# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 21:42:47 2022
#   Inital geometry file: a 111 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CCC[C@@]3(OC1=O)[C@@H]4CC[C@@H]5C[C@]4(CC5=C)[C@H]([C@H]23)C(O)=O
#
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
 J5X  J5X  "Gibberellin A9"  ligand  46  23  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J5X
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
 J5X  C1   C  CH2    0  -0.420  14.2189  10.8452  16.6538
 J5X  C2   C  CH2    0  -0.476  12.9682  11.3059  17.4115
 J5X  C3   C  CH2    0  -0.398  13.2787  11.8781  18.8010
 J5X  C4   C  CT     0  -0.244  14.3497  11.0702  19.5725
 J5X  C5   C  CH1    0  -0.219  15.6212  11.0829  18.7300
 J5X  C6   C  CH1    0  -0.352  16.8679  10.4269  19.3116
 J5X  C7   C  C      0   0.428  17.7781  11.3521  20.1438
 J5X  C8   C  CT     0  -0.068  17.5822   9.8101  18.0853
 J5X  C9   C  CH1    0  -0.211  16.4746   9.6149  16.9914
 J5X  C10  C  CT     0   0.233  15.1913  10.1596  17.5978
 J5X  C11  C  CH2    0  -0.449  16.4210   8.1938  16.4414
 J5X  C12  C  CH2    0  -0.409  17.8127   7.7205  16.0031
 J5X  C13  C  CH1    0  -0.317  18.9195   8.2383  16.9516
 J5X  C14  C  CH2    0  -0.428  18.3163   8.4901  18.3361
 J5X  C15  C  CH2    0  -0.486  18.7213  10.6319  17.4627
 J5X  C16  C  C      0   0.210  19.3864   9.6274  16.5510
 J5X  C17  C  C2     0  -0.632  20.2313   9.9007  15.5634
 J5X  C18  C  CH3    0  -0.658  14.4766  11.5353  21.0086
 J5X  C19  C  C      0   0.573  13.9685   9.6059  19.4458
 J5X  O91  O  O      0  -0.425  13.3044   8.9325  20.1884
 J5X  O92  O  O2     0  -0.464  14.4677   9.1148  18.3097
 J5X  O71  O  O      0  -0.596  17.6880  12.5807  19.9472
 J5X  O72  O  OC    -1  -0.606  18.5589  10.7819  20.9343
 J5X  H1   H  HCH2   0   0.243  13.9375  10.1891  15.8251
 J5X  H2   H  HCH2   0   0.232  14.7367  11.7020  16.2153
 J5X  H3   H  HCH2   0   0.248  12.4350  12.0538  16.8227
 J5X  H4   H  HCH2   0   0.233  12.2749  10.4672  17.5138
 J5X  H5   H  HCH2   0   0.240  13.6513  12.9026  18.7170
 J5X  H6   H  HCH2   0   0.244  12.3583  11.9249  19.3881
 J5X  H7   H  HCH1   0   0.249  15.8582  12.0844  18.3646
 J5X  H8   H  HCH1   0   0.219  16.5787   9.5905  19.9613
 J5X  H9   H  HCH1   0   0.242  16.7062  10.2803  16.1507
 J5X  H10  H  HCH2   0   0.235  15.7236   8.1363  15.6021
 J5X  H11  H  HCH2   0   0.227  16.0367   7.5156  17.2046
 J5X  H12  H  HCH2   0   0.228  17.8274   6.6282  15.9879
 J5X  H13  H  HCH2   0   0.223  18.0263   8.0475  14.9832
 J5X  H14  H  HCH1   0   0.239  19.7526   7.5324  16.9585
 J5X  H15  H  HCH2   0   0.232  17.6700   7.6833  18.6884
 J5X  H16  H  HCH2   0   0.239  19.0895   8.6403  19.0930
 J5X  H17  H  HCH2   0   0.248  19.4319  10.9434  18.2344
 J5X  H18  H  HCH2   0   0.241  18.3880  11.5324  16.9430
 J5X  H19  H  H      0   0.224  20.5062  10.9186  15.3136
 J5X  H20  H  H      0   0.224  20.6786   9.1158  14.9644
 J5X  H21  H  HCH3   0   0.232  13.5292  11.4386  21.5405
 J5X  H22  H  HCH3   0   0.236  15.2275  10.9645  21.5554
 J5X  H23  H  HCH3   0   0.233  14.7694  12.5848  21.0384

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
 J5X  C17  C16  double  1.328  0.020  1.328
 J5X  C12  C11  single  1.534  0.020  1.534
 J5X  C12  C13  single  1.547  0.020  1.547
 J5X  C11  C9   single  1.525  0.020  1.525
 J5X  C16  C13  single  1.519  0.020  1.519
 J5X  C16  C15  single  1.511  0.020  1.511
 J5X  C1   C2   single  1.533  0.020  1.533
 J5X  C1   C10  single  1.519  0.020  1.519
 J5X  C9   C10  single  1.520  0.020  1.520
 J5X  C9   C8   single  1.569  0.020  1.569
 J5X  C13  C14  single  1.531  0.020  1.531
 J5X  C15  C8   single  1.536  0.020  1.536
 J5X  C2   C3   single  1.534  0.020  1.534
 J5X  C10  O92  single  1.457  0.020  1.457
 J5X  C10  C5   single  1.523  0.020  1.523
 J5X  C8   C14  single  1.531  0.020  1.531
 J5X  C8   C6   single  1.547  0.020  1.547
 J5X  O92  C19  single  1.335  0.020  1.335
 J5X  C5   C6   single  1.524  0.020  1.524
 J5X  C5   C4   single  1.525  0.020  1.525
 J5X  C3   C4   single  1.548  0.020  1.548
 J5X  C6   C7   single  1.542  0.020  1.542
 J5X  C19  C4   single  1.518  0.020  1.518
 J5X  C19  O91  double  1.202  0.020  1.202
 J5X  C4   C18  single  1.515  0.020  1.515
 J5X  O71  C7   deloc   1.247  0.020  1.247
 J5X  C7   O72  deloc   1.249  0.020  1.249
 J5X  C1   H1   single  0.970  0.020  1.090
 J5X  C1   H2   single  0.970  0.020  1.090
 J5X  C2   H3   single  0.970  0.020  1.090
 J5X  C2   H4   single  0.970  0.020  1.090
 J5X  C3   H5   single  0.970  0.020  1.090
 J5X  C3   H6   single  0.970  0.020  1.090
 J5X  C5   H7   single  0.970  0.020  1.090
 J5X  C6   H8   single  0.970  0.020  1.090
 J5X  C9   H9   single  0.970  0.020  1.090
 J5X  C11  H10  single  0.970  0.020  1.090
 J5X  C11  H11  single  0.970  0.020  1.090
 J5X  C12  H12  single  0.970  0.020  1.090
 J5X  C12  H13  single  0.970  0.020  1.090
 J5X  C13  H14  single  0.970  0.020  1.090
 J5X  C14  H15  single  0.970  0.020  1.090
 J5X  C14  H16  single  0.970  0.020  1.090
 J5X  C15  H17  single  0.970  0.020  1.090
 J5X  C15  H18  single  0.970  0.020  1.090
 J5X  C17  H19  single  0.930  0.020  1.080
 J5X  C17  H20  single  0.930  0.020  1.080
 J5X  C18  H21  single  0.970  0.020  1.090
 J5X  C18  H22  single  0.970  0.020  1.090
 J5X  C18  H23  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
 J5X  H2   C1   H1   106.75  3.000
 J5X  H2   C1   C10  107.45  3.000
 J5X  H1   C1   C10  111.40  3.000
 J5X  H2   C1   C2   110.44  3.000
 J5X  H1   C1   C2   110.17  3.000
 J5X  C10  C1   C2   110.53  3.000
 J5X  H4   C2   H3   105.46  3.000
 J5X  H4   C2   C3   109.25  3.000
 J5X  H3   C2   C3   109.39  3.000
 J5X  H4   C2   C1   109.46  3.000
 J5X  H3   C2   C1   109.75  3.000
 J5X  C3   C2   C1   113.24  3.000
 J5X  H6   C3   H5   106.75  3.000
 J5X  H6   C3   C4   109.72  3.000
 J5X  H5   C3   C4   106.95  3.000
 J5X  H6   C3   C2   109.40  3.000
 J5X  H5   C3   C2   110.42  3.000
 J5X  C4   C3   C2   113.38  3.000
 J5X  C19  C4   C18  113.34  3.000
 J5X  C18  C4   C5   116.82  3.000
 J5X  C19  C4   C5    99.86  3.000
 J5X  C18  C4   C3   111.73  3.000
 J5X  C19  C4   C3   106.74  3.000
 J5X  C5   C4   C3   107.29  3.000
 J5X  H7   C5   C10  111.63  3.000
 J5X  H7   C5   C6   110.17  3.000
 J5X  C10  C5   C6   104.69  3.000
 J5X  H7   C5   C4   111.92  3.000
 J5X  C6   C5   C4   117.87  3.000
 J5X  C10  C5   C4    99.81  3.000
 J5X  H8   C6   C8   106.68  3.000
 J5X  H8   C6   C7   107.05  3.000
 J5X  C8   C6   C7   113.24  3.000
 J5X  H8   C6   C5   109.77  3.000
 J5X  C7   C6   C5   115.50  3.000
 J5X  C8   C6   C5   104.29  3.000
 J5X  O72  C7   O71  126.48  3.000
 J5X  O72  C7   C6   115.90  3.000
 J5X  O71  C7   C6   117.60  3.000
 J5X  C15  C8   C14   99.90  3.000
 J5X  C14  C8   C9   110.21  3.000
 J5X  C15  C8   C9   107.91  3.000
 J5X  C14  C8   C6   115.79  3.000
 J5X  C15  C8   C6   116.75  3.000
 J5X  C9   C8   C6   106.04  3.000
 J5X  H9   C9   C11  107.24  3.000
 J5X  H9   C9   C10  105.46  3.000
 J5X  C11  C9   C10  116.62  3.000
 J5X  H9   C9   C8   108.05  3.000
 J5X  C10  C9   C8   105.86  3.000
 J5X  C11  C9   C8   113.10  3.000
 J5X  O92  C10  C9   110.93  3.000
 J5X  O92  C10  C5   102.23  3.000
 J5X  C9   C10  C5   105.99  3.000
 J5X  C5   C10  C1   111.66  3.000
 J5X  O92  C10  C1   108.03  3.000
 J5X  C9   C10  C1   117.02  3.000
 J5X  H11  C11  H10  106.25  3.000
 J5X  H11  C11  C12  109.13  3.000
 J5X  H10  C11  C12  110.08  3.000
 J5X  H11  C11  C9   109.84  3.000
 J5X  H10  C11  C9   110.40  3.000
 J5X  C12  C11  C9   111.02  3.000
 J5X  H13  C12  H12  106.48  3.000
 J5X  H13  C12  C13  109.42  3.000
 J5X  H12  C12  C13  109.49  3.000
 J5X  H13  C12  C11  110.60  3.000
 J5X  H12  C12  C11  108.95  3.000
 J5X  C13  C12  C11  111.76  3.000
 J5X  H14  C13  C16  111.00  3.000
 J5X  H14  C13  C14  113.65  3.000
 J5X  C16  C13  C14  102.08  3.000
 J5X  H14  C13  C12  109.47  3.000
 J5X  C14  C13  C12  109.12  3.000
 J5X  C16  C13  C12  111.36  3.000
 J5X  H16  C14  H15  107.28  3.000
 J5X  H16  C14  C13  111.74  3.000
 J5X  H15  C14  C13  113.79  3.000
 J5X  H16  C14  C8   109.53  3.000
 J5X  H15  C14  C8   113.95  3.000
 J5X  C13  C14  C8   100.52  3.000
 J5X  H18  C15  H17  107.40  3.000
 J5X  H18  C15  C16  113.30  3.000
 J5X  H17  C15  C16  109.21  3.000
 J5X  H18  C15  C8   114.06  3.000
 J5X  H17  C15  C8   110.37  3.000
 J5X  C16  C15  C8   102.43  3.000
 J5X  C17  C16  C15  126.29  3.000
 J5X  C15  C16  C13  108.27  3.000
 J5X  C17  C16  C13  125.44  3.000
 J5X  H20  C17  H19  116.62  3.000
 J5X  H20  C17  C16  121.63  3.000
 J5X  H19  C17  C16  121.75  3.000
 J5X  H23  C18  H22  107.78  3.000
 J5X  H23  C18  H21  107.78  3.000
 J5X  H22  C18  H21  107.89  3.000
 J5X  H23  C18  C4   110.12  3.000
 J5X  H22  C18  C4   111.86  3.000
 J5X  H21  C18  C4   111.24  3.000
 J5X  O92  C19  O91  121.75  3.000
 J5X  O91  C19  C4   128.85  3.000
 J5X  O92  C19  C4   109.39  3.000
 J5X  C19  O92  C10  109.75  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
 J5X  Var_01  C4   C3   C2   C1    -41.51  30.0  1
 J5X  Var_02  C10  C1   C2   C3     39.66  30.0  1
 J5X  Var_03  C10  O92  C19  C4     -0.29  30.0  3
 J5X  Var_04  C13  C16  C15  C8    -16.03  30.0  3
 J5X  Var_05  C13  C12  C11  C9     37.11  30.0  1
 J5X  Var_06  C17  C16  C15  C8    163.75  30.0  3
 J5X  Var_07  O91  C19  O92  C10   178.32  30.0  3
 J5X  Var_08  H5   C3   C2   C1     78.48  30.0  1
 J5X  Var_09  H6   C3   C2   C1   -164.32  30.0  1
 J5X  Var_10  H1   C1   C2   C3    163.21  30.0  1
 J5X  Var_11  H2   C1   C2   C3    -79.11  30.0  1
 J5X  Var_12  H3   C2   C3   C4   -164.26  30.0  1
 J5X  Var_13  H4   C2   C3   C4     80.76  30.0  1
 J5X  Var_14  H12  C12  C11  C9    158.23  30.0  1
 J5X  Var_15  H13  C12  C11  C9    -85.06  30.0  1
 J5X  Var_16  H3   C2   C1   C10   162.21  30.0  1
 J5X  Var_17  H4   C2   C1   C10   -82.50  30.0  1
 J5X  Var_18  H10  C11  C12  C13   159.66  30.0  1
 J5X  Var_19  H11  C11  C12  C13   -84.09  30.0  1
 J5X  Var_20  H17  C15  C16  C13   100.98  30.0  3
 J5X  Var_21  H18  C15  C16  C13  -139.36  30.0  3
 J5X  Var_22  H19  C17  C16  C13   178.52   0.0  2
 J5X  Var_23  H20  C17  C16  C13    -1.29   0.0  2
 J5X  Var_24  H19  C17  C16  C15    -1.22   0.0  2
 J5X  Var_25  H20  C17  C16  C15   178.96   0.0  2
 J5X  Var_26  H17  C15  C16  C17   -79.24  30.0  3
 J5X  Var_27  H18  C15  C16  C17    40.42  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
 J5X  chir_01  C4   C3   C5   C18  negativ
 J5X  chir_02  C5   C4   C6   C10  negativ
 J5X  chir_03  C6   C7   C5   C8   negativ
 J5X  chir_04  C8   C14  C6   C9   positiv
 J5X  chir_05  C9   C8   C10  C11  positiv
 J5X  chir_06  C10  C1   C9   C5   negativ
 J5X  chir_07  C13  C12  C16  C14  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
 J5X  plan-1  C6   0.020
 J5X  plan-1  C7   0.020
 J5X  plan-1  O71  0.020
 J5X  plan-1  O72  0.020
 J5X  plan-2  C4   0.020
 J5X  plan-2  C19  0.020
 J5X  plan-2  O91  0.020
 J5X  plan-2  O92  0.020
 J5X  plan-3  C13  0.020
 J5X  plan-3  C15  0.020
 J5X  plan-3  C16  0.020
 J5X  plan-3  C17  0.020
 J5X  plan-3  H19  0.020
 J5X  plan-3  H20  0.020

