# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 05:47:32 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  49  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 PERFECT
;

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  OP    -1  -0.922    6.4655  -0.4276  -0.6843
 714  P1    P  P      0   1.179    5.5849  -0.1114   0.5312
 714  O3    O  OP    -1  -0.921    5.5106  -1.2403   1.5647
 714  O2    O  O      0  -0.937    5.9735   1.2404   1.1781
 714  C1    C  CH1    0  -0.746    3.8614   0.1799  -0.1183
 714  P2    P  P      0   1.188    2.9090  -1.2971  -0.7369
 714  O4    O  O      0  -0.902    1.7885  -0.6882  -1.6073
 714  O5    O  OP    -1  -0.908    3.8675  -2.1678  -1.5575
 714  O6    O  OP    -1  -0.910    2.3448  -1.9993   0.5115
 714  C2    C  CH2    0  -0.322    3.0610   0.9158   0.9434
 714  N1    N  NR6    1  -0.369    1.7931   1.4719   0.4233
 714  C7    C  CR16   0   0.031    0.6934   0.7303   0.4417
 714  C6    C  CR6    0   0.308   -0.4986   1.2133  -0.0921
 714  C5    C  CR16   0  -0.224   -0.4978   2.4623  -0.6916
 714  C4    C  CR16   0  -0.278    0.6833   3.1926  -0.7226
 714  C3    C  CR16   0   0.086    1.8190   2.6815  -0.1551
 714  O7    O  O2     0  -0.458   -1.5535   0.4027   0.0276
 714  C8    C  CH2    0  -0.140   -2.8218   0.8803  -0.3927
 714  C9    C  CH2    0  -0.436   -3.8832  -0.0961   0.0648
 714  C10   C  CH2    0  -0.413   -5.2691   0.3570  -0.3782
 714  C11   C  CH2    0  -0.401   -6.3911  -0.5022   0.1891
 714  C12   C  CH2    0  -0.406   -7.7722  -0.0477  -0.2653
 714  C13   C  CH2    0  -0.399   -8.9094  -0.8456   0.3587
 714  C14   C  CH2    0  -0.410  -10.2888  -0.3902  -0.1010
 714  C15   C  CH3    0  -0.646  -11.4203  -1.1745   0.5474
 714  H1    H  HCH1   0   0.180    3.9815   0.8672  -0.9676
 714  H2    H  HCH2   0   0.245    2.8121   0.2458   1.7635
 714  H2A   H  HCH2   0   0.244    3.6205   1.7582   1.3451
 714  H7    H  HCR6   0   0.301    0.7721  -0.2494   0.8916
 714  H5    H  HCR6   0   0.277   -1.3832   2.8916  -1.1354
 714  H4    H  HCR6   0   0.270    0.7073   4.1679  -1.1791
 714  H3    H  HCR6   0   0.290    2.7493   3.2248  -0.1307
 714  H8    H  HCH2   0   0.212   -3.0178   1.8657   0.0449
 714  H8A   H  HCH2   0   0.211   -2.8395   0.9903  -1.4830
 714  H9    H  HCH2   0   0.223   -3.6669  -1.0913  -0.3315
 714  H9A   H  HCH2   0   0.229   -3.8455  -0.1666   1.1546
 714  H10   H  HCH2   0   0.208   -5.4273   1.3958  -0.0694
 714  H10A  H  HCH2   0   0.206   -5.3253   0.3570  -1.4717
 714  H11   H  HCH2   0   0.204   -6.2379  -1.5483  -0.0960
 714  H11A  H  HCH2   0   0.205   -6.3422  -0.4782   1.2829
 714  H12   H  HCH2   0   0.202   -7.9005   1.0130  -0.0223
 714  H12A  H  HCH2   0   0.201   -7.8368  -0.1145  -1.3571
 714  H13   H  HCH2   0   0.201   -8.7824  -1.9085   0.1256
 714  H13A  H  HCH2   0   0.202   -8.8476  -0.7693   1.4500
 714  H14   H  HCH2   0   0.205  -10.4083   0.6751   0.1186
 714  H14A  H  HCH2   0   0.204  -10.3556  -0.4813  -1.1895
 714  H15   H  HCH3   0   0.217  -12.3965  -0.8352   0.1998
 714  H15A  H  HCH3   0   0.209  -11.3425  -2.2398   0.3227
 714  H15B  H  HCH3   0   0.210  -11.4014  -1.0685   1.6335

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    deloc     1.534  0.020  1.534
 714  O2   P1    deloc     1.548  0.020  1.548
 714  P1   O3    deloc     1.532  0.020  1.532
 714  P1   C1    single    1.865  0.020  1.865
 714  C1   C2    single    1.520  0.020  1.520
 714  C1   P2    single    1.863  0.020  1.863
 714  C1   H1    single    0.970  0.020  1.090
 714  O4   P2    deloc     1.544  0.020  1.544
 714  O6   P2    deloc     1.539  0.020  1.539
 714  P2   O5    deloc     1.533  0.020  1.533
 714  C2   N1    single    1.479  0.020  1.479
 714  C2   H2    single    0.970  0.020  1.090
 714  C2   H2A   single    0.970  0.020  1.090
 714  N1   C7    aromatic  1.327  0.020  1.327
 714  N1   C3    aromatic  1.341  0.020  1.341
 714  C7   C6    aromatic  1.393  0.020  1.393
 714  C7   H7    single    0.930  0.020  1.080
 714  C6   O7    single    1.336  0.020  1.336
 714  C6   C5    aromatic  1.385  0.020  1.385
 714  C4   C5    aromatic  1.389  0.020  1.389
 714  C5   H5    single    0.930  0.020  1.080
 714  C3   C4    aromatic  1.369  0.020  1.369
 714  C4   H4    single    0.930  0.020  1.080
 714  C3   H3    single    0.930  0.020  1.080
 714  O7   C8    single    1.419  0.020  1.419
 714  C8   C9    single    1.513  0.020  1.513
 714  C8   H8    single    0.970  0.020  1.090
 714  C8   H8A   single    0.970  0.020  1.090
 714  C9   C10   single    1.524  0.020  1.524
 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  C1    P1   O2    103.96  3.000
 714  C1    P1   O3    107.77  3.000
 714  O2    P1   O3    111.94  3.000
 714  C1    P1   O1    106.67  3.000
 714  O3    P1   O1    114.23  3.000
 714  O2    P1   O1    111.53  3.000
 714  H1    C1   C2    107.13  3.000
 714  H1    C1   P2    107.16  3.000
 714  C2    C1   P2    110.28  3.000
 714  H1    C1   P1    105.41  3.000
 714  P2    C1   P1    117.66  3.000
 714  C2    C1   P1    108.61  3.000
 714  O6    P2   O5    113.84  3.000
 714  O5    P2   O4    112.08  3.000
 714  O6    P2   O4    111.79  3.000
 714  O5    P2   C1    107.96  3.000
 714  O6    P2   C1    106.24  3.000
 714  O4    P2   C1    104.21  3.000
 714  H2A   C2   H2    108.43  3.000
 714  H2A   C2   N1    106.23  3.000
 714  H2    C2   N1    107.49  3.000
 714  H2A   C2   C1    111.22  3.000
 714  H2    C2   C1    110.42  3.000
 714  N1    C2   C1    112.83  3.000
 714  C3    N1   C7    121.75  3.000
 714  C3    N1   C2    118.31  3.000
 714  C7    N1   C2    119.71  3.000
 714  H7    C7   C6    122.42  3.000
 714  H7    C7   N1    116.88  3.000
 714  C6    C7   N1    120.69  3.000
 714  O7    C6   C5    125.90  3.000
 714  C5    C6   C7    118.56  3.000
 714  O7    C6   C7    115.54  3.000
 714  H5    C5   C4    118.63  3.000
 714  H5    C5   C6    122.41  3.000
 714  C4    C5   C6    118.96  3.000
 714  H4    C4   C3    119.70  3.000
 714  H4    C4   C5    120.29  3.000
 714  C3    C4   C5    120.00  3.000
 714  H3    C3   C4    122.51  3.000
 714  H3    C3   N1    117.50  3.000
 714  C4    C3   N1    119.98  3.000
 714  C8    O7   C6    118.36  3.000
 714  H8A   C8   H8    107.70  3.000
 714  H8A   C8   C9    110.74  3.000
 714  H8    C8   C9    109.52  3.000
 714  H8A   C8   O7    110.06  3.000
 714  H8    C8   O7    110.14  3.000
 714  C9    C8   O7    108.68  3.000
 714  H9A   C9   H9    107.22  3.000
 714  H9A   C9   C10   109.91  3.000
 714  H9    C9   C10   110.20  3.000
 714  H9A   C9   C8    108.60  3.000
 714  H9    C9   C8    109.83  3.000
 714  C10   C9   C8    110.99  3.000
 714  H10A  C10  H10   105.91  3.000
 714  H10A  C10  C11   109.52  3.000
 714  H10   C10  C11   108.89  3.000
 714  H10A  C10  C9    109.70  3.000
 714  H10   C10  C9    109.36  3.000
 714  C11   C10  C9    113.21  3.000
 714  H11A  C11  H11   105.94  3.000
 714  H11A  C11  C12   109.38  3.000
 714  H11   C11  C12   109.52  3.000
 714  H11A  C11  C10   109.08  3.000
 714  H11   C11  C10   109.81  3.000
 714  C12   C11  C10   112.87  3.000
 714  H12A  C12  H12   105.85  3.000
 714  H12A  C12  C13   109.41  3.000
 714  H12   C12  C13   109.20  3.000
 714  H12A  C12  C11   109.42  3.000
 714  H12   C12  C11   109.19  3.000
 714  C13   C12  C11   113.48  3.000
 714  H13A  C13  H13   105.84  3.000
 714  H13A  C13  C14   109.31  3.000
 714  H13   C13  C14   109.31  3.000
 714  H13A  C13  C12   109.24  3.000
 714  H13   C13  C12   109.55  3.000
 714  C14   C13  C12   113.32  3.000
 714  H14A  C14  H14   105.90  3.000
 714  H14A  C14  C15   109.60  3.000
 714  H14   C14  C15   109.58  3.000
 714  H14A  C14  C13   109.30  3.000
 714  H14   C14  C13   109.23  3.000
 714  C15   C14  C13   112.99  3.000
 714  H15B  C15  H15A  107.36  3.000
 714  H15B  C15  H15   107.61  3.000
 714  H15A  C15  H15   107.58  3.000
 714  H15B  C15  C14   111.16  3.000
 714  H15A  C15  C14   111.24  3.000
 714  H15   C15  C14   111.68  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     88.81  30.0  2
 714  Var_02    N1   C2   C1   P1    166.62  30.0  3
 714  Var_03    C9   C8   O7   C6   -169.87  30.0  3
 714  Var_04    C2   C1   P1   O1   -162.17  30.0  3
 714  Var_05    O4   P2   C1   P1   -161.61  30.0  3
 714  Var_06    C10  C9   C8   O7   -179.16  30.0  3
 714  Var_07    C11  C10  C9   C8   -173.44  30.0  3
 714  Var_08    C12  C11  C10  C9   -179.65  30.0  1
 714  Var_09    C13  C12  C11  C10  -176.59  30.0  3
 714  Var_10    C14  C13  C12  C11  -179.86  30.0  3
 714  Var_11    C15  C14  C13  C12  -178.89  30.0  1
 714  Var_12    H15  C15  C14  C13  -179.70  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

