0  -0.418   -0.8611   2.5567  -0.9643
 D3V  C15  C  CH2   0  -0.436    0.5526   3.0781  -1.2268
 D3V  C24  C  CH1   0  -0.029    5.5427  -2.1371   0.3227
 D3V  C23  C  CH2   0  -0.489    6.9431  -1.7105  -0.0954
 D3V  C22  C  CH1   0   0.071    6.9570  -0.3293  -0.7351
 D3V  O1   O  OH1   0  -0.674    8.3000  -0.0159  -1.0403
 D3V  C21  C  CH2   0  -0.532    6.3376   0.6974   0.2177
 D3V  C25  C  C     0   0.069    4.9043  -1.0835   1.2004
 D3V  C26  C  C2    0  -0.587    4.3829  -1.3901   2.3867
 D3V  C20  C  C     0   0.095    4.9549   0.2794   0.6389
 D3V  C19  C  C1    0  -0.299    3.8892   1.0765   0.4505
 D3V  C17  C  C     0   0.153    1.4443   1.5455   0.5447
 D3V  C    C  CH1   0  -0.245    0.0429   1.1169   0.8433
 D3V  C16  C  CH2   0  -0.505    1.4778   2.9428  -0.0104
 D3V  C3   C  CH1   0  -0.175   -2.1895   0.6383   0.2115
 D3V  C2   C  CH2   0  -0.454   -1.7498  -0.4242   1.2580
 D3V  C1   C  CH2   0  -0.449   -0.2427  -0.2228   1.4992
 D3V  O    O  OH1   0  -0.677   -3.0985  -1.0057  -1.3934
 D3V  H9   H  HCH3  0   0.236   -2.9416   1.3265  -2.4762
 D3V  H8   H  HCH3  0   0.238   -4.6444   0.9644  -2.2504
 D3V  H10  H  HCH3  0   0.222   -3.8769   2.2051  -1.2680
 D3V  H12  H  HCH2  0   0.234   -4.2999  -0.6500   1.1120
 D3V  H13  H  HCH2  0   0.216   -4.8765   0.9381   0.6828
 D3V  H15  H  HCH2  0   0.218   -6.1341  -0.1068  -1.2622
 D3V  H14  H  HCH2  0   0.209   -5.5702  -1.6781  -0.7366
 D3V  H16  H  HCH2  0   0.211   -6.6357  -1.2661   1.5143
 D3V  H17  H  HCH2  0   0.202   -7.2807   0.2441   0.9076
 D3V  H18  H  HCH1  0   0.208   -7.8999  -2.5241  -0.1957
 D3V  H20  H  HCH3  0   0.211   -9.6114  -0.6363   1.4923
 D3V  H21  H  HCH3  0   0.223  -10.1392  -2.1857   0.8394
 D3V  H19  H  HCH3  0   0.222   -8.8720  -2.1319   2.0618
 D3V  H23  H  HCH3  0   0.227   -8.1185  -0.8413  -1.9992
 D3V  H22  H  HCH3  0   0.224   -9.7121  -1.3725  -1.4828
 D3V  H24  H  HCH3  0   0.210   -9.0907   0.1878  -0.9492
 D3V  H26  H  HCH3  0   0.228   -0.9146   0.1716  -2.3781
 D3V  H27  H  HCH3  0   0.224    0.7114   0.3884  -1.7386
 D3V  H25  H  HCH3  0   0.224   -0.3193  -0.8837  -1.1138
 D3V  H28  H  HCH2  0   0.231   -1.4431   2.6347  -1.8832
 D3V  H29  H  HCH2  0   0.211   -1.3528   3.2093  -0.2326
 D3V  H30  H  HCH2  0   0.222    0.9946   2.5471  -2.0738
 D3V  H31  H  HCH2  0   0.234    0.5018   4.1285  -1.5228
 D3V  H3   H  HCH1  0   0.226    5.6129  -3.0755   0.8889
 D3V  H39  H  HCH2  0   0.238    7.5781  -1.6987   0.7960
 D3V  H40  H  HCH2  0   0.250    7.3641  -2.4527  -0.7797
 D3V  H2   H  HCH1  0   0.205    6.3533  -0.3512  -1.6521
 D3V  H38  H  HOH1  0   0.449    8.3113   0.8175  -1.5214
 D3V  H37  H  HCH2  0   0.236    6.9865   0.7719   1.0992
 D3V  H36  H  HCH2  0   0.245    6.3099   1.6841  -0.2533
 D3V  H42  H  H     0   0.245    3.9459  -0.6392   3.0328
 D3V  H43  H  H     0   0.243    4.3909  -2.4089   2.7561
 D3V  H35  H  H     0   0.232    4.0892   2.0497   0.0131
 D3V  H    H  HCH1  0   0.230   -0.3804   1.8909   1.5030
 D3V  H32  H  HCH2  0   0.244    2.4837   3.2643  -0.2799
 D3V  H33  H  HCH2  0   0.231    1.1311   3.6308   0.7705
 D3V  H1   H  HCH1  0   0.217   -2.5712   1.4994   0.7743
 D3V  H6   H  HCH2  0   0.239   -2.3151  -0.3048   2.1823
 D3V  H7   H  HCH2  0   0.210   -1.9425  -1.4473   0.9251
 D3V  H5   H  HCH2  0   0.223    0.3330  -1.0242   1.0317
 D3V  H4   H  HCH2  0   0.237    0.0156  -0.2277   2.5592
 D3V  H11  H  HOH1  0   0.438   -2.9274  -1.7177  -0.7693
 D3V  C18  C  C1    0  -0.355    2.5073   0.7489   0.7393
 D3V  O2   O  OH1   0  -0.663    4.7811  -2.3199  -0.8562
 D3V  H41  H  HOH1  0   0.448    3.8834  -2.5535  -0.5998
 D3V  H34  H  H     0   0.229    2.3259  -0.2446   1.1329

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
 D3V  C11  C9   single  1.526  0.020  1.526
 D3V  C9   C10  single  1.526  0.020  1.526
 D3V  C9   C8   single  1.530  0.020  1.530
 D3V  C8   C7   single  1.525  0.020  1.525
 D3V  C7   C6   single  1.525  0.020  1.525
 D3V  C6   C4   single  1.545  0.020  1.545
 D3V  O    C4   single  1.419  0.020  1.419
 D3V  C13  C12  single  1.530  0.020  1.530
 D3V  C26  C25  double  1.332  0.020  1.332
 D3V  C15  C14  single  1.529  0.020  1.529
 D3V  C15  C16  single  1.534  0.020  1.534
 D3V  C14  C12  single  1.533  0.020  1.533
 D3V  C4   C5   single  1.524  0.020  1.524
 D3V  C4   C3   single  1.549  0.020  1.549
 D3V  C12  C3   single  1.551  0.020  1.551
 D3V  C12  C    single  1.553  0.020  1.553
 D3V  C23  C22  single  1.522  0.020  1.522
 D3V  C23  C24  single  1.522  0.020  1.522
 D3V  C25  C20  single  1.475  0.020  1.475
 D3V  C25  C24  single  1.513  0.020  1.513
 D3V  O2   C24  single  1.415  0.020  1.415
 D3V  C21  C20  single  1.505  0.020  1.505
 D3V  C21  C22  single  1.531  0.020  1.531
 D3V  C20  C19  double  1.344  0.020  1.344
 D3V  C3   C2   single  1.555  0.020  1.555
 D3V  C22  O1   single  1.412  0.020  1.412
 D3V  C19  C18  single  1.449  0.020  1.449
 D3V  C16  C17  single  1.504  0.020  1.504
 D3V  C18  C17  double  1.343  0.020  1.343
 D3V  C17  C    single  1.496  0.020  1.496
 D3V  C    C1   single  1.519  0.020  1.519
 D3V  C2   C1   single  1.540  0.020  1.540
 D3V  C5   H9   single  0.970  0.020  1.090
 D3V  C5   H8   single  0.970  0.020  1.090
 D3V  C5   H10  single  0.970  0.020  1.090
 D3V  C6   H12  single  0.970  0.020  1.090
 D3V  C6   H13  single  0.970  0.020  1.090
 D3V  C7   H15  single  0.970  0.020  1.090
 D3V  C7   H14  single  0.970  0.020  1.090
 D3V  C8   H16  single  0.970  0.020  1.090
 D3V  C8   H17  single  0.970  0.020  1.090
 D3V  C9   H18  single  0.970  0.020  1.090
 D3V  C10  H20  single  0.970  0.020  1.090
 D3V  C10  H21  single  0.970  0.020  1.090
 D3V  C10  H19  single  0.970  0.020  1.090
 D3V  C11  H23  single  0.970  0.020  1.090
 D3V  C11  H22  single  0.970  0.020  1.090
 D3V  C11  H24  single  0.970  0.020  1.090
 D3V  C13  H26  single  0.970  0.020  1.090
 D3V  C13  H27  single  0.970  0.020  1.090
 D3V  C13  H25  single  0.970  0.020  1.090
 D3V  C14  H28  single  0.970  0.020  1.090
 D3V  C14  H29  single  0.970  0.020  1.090
 D3V  C15  H30  single  0.970  0.020  1.090
 D3V  C15  H31  single  0.970  0.020  1.090
 D3V  O2   H41  single  0.850  0.020  0.980
 D3V  C24  H3   single  0.970  0.020  1.090
 D3V  C23  H39  single  0.970  0.020  1.090
 D3V  C23  H40  single  0.970  0.020  1.090
 D3V  C22  H2   single  0.970  0.020  1.090
 D3V  O1   H38  single  0.850  0.020  0.980
 D3V  C21  H37  single  0.970  0.020  1.090
 D3V  C21  H36  single  0.970  0.020  1.090
 D3V  C26  H42  single  0.930  0.020  1.080
 D3V  C26  H43  single  0.930  0.020  1.080
 D3V  C19  H35  single  0.930  0.020  1.080
 D3V  C18  H34  single  0.930  0.020  1.080
 D3V  C    H    single  0.970  0.020  1.090
 D3V  C16  H32  single  0.970  0.020  1.090
 D3V  C16  H33  single  0.970  0.020  1.090
 D3V  C3   H1   single  0.970  0.020  1.090
 D3V  C2   H6   single  0.970  0.020  1.090
 D3V  C2   H7   single  0.970  0.020  1.090
 D3V  C1   H5   single  0.970  0.020  1.090
 D3V  C1   H4   single  0.970  0.020  1.090
 D3V  O    H11  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
 D3V  O    C4   C3   112.60  3.000
 D3V  C3   C4   C6   107.62  3.000
 D3V  O    C4   C6   110.16  3.000
 D3V  C3   C4   C5   111.58  3.000
 D3V  O    C4   C5   105.46  3.000
 D3V  C6   C4   C5   109.41  3.000
 D3V  H10  C5   H8   107.55  3.000
 D3V  H10  C5   H9   107.96  3.000
 D3V  H8   C5   H9   107.29  3.000
 D3V  H10  C5   C4   110.79  3.000
 D3V  H8   C5   C4   111.03  3.000
 D3V  H9   C5   C4   112.02  3.000
 D3V  H13  C6   H12  105.44  3.000
 D3V  H13  C6   C7   109.24  3.000
 D3V  H12  C6   C7   107.81  3.000
 D3V  H13  C6   C4   108.19  3.000
 D3V  H12  C6   C4   109.58  3.000
 D3V  C7   C6   C4   116.06  3.000
 D3V  H14  C7   H15  106.36  3.000
 D3V  H14  C7   C8   109.19  3.000
 D3V  H15  C7   C8   109.47  3.000
 D3V  H14  C7   C6   109.77  3.000
 D3V  H15  C7   C6   110.41  3.000
 D3V  C8   C7   C6   111.50  3.000
 D3V  H17  C8   H16  105.93  3.000
 D3V  H17  C8   C9   108.90  3.000
 D3V  H16  C8   C9   108.47  3.000
 D3V  H17  C8   C7   109.33  3.000
 D3V  H16  C8   C7   108.88  3.000
 D3V  C9   C8   C7   114.94  3.000
 D3V  H18  C9   C11  107.99  3.000
 D3V  H18  C9   C10  108.02  3.000
 D3V  C11  C9   C10  110.29  3.000
 D3V  H18  C9   C8   107.74  3.000
 D3V  C10  C9   C8   110.24  3.000
 D3V  C11  C9   C8   112.40  3.000
 D3V  H19  C10  H21  107.56  3.000
 D3V  H19  C10  H20  107.61  3.000
 D3V  H21  C10  H20  107.54  3.000
 D3V  H19  C10  C9   111.59  3.000
 D3V  H21  C10  C9   111.47  3.000
 D3V  H20  C10  C9   110.86  3.000
 D3V  H24  C11  H22  107.54  3.000
 D3V  H24  C11  H23  107.66  3.000
 D3V  H22  C11  H23  107.31  3.000
 D3V  H24  C11  C9   110.88  3.000
 D3V  H22  C11  C9   110.89  3.000
 D3V  H23  C11  C9   112.35  3.000
 D3V  C3   C12  C     99.50  3.000
 D3V  C    C12  C14  107.04  3.000
 D3V  C3   C12  C14  115.78  3.000
 D3V  C    C12  C13  110.44  3.000
 D3V  C3   C12  C13  112.55  3.000
 D3V  C14  C12  C13  110.76  3.000
 D3V  H25  C13  H27  107.01  3.000
 D3V  H25  C13  H26  106.94  3.000
 D3V  H27  C13  H26  107.76  3.000
 D3V  H25  C13  C12  112.33  3.000
 D3V  H27  C13  C12  111.26  3.000
 D3V  H26  C13  C12  111.28  3.000
 D3V  H29  C14  H28  106.27  3.000
 D3V  H29  C14  C15  109.03  3.000
 D3V  H28  C14  C15  108.92  3.000
 D3V  H29  C14  C12  108.72  3.000
 D3V  H28  C14  C12  111.50  3.000
 D3V  C15  C14  C12  112.20  3.000
 D3V  H31  C15  H30  106.02  3.000
 D3V  H31  C15  C16  109.13  3.000
 D3V  H30  C15  C16  109.13  3.000
 D3V  H31  C15  C14  109.34  3.000
 D3V  H30  C15  C14  109.95  3.000
 D3V  C16  C15  C14  113.03  3.000
 D3V  H3   C24  C25  108.85  3.000
 D3V  H3   C24  C23  108.80  3.000
 D3V  C25  C24  C23  110.64  3.000
 D3V  H3   C24  O2   110.69  3.000
 D3V  C25  C24  O2   110.25  3.000
 D3V  C23  C24  O2   107.60  3.000
 D3V  H40  C23  H39  107.07  3.000
 D3V  H40  C23  C22  110.45  3.000
 D3V  H39  C23  C22  109.09  3.000
 D3V  H40  C23  C24  109.62  3.000
 D3V  H39  C23  C24  108.24  3.000
 D3V  C22  C23  C24  112.21  3.000
 D3V  H2   C22  C21  108.10  3.000
 D3V  H2   C22  O1   110.28  3.000
 D3V  C21  C22  O1   111.73  3.000
 D3V  H2   C22  C23  109.13  3.000
 D3V  O1   C22  C23  107.51  3.000
 D3V  C21  C22  C23  110.07  3.000
 D3V  H38  O1   C22  108.14  3.000
 D3V  H36  C21  H37  107.44  3.000
 D3V  H36  C21  C20  110.36  3.000
 D3V  H37  C21  C20  109.72  3.000
 D3V  H36  C21  C22  110.31  3.000
 D3V  H37  C21  C22  107.83  3.000
 D3V  C20  C21  C22  111.07  3.000
 D3V  C20  C25  C26  124.43  3.000
 D3V  C20  C25  C24  114.10  3.000
 D3V  C26  C25  C24  121.45  3.000
 D3V  H43  C26  H42  116.84  3.000
 D3V  H43  C26  C25  121.15  3.000
 D3V  H42  C26  C25  122.00  3.000
 D3V  C19  C20  C25  125.04  3.000
 D3V  C19  C20  C21  121.65  3.000
 D3V  C25  C20  C21  113.25  3.000
 D3V  H35  C19  C18  117.30  3.000
 D3V  H35  C19  C20  116.23  3.000
 D3V  C18  C19  C20  126.44  3.000
 D3V  C16  C17  C    111.15  3.000
 D3V  C    C17  C18  122.88  3.000
 D3V  C16  C17  C18  125.96  3.000
 D3V  H    C    C1   106.79  3.000
 D3V  H    C    C17  106.16  3.000
 D3V  C1   C    C17  121.02  3.000
 D3V  H    C    C12  105.19  3.000
 D3V  C1   C    C12  104.23  3.000
 D3V  C17  C    C12  112.35  3.000
 D3V  H33  C16  H32  106.42  3.000
 D3V  H33  C16  C17  108.24  3.000
 D3V  H32  C16  C17  112.70  3.000
 D3V  H33  C16  C15  108.58  3.000
 D3V  H32  C16  C15  109.54  3.000
 D3V  C17  C16  C15  111.17  3.000
 D3V  H1   C3   C2   106.83  3.000
 D3V  H1   C3   C12  105.22  3.000
 D3V  C2   C3   C12  104.19  3.000
 D3V  H1   C3   C4   104.80  3.000
 D3V  C2   C3   C4   113.58  3.000
 D3V  C12  C3   C4   121.21  3.000
 D3V  H7   C2   H6   105.63  3.000
 D3V  H7   C2   C1   110.05  3.000
 D3V  H6   C2   C1   111.13  3.000
 D3V  H7   C2   C3   112.63  3.000
 D3V  H6   C2   C3   110.44  3.000
 D3V  C1   C2   C3   107.03  3.000
 D3V  H4   C1   H5   106.73  3.000
 D3V  H4   C1   C2   112.54  3.000
 D3V  H5   C1   C2   110.67  3.000
 D3V  H4   C1   C    112.27  3.000
 D3V  H5   C1   C    111.31  3.000
 D3V  C2   C1   C    103.41  3.000
 D3V  H11  O    C4   108.97  3.000
 D3V  H34  C18  C17  117.65  3.000
 D3V  H34  C18  C19  116.05  3.000
 D3V  C17  C18  C19  126.29  3.000
 D3V  H41  O2   C24  108.14  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
 D3V  Var_01  C16  C15  C14  C12   -53.04  30.0  1
 D3V  Var_02  C17  C16  C15  C14    50.84  30.0  1
 D3V  Var_03  C    C17  C16  C15   -53.95  30.0  1
 D3V  Var_04  C21  C20  C25  C24   -51.86  30.0  1
 D3V  Var_05  C25  C20  C21  C22    53.44  30.0  1
 D3V  Var_06  C3   C2   C1   C      12.45  30.0  1
 D3V  Var_07  C18  C19  C20  C21   175.99  30.0  2
 D3V  Var_08  C17  C18  C19  C20  -179.70  30.0  2
 D3V  Var_09  H42  C26  C25  C24   178.45  30.0  2
 D3V  Var_10  C8   C7   C6   C4   -176.83  30.0  1
 D3V  Var_11  C9   C8   C7   C6   -174.89  30.0  1
 D3V  Var_12  C11  C9   C8   C7    -60.51  30.0  2
 D3V  Var_13  H23  C11  C9   C8     62.39  30.0  3
 D3V  Var_14  H20  C10  C9   C8     62.38  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
 D3V  chir_01  C4   O    C5   C3   positiv
 D3V  chir_02  C12  C3   C14  C    negativ
 D3V  chir_03  C24  C23  C25  O2   negativ
 D3V  chir_04  C22  O1   C23  C21  negativ
 D3V  chir_05  C    C12  C17  C1   positiv
 D3V  chir_06  C3   C2   C12  C4   negativ

