# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 03:21:09 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-butyl-1-(2,2-diphosphonoethyl)pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCc1ccc[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
 476  476  3-butyl-1-(2,2-diphosphonoethyl)pyridinium  ligand  40  20  .  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_476
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
 476  O11  O  O     0  -0.681   2.1986   2.1989   0.4989
 476  P10  P  P     0   1.419   1.8490   1.3040  -0.6226
 476  O13  O  OH1   0  -0.731   0.5870   1.8864  -1.4138
 476  O12  O  OH1   0  -0.746   2.9821   0.9772  -1.7051
 476  C8   C  CH1   0  -0.872   1.3917  -0.3894  -0.1071
 476  P9   P  P     0   1.405   2.8919  -1.4079   0.1855
 476  O15  O  OH1   0  -0.730   3.3678  -1.8867  -1.2601
 476  O14  O  O     0  -0.684   3.8764  -0.7205   1.0487
 476  O16  O  OH1   0  -0.733   2.2962  -2.7856   0.7297
 476  C7   C  CH2   0  -0.347   0.5427  -0.3446   1.1679
 476  N2   N  NR6   1  -0.413  -0.6596   0.4894   0.9983
 476  C1   C  CR16  0   0.050  -1.6339   0.0468   0.1879
 476  C6   C  CR6   0   0.017  -2.7695   0.7907  -0.0475
 476  C5   C  CR16  0  -0.131  -2.8710   2.0228   0.5964
 476  C4   C  CR16  0  -0.333  -1.8616   2.4598   1.4353
 476  C3   C  CR16  0   0.066  -0.7507   1.6704   1.6223
 476  C17  C  CH2   0  -0.515  -3.8663   0.2564  -0.9153
 476  C18  C  CH2   0  -0.413  -4.8554  -0.5902  -0.1095
 476  C19  C  CH2   0  -0.426  -6.0281  -1.0712  -0.9533
 476  C20  C  CH3   0  -0.662  -6.9963  -1.9362  -0.1588
 476  H1   H  HOH1  0   0.499   0.3748   1.4738  -2.2619
 476  H2   H  HOH1  0   0.513   3.5203   1.7311  -1.9896
 476  H3   H  HCH1  0   0.360   0.8268  -0.8722  -0.9119
 476  H4   H  HOH1  0   0.500   3.7189  -1.1782  -1.8185
 476  H5   H  HOH1  0   0.507   2.6462  -3.0519   1.5910
 476  H6   H  HCH2  0   0.340   0.2068  -1.3436   1.4363
 476  H7   H  HCH2  0   0.323   1.1045   0.0579   2.0067
 476  H8   H  HCR6  0   0.345  -1.4787  -0.9237  -0.2634
 476  H9   H  HCR6  0   0.305  -3.7446   2.6421   0.4387
 476  H10  H  HCR6  0   0.318  -1.9228   3.4095   1.9447
 476  H11  H  HCR6  0   0.354   0.0699   1.9574   2.2608
 476  H12  H  HCH2  0   0.264  -4.3907   1.0944  -1.3789
 476  H13  H  HCH2  0   0.263  -3.4433  -0.3418  -1.7249
 476  H14  H  HCH2  0   0.231  -4.3299  -1.4502   0.3176
 476  H15  H  HCH2  0   0.232  -5.2275  -0.0052   0.7378
 476  H16  H  HCH2  0   0.220  -6.5560  -0.2045  -1.3617
 476  H17  H  HCH2  0   0.220  -5.6530  -1.6332  -1.8140
 476  H18  H  HCH3  0   0.219  -6.5036  -2.8342   0.2180
 476  H19  H  HCH3  0   0.219  -7.3943  -1.3933   0.7002
 476  H20  H  HCH3  0   0.230  -7.8414  -2.2542  -0.7699

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
 476  C20  C19  single    1.522  0.020  1.522
 476  C18  C19  single    1.523  0.020  1.523
 476  C18  C17  single    1.531  0.020  1.531
 476  C5   C4   aromatic  1.383  0.020  1.383
 476  C5   C6   aromatic  1.394  0.020  1.394
 476  C4   C3   aromatic  1.376  0.020  1.376
 476  C6   C17  single    1.497  0.020  1.497
 476  C6   C1   aromatic  1.378  0.020  1.378
 476  C3   N2   aromatic  1.339  0.020  1.339
 476  C1   N2   aromatic  1.342  0.020  1.342
 476  N2   C7   single    1.473  0.020  1.473
 476  C7   C8   single    1.532  0.020  1.532
 476  O14  P9   double    1.479  0.020  1.479
 476  C8   P9   single    1.837  0.020  1.837
 476  C8   P10  single    1.828  0.020  1.828
 476  O11  P10  double    1.477  0.020  1.477
 476  P9   O16  single    1.597  0.020  1.597
 476  P9   O15  single    1.595  0.020  1.595
 476  P10  O12  single    1.601  0.020  1.601
 476  P10  O13  single    1.599  0.020  1.599
 476  O13  H1   single    0.850  0.020  0.980
 476  O12  H2   single    0.850  0.020  0.980
 476  C8   H3   single    0.970  0.020  1.090
 476  O15  H4   single    0.850  0.020  0.980
 476  O16  H5   single    0.850  0.020  0.980
 476  C7   H6   single    0.970  0.020  1.090
 476  C7   H7   single    0.970  0.020  1.090
 476  C1   H8   single    0.930  0.020  1.080
 476  C5   H9   single    0.930  0.020  1.080
 476  C4   H10  single    0.930  0.020  1.080
 476  C3   H11  single    0.930  0.020  1.080
 476  C17  H12  single    0.970  0.020  1.090
 476  C17  H13  single    0.970  0.020  1.090
 476  C18  H14  single    0.970  0.020  1.090
 476  C18  H15  single    0.970  0.020  1.090
 476  C19  H16  single    0.970  0.020  1.090
 476  C19  H17  single    0.970  0.020  1.090
 476  C20  H18  single    0.970  0.020  1.090
 476  C20  H19  single    0.970  0.020  1.090
 476  C20  H20  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
 476  C8   P10  O12  100.29  3.000
 476  O12  P10  O13  107.36  3.000
 476  C8   P10  O13  106.22  3.000
 476  O13  P10  O11  109.98  3.000
 476  O12  P10  O11  118.02  3.000
 476  C8   P10  O11  113.97  3.000
 476  H1   O13  P10  116.85  3.000
 476  H2   O12  P10  115.65  3.000
 476  H3   C8   C7   109.78  3.000
 476  H3   C8   P9   107.09  3.000
 476  C7   C8   P9   109.65  3.000
 476  H3   C8   P10  109.27  3.000
 476  P9   C8   P10  110.75  3.000
 476  C7   C8   P10  110.25  3.000
 476  O16  P9   O14  116.78  3.000
 476  O16  P9   O15   99.27  3.000
 476  O14  P9   O15  118.02  3.000
 476  O15  P9   C8   105.41  3.000
 476  O16  P9   C8   103.18  3.000
 476  O14  P9   C8   112.27  3.000
 476  H4   O15  P9   114.28  3.000
 476  H5   O16  P9   113.96  3.000
 476  H7   C7   H6   108.02  3.000
 476  H7   C7   N2   107.52  3.000
 476  H6   C7   N2   107.23  3.000
 476  H7   C7   C8   111.51  3.000
 476  H6   C7   C8   110.46  3.000
 476  N2   C7   C8   111.90  3.000
 476  C3   N2   C1   121.52  3.000
 476  C1   N2   C7   118.38  3.000
 476  C3   N2   C7   120.09  3.000
 476  H8   C1   C6   122.10  3.000
 476  H8   C1   N2   116.34  3.000
 476  C6   C1   N2   121.56  3.000
 476  C17  C6   C5   121.99  3.000
 476  C17  C6   C1   120.68  3.000
 476  C5   C6   C1   117.28  3.000
 476  H9   C5   C4   119.77  3.000
 476  H9   C5   C6   119.82  3.000
 476  C4   C5   C6   120.41  3.000
 476  H10  C4   C3   119.11  3.000
 476  H10  C4   C5   121.52  3.000
 476  C3   C4   C5   119.37  3.000
 476  H11  C3   C4   122.83  3.000
 476  H11  C3   N2   117.31  3.000
 476  C4   C3   N2   119.86  3.000
 476  H13  C17  H12  106.96  3.000
 476  H13  C17  C18  109.72  3.000
 476  H12  C17  C18  109.73  3.000
 476  H13  C17  C6   109.97  3.000
 476  H12  C17  C6   108.91  3.000
 476  C18  C17  C6   111.44  3.000
 476  H15  C18  H14  106.32  3.000
 476  H15  C18  C19  109.63  3.000
 476  H14  C18  C19  109.74  3.000
 476  H15  C18  C17  109.35  3.000
 476  H14  C18  C17  109.24  3.000
 476  C19  C18  C17  112.37  3.000
 476  H17  C19  H16  106.18  3.000
 476  H17  C19  C20  109.68  3.000
 476  H16  C19  C20  109.76  3.000
 476  H17  C19  C18  109.52  3.000
 476  H16  C19  C18  109.16  3.000
 476  C20  C19  C18  112.34  3.000
 476  H20  C20  H19  107.68  3.000
 476  H20  C20  H18  107.67  3.000
 476  H19  C20  H18  107.59  3.000
 476  H20  C20  C19  111.48  3.000
 476  H19  C20  C19  111.11  3.000
 476  H18  C20  C19  111.14  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
 476  CONST_01  C5   C4   C3   N2      0.00   0.0  0
 476  CONST_02  C5   C6   C1   N2      0.00   0.0  0
 476  CONST_03  C4   C5   C6   C1      0.00   0.0  0
 476  CONST_04  C4   C3   N2   C1      0.00   0.0  0
 476  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 476  CONST_06  C3   N2   C1   C6      0.00   0.0  0
 476  CONST_07  C4   C3   N2   C7    180.00   0.0  0
 476  CONST_08  C6   C1   N2   C7    180.00   0.0  0
 476  CONST_09  C17  C6   C1   N2    180.00   0.0  0
 476  CONST_10  C17  C6   C5   C4    180.00   0.0  0
 476  CONST_11  H10  C4   C3   N2    180.00   0.0  0
 476  CONST_12  H9   C5   C6   C1    180.00   0.0  0
 476  CONST_13  H11  C3   N2   C1    180.00   0.0  0
 476  CONST_14  H8   C1   C6   C5    180.00   0.0  0
 476  Var_01    C3   N2   C7   C8   -109.22  30.0  3
 476  Var_02    C18  C17  C6   C1     86.96  30.0  2
 476  Var_03    N2   C7   C8   P10    56.40  30.0  2
 476  Var_04    C19  C18  C17  C6    176.36  30.0  1
 476  Var_05    C7   C8   P10  O11    39.75  30.0  2
 476  Var_06    O14  P9   C8   P10    49.09  30.0  3
 476  Var_07    C20  C19  C18  C17   178.84  30.0  3
 476  Var_08    H18  C20  C19  C18   -61.16  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
 476  plan-1  C7   0.020
 476  plan-1  N2   0.020
 476  plan-1  C1   0.020
 476  plan-1  C6   0.020
 476  plan-1  C5   0.020
 476  plan-1  C4   0.020
 476  plan-1  C3   0.020
 476  plan-1  C17  0.020
 476  plan-1  H8   0.020
 476  plan-1  H9   0.020
 476  plan-1  H10  0.020
 476  plan-1  H11  0.020

