# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 16:31:35 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 3-butoxy-1-(2,2-diphosphonoethyl)pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCOc1ccc[n+](CC([P](O)(O)=O)[P](O)(O)=O)c1
#
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
 721  721  3-butoxy-1-(2,2-diphosphonoethyl)pyridinium  ligand  41  21  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_721
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
 721  O6    O  O     0  -0.681  -0.7304   1.9703  -0.4226
 721  P2    P  P     0   1.416  -1.4274   1.2828   0.6829
 721  O5    O  OH1   0  -0.731  -0.3880   0.9264   1.8459
 721  O4    O  OH1   0  -0.744  -2.6747   2.0182   1.3628
 721  C1    C  CH1   0  -0.863  -2.2064  -0.2963   0.1896
 721  P1    P  P     0   1.404  -3.8132   0.0046  -0.6511
 721  O3    O  O     0  -0.683  -3.7137   1.0348  -1.7065
 721  O2    O  OH1   0  -0.733  -4.2631  -1.4577  -1.1082
 721  O1    O  OH1   0  -0.729  -4.8702   0.2327   0.5218
 721  C2    C  CH2   0  -0.353  -1.2800  -1.0731  -0.7513
 721  N1    N  NR6   1  -0.395   0.0308  -1.3465  -0.1342
 721  C3    C  CR16  0   0.042   0.0951  -2.2564   0.8496
 721  C4    C  CR16  0  -0.315   1.2967  -2.5039   1.4645
 721  C5    C  CR16  0  -0.238   2.4358  -1.8168   1.0755
 721  C7    C  CR16  0  -0.015   1.1028  -0.6674  -0.5420
 721  C6    C  CR6   0   0.327   2.3441  -0.8779   0.0511
 721  O7    O  O2    0  -0.453   3.3404  -0.1459  -0.4254
 721  C8    C  CH2   0  -0.190   4.6548  -0.3291   0.1100
 721  C9    C  CH2   0  -0.453   5.5879   0.6250  -0.6006
 721  C10   C  CH2   0  -0.432   7.0247   0.4576  -0.1193
 721  C11   C  CH3   0  -0.662   7.9792   1.4177  -0.8148
 721  HO5   H  HOH1  0   0.498  -0.7569   0.6198   2.6853
 721  HO4   H  HOH1  0   0.512  -2.5420   2.9530   1.5815
 721  H1    H  HCH1  0   0.359  -2.4218  -0.8941   1.0817
 721  HO2   H  HOH1  0   0.507  -4.3827  -1.5540  -2.0628
 721  HO1   H  HOH1  0   0.500  -4.7916   1.0845   0.9735
 721  H2    H  HCH2  0   0.343  -1.7161  -2.0348  -1.0101
 721  H2A   H  HCH2  0   0.325  -1.1004  -0.5275  -1.6749
 721  H3    H  HCR6  0   0.351  -0.8162  -2.7727   1.1086
 721  H4    H  HCR6  0   0.323   1.3412  -3.2405   2.2522
 721  H5    H  HCR6  0   0.334   3.3739  -2.0247   1.5704
 721  H7    H  HCR6  0   0.359   0.9711   0.0459  -1.3417
 721  H8    H  HCH2  0   0.241   4.6474  -0.1322   1.1871
 721  H8A   H  HCH2  0   0.241   4.9706  -1.3662  -0.0443
 721  H9    H  HCH2  0   0.236   5.5396   0.4456  -1.6784
 721  H9A   H  HCH2  0   0.235   5.2583   1.6538  -0.4295
 721  H10   H  HCH2  0   0.223   7.0720   0.6156   0.9622
 721  H10A  H  HCH2  0   0.223   7.3501  -0.5722  -0.2928
 721  H11   H  HCH3  0   0.220   7.9549   1.2826  -1.8975
 721  H11A  H  HCH3  0   0.221   7.7172   2.4559  -0.6052
 721  H11B  H  HCH3  0   0.231   9.0065   1.2632  -0.4846

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
 721  O6   P2    double    1.477  0.020  1.477
 721  O5   P2    single    1.600  0.020  1.600
 721  O4   P2    single    1.600  0.020  1.600
 721  P2   C1    single    1.829  0.020  1.829
 721  O5   HO5   single    0.850  0.020  0.980
 721  O4   HO4   single    0.850  0.020  0.980
 721  C1   C2    single    1.532  0.020  1.532
 721  C1   P1    single    1.838  0.020  1.838
 721  C1   H1    single    0.970  0.020  1.090
 721  O3   P1    double    1.478  0.020  1.478
 721  O1   P1    single    1.595  0.020  1.595
 721  P1   O2    single    1.597  0.020  1.597
 721  O2   HO2   single    0.850  0.020  0.980
 721  O1   HO1   single    0.850  0.020  0.980
 721  N1   C2    single    1.474  0.020  1.474
 721  C2   H2    single    0.970  0.020  1.090
 721  C2   H2A   single    0.970  0.020  1.090
 721  C7   N1    aromatic  1.333  0.020  1.333
 721  C3   N1    aromatic  1.342  0.020  1.342
 721  C4   C3    aromatic  1.372  0.020  1.372
 721  C3   H3    single    0.930  0.020  1.080
 721  C5   C4    aromatic  1.386  0.020  1.386
 721  C4   H4    single    0.930  0.020  1.080
 721  C5   C6    aromatic  1.393  0.020  1.393
 721  C5   H5    single    0.930  0.020  1.080
 721  C6   C7    aromatic  1.392  0.020  1.392
 721  C7   H7    single    0.930  0.020  1.080
 721  O7   C6    single    1.325  0.020  1.325
 721  C8   O7    single    1.431  0.020  1.431
 721  C9   C8    single    1.512  0.020  1.512
 721  C8   H8    single    0.970  0.020  1.090
 721  C8   H8A   single    0.970  0.020  1.090
 721  C10  C9    single    1.524  0.020  1.524
 721  C9   H9    single    0.970  0.020  1.090
 721  C9   H9A   single    0.970  0.020  1.090
 721  C11  C10   single    1.522  0.020  1.522
 721  C10  H10   single    0.970  0.020  1.090
 721  C10  H10A  single    0.970  0.020  1.090
 721  C11  H11   single    0.970  0.020  1.090
 721  C11  H11A  single    0.970  0.020  1.090
 721  C11  H11B  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
 721  C1    P2   O4    100.34  3.000
 721  C1    P2   O5    106.29  3.000
 721  O4    P2   O5    107.45  3.000
 721  C1    P2   O6    113.65  3.000
 721  O4    P2   O6    118.18  3.000
 721  O5    P2   O6    109.95  3.000
 721  HO5   O5   P2    116.99  3.000
 721  HO4   O4   P2    115.63  3.000
 721  H1    C1   C2    110.03  3.000
 721  H1    C1   P1    106.85  3.000
 721  C2    C1   P1    109.31  3.000
 721  H1    C1   P2    109.59  3.000
 721  P1    C1   P2    110.76  3.000
 721  C2    C1   P2    110.24  3.000
 721  O1    P1   O2     98.90  3.000
 721  O2    P1   O3    116.93  3.000
 721  O1    P1   O3    118.03  3.000
 721  O2    P1   C1    103.14  3.000
 721  O1    P1   C1    105.44  3.000
 721  O3    P1   C1    112.44  3.000
 721  HO2   O2   P1    114.12  3.000
 721  HO1   O1   P1    114.54  3.000
 721  H2A   C2   H2    107.93  3.000
 721  H2A   C2   N1    107.56  3.000
 721  H2    C2   N1    106.99  3.000
 721  H2A   C2   C1    111.53  3.000
 721  H2    C2   C1    110.62  3.000
 721  N1    C2   C1    111.99  3.000
 721  C7    N1   C3    122.09  3.000
 721  C3    N1   C2    118.38  3.000
 721  C7    N1   C2    119.50  3.000
 721  H3    C3   C4    123.07  3.000
 721  H3    C3   N1    117.39  3.000
 721  C4    C3   N1    119.53  3.000
 721  H4    C4   C5    120.61  3.000
 721  H4    C4   C3    119.09  3.000
 721  C5    C4   C3    120.29  3.000
 721  H5    C5   C6    121.58  3.000
 721  H5    C5   C4    119.30  3.000
 721  C6    C5   C4    119.11  3.000
 721  H7    C7   C6    121.63  3.000
 721  H7    C7   N1    117.72  3.000
 721  C6    C7   N1    120.66  3.000
 721  O7    C6   C7    115.71  3.000
 721  O7    C6   C5    125.98  3.000
 721  C7    C6   C5    118.31  3.000
 721  C8    O7   C6    119.03  3.000
 721  H8A   C8   H8    108.11  3.000
 721  H8A   C8   C9    110.70  3.000
 721  H8    C8   C9    110.67  3.000
 721  H8A   C8   O7    109.48  3.000
 721  H8    C8   O7    109.80  3.000
 721  C9    C8   O7    108.07  3.000
 721  H9A   C9   H9    107.16  3.000
 721  H9A   C9   C10   109.75  3.000
 721  H9    C9   C10   109.56  3.000
 721  H9A   C9   C8    109.52  3.000
 721  H9    C9   C8    109.42  3.000
 721  C10   C9   C8    111.35  3.000
 721  H10A  C10  H10   106.26  3.000
 721  H10A  C10  C11   109.56  3.000
 721  H10   C10  C11   109.48  3.000
 721  H10A  C10  C9    109.49  3.000
 721  H10   C10  C9    109.69  3.000
 721  C11   C10  C9    112.18  3.000
 721  H11B  C11  H11A  107.64  3.000
 721  H11B  C11  H11   107.70  3.000
 721  H11A  C11  H11   107.63  3.000
 721  H11B  C11  C10   111.29  3.000
 721  H11A  C11  C10   111.21  3.000
 721  H11   C11  C10   111.18  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
 721  CONST_01  C5   C6   C7   N1     0.00   0.0  0
 721  CONST_02  C5   C4   C3   N1     0.00   0.0  0
 721  CONST_03  C6   C7   N1   C3     0.00   0.0  0
 721  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 721  CONST_05  C7   N1   C3   C4     0.00   0.0  0
 721  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 721  CONST_07  C6   C7   N1   C2   180.00   0.0  0
 721  CONST_08  C4   C3   N1   C2   180.00   0.0  0
 721  CONST_09  O7   C6   C7   N1   180.00   0.0  0
 721  CONST_10  O7   C6   C5   C4   180.00   0.0  0
 721  CONST_11  H4   C4   C3   N1   180.00   0.0  0
 721  CONST_12  H7   C7   N1   C3   180.00   0.0  0
 721  CONST_13  H5   C5   C4   C3   180.00   0.0  0
 721  CONST_14  H3   C3   C4   C5   180.00   0.0  0
 721  Var_01    C7   N1   C2   C1  -106.67  30.0  3
 721  Var_02    N1   C2   C1   P2    57.99  30.0  3
 721  Var_03    C9   C8   O7   C6  -179.79  30.0  1
 721  Var_04    C2   C1   P2   O6    41.07  30.0  3
 721  Var_05    O3   P1   C1   P2    48.45  30.0  3
 721  Var_06    C10  C9   C8   O7  -178.02  30.0  2
 721  Var_07    C11  C10  C9   C8  -179.53  30.0  1
 721  Var_08    H11  C11  C10  C9   -58.04  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
 721  plan-1  C2  0.020
 721  plan-1  N1  0.020
 721  plan-1  C3  0.020
 721  plan-1  C4  0.020
 721  plan-1  C5  0.020
 721  plan-1  C7  0.020
 721  plan-1  C6  0.020
 721  plan-1  O7  0.020
 721  plan-1  H3  0.020
 721  plan-1  H4  0.020
 721  plan-1  H5  0.020
 721  plan-1  H7  0.020

