# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:19:21 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: [(~{E})-3-methylhex-2-enyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(/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
 9GB  9GB  '[(~{E})-3-methylhex-2-enyl] dihydrogen phosphate'  ligand  27  12  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9GB
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
 9GB  C2   C  C1    0  -0.328   1.0208  -0.2704  -0.8545
 9GB  C4   C  CH3   0  -0.734   2.1273  -1.6602   0.9266
 9GB  C5   C  CH2   0  -0.479   3.4553  -0.0748  -0.5419
 9GB  C6   C  CH2   0  -0.429   4.1359   0.6832   0.5994
 9GB  O3A  O  O     0  -0.715  -3.4549  -0.5348  -1.1798
 9GB  PA   P  P     0   1.458  -2.7577   0.1189  -0.0559
 9GB  O1A  O  OH1   0  -0.733  -3.1197   1.6396   0.2607
 9GB  O2A  O  OH1   0  -0.743  -2.9973  -0.7261   1.2811
 9GB  O1   O  O2    0  -0.589  -1.1842   0.3246  -0.2075
 9GB  C1   C  CH2   0  -0.232  -0.3666  -0.7763  -0.6670
 9GB  C3   C  C     0   0.143   2.1121  -0.6518  -0.1840
 9GB  C7   C  CH3   0  -0.661   5.4846   1.2494   0.1783
 9GB  H1   H  H     0   0.242   1.1343   0.4674  -1.6438
 9GB  H2   H  HCH3  0   0.249   2.3897  -1.1886   1.8758
 9GB  H3   H  HCH3  0   0.246   1.1782  -2.1713   1.0678
 9GB  H4   H  HCH3  0   0.243   2.8894  -2.4190   0.7366
 9GB  H5   H  HCH2  0   0.233   3.3553   0.5910  -1.4032
 9GB  H6   H  HCH2  0   0.229   4.1126  -0.8946  -0.8564
 9GB  H7   H  HCH2  0   0.222   3.4834   1.4942   0.9352
 9GB  H8   H  HCH2  0   0.224   4.2717   0.0217   1.4583
 9GB  H9   H  HOH1  0   0.503  -4.0681   1.8120   0.3336
 9GB  H10  H  HOH1  0   0.495  -2.6128  -0.3524   2.0855
 9GB  H11  H  HCH2  0   0.247  -0.7640  -1.1405  -1.6176
 9GB  H12  H  HCH2  0   0.244  -0.4179  -1.5952   0.0519
 9GB  H13  H  HCH3  0   0.219   5.3757   1.9569  -0.6452
 9GB  H14  H  HCH3  0   0.230   5.9720   1.7719   1.0018
 9GB  H15  H  HCH3  0   0.218   6.1571   0.4567  -0.1554

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
 9GB  C6   C5   single  1.530  0.020  1.530
 9GB  C6   C7   single  1.522  0.020  1.522
 9GB  C5   C3   single  1.505  0.020  1.505
 9GB  C3   C4   single  1.500  0.020  1.500
 9GB  C3   C2   double  1.336  0.020  1.336
 9GB  C2   C1   single  1.489  0.020  1.489
 9GB  O1   C1   single  1.446  0.020  1.446
 9GB  O1   PA   single  1.594  0.020  1.594
 9GB  O3A  PA   double  1.475  0.020  1.475
 9GB  PA   O1A  single  1.595  0.020  1.595
 9GB  PA   O2A  single  1.600  0.020  1.600
 9GB  C2   H1   single  0.930  0.020  1.080
 9GB  C4   H2   single  0.970  0.020  1.090
 9GB  C4   H3   single  0.970  0.020  1.090
 9GB  C4   H4   single  0.970  0.020  1.090
 9GB  C5   H5   single  0.970  0.020  1.090
 9GB  C5   H6   single  0.970  0.020  1.090
 9GB  C6   H7   single  0.970  0.020  1.090
 9GB  C6   H8   single  0.970  0.020  1.090
 9GB  O1A  H9   single  0.850  0.020  0.980
 9GB  O2A  H10  single  0.850  0.020  0.980
 9GB  C1   H11  single  0.970  0.020  1.090
 9GB  C1   H12  single  0.970  0.020  1.090
 9GB  C7   H13  single  0.970  0.020  1.090
 9GB  C7   H14  single  0.970  0.020  1.090
 9GB  C7   H15  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
 9GB  H1   C2   C3   118.23  3.000
 9GB  H1   C2   C1   114.81  3.000
 9GB  C3   C2   C1   126.94  3.000
 9GB  H4   C4   H3   107.77  3.000
 9GB  H4   C4   H2   106.48  3.000
 9GB  H3   C4   H2   107.46  3.000
 9GB  H4   C4   C3   110.20  3.000
 9GB  H3   C4   C3   113.78  3.000
 9GB  H2   C4   C3   110.83  3.000
 9GB  H6   C5   H5   106.51  3.000
 9GB  H6   C5   C3   108.45  3.000
 9GB  H5   C5   C3   109.83  3.000
 9GB  H6   C5   C6   108.52  3.000
 9GB  H5   C5   C6   109.07  3.000
 9GB  C3   C5   C6   114.18  3.000
 9GB  H8   C6   H7   106.36  3.000
 9GB  H8   C6   C7   109.43  3.000
 9GB  H7   C6   C7   109.74  3.000
 9GB  H8   C6   C5   109.99  3.000
 9GB  H7   C6   C5   109.33  3.000
 9GB  C7   C6   C5   111.85  3.000
 9GB  O1   PA   O2A  107.19  3.000
 9GB  O2A  PA   O1A  107.68  3.000
 9GB  O1   PA   O1A   96.89  3.000
 9GB  O2A  PA   O3A  109.38  3.000
 9GB  O1A  PA   O3A  117.80  3.000
 9GB  O1   PA   O3A  116.82  3.000
 9GB  H9   O1A  PA   114.06  3.000
 9GB  H10  O2A  PA   115.58  3.000
 9GB  C1   O1   PA   119.34  3.000
 9GB  H12  C1   H11  107.81  3.000
 9GB  H12  C1   O1   109.60  3.000
 9GB  H11  C1   O1   108.94  3.000
 9GB  H12  C1   C2   112.45  3.000
 9GB  H11  C1   C2   110.04  3.000
 9GB  O1   C1   C2   107.96  3.000
 9GB  C5   C3   C4   115.13  3.000
 9GB  C4   C3   C2   124.86  3.000
 9GB  C5   C3   C2   120.00  3.000
 9GB  H15  C7   H14  107.67  3.000
 9GB  H15  C7   H13  107.56  3.000
 9GB  H14  C7   H13  107.69  3.000
 9GB  H15  C7   C6   111.11  3.000
 9GB  H14  C7   C6   111.43  3.000
 9GB  H13  C7   C6   111.20  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
 9GB  Var_01  C1   C2  C3  C4    -1.53   0.0  2
 9GB  Var_02  C6   C5  C3  C2   119.70  30.0  1
 9GB  Var_03  C3   C2  C1  O1   116.08  30.0  1
 9GB  Var_04  C7   C6  C5  C3  -179.71  30.0  1
 9GB  Var_05  H2   C4  C3  C2  -113.50  30.0  3
 9GB  Var_06  H13  C7  C6  C5    60.91  30.0  3
 9GB  Var_07  H11  C1  O1  PA    54.55  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
 9GB  plan-1  C2  0.020
 9GB  plan-1  C4  0.020
 9GB  plan-1  C5  0.020
 9GB  plan-1  C1  0.020
 9GB  plan-1  C3  0.020
 9GB  plan-1  H1  0.020

