# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 15:23:43 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  36  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.901   2.4892   1.8135   1.1579
 476  P10  P  P      0   1.192   2.2451   1.3688  -0.2986
 476  O13  O  OP    -1  -0.897   1.1071   2.1786  -0.9595
 476  O12  O  OP    -1  -0.891   3.5105   1.3249  -1.1562
 476  C8   C  CH1    0  -0.747   1.5534  -0.3633  -0.1955
 476  P9   P  P      0   1.178   2.7518  -1.7799   0.0863
 476  O15  O  OP    -1  -0.909   3.5540  -1.9388  -1.2089
 476  O14  O  O      0  -0.915   3.5894  -1.4116   1.3155
 476  O16  O  OP    -1  -0.926   1.8313  -2.9933   0.3487
 476  C7   C  CH2    0  -0.330   0.4969  -0.4485   0.8889
 476  N2   N  NR6    1  -0.384  -0.6701   0.4391   0.6650
 476  C1   C  CR16   0   0.036  -1.7265  -0.0410  -0.0032
 476  C6   C  CR6    0  -0.002  -2.8299   0.7366  -0.2786
 476  C5   C  CR16   0  -0.155  -2.8089   2.0550   0.1783
 476  C4   C  CR16   0  -0.359  -1.7019   2.5414   0.8438
 476  C3   C  CR16   0   0.096  -0.6153   1.7146   1.0532
 476  C17  C  CH2    0  -0.510  -4.0212   0.1514  -0.9777
 476  C18  C  CH2    0  -0.410  -4.8973  -0.6725  -0.0329
 476  C19  C  CH2    0  -0.424  -6.1396  -1.2246  -0.7197
 476  C20  C  CH3    0  -0.662  -6.9940  -2.0760   0.2084
 476  H3   H  HCH1   0   0.171   1.0637  -0.5810  -1.1557
 476  H6   H  HCH2   0   0.246   0.0998  -1.4591   0.9682
 476  H7   H  HCH2   0   0.248   0.9209  -0.1693   1.8512
 476  H8   H  HCR6   0   0.314  -1.6664  -1.0787  -0.3022
 476  H9   H  HCR6   0   0.282  -3.6633   2.6970   0.0033
 476  H10  H  HCR6   0   0.289  -1.6619   3.5621   1.1944
 476  H11  H  HCR6   0   0.318   0.2925   2.0189   1.5569
 476  H12  H  HCH2   0   0.251  -4.6109   0.9613  -1.4133
 476  H13  H  HCH2   0   0.253  -3.6919  -0.4763  -1.8098
 476  H14  H  HCH2   0   0.225  -4.3077  -1.4985   0.3782
 476  H15  H  HCH2   0   0.226  -5.1939  -0.0545   0.8207
 476  H16  H  HCH2   0   0.217  -6.7344  -0.3927  -1.1090
 476  H17  H  HCH2   0   0.217  -5.8405  -1.8160  -1.5904
 476  H18  H  HCH3   0   0.218  -6.4403  -2.9450   0.5681
 476  H19  H  HCH3   0   0.217  -7.3162  -1.5067   1.0822
 476  H20  H  HCH3   0   0.228  -7.8888  -2.4406  -0.2969

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    1.529  0.020  1.529
 476  C5   C4   aromatic  1.380  0.020  1.380
 476  C5   C6   aromatic  1.395  0.020  1.395
 476  C4   C3   aromatic  1.381  0.020  1.381
 476  C6   C17  single    1.500  0.020  1.500
 476  C6   C1   aromatic  1.378  0.020  1.378
 476  C3   N2   aromatic  1.334  0.020  1.334
 476  C1   N2   aromatic  1.339  0.020  1.339
 476  N2   C7   single    1.483  0.020  1.483
 476  C7   C8   single    1.516  0.020  1.516
 476  O14  P9   deloc     1.532  0.020  1.532
 476  C8   P9   single    1.877  0.020  1.877
 476  C8   P10  single    1.868  0.020  1.868
 476  O11  P10  deloc     1.542  0.020  1.542
 476  P9   O16  deloc     1.545  0.020  1.545
 476  P9   O15  deloc     1.532  0.020  1.532
 476  P10  O12  deloc     1.529  0.020  1.529
 476  P10  O13  deloc     1.545  0.020  1.545
 476  C8   H3   single    0.970  0.020  1.090
 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  108.10  3.000
 476  O12  P10  O13  112.62  3.000
 476  C8   P10  O13  103.70  3.000
 476  O13  P10  O11  111.68  3.000
 476  O12  P10  O11  114.02  3.000
 476  C8   P10  O11  105.89  3.000
 476  H3   C8   C7   107.64  3.000
 476  H3   C8   P9   105.43  3.000
 476  C7   C8   P9   107.16  3.000
 476  H3   C8   P10  107.47  3.000
 476  P9   C8   P10  118.15  3.000
 476  C7   C8   P10  110.46  3.000
 476  O16  P9   O14  112.22  3.000
 476  O16  P9   O15  111.97  3.000
 476  O14  P9   O15  114.64  3.000
 476  O15  P9   C8   106.60  3.000
 476  O16  P9   C8   103.76  3.000
 476  O14  P9   C8   106.74  3.000
 476  H7   C7   H6   108.42  3.000
 476  H7   C7   N2   106.65  3.000
 476  H6   C7   N2   106.23  3.000
 476  H7   C7   C8   110.27  3.000
 476  H6   C7   C8   111.00  3.000
 476  N2   C7   C8   113.99  3.000
 476  C3   N2   C1   121.35  3.000
 476  C1   N2   C7   118.79  3.000
 476  C3   N2   C7   119.72  3.000
 476  H8   C1   C6   122.06  3.000
 476  H8   C1   N2   115.98  3.000
 476  C6   C1   N2   121.96  3.000
 476  C17  C6   C5   122.21  3.000
 476  C17  C6   C1   120.60  3.000
 476  C5   C6   C1   117.11  3.000
 476  H9   C5   C4   120.12  3.000
 476  H9   C5   C6   119.69  3.000
 476  C4   C5   C6   120.19  3.000
 476  H10  C4   C3   119.17  3.000
 476  H10  C4   C5   121.29  3.000
 476  C3   C4   C5   119.54  3.000
 476  H11  C3   C4   124.21  3.000
 476  H11  C3   N2   116.03  3.000
 476  C4   C3   N2   119.72  3.000
 476  H13  C17  H12  106.55  3.000
 476  H13  C17  C18  109.48  3.000
 476  H12  C17  C18  109.66  3.000
 476  H13  C17  C6   109.85  3.000
 476  H12  C17  C6   108.99  3.000
 476  C18  C17  C6   112.16  3.000
 476  H15  C18  H14  106.21  3.000
 476  H15  C18  C19  109.58  3.000
 476  H14  C18  C19  109.58  3.000
 476  H15  C18  C17  109.43  3.000
 476  H14  C18  C17  109.26  3.000
 476  C19  C18  C17  112.58  3.000
 476  H17  C19  H16  106.05  3.000
 476  H17  C19  C20  109.66  3.000
 476  H16  C19  C20  109.70  3.000
 476  H17  C19  C18  109.37  3.000
 476  H16  C19  C18  109.16  3.000
 476  C20  C19  C18  112.68  3.000
 476  H20  C20  H19  107.64  3.000
 476  H20  C20  H18  107.63  3.000
 476  H19  C20  H18  107.53  3.000
 476  H20  C20  C19  111.42  3.000
 476  H19  C20  C19  111.23  3.000
 476  H18  C20  C19  111.20  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   -84.51  30.0  2
 476  Var_02    C18  C17  C6   C1    78.37  30.0  2
 476  Var_03    N2   C7   C8   P10   61.07  30.0  1
 476  Var_04    C19  C18  C17  C6   177.68  30.0  1
 476  Var_05    C7   C8   P10  O11   44.33  30.0  3
 476  Var_06    O14  P9   C8   P10   52.25  30.0  3
 476  Var_07    C20  C19  C18  C17  178.45  30.0  3
 476  Var_08    H18  C20  C19  C18  -61.28  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

