# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 12:42:41 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-[(1E)-but-1-en-1-yl]-1-(2,2-diphosphonoethyl)pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC/C=C/c1ccc[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
 PB6  PB6  3-[(1E)-but-1-en-1-yl]-1-(2,2-diphosphonoethyl)pyridinium  ligand  34  20  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PB6
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
 PB6  C7    C  CH2    0  -0.329  -1.0205  -1.2114  -0.6392
 PB6  C8    C  CH1    0  -0.748  -1.8190  -0.2321   0.2011
 PB6  P9    P  P      0   1.195  -0.9954   1.4431   0.1996
 PB6  O10   O  OP    -1  -0.882   0.2708   1.2346   1.0657
 PB6  O11   O  O      0  -0.901  -0.6287   1.7264  -1.2696
 PB6  N12   N  NR6    1  -0.387   0.3558  -1.4340  -0.1373
 PB6  O12   O  OP    -1  -0.889  -1.9674   2.4517   0.8120
 PB6  C13   C  CR16   0   0.041   0.5825  -2.4378   0.7214
 PB6  C14   C  CR16   0  -0.349   1.8321  -2.6278   1.2550
 PB6  P14   P  P      0   1.179  -3.6032  -0.3205  -0.3719
 PB6  C15   C  CR16   0  -0.180   2.8638  -1.7718   0.8878
 PB6  O15   O  OP    -1  -0.924  -3.8697  -1.8345  -0.5230
 PB6  C16   C  CR6    0   0.008   2.6195  -0.7302   0.0039
 PB6  O16   O  OP    -1  -0.909  -4.4427   0.3082   0.7446
 PB6  C17   C  CR16   0   0.089   1.3149  -0.5662  -0.4572
 PB6  O17   O  O      0  -0.915  -3.6750   0.4177  -1.7137
 PB6  C18   C  C1     0  -0.298   3.6344   0.2163  -0.4591
 PB6  C19   C  C1     0  -0.196   4.9514   0.0077  -0.4381
 PB6  C20   C  CH2    0  -0.485   5.9741   0.9819  -0.9201
 PB6  C21   C  CH3    0  -0.662   6.9455   1.3883   0.1870
 PB6  H7    H  HCH2   0   0.244  -1.5012  -2.1874  -0.6688
 PB6  H7A   H  HCH2   0   0.249  -0.9272  -0.8431  -1.6590
 PB6  H8    H  HCH1   0   0.174  -1.8195  -0.6046   1.2355
 PB6  H13   H  HCR6   0   0.322  -0.2573  -3.0752   0.9550
 PB6  H14   H  HCR6   0   0.294   1.9971  -3.4427   1.9437
 PB6  H15   H  HCR6   0   0.281   3.8511  -1.9202   1.3057
 PB6  H17   H  HCR6   0   0.316   1.0340   0.2132  -1.1542
 PB6  H18   H  H      0   0.252   3.2526   1.1435  -0.8767
 PB6  H19   H  H      0   0.250   5.3428  -0.9289  -0.0478
 PB6  H20   H  HCH2   0   0.240   6.5417   0.5221  -1.7353
 PB6  H20A  H  HCH2   0   0.238   5.4852   1.8657  -1.3355
 PB6  H21   H  HCH3   0   0.234   7.7219   2.0476  -0.2015
 PB6  H21A  H  HCH3   0   0.227   6.4283   1.9132   0.9902
 PB6  H21B  H  HCH3   0   0.225   7.4368   0.5157   0.6202

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
 PB6  C7   C8    single    1.517  0.020  1.517
 PB6  C7   N12   single    1.482  0.020  1.482
 PB6  C7   H7    single    0.970  0.020  1.090
 PB6  C7   H7A   single    0.970  0.020  1.090
 PB6  C8   P9    single    1.867  0.020  1.867
 PB6  C8   P14   single    1.876  0.020  1.876
 PB6  C8   H8    single    0.970  0.020  1.090
 PB6  P9   O10   deloc     1.548  0.020  1.548
 PB6  P9   O11   deloc     1.541  0.020  1.541
 PB6  P9   O12   deloc     1.529  0.020  1.529
 PB6  N12  C13   aromatic  1.340  0.020  1.340
 PB6  N12  C17   aromatic  1.332  0.020  1.332
 PB6  C13  C14   aromatic  1.372  0.020  1.372
 PB6  C13  H13   single    0.930  0.020  1.080
 PB6  C14  C15   aromatic  1.390  0.020  1.390
 PB6  C14  H14   single    0.930  0.020  1.080
 PB6  P14  O15   deloc     1.545  0.020  1.545
 PB6  P14  O16   deloc     1.532  0.020  1.532
 PB6  P14  O17   deloc     1.533  0.020  1.533
 PB6  C15  C16   aromatic  1.388  0.020  1.388
 PB6  C15  H15   single    0.930  0.020  1.080
 PB6  C16  C17   aromatic  1.393  0.020  1.393
 PB6  C16  C18   single    1.463  0.020  1.463
 PB6  C17  H17   single    0.930  0.020  1.080
 PB6  C18  C19   double    1.334  0.020  1.334
 PB6  C18  H18   single    0.930  0.020  1.080
 PB6  C19  C20   single    1.492  0.020  1.492
 PB6  C19  H19   single    0.930  0.020  1.080
 PB6  C20  C21   single    1.528  0.020  1.528
 PB6  C20  H20   single    0.970  0.020  1.090
 PB6  C20  H20A  single    0.970  0.020  1.090
 PB6  C21  H21   single    0.970  0.020  1.090
 PB6  C21  H21A  single    0.970  0.020  1.090
 PB6  C21  H21B  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
 PB6  H7A   C7   H7    108.41  3.000
 PB6  H7A   C7   N12   106.77  3.000
 PB6  H7    C7   N12   106.55  3.000
 PB6  H7A   C7   C8    110.22  3.000
 PB6  H7    C7   C8    111.19  3.000
 PB6  N12   C7   C8    113.46  3.000
 PB6  H8    C8   P14   105.73  3.000
 PB6  H8    C8   P9    107.76  3.000
 PB6  P14   C8   P9    117.49  3.000
 PB6  H8    C8   C7    107.61  3.000
 PB6  P14   C8   C7    107.51  3.000
 PB6  P9    C8   C7    110.28  3.000
 PB6  O12   P9   O11   114.34  3.000
 PB6  O12   P9   O10   112.63  3.000
 PB6  O11   P9   O10   111.32  3.000
 PB6  O12   P9   C8    108.13  3.000
 PB6  O11   P9   C8    105.71  3.000
 PB6  O10   P9   C8    103.86  3.000
 PB6  C17   N12  C13   121.33  3.000
 PB6  C17   N12  C7    119.30  3.000
 PB6  C13   N12  C7    119.11  3.000
 PB6  H13   C13  C14   122.85  3.000
 PB6  H13   C13  N12   116.69  3.000
 PB6  C14   C13  N12   120.46  3.000
 PB6  H14   C14  C15   121.32  3.000
 PB6  H14   C14  C13   119.46  3.000
 PB6  C15   C14  C13   119.21  3.000
 PB6  O17   P14  O16   114.49  3.000
 PB6  O17   P14  O15   112.23  3.000
 PB6  O16   P14  O15   112.27  3.000
 PB6  O17   P14  C8    106.81  3.000
 PB6  O16   P14  C8    106.21  3.000
 PB6  O15   P14  C8    103.90  3.000
 PB6  H15   C15  C16   120.62  3.000
 PB6  H15   C15  C14   119.39  3.000
 PB6  C16   C15  C14   119.99  3.000
 PB6  C18   C16  C17   117.95  3.000
 PB6  C18   C16  C15   124.41  3.000
 PB6  C17   C16  C15   117.64  3.000
 PB6  H17   C17  C16   122.73  3.000
 PB6  H17   C17  N12   115.89  3.000
 PB6  C16   C17  N12   121.19  3.000
 PB6  H18   C18  C19   119.13  3.000
 PB6  H18   C18  C16   115.47  3.000
 PB6  C19   C18  C16   125.37  3.000
 PB6  H19   C19  C20   115.56  3.000
 PB6  H19   C19  C18   119.72  3.000
 PB6  C20   C19  C18   124.72  3.000
 PB6  H20A  C20  H20   106.79  3.000
 PB6  H20A  C20  C21   110.19  3.000
 PB6  H20   C20  C21   108.76  3.000
 PB6  H20A  C20  C19   110.14  3.000
 PB6  H20   C20  C19   108.76  3.000
 PB6  C21   C20  C19   112.04  3.000
 PB6  H21B  C21  H21A  107.83  3.000
 PB6  H21B  C21  H21   107.73  3.000
 PB6  H21A  C21  H21   108.01  3.000
 PB6  H21B  C21  C20   111.19  3.000
 PB6  H21A  C21  C20   111.12  3.000
 PB6  H21   C21  C20   110.82  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
 PB6  CONST_01  C15  C14  C13  N12    0.00   0.0  0
 PB6  CONST_02  C15  C16  C17  N12    0.00   0.0  0
 PB6  CONST_03  C16  C17  N12  C13    0.00   0.0  0
 PB6  CONST_04  C16  C15  C14  C13    0.00   0.0  0
 PB6  CONST_05  C17  N12  C13  C14    0.00   0.0  0
 PB6  CONST_06  C17  C16  C15  C14    0.00   0.0  0
 PB6  CONST_07  C14  C13  N12  C7   180.00   0.0  0
 PB6  CONST_08  C16  C17  N12  C7   180.00   0.0  0
 PB6  CONST_09  C18  C16  C17  N12  180.00   0.0  0
 PB6  CONST_10  C18  C16  C15  C14  180.00   0.0  0
 PB6  CONST_11  H14  C14  C13  N12  180.00   0.0  0
 PB6  CONST_12  H17  C17  N12  C13  180.00   0.0  0
 PB6  CONST_13  H15  C15  C14  C13  180.00   0.0  0
 PB6  CONST_14  H13  C13  C14  C15  180.00   0.0  0
 PB6  Var_01    C13  N12  C7   C8    91.70  30.0  2
 PB6  Var_02    C19  C18  C16  C15   20.93  30.0  2
 PB6  Var_03    C20  C19  C18  C16  179.72   0.0  2
 PB6  Var_04    N12  C7   C8   P9    61.34  30.0  1
 PB6  Var_05    O10  P9   C8   C7   -71.40  30.0  3
 PB6  Var_06    O15  P14  C8   C7    43.80  30.0  3
 PB6  Var_07    C21  C20  C19  C18  120.26  30.0  3
 PB6  Var_08    H21  C21  C20  C19  176.27  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
 PB6  plan-1  C7   0.020
 PB6  plan-1  N12  0.020
 PB6  plan-1  C13  0.020
 PB6  plan-1  C14  0.020
 PB6  plan-1  C15  0.020
 PB6  plan-1  C16  0.020
 PB6  plan-1  C17  0.020
 PB6  plan-1  C18  0.020
 PB6  plan-1  H13  0.020
 PB6  plan-1  H14  0.020
 PB6  plan-1  H15  0.020
 PB6  plan-1  H17  0.020
 PB6  plan-2  C16  0.020
 PB6  plan-2  C18  0.020
 PB6  plan-2  C19  0.020
 PB6  plan-2  C20  0.020
 PB6  plan-2  H18  0.020
 PB6  plan-2  H19  0.020

