# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 16:10:55 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: [(2~{Z})-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCC\C(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
 HZZ  HZZ  '[(2~{Z})-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate'  ligand  34  15  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HZZ
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
 HZZ  C06  C  CH2   0  -0.240   1.3516  -1.2965   0.8339
 HZZ  C07  C  C1    0  -0.315   0.4618  -2.3710   0.3151
 HZZ  C08  C  C     0   0.143  -0.8729  -2.3231   0.2864
 HZZ  C09  C  CH2   0  -0.522  -1.6780  -1.1338   0.7403
 HZZ  C10  C  CH3   0  -0.718  -1.6718  -3.4600  -0.2729
 HZZ  C11  C  CH2   0  -0.491  -1.8097  -0.0851  -0.3779
 HZZ  C12  C  C1    0  -0.262  -2.6100   1.1025   0.0585
 HZZ  C13  C  C     0   0.088  -3.8892   1.3653  -0.2203
 HZZ  C14  C  CH3   0  -0.706  -4.5602   2.5970   0.3142
 HZZ  C15  C  CH3   0  -0.719  -4.7703   0.4939  -1.0648
 HZZ  O01  O  OH1   0  -0.745   1.5854   1.8806   0.2338
 HZZ  O03  O  OH1   0  -0.732   3.2122   0.9770  -1.5507
 HZZ  O04  O  O     0  -0.712   3.7027   0.7879   1.0283
 HZZ  O05  O  O2    0  -0.588   1.9341  -0.6067  -0.3006
 HZZ  P02  P  P     0   1.454   2.7021   0.7674  -0.0548
 HZZ  H1   H  HCH2  0   0.241   0.8046  -0.5874   1.4582
 HZZ  H2   H  HCH2  0   0.257   2.1593  -1.7197   1.4339
 HZZ  H3   H  H     0   0.243   0.9614  -3.2519  -0.0767
 HZZ  H4   H  HCH2  0   0.250  -2.6784  -1.4605   1.0351
 HZZ  H5   H  HCH2  0   0.248  -1.2403  -0.6630   1.6236
 HZZ  H6   H  HCH3  0   0.244  -2.2978  -3.9097   0.5015
 HZZ  H7   H  HCH3  0   0.238  -2.3504  -3.1104  -1.0549
 HZZ  H8   H  HCH3  0   0.242  -1.0411  -4.2411  -0.6956
 HZZ  H9   H  HCH2  0   0.229  -0.8064   0.2394  -0.6668
 HZZ  H10  H  HCH2  0   0.241  -2.2373  -0.5531  -1.2671
 HZZ  H11  H  H     0   0.223  -2.0809   1.8028   0.7011
 HZZ  H12  H  HCH3  0   0.231  -4.9557   3.2110  -0.4992
 HZZ  H13  H  HCH3  0   0.232  -5.4141   2.3347   0.9444
 HZZ  H14  H  HCH3  0   0.236  -3.8808   3.2121   0.9036
 HZZ  H15  H  HCH3  0   0.236  -4.2911  -0.4282  -1.3870
 HZZ  H16  H  HCH3  0   0.237  -5.6751   0.2225  -0.5155
 HZZ  H17  H  HCH3  0   0.237  -5.1023   1.0295  -1.9579
 HZZ  H18  H  HOH1  0   0.493   0.9528   2.0371  -0.4795
 HZZ  H19  H  HOH1  0   0.504   3.8070   1.7311  -1.6619

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
 HZZ  C10  C08  single  1.498  0.020  1.498
 HZZ  C08  C07  double  1.336  0.020  1.336
 HZZ  C08  C09  single  1.506  0.020  1.506
 HZZ  C12  C11  single  1.497  0.020  1.497
 HZZ  C12  C13  double  1.335  0.020  1.335
 HZZ  C11  C09  single  1.539  0.020  1.539
 HZZ  C07  C06  single  1.488  0.020  1.488
 HZZ  C14  C13  single  1.501  0.020  1.501
 HZZ  C13  C15  single  1.500  0.020  1.500
 HZZ  C06  O05  single  1.450  0.020  1.450
 HZZ  O05  P02  single  1.593  0.020  1.593
 HZZ  O04  P02  double  1.475  0.020  1.475
 HZZ  P02  O03  single  1.594  0.020  1.594
 HZZ  P02  O01  single  1.603  0.020  1.603
 HZZ  C06  H1   single  0.970  0.020  1.090
 HZZ  C06  H2   single  0.970  0.020  1.090
 HZZ  C07  H3   single  0.930  0.020  1.080
 HZZ  C09  H4   single  0.970  0.020  1.090
 HZZ  C09  H5   single  0.970  0.020  1.090
 HZZ  C10  H6   single  0.970  0.020  1.090
 HZZ  C10  H7   single  0.970  0.020  1.090
 HZZ  C10  H8   single  0.970  0.020  1.090
 HZZ  C11  H9   single  0.970  0.020  1.090
 HZZ  C11  H10  single  0.970  0.020  1.090
 HZZ  C12  H11  single  0.930  0.020  1.080
 HZZ  C14  H12  single  0.970  0.020  1.090
 HZZ  C14  H13  single  0.970  0.020  1.090
 HZZ  C14  H14  single  0.970  0.020  1.090
 HZZ  C15  H15  single  0.970  0.020  1.090
 HZZ  C15  H16  single  0.970  0.020  1.090
 HZZ  C15  H17  single  0.970  0.020  1.090
 HZZ  O01  H18  single  0.850  0.020  0.980
 HZZ  O03  H19  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
 HZZ  H2   C06  H1   107.95  3.000
 HZZ  H2   C06  O05  108.50  3.000
 HZZ  H1   C06  O05  109.86  3.000
 HZZ  H2   C06  C07  110.74  3.000
 HZZ  H1   C06  C07  111.63  3.000
 HZZ  O05  C06  C07  108.12  3.000
 HZZ  H3   C07  C08  118.75  3.000
 HZZ  H3   C07  C06  115.87  3.000
 HZZ  C08  C07  C06  125.37  3.000
 HZZ  C10  C08  C09  115.26  3.000
 HZZ  C09  C08  C07  123.77  3.000
 HZZ  C10  C08  C07  120.91  3.000
 HZZ  H5   C09  H4   106.11  3.000
 HZZ  H5   C09  C11  109.16  3.000
 HZZ  H4   C09  C11  108.75  3.000
 HZZ  H5   C09  C08  111.70  3.000
 HZZ  H4   C09  C08  109.54  3.000
 HZZ  C11  C09  C08  111.40  3.000
 HZZ  H8   C10  H7   108.13  3.000
 HZZ  H8   C10  H6   108.16  3.000
 HZZ  H7   C10  H6   106.44  3.000
 HZZ  H8   C10  C08  112.35  3.000
 HZZ  H7   C10  C08  110.83  3.000
 HZZ  H6   C10  C08  110.69  3.000
 HZZ  H10  C11  H9   105.75  3.000
 HZZ  H10  C11  C12  111.60  3.000
 HZZ  H9   C11  C12  109.40  3.000
 HZZ  H10  C11  C09  109.46  3.000
 HZZ  H9   C11  C09  108.41  3.000
 HZZ  C12  C11  C09  111.99  3.000
 HZZ  H11  C12  C13  117.56  3.000
 HZZ  H11  C12  C11  115.02  3.000
 HZZ  C13  C12  C11  127.39  3.000
 HZZ  C15  C13  C14  114.50  3.000
 HZZ  C15  C13  C12  124.48  3.000
 HZZ  C14  C13  C12  121.02  3.000
 HZZ  H14  C14  H13  108.10  3.000
 HZZ  H14  C14  H12  108.12  3.000
 HZZ  H13  C14  H12  106.32  3.000
 HZZ  H14  C14  C13  112.16  3.000
 HZZ  H13  C14  C13  110.95  3.000
 HZZ  H12  C14  C13  110.95  3.000
 HZZ  H17  C15  H16  106.32  3.000
 HZZ  H17  C15  H15  107.89  3.000
 HZZ  H16  C15  H15  107.64  3.000
 HZZ  H17  C15  C13  110.72  3.000
 HZZ  H16  C15  C13  110.35  3.000
 HZZ  H15  C15  C13  113.60  3.000
 HZZ  H18  O01  P02  115.83  3.000
 HZZ  H19  O03  P02  114.03  3.000
 HZZ  P02  O05  C06  118.90  3.000
 HZZ  O05  P02  O04  116.89  3.000
 HZZ  O04  P02  O03  118.05  3.000
 HZZ  O05  P02  O03   97.05  3.000
 HZZ  O03  P02  O01  107.49  3.000
 HZZ  O04  P02  O01  109.32  3.000
 HZZ  O05  P02  O01  106.91  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
 HZZ  Var_01  C10  C08  C07  C06   179.36   0.0  2
 HZZ  Var_02  C14  C13  C12  C11   178.98   0.0  2
 HZZ  Var_03  O04  P02  O05  C06    48.82  30.0  3
 HZZ  Var_04  C11  C09  C08  C07    84.26  30.0  3
 HZZ  Var_05  O05  C06  C07  C08  -104.01  30.0  3
 HZZ  Var_06  C12  C11  C09  C08   179.91  30.0  1
 HZZ  Var_07  C13  C12  C11  C09  -100.99  30.0  1
 HZZ  Var_08  H6   C10  C08  C07   116.73  30.0  3
 HZZ  Var_09  H12  C14  C13  C12   122.35  30.0  3
 HZZ  Var_10  H15  C15  C13  C12     3.93  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
 HZZ  plan-1  C06  0.020
 HZZ  plan-1  C07  0.020
 HZZ  plan-1  C08  0.020
 HZZ  plan-1  C09  0.020
 HZZ  plan-1  C10  0.020
 HZZ  plan-1  H3   0.020
 HZZ  plan-2  C11  0.020
 HZZ  plan-2  C12  0.020
 HZZ  plan-2  C13  0.020
 HZZ  plan-2  C14  0.020
 HZZ  plan-2  C15  0.020
 HZZ  plan-2  H11  0.020

