# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:22:02 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: [1-(4-oxidanylphenoxy)-1-phosphono-ethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(Oc1ccc(O)cc1)([P](O)(O)=O)[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
 L69  L69  '[1-(4-oxidanylphenoxy)-1-phosphono-ethyl]phosphonic acid'  ligand  26  18  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L69
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
 L69  O5   O  OP    -1  -0.895  -2.3839  -2.2135   0.0956
 L69  P1   P  P      0   1.177  -0.9213  -1.7615   0.0594
 L69  O4   O  OP    -1  -0.909  -0.1944  -1.8784   1.4031
 L69  O6   O  O      0  -0.904  -0.1608  -2.4668  -1.0933
 L69  C6   C  CT     0  -0.296  -0.9164   0.0839  -0.3730
 L69  C7   C  CH3    0  -0.684  -0.7756   0.3172  -1.8698
 L69  P    P  P      0   1.178  -2.4522   1.0205   0.2056
 L69  O3   O  O      0  -0.923  -2.6342   0.7012   1.6956
 L69  O2   O  OP    -1  -0.935  -2.1042   2.5042  -0.0297
 L69  O1   O  OP    -1  -0.920  -3.6092   0.5625  -0.6917
 L69  O    O  O2     0  -0.502   0.1360   0.7973   0.3366
 L69  C5   C  CR6    0   0.356   1.4442   0.6492   0.1203
 L69  C    C  CR16   0  -0.362   2.2650   1.6709   0.6162
 L69  C4   C  CR16   0  -0.397   2.0636  -0.4177  -0.5356
 L69  C3   C  CR16   0  -0.385   3.4467  -0.4461  -0.6793
 L69  C2   C  CR6    0   0.308   4.2520   0.5672  -0.1743
 L69  O7   O  OH1    0  -0.655   5.6086   0.5681  -0.2924
 L69  C1   C  CR16   0  -0.329   3.6443   1.6317   0.4818
 L69  H3   H  HCH3   0   0.202  -1.6089  -0.1633  -2.3804
 L69  H4   H  HCH3   0   0.183  -0.8235   1.3847  -2.1009
 L69  H5   H  HCH3   0   0.202   0.1435  -0.0859  -2.2964
 L69  H8   H  HCR6   0   0.236   1.8061   2.5137   1.1199
 L69  H9   H  HCR6   0   0.299   1.4690  -1.2425  -0.9194
 L69  H10  H  HCR6   0   0.248   3.8998  -1.2905  -1.1898
 L69  H11  H  HOH1   0   0.464   5.8974  -0.2397  -0.7292
 L69  H12  H  HCR6   0   0.244   4.2479   2.4374   0.8833

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
 L69  O6  P1   deloc     1.551  0.020  1.551
 L69  O3  P    deloc     1.535  0.020  1.535
 L69  P1  O5   deloc     1.531  0.020  1.531
 L69  P1  O4   deloc     1.532  0.020  1.532
 L69  P1  C6   single    1.895  0.020  1.895
 L69  P   O1   deloc     1.534  0.020  1.534
 L69  P   C6   single    1.890  0.020  1.890
 L69  P   O2   deloc     1.542  0.020  1.542
 L69  C6  C7   single    1.521  0.020  1.521
 L69  C6  O    single    1.456  0.020  1.456
 L69  O   C5   single    1.334  0.020  1.334
 L69  C5  C    aromatic  1.401  0.020  1.401
 L69  C5  C4   aromatic  1.397  0.020  1.397
 L69  C   C1   aromatic  1.386  0.020  1.386
 L69  C4  C3   aromatic  1.391  0.020  1.391
 L69  C1  C2   aromatic  1.390  0.020  1.390
 L69  C3  C2   aromatic  1.389  0.020  1.389
 L69  C2  O7   single    1.362  0.020  1.362
 L69  C7  H3   single    0.970  0.020  1.090
 L69  C7  H4   single    0.970  0.020  1.090
 L69  C7  H5   single    0.970  0.020  1.090
 L69  C   H8   single    0.930  0.020  1.080
 L69  C4  H9   single    0.930  0.020  1.080
 L69  C3  H10  single    0.930  0.020  1.080
 L69  O7  H11  single    0.850  0.020  0.980
 L69  C1  H12  single    0.930  0.020  1.080

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
 L69  C6   P1  O6  105.78  3.000
 L69  C6   P1  O4  105.86  3.000
 L69  O6   P1  O4  112.62  3.000
 L69  C6   P1  O5  107.17  3.000
 L69  O4   P1  O5  114.20  3.000
 L69  O6   P1  O5  110.59  3.000
 L69  O    C6  P   101.27  3.000
 L69  O    C6  C7  109.72  3.000
 L69  P    C6  C7  107.48  3.000
 L69  O    C6  P1  111.58  3.000
 L69  C7   C6  P1  111.97  3.000
 L69  P    C6  P1  114.25  3.000
 L69  H5   C7  H4  108.37  3.000
 L69  H5   C7  H3  107.36  3.000
 L69  H4   C7  H3  107.35  3.000
 L69  H5   C7  C6  113.96  3.000
 L69  H4   C7  C6  110.72  3.000
 L69  H3   C7  C6  108.83  3.000
 L69  O1   P   O2  111.60  3.000
 L69  O2   P   O3  112.03  3.000
 L69  O1   P   O3  114.60  3.000
 L69  O2   P   C6  104.29  3.000
 L69  O1   P   C6  106.61  3.000
 L69  O3   P   C6  106.89  3.000
 L69  C5   O   C6  125.12  3.000
 L69  C4   C5  C   117.59  3.000
 L69  C4   C5  O   126.56  3.000
 L69  C    C5  O   115.85  3.000
 L69  H8   C   C1  119.22  3.000
 L69  H8   C   C5  118.91  3.000
 L69  C1   C   C5  121.87  3.000
 L69  H9   C4  C3  119.48  3.000
 L69  H9   C4  C5  120.18  3.000
 L69  C3   C4  C5  120.33  3.000
 L69  H10  C3  C2  119.75  3.000
 L69  H10  C3  C4  118.65  3.000
 L69  C2   C3  C4  121.59  3.000
 L69  C1   C2  O7  118.41  3.000
 L69  O7   C2  C3  123.12  3.000
 L69  C1   C2  C3  118.47  3.000
 L69  H11  O7  C2  109.73  3.000
 L69  H12  C1  C2  120.04  3.000
 L69  H12  C1  C   119.81  3.000
 L69  C2   C1  C   120.14  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
 L69  CONST_01  C2   C1  C   C5    0.00   0.0  0
 L69  CONST_02  C2   C3  C4  C5    0.00   0.0  0
 L69  CONST_03  C3   C4  C5  C     0.00   0.0  0
 L69  CONST_04  C3   C2  C1  C     0.00   0.0  0
 L69  CONST_05  C1   C   C5  C4    0.00   0.0  0
 L69  CONST_06  C1   C2  C3  C4    0.00   0.0  0
 L69  CONST_07  C1   C   C5  O   180.00   0.0  0
 L69  CONST_08  C3   C4  C5  O   180.00   0.0  0
 L69  CONST_09  O7   C2  C1  C   180.00   0.0  0
 L69  CONST_10  O7   C2  C3  C4  180.00   0.0  0
 L69  CONST_11  H12  C1  C   C5  180.00   0.0  0
 L69  CONST_12  H10  C3  C4  C5  180.00   0.0  0
 L69  CONST_13  H9   C4  C5  C   180.00   0.0  0
 L69  CONST_14  H8   C   C5  C4  180.00   0.0  0
 L69  Var_01    C    C5  O   C6  162.56  30.0  2
 L69  Var_02    P    C6  P1  O5   29.47  30.0  3
 L69  Var_03    O3   P   C6  P1   51.45  30.0  3
 L69  Var_04    H3   C7  C6  P1   59.52  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
 L69  plan-1  O    0.020
 L69  plan-1  C5   0.020
 L69  plan-1  C    0.020
 L69  plan-1  C4   0.020
 L69  plan-1  C3   0.020
 L69  plan-1  C2   0.020
 L69  plan-1  O7   0.020
 L69  plan-1  C1   0.020
 L69  plan-1  H8   0.020
 L69  plan-1  H9   0.020
 L69  plan-1  H10  0.020
 L69  plan-1  H12  0.020

