# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Nov 22 18:02:06 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: (2E)-3-methylhept-2-en-1-yl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC(/C)=C/CO[P](O)(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
 WOG  WOG  "(2E)-3-methylhept-2-en-1-yl dihydrogen phosphate"  ligand  30  13  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WOG
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
 WOG  C01  C  CH3   0  -0.731  -17.5051  -11.2912   8.6403
 WOG  C02  C  C     0   0.142  -18.5490  -11.7246   7.6564
 WOG  C03  C  CH2   0  -0.491  -18.7298  -13.2118   7.5184
 WOG  C04  C  CH2   0  -0.435  -19.1277  -13.9758   8.7861
 WOG  C05  C  CH2   0  -0.421  -20.5108  -13.6432   9.3459
 WOG  C06  C  CH3   0  -0.665  -20.5771  -12.3810  10.1976
 WOG  C08  C  C1    0  -0.310  -19.2547  -10.8896   6.8868
 WOG  C09  C  CH2   0  -0.260  -19.1433   -9.4003   6.8834
 WOG  O10  O  O2    0  -0.581  -18.0986   -8.9348   5.9947
 WOG  O12  O  OH1   0  -0.737  -19.0331   -7.2918   4.4012
 WOG  O13  O  O     0  -0.704  -19.1176   -9.8194   3.7538
 WOG  O14  O  OH1   0  -0.731  -16.8989   -8.4482   3.8903
 WOG  P11  P  P     0   1.437  -18.3697   -8.7454   4.4380
 WOG  H1   H  HCH3  0   0.244  -16.5529  -11.7746   8.4088
 WOG  H2   H  HCH3  0   0.245  -17.3348  -10.2172   8.6547
 WOG  H3   H  HCH3  0   0.248  -17.7694  -11.5992   9.6536
 WOG  H4   H  HCH2  0   0.233  -19.4681  -13.4178   6.7386
 WOG  H5   H  HCH2  0   0.237  -17.7810  -13.6299   7.1628
 WOG  H6   H  HCH2  0   0.232  -19.1017  -15.0382   8.5308
 WOG  H7   H  HCH2  0   0.218  -18.3717  -13.8427   9.5659
 WOG  H8   H  HCH2  0   0.211  -21.2253  -13.5691   8.5197
 WOG  H9   H  HCH2  0   0.220  -20.8476  -14.4863   9.9547
 WOG  H10  H  HCH3  0   0.226  -21.5780  -12.2420  10.6089
 WOG  H11  H  HCH3  0   0.214  -19.8841  -12.4409  11.0394
 WOG  H12  H  HCH3  0   0.224  -20.3305  -11.4855   9.6284
 WOG  H13  H  H     0   0.238  -19.9652  -11.3167   6.1869
 WOG  H14  H  HCH2  0   0.255  -18.8745   -9.0059   7.8617
 WOG  H15  H  HCH2  0   0.249  -20.0988   -8.9472   6.6084
 WOG  H16  H  HOH1  0   0.496  -19.5439   -7.1085   3.6015
 WOG  H17  H  HOH1  0   0.496  -16.3957   -9.2421   3.6637

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
 WOG  O13  P11  double  1.477  0.020  1.477
 WOG  O14  P11  single  1.597  0.020  1.597
 WOG  P11  O12  single  1.598  0.020  1.598
 WOG  P11  O10  single  1.591  0.020  1.591
 WOG  O10  C09  single  1.448  0.020  1.448
 WOG  C09  C08  single  1.493  0.020  1.493
 WOG  C08  C02  double  1.337  0.020  1.337
 WOG  C02  C03  single  1.504  0.020  1.504
 WOG  C02  C01  single  1.499  0.020  1.499
 WOG  C03  C04  single  1.533  0.020  1.533
 WOG  C04  C05  single  1.529  0.020  1.529
 WOG  C05  C06  single  1.524  0.020  1.524
 WOG  C01  H1   single  0.970  0.020  1.090
 WOG  C01  H2   single  0.970  0.020  1.090
 WOG  C01  H3   single  0.970  0.020  1.090
 WOG  C03  H4   single  0.970  0.020  1.090
 WOG  C03  H5   single  0.970  0.020  1.090
 WOG  C04  H6   single  0.970  0.020  1.090
 WOG  C04  H7   single  0.970  0.020  1.090
 WOG  C05  H8   single  0.970  0.020  1.090
 WOG  C05  H9   single  0.970  0.020  1.090
 WOG  C06  H10  single  0.970  0.020  1.090
 WOG  C06  H11  single  0.970  0.020  1.090
 WOG  C06  H12  single  0.970  0.020  1.090
 WOG  C08  H13  single  0.930  0.020  1.080
 WOG  C09  H14  single  0.970  0.020  1.090
 WOG  C09  H15  single  0.970  0.020  1.090
 WOG  O12  H16  single  0.850  0.020  0.980
 WOG  O14  H17  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
 WOG  H3   C01  H2   107.72  3.000
 WOG  H3   C01  H1   106.43  3.000
 WOG  H2   C01  H1   107.66  3.000
 WOG  H3   C01  C02  111.05  3.000
 WOG  H2   C01  C02  113.79  3.000
 WOG  H1   C01  C02  109.87  3.000
 WOG  C08  C02  C03  120.08  3.000
 WOG  C03  C02  C01  115.46  3.000
 WOG  C08  C02  C01  124.40  3.000
 WOG  H5   C03  H4   106.33  3.000
 WOG  H5   C03  C04  107.63  3.000
 WOG  H4   C03  C04  108.70  3.000
 WOG  H5   C03  C02  107.63  3.000
 WOG  H4   C03  C02  109.44  3.000
 WOG  C04  C03  C02  116.62  3.000
 WOG  H7   C04  H6   105.56  3.000
 WOG  H7   C04  C05  109.73  3.000
 WOG  H6   C04  C05  108.58  3.000
 WOG  H7   C04  C03  110.45  3.000
 WOG  H6   C04  C03  106.57  3.000
 WOG  C05  C04  C03  115.42  3.000
 WOG  H9   C05  H8   105.75  3.000
 WOG  H9   C05  C06  108.31  3.000
 WOG  H8   C05  C06  109.71  3.000
 WOG  H9   C05  C04  108.35  3.000
 WOG  H8   C05  C04  109.20  3.000
 WOG  C06  C05  C04  115.10  3.000
 WOG  H12  C06  H11  107.71  3.000
 WOG  H12  C06  H10  107.45  3.000
 WOG  H11  C06  H10  107.38  3.000
 WOG  H12  C06  C05  112.27  3.000
 WOG  H11  C06  C05  110.96  3.000
 WOG  H10  C06  C05  110.86  3.000
 WOG  H13  C08  C09  116.10  3.000
 WOG  H13  C08  C02  118.10  3.000
 WOG  C09  C08  C02  125.79  3.000
 WOG  H15  C09  H14  106.97  3.000
 WOG  H15  C09  O10  110.06  3.000
 WOG  H14  C09  O10  104.88  3.000
 WOG  H15  C09  C08  110.42  3.000
 WOG  H14  C09  C08  112.19  3.000
 WOG  O10  C09  C08  112.07  3.000
 WOG  P11  O10  C09  121.04  3.000
 WOG  H16  O12  P11  114.26  3.000
 WOG  H17  O14  P11  114.01  3.000
 WOG  O14  P11  O13  116.28  3.000
 WOG  O14  P11  O12  101.84  3.000
 WOG  O13  P11  O12  116.14  3.000
 WOG  O12  P11  O10  101.62  3.000
 WOG  O14  P11  O10  101.58  3.000
 WOG  O13  P11  O10  116.93  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
 WOG  Var_01  C09  C08  C02  C01    -0.85   0.0  2
 WOG  Var_02  C09  C08  C02  C03  -177.77   0.0  2
 WOG  Var_03  C04  C03  C02  C01    59.42  30.0  3
 WOG  Var_04  O10  C09  C08  C02    86.45  30.0  1
 WOG  Var_05  C05  C04  C03  C02    65.69  30.0  3
 WOG  Var_06  C06  C05  C04  C03   -81.46  30.0  3
 WOG  Var_07  C08  C02  C03  C04  -123.39  30.0  1
 WOG  Var_08  P11  O10  C09  C08    83.82  30.0  1
 WOG  Var_09  O13  P11  O10  C09   -44.13  30.0  3
 WOG  Var_10  O14  P11  O10  C09  -171.80  30.0  3
 WOG  Var_11  O12  P11  O10  C09    83.37  30.0  3
 WOG  Var_12  H13  C08  C02  C01   178.19   0.0  2
 WOG  Var_13  H13  C08  C02  C03     1.27   0.0  2
 WOG  Var_14  H4   C03  C02  C01  -176.72  30.0  3
 WOG  Var_15  H5   C03  C02  C01   -61.56  30.0  3
 WOG  Var_16  H14  C09  C08  C02   -31.24  30.0  1
 WOG  Var_17  H15  C09  C08  C02  -150.46  30.0  1
 WOG  Var_18  H6   C04  C03  C02  -173.68  30.0  3
 WOG  Var_19  H7   C04  C03  C02   -59.49  30.0  3
 WOG  Var_20  H1   C01  C02  C03    54.08  30.0  3
 WOG  Var_21  H2   C01  C02  C03   174.86  30.0  3
 WOG  Var_22  H3   C01  C02  C03   -63.40  30.0  3
 WOG  Var_23  H8   C05  C04  C03    42.42  30.0  3
 WOG  Var_24  H9   C05  C04  C03   157.15  30.0  3
 WOG  Var_25  H10  C06  C05  C04  -176.63  30.0  3
 WOG  Var_26  H11  C06  C05  C04   -57.40  30.0  3
 WOG  Var_27  H12  C06  C05  C04    63.19  30.0  3
 WOG  Var_28  H4   C03  C04  C05   -58.55  30.0  1
 WOG  Var_29  H5   C03  C04  C05  -173.32  30.0  1
 WOG  Var_30  H6   C04  C05  C06   159.01  30.0  1
 WOG  Var_31  H7   C04  C05  C06    44.09  30.0  1
 WOG  Var_32  H4   C03  C02  C08     0.47  30.0  3
 WOG  Var_33  H5   C03  C02  C08   115.62  30.0  3
 WOG  Var_34  H1   C01  C02  C08  -122.97  30.0  3
 WOG  Var_35  H2   C01  C02  C08    -2.19  30.0  3
 WOG  Var_36  H3   C01  C02  C08   119.55  30.0  3
 WOG  Var_37  H13  C08  C09  O10   -92.60  30.0  3
 WOG  Var_38  H14  C09  O10  P11  -154.22  30.0  3
 WOG  Var_39  H15  C09  O10  P11   -39.47  30.0  3

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
 WOG  plan-1  C01  0.020
 WOG  plan-1  C02  0.020
 WOG  plan-1  C03  0.020
 WOG  plan-1  C08  0.020
 WOG  plan-1  C09  0.020
 WOG  plan-1  H13  0.020

