# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 17:17:38 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-(2,2-diphosphonoethyl)-3-(octyloxy)pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCOc1ccc[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
 714  714  1-(2,2-diphosphonoethyl)-3-(octyloxy)pyridinium  ligand  53  25  .  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_714
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
 714  O1    O  OH1   0  -0.750    6.3882  -0.6873  -0.3013
 714  P1    P  P     0   1.416    5.5514   0.0560   0.8437
 714  O3    O  OH1   0  -0.740    5.3157  -0.9752   2.0382
 714  O2    O  O     0  -0.678    6.0874   1.3295   1.3632
 714  C1    C  CH1   0  -0.881    3.9491   0.2438  -0.0256
 714  P2    P  P     0   1.413    3.3639  -1.2082  -0.9689
 714  O4    O  O     0  -0.672    1.9538  -1.1167  -1.4020
 714  O5    O  OH1   0  -0.731    4.3312  -1.3709  -2.2233
 714  O6    O  OH1   0  -0.755    3.7066  -2.3699   0.0844
 714  C2    C  CH2   0  -0.352    2.9152   0.7356   0.9968
 714  N1    N  NR6   1  -0.387    1.6999   1.2615   0.3553
 714  C7    C  CR16  0   0.012    0.5503   0.6054   0.4905
 714  C6    C  CR6   0   0.319   -0.6144   1.0800  -0.1056
 714  C5    C  CR16  0  -0.236   -0.5403   2.2460  -0.8615
 714  C4    C  CR16  0  -0.321    0.6783   2.8983  -0.9769
 714  C3    C  CR16  0   0.045    1.7934   2.3952  -0.3572
 714  O7    O  O2    0  -0.455   -1.7062   0.3592   0.1103
 714  C8    C  CH2   0  -0.190   -2.9572   0.8287  -0.3988
 714  C9    C  CH2   0  -0.458   -4.0474  -0.0801   0.1209
 714  C10   C  CH2   0  -0.428   -5.4188   0.3713  -0.3697
 714  C11   C  CH2   0  -0.413   -6.5560  -0.4404   0.2372
 714  C12   C  CH2   0  -0.413   -7.9303   0.0080  -0.2433
 714  C13   C  CH2   0  -0.407   -9.0733  -0.7594   0.4083
 714  C14   C  CH2   0  -0.419  -10.4498  -0.3112  -0.0675
 714  C15   C  CH3   0  -0.663  -11.5849  -1.0715   0.6040
 714  HO1   H  HOH1  0   0.514    7.3128  -0.8870  -0.0907
 714  HO3   H  HOH1  0   0.499    4.9596  -1.8390   1.7805
 714  H1    H  HCH1  0   0.373    4.1293   1.0317  -0.7668
 714  HO5   H  HOH1  0   0.499    5.2781  -1.4158  -2.0219
 714  HO6   H  HOH1  0   0.512    3.3846  -3.2548  -0.1440
 714  H2    H  HCH2  0   0.326    2.6170  -0.0501   1.6857
 714  H2A   H  HCH2  0   0.342    3.3326   1.5479   1.5911
 714  H7    H  HCR6  0   0.354    0.5499  -0.2967   1.0837
 714  H5    H  HCR6  0   0.332   -1.4074   2.6583  -1.3578
 714  H4    H  HCR6  0   0.322    0.7613   3.8096  -1.5494
 714  H3    H  HCR6  0   0.349    2.7580   2.8774  -0.4020
 714  H8    H  HCH2  0   0.239   -3.1287   1.8568  -0.0629
 714  H8A   H  HCH2  0   0.242   -2.9329   0.8286  -1.4936
 714  H9    H  HCH2  0   0.238   -3.8582  -1.1082  -0.1987
 714  H9A   H  HCH2  0   0.235   -4.0287  -0.0723   1.2144
 714  H10   H  HCH2  0   0.218   -5.5632   1.4290  -0.1249
 714  H10A  H  HCH2  0   0.221   -5.4613   0.3022  -1.4616
 714  H11   H  HCH2  0   0.212   -6.4163  -1.5012   0.0041
 714  H11A  H  HCH2  0   0.211   -6.5096  -0.3607   1.3289
 714  H12   H  HCH2  0   0.208   -8.0514   1.0781  -0.0419
 714  H12A  H  HCH2  0   0.209   -7.9901  -0.1034  -1.3316
 714  H13   H  HCH2  0   0.207   -8.9536  -1.8306   0.2116
 714  H13A  H  HCH2  0   0.206   -9.0113  -0.6443   1.4964
 714  H14   H  HCH2  0   0.210  -10.5643   0.7609   0.1200
 714  H14A  H  HCH2  0   0.210  -10.5157  -0.4365  -1.1529
 714  H15   H  HCH3  0   0.226  -12.5595  -0.7369   0.2471
 714  H15A  H  HCH3  0   0.216  -11.5118  -2.1430   0.4085
 714  H15B  H  HCH3  0   0.216  -11.5642  -0.9345   1.6869

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
 714  O1   P1    single    1.601  0.020  1.601
 714  O1   HO1   single    0.850  0.020  0.980
 714  O2   P1    double    1.476  0.020  1.476
 714  P1   O3    single    1.596  0.020  1.596
 714  P1   C1    single    1.833  0.020  1.833
 714  O3   HO3   single    0.850  0.020  0.980
 714  C1   C2    single    1.535  0.020  1.535
 714  C1   P2    single    1.828  0.020  1.828
 714  C1   H1    single    0.970  0.020  1.090
 714  O4   P2    double    1.478  0.020  1.478
 714  O6   P2    single    1.605  0.020  1.605
 714  P2   O5    single    1.592  0.020  1.592
 714  O5   HO5   single    0.850  0.020  0.980
 714  O6   HO6   single    0.850  0.020  0.980
 714  C2   N1    single    1.471  0.020  1.471
 714  C2   H2    single    0.970  0.020  1.090
 714  C2   H2A   single    0.970  0.020  1.090
 714  N1   C7    aromatic  1.331  0.020  1.331
 714  N1   C3    aromatic  1.342  0.020  1.342
 714  C7   C6    aromatic  1.392  0.020  1.392
 714  C7   H7    single    0.930  0.020  1.080
 714  C6   O7    single    1.326  0.020  1.326
 714  C6   C5    aromatic  1.392  0.020  1.392
 714  C4   C5    aromatic  1.387  0.020  1.387
 714  C5   H5    single    0.930  0.020  1.080
 714  C3   C4    aromatic  1.371  0.020  1.371
 714  C4   H4    single    0.930  0.020  1.080
 714  C3   H3    single    0.930  0.020  1.080
 714  O7   C8    single    1.430  0.020  1.430
 714  C8   C9    single    1.512  0.020  1.512
 714  C8   H8    single    0.970  0.020  1.090
 714  C8   H8A   single    0.970  0.020  1.090
 714  C9   C10   single    1.525  0.020  1.525
 714  C9   H9    single    0.970  0.020  1.090
 714  C9   H9A   single    0.970  0.020  1.090
 714  C11  C10   single    1.523  0.020  1.523
 714  C10  H10   single    0.970  0.020  1.090
 714  C10  H10A  single    0.970  0.020  1.090
 714  C11  C12   single    1.523  0.020  1.523
 714  C11  H11   single    0.970  0.020  1.090
 714  C11  H11A  single    0.970  0.020  1.090
 714  C12  C13   single    1.523  0.020  1.523
 714  C12  H12   single    0.970  0.020  1.090
 714  C12  H12A  single    0.970  0.020  1.090
 714  C14  C13   single    1.524  0.020  1.524
 714  C13  H13   single    0.970  0.020  1.090
 714  C13  H13A  single    0.970  0.020  1.090
 714  C14  C15   single    1.522  0.020  1.522
 714  C14  H14   single    0.970  0.020  1.090
 714  C14  H14A  single    0.970  0.020  1.090
 714  C15  H15   single    0.970  0.020  1.090
 714  C15  H15A  single    0.970  0.020  1.090
 714  C15  H15B  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
 714  HO1   O1   P1    116.03  3.000
 714  C1    P1   O2    113.33  3.000
 714  C1    P1   O3    106.99  3.000
 714  O2    P1   O3    110.35  3.000
 714  C1    P1   O1     99.52  3.000
 714  O3    P1   O1    108.21  3.000
 714  O2    P1   O1    117.54  3.000
 714  HO3   O3   P1    115.54  3.000
 714  H1    C1   C2    109.31  3.000
 714  H1    C1   P2    105.93  3.000
 714  C2    C1   P2    112.50  3.000
 714  H1    C1   P1    104.51  3.000
 714  P2    C1   P1    116.32  3.000
 714  C2    C1   P1    107.81  3.000
 714  O6    P2   O5    108.25  3.000
 714  O5    P2   O4    110.80  3.000
 714  O6    P2   O4    116.16  3.000
 714  O5    P2   C1    107.06  3.000
 714  O6    P2   C1     99.67  3.000
 714  O4    P2   C1    114.05  3.000
 714  HO5   O5   P2    115.76  3.000
 714  HO6   O6   P2    115.81  3.000
 714  H2A   C2   H2    107.36  3.000
 714  H2A   C2   N1    106.72  3.000
 714  H2    C2   N1    107.95  3.000
 714  H2A   C2   C1    110.13  3.000
 714  H2    C2   C1    112.05  3.000
 714  N1    C2   C1    112.36  3.000
 714  C3    N1   C7    122.05  3.000
 714  C3    N1   C2    118.41  3.000
 714  C7    N1   C2    119.54  3.000
 714  H7    C7   C6    121.33  3.000
 714  H7    C7   N1    117.91  3.000
 714  C6    C7   N1    120.75  3.000
 714  O7    C6   C5    126.00  3.000
 714  C5    C6   C7    118.28  3.000
 714  O7    C6   C7    115.71  3.000
 714  H5    C5   C4    119.16  3.000
 714  H5    C5   C6    121.76  3.000
 714  C4    C5   C6    119.08  3.000
 714  H4    C4   C3    119.13  3.000
 714  H4    C4   C5    120.58  3.000
 714  C3    C4   C5    120.29  3.000
 714  H3    C3   C4    122.96  3.000
 714  H3    C3   N1    117.49  3.000
 714  C4    C3   N1    119.54  3.000
 714  C8    O7   C6    118.94  3.000
 714  H8A   C8   H8    108.07  3.000
 714  H8A   C8   C9    111.09  3.000
 714  H8    C8   C9    110.24  3.000
 714  H8A   C8   O7    109.67  3.000
 714  H8    C8   O7    109.64  3.000
 714  C9    C8   O7    108.13  3.000
 714  H9A   C9   H9    107.23  3.000
 714  H9A   C9   C10   109.57  3.000
 714  H9    C9   C10   109.88  3.000
 714  H9A   C9   C8    109.10  3.000
 714  H9    C9   C8    109.88  3.000
 714  C10   C9   C8    111.11  3.000
 714  H10A  C10  H10   106.19  3.000
 714  H10A  C10  C11   109.56  3.000
 714  H10   C10  C11   109.09  3.000
 714  H10A  C10  C9    109.70  3.000
 714  H10   C10  C9    109.42  3.000
 714  C11   C10  C9    112.67  3.000
 714  H11A  C11  H11   106.09  3.000
 714  H11A  C11  C12   109.34  3.000
 714  H11   C11  C12   109.45  3.000
 714  H11A  C11  C10   109.07  3.000
 714  H11   C11  C10   109.64  3.000
 714  C12   C11  C10   113.01  3.000
 714  H12A  C12  H12   106.01  3.000
 714  H12A  C12  C13   109.44  3.000
 714  H12   C12  C13   109.30  3.000
 714  H12A  C12  C11   109.43  3.000
 714  H12   C12  C11   109.22  3.000
 714  C13   C12  C11   113.19  3.000
 714  H13A  C13  H13   105.95  3.000
 714  H13A  C13  C14   109.28  3.000
 714  H13   C13  C14   109.28  3.000
 714  H13A  C13  C12   109.23  3.000
 714  H13   C13  C12   109.50  3.000
 714  C14   C13  C12   113.34  3.000
 714  H14A  C14  H14   106.00  3.000
 714  H14A  C14  C15   109.60  3.000
 714  H14   C14  C15   109.61  3.000
 714  H14A  C14  C13   109.29  3.000
 714  H14   C14  C13   109.21  3.000
 714  C15   C14  C13   112.89  3.000
 714  H15B  C15  H15A  107.43  3.000
 714  H15B  C15  H15   107.64  3.000
 714  H15A  C15  H15   107.60  3.000
 714  H15B  C15  C14   111.14  3.000
 714  H15A  C15  C14   111.18  3.000
 714  H15   C15  C14   111.64  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
 714  CONST_01  C5   C6   C7   N1      0.00   0.0  0
 714  CONST_02  C5   C4   C3   N1      0.00   0.0  0
 714  CONST_03  C4   C3   N1   C7      0.00   0.0  0
 714  CONST_04  C4   C5   C6   C7      0.00   0.0  0
 714  CONST_05  C3   N1   C7   C6      0.00   0.0  0
 714  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 714  CONST_07  C6   C7   N1   C2    180.00   0.0  0
 714  CONST_08  C4   C3   N1   C2    180.00   0.0  0
 714  CONST_09  O7   C6   C7   N1    180.00   0.0  0
 714  CONST_10  O7   C6   C5   C4    180.00   0.0  0
 714  CONST_11  H4   C4   C3   N1    180.00   0.0  0
 714  CONST_12  H3   C3   N1   C7    180.00   0.0  0
 714  CONST_13  H5   C5   C6   C7    180.00   0.0  0
 714  CONST_14  H7   C7   C6   C5    180.00   0.0  0
 714  Var_01    C7   N1   C2   C1    112.20  30.0  2
 714  Var_02    N1   C2   C1   P1    164.69  30.0  3
 714  Var_03    C9   C8   O7   C6   -173.40  30.0  3
 714  Var_04    C2   C1   P1   O1    170.65  30.0  3
 714  Var_05    O4   P2   C1   P1    167.42  30.0  3
 714  Var_06    C10  C9   C8   O7    179.31  30.0  3
 714  Var_07    C11  C10  C9   C8   -174.63  30.0  3
 714  Var_08    C12  C11  C10  C9    179.76  30.0  1
 714  Var_09    C13  C12  C11  C10  -177.42  30.0  3
 714  Var_10    C14  C13  C12  C11   179.86  30.0  3
 714  Var_11    C15  C14  C13  C12  -179.22  30.0  1
 714  Var_12    H15  C15  C14  C13  -179.85  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
 714  plan-1  C2  0.020
 714  plan-1  N1  0.020
 714  plan-1  C7  0.020
 714  plan-1  C6  0.020
 714  plan-1  C5  0.020
 714  plan-1  C4  0.020
 714  plan-1  C3  0.020
 714  plan-1  O7  0.020
 714  plan-1  H7  0.020
 714  plan-1  H5  0.020
 714  plan-1  H4  0.020
 714  plan-1  H3  0.020

