# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 06:31:23 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: (2~{S})-3-dimethoxyphosphoryloxy-2-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[P](=O)(OC)OC[C@H](OC\C=C(/C)CC\C=C(/C)CCC=C(C)C)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
 C0X  C0X  '(2~{S})-3-dimethoxyphosphoryloxy-2-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoic acid'  ligand  62  28  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C0X
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
 C0X  C15  C  CH2    0  -0.185  -1.1587   2.2404  -0.4725
 C0X  C17  C  CH1    0  -0.095  -3.3938   1.5768  -0.8644
 C0X  C14  C  C1     0  -0.328   0.2050   1.6502  -0.3283
 C0X  C13  C  CH3    0  -0.720   7.6503  -2.8096   1.6342
 C0X  C12  C  CH3    0  -0.705   9.9355  -3.1103   0.6119
 C0X  C1   C  CH3    0  -0.736   0.9819   3.0480   1.6104
 C0X  C2   C  C      0   0.126   1.1454   1.9906   0.5566
 C0X  C4   C  CH2    0  -0.493   3.6378   2.2703   0.1482
 C0X  C6   C  C      0   0.113   5.7137   1.1336  -0.7925
 C0X  C7   C  CH3    0  -0.732   5.3564   1.2850  -2.2424
 C0X  C8   C  CH2    0  -0.482   6.9973   0.3977  -0.5134
 C0X  C9   C  CH2    0  -0.493   6.9207  -1.1013  -0.8473
 C0X  C24  C  CH3    0  -0.441  -7.4301  -0.3977   0.0871
 C0X  O23  O  O2     0  -0.589  -6.7429  -1.3495  -0.7339
 C0X  C3   C  CH2    0  -0.483   2.4915   1.3192   0.5280
 C0X  C5   C  C1     0  -0.269   4.9634   1.5792   0.2188
 C0X  C10  C  C1     0  -0.261   8.2248  -1.7905  -0.5887
 C0X  C11  C  C      0   0.085   8.5617  -2.5194   0.4785
 C0X  O16  O  O2     0  -0.497  -2.0973   1.1867  -0.4963
 C0X  C18  C  CH2    0  -0.197  -4.1317   0.3534  -1.3573
 C0X  O19  O  O2     0  -0.590  -4.3717  -0.5131  -0.2342
 C0X  P20  P  P      0   1.506  -5.2525  -1.8237  -0.4148
 C0X  O21  O  O2     0  -0.585  -5.2233  -2.2960   1.1067
 C0X  C22  C  CH3    0  -0.417  -5.7373  -3.5847   1.4594
 C0X  O25  O  O      0  -0.706  -4.8170  -2.8038  -1.4273
 C0X  C26  C  C      0   0.396  -4.2000   2.2756   0.2622
 C0X  O27  O  OC    -1  -0.613  -5.3426   2.6470  -0.0770
 C0X  H1   H  HCH2   0   0.215  -1.3802   2.9524   0.3267
 C0X  H2   H  HCH2   0   0.199  -1.2093   2.8034  -1.4186
 C0X  H3   H  HCH1   0   0.217  -3.3556   2.2647  -1.7258
 C0X  H4   H  H      0   0.227   0.4445   0.8771  -1.0552
 C0X  H5   H  HCH3   0   0.233   7.5913  -3.8853   1.8181
 C0X  H6   H  HCH3   0   0.236   8.0438  -2.3627   2.5508
 C0X  H7   H  HCH3   0   0.238   6.6363  -2.4391   1.4968
 C0X  H8   H  HCH3   0   0.230   9.8865  -4.1979   0.7110
 C0X  H9   H  HCH3   0   0.235  10.5702  -2.8769  -0.2428
 C0X  H10  H  HCH3   0   0.230  10.4336  -2.7416   1.5129
 C0X  H11  H  HCH3   0   0.237   1.4163   2.7154   2.5551
 C0X  H12  H  HCH3   0   0.244   1.5063   3.9656   1.3325
 C0X  H13  H  HCH3   0   0.246  -0.0569   3.3146   1.7959
 C0X  H14  H  HCH2   0   0.237   3.4440   2.6773  -0.8461
 C0X  H15  H  HCH2   0   0.236   3.6455   3.1209   0.8359
 C0X  H16  H  HCH3   0   0.240   5.0947   0.3223  -2.6883
 C0X  H17  H  HCH3   0   0.241   4.5148   1.9549  -2.4090
 C0X  H18  H  HCH3   0   0.233   6.2065   1.6686  -2.8115
 C0X  H19  H  HCH2   0   0.225   7.8151   0.8462  -1.0886
 C0X  H20  H  HCH2   0   0.234   7.2641   0.5017   0.5414
 C0X  H21  H  HCH2   0   0.235   6.1077  -1.5454  -0.2701
 C0X  H22  H  HCH2   0   0.235   6.6543  -1.2283  -1.9003
 C0X  H23  H  HCH3   0   0.237  -7.5992  -0.7911   1.0897
 C0X  H24  H  HCH3   0   0.247  -6.8829   0.5431   0.1528
 C0X  H25  H  HCH3   0   0.251  -8.3919  -0.2156  -0.3850
 C0X  H26  H  HCH2   0   0.230   2.7027   0.8950   1.5163
 C0X  H27  H  HCH2   0   0.236   2.4816   0.4838  -0.1762
 C0X  H28  H  H      0   0.221   5.3237   1.3898   1.2282
 C0X  H29  H  H      0   0.221   8.9869  -1.6338  -1.3490
 C0X  H30  H  HCH2   0   0.241  -5.0743   0.6644  -1.8094
 C0X  H31  H  HCH2   0   0.250  -3.5419  -0.1761  -2.1097
 C0X  H32  H  HCH3   0   0.238  -6.7965  -3.6737   1.2152
 C0X  H33  H  HCH3   0   0.243  -5.1847  -4.3803   0.9608
 C0X  H34  H  HCH3   0   0.257  -5.6167  -3.6853   2.5342
 C0X  O28  O  O      0  -0.583  -3.6592   2.4054   1.3703

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
 C0X  O25  P20  double  1.475  0.020  1.475
 C0X  C24  O23  single  1.433  0.020  1.433
 C0X  P20  O21  single  1.593  0.020  1.593
 C0X  P20  O23  single  1.596  0.020  1.596
 C0X  P20  O19  single  1.589  0.020  1.589
 C0X  O21  C22  single  1.432  0.020  1.432
 C0X  O19  C18  single  1.439  0.020  1.439
 C0X  C18  C17  single  1.511  0.020  1.511
 C0X  O28  C26  deloc   1.240  0.020  1.240
 C0X  C17  C26  single  1.552  0.020  1.552
 C0X  C17  O16  single  1.403  0.020  1.403
 C0X  C26  O27  deloc   1.248  0.020  1.248
 C0X  O16  C15  single  1.411  0.020  1.411
 C0X  C14  C15  single  1.493  0.020  1.493
 C0X  C14  C2   double  1.335  0.020  1.335
 C0X  C3   C2   single  1.504  0.020  1.504
 C0X  C3   C4   single  1.537  0.020  1.537
 C0X  C2   C1   single  1.502  0.020  1.502
 C0X  C4   C5   single  1.497  0.020  1.497
 C0X  C5   C6   double  1.336  0.020  1.336
 C0X  C8   C6   single  1.506  0.020  1.506
 C0X  C8   C9   single  1.538  0.020  1.538
 C0X  C6   C7   single  1.501  0.020  1.501
 C0X  C10  C9   single  1.498  0.020  1.498
 C0X  C10  C11  double  1.336  0.020  1.336
 C0X  C13  C11  single  1.500  0.020  1.500
 C0X  C11  C12  single  1.501  0.020  1.501
 C0X  C15  H1   single  0.970  0.020  1.090
 C0X  C15  H2   single  0.970  0.020  1.090
 C0X  C17  H3   single  0.970  0.020  1.090
 C0X  C14  H4   single  0.930  0.020  1.080
 C0X  C13  H5   single  0.970  0.020  1.090
 C0X  C13  H6   single  0.970  0.020  1.090
 C0X  C13  H7   single  0.970  0.020  1.090
 C0X  C12  H8   single  0.970  0.020  1.090
 C0X  C12  H9   single  0.970  0.020  1.090
 C0X  C12  H10  single  0.970  0.020  1.090
 C0X  C1   H11  single  0.970  0.020  1.090
 C0X  C1   H12  single  0.970  0.020  1.090
 C0X  C1   H13  single  0.970  0.020  1.090
 C0X  C4   H14  single  0.970  0.020  1.090
 C0X  C4   H15  single  0.970  0.020  1.090
 C0X  C7   H16  single  0.970  0.020  1.090
 C0X  C7   H17  single  0.970  0.020  1.090
 C0X  C7   H18  single  0.970  0.020  1.090
 C0X  C8   H19  single  0.970  0.020  1.090
 C0X  C8   H20  single  0.970  0.020  1.090
 C0X  C9   H21  single  0.970  0.020  1.090
 C0X  C9   H22  single  0.970  0.020  1.090
 C0X  C24  H23  single  0.970  0.020  1.090
 C0X  C24  H24  single  0.970  0.020  1.090
 C0X  C24  H25  single  0.970  0.020  1.090
 C0X  C3   H26  single  0.970  0.020  1.090
 C0X  C3   H27  single  0.970  0.020  1.090
 C0X  C5   H28  single  0.930  0.020  1.080
 C0X  C10  H29  single  0.930  0.020  1.080
 C0X  C18  H30  single  0.970  0.020  1.090
 C0X  C18  H31  single  0.970  0.020  1.090
 C0X  C22  H32  single  0.970  0.020  1.090
 C0X  C22  H33  single  0.970  0.020  1.090
 C0X  C22  H34  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
 C0X  H2   C15  H1   106.60  3.000
 C0X  H2   C15  O16  109.66  3.000
 C0X  H1   C15  O16  111.34  3.000
 C0X  H2   C15  C14  109.08  3.000
 C0X  H1   C15  C14  111.84  3.000
 C0X  O16  C15  C14  108.30  3.000
 C0X  H3   C17  C26  107.71  3.000
 C0X  H3   C17  C18  105.49  3.000
 C0X  C26  C17  C18  110.35  3.000
 C0X  H3   C17  O16  110.26  3.000
 C0X  C26  C17  O16  114.51  3.000
 C0X  C18  C17  O16  108.16  3.000
 C0X  H4   C14  C2   117.97  3.000
 C0X  H4   C14  C15  114.68  3.000
 C0X  C2   C14  C15  127.34  3.000
 C0X  H7   C13  H6   107.58  3.000
 C0X  H7   C13  H5   107.82  3.000
 C0X  H6   C13  H5   106.30  3.000
 C0X  H7   C13  C11  113.77  3.000
 C0X  H6   C13  C11  110.38  3.000
 C0X  H5   C13  C11  110.66  3.000
 C0X  H10  C12  H9   107.97  3.000
 C0X  H10  C12  H8   106.33  3.000
 C0X  H9   C12  H8   108.07  3.000
 C0X  H10  C12  C11  110.94  3.000
 C0X  H9   C12  C11  112.27  3.000
 C0X  H8   C12  C11  111.01  3.000
 C0X  H13  C1   H12  107.20  3.000
 C0X  H13  C1   H11  107.88  3.000
 C0X  H12  C1   H11  106.55  3.000
 C0X  H13  C1   C2   113.33  3.000
 C0X  H12  C1   C2   111.13  3.000
 C0X  H11  C1   C2   110.45  3.000
 C0X  C3   C2   C1   115.15  3.000
 C0X  C1   C2   C14  124.60  3.000
 C0X  C3   C2   C14  120.24  3.000
 C0X  H15  C4   H14  106.50  3.000
 C0X  H15  C4   C5   108.86  3.000
 C0X  H14  C4   C5   111.86  3.000
 C0X  H15  C4   C3   109.34  3.000
 C0X  H14  C4   C3   108.86  3.000
 C0X  C5   C4   C3   111.29  3.000
 C0X  C5   C6   C8   120.10  3.000
 C0X  C8   C6   C7   115.56  3.000
 C0X  C5   C6   C7   124.33  3.000
 C0X  H18  C7   H17  107.81  3.000
 C0X  H18  C7   H16  106.44  3.000
 C0X  H17  C7   H16  107.13  3.000
 C0X  H18  C7   C6   110.69  3.000
 C0X  H17  C7   C6   113.21  3.000
 C0X  H16  C7   C6   111.24  3.000
 C0X  H20  C8   H19  106.59  3.000
 C0X  H20  C8   C9   108.33  3.000
 C0X  H19  C8   C9   108.79  3.000
 C0X  H20  C8   C6   109.91  3.000
 C0X  H19  C8   C6   109.81  3.000
 C0X  C9   C8   C6   113.19  3.000
 C0X  H22  C9   H21  106.29  3.000
 C0X  H22  C9   C10  108.97  3.000
 C0X  H21  C9   C10  111.72  3.000
 C0X  H22  C9   C8   109.54  3.000
 C0X  H21  C9   C8   108.59  3.000
 C0X  C10  C9   C8   111.58  3.000
 C0X  H25  C24  H24  109.01  3.000
 C0X  H25  C24  H23  108.83  3.000
 C0X  H24  C24  H23  109.49  3.000
 C0X  H25  C24  O23  106.67  3.000
 C0X  H24  C24  O23  111.54  3.000
 C0X  H23  C24  O23  111.20  3.000
 C0X  P20  O23  C24  122.05  3.000
 C0X  H27  C3   H26  106.68  3.000
 C0X  H27  C3   C4   108.70  3.000
 C0X  H26  C3   C4   108.57  3.000
 C0X  H27  C3   C2   110.21  3.000
 C0X  H26  C3   C2   109.15  3.000
 C0X  C4   C3   C2   113.31  3.000
 C0X  H28  C5   C6   117.27  3.000
 C0X  H28  C5   C4   114.66  3.000
 C0X  C6   C5   C4   128.02  3.000
 C0X  H29  C10  C11  117.42  3.000
 C0X  H29  C10  C9   115.03  3.000
 C0X  C11  C10  C9   127.50  3.000
 C0X  C10  C11  C12  121.10  3.000
 C0X  C12  C11  C13  114.29  3.000
 C0X  C10  C11  C13  124.61  3.000
 C0X  C17  O16  C15  114.29  3.000
 C0X  H31  C18  H30  108.62  3.000
 C0X  H31  C18  O19  109.62  3.000
 C0X  H30  C18  O19  110.56  3.000
 C0X  H31  C18  C17  110.68  3.000
 C0X  H30  C18  C17  109.04  3.000
 C0X  O19  C18  C17  108.33  3.000
 C0X  P20  O19  C18  120.03  3.000
 C0X  O25  P20  O21  116.94  3.000
 C0X  O21  P20  O19   97.22  3.000
 C0X  O25  P20  O19  117.54  3.000
 C0X  O19  P20  O23  107.17  3.000
 C0X  O21  P20  O23  107.22  3.000
 C0X  O25  P20  O23  109.63  3.000
 C0X  C22  O21  P20  119.70  3.000
 C0X  H34  C22  H33  109.20  3.000
 C0X  H34  C22  H32  108.77  3.000
 C0X  H33  C22  H32  109.30  3.000
 C0X  H34  C22  O21  106.70  3.000
 C0X  H33  C22  O21  111.26  3.000
 C0X  H32  C22  O21  111.53  3.000
 C0X  O27  C26  O28  127.66  3.000
 C0X  O27  C26  C17  114.34  3.000
 C0X  O28  C26  C17  118.00  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
 C0X  Var_01  C3   C2   C14  C15  -177.80   0.0  2
 C0X  Var_02  C9   C10  C11  C13     1.37   0.0  2
 C0X  Var_03  C8   C6   C5   C4   -176.98   0.0  2
 C0X  Var_04  C14  C15  O16  C17  -169.24  30.0  3
 C0X  Var_05  C4   C3   C2   C14   113.77  30.0  2
 C0X  Var_06  O16  C15  C14  C2   -129.42  30.0  3
 C0X  Var_07  C5   C4   C3   C2    176.36  30.0  3
 C0X  Var_08  C3   C4   C5   C6    103.86  30.0  2
 C0X  Var_09  C10  C9   C8   C6    178.58  30.0  3
 C0X  Var_10  C9   C8   C6   C7    -69.30  30.0  2
 C0X  Var_11  C11  C10  C9   C8     99.52  30.0  1
 C0X  Var_12  O25  P20  O23  C24   179.87  30.0  2
 C0X  Var_13  H11  C1   C2   C14   138.50  30.0  3
 C0X  Var_14  H8   C12  C11  C13    59.10  30.0  3
 C0X  Var_15  H5   C13  C11  C12   -54.27  30.0  3
 C0X  Var_16  H16  C7   C6   C8     68.58  30.0  3
 C0X  Var_17  H32  C22  O21  P20   -61.20  30.0  3
 C0X  Var_18  H23  C24  O23  P20   -64.66  30.0  3
 C0X  Var_19  H30  C18  O19  P20    54.86  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
 C0X  chir_01  C17  C18  C26  O16  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
 C0X  plan-1  C17  0.020
 C0X  plan-1  C26  0.020
 C0X  plan-1  O27  0.020
 C0X  plan-1  O28  0.020
 C0X  plan-2  C15  0.020
 C0X  plan-2  C14  0.020
 C0X  plan-2  C1   0.020
 C0X  plan-2  C2   0.020
 C0X  plan-2  C3   0.020
 C0X  plan-2  H4   0.020
 C0X  plan-3  C4   0.020
 C0X  plan-3  C6   0.020
 C0X  plan-3  C7   0.020
 C0X  plan-3  C8   0.020
 C0X  plan-3  C5   0.020
 C0X  plan-3  H28  0.020
 C0X  plan-4  C13  0.020
 C0X  plan-4  C12  0.020
 C0X  plan-4  C9   0.020
 C0X  plan-4  C10  0.020
 C0X  plan-4  C11  0.020
 C0X  plan-4  H29  0.020

