# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 01:23:55 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: [2-(1-methylpyridin-2-yl)-1-phosphono-ethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n]1ccccc1CC([P](O)(O)=O)[P](O)(O)=O
#
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
 C6J  C6J  '[2-(1-methylpyridin-2-yl)-1-phosphono-ethyl]phosphonic acid'  ligand  31  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C6J
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
 C6J  OAL  O  OH1   0  -0.734  40.2744  16.2697  10.9988
 C6J  PAK  P  P     0   1.393  41.5660  17.1963  10.8349
 C6J  OAN  O  O     0  -0.695  41.6138  18.0935   9.6580
 C6J  OAM  O  OH1   0  -0.738  42.7497  16.1062  10.8957
 C6J  CAH  C  CH1   0  -0.848  41.5917  18.0465  12.4479
 C6J  PAI  P  P     0   1.405  39.9806  18.8202  12.8097
 C6J  OAO  O  OH1   0  -0.741  40.2566  19.7890  14.0641
 C6J  OAQ  O  O     0  -0.699  39.3374  19.4853  11.6530
 C6J  OAP  O  OH1   0  -0.733  39.1973  17.6105  13.4984
 C6J  CAG  C  CH2   0  -0.558  42.7281  19.1000  12.4689
 C6J  CAE  C  CR6   0   0.299  44.0748  18.5578  12.1000
 C6J  CAD  C  CR16  0  -0.369  44.6442  18.8353  10.8886
 C6J  CAC  C  CR16  0  -0.260  45.8773  18.2822  10.4840
 C6J  CAB  C  CR16  0  -0.345  46.5037  17.3985  11.3916
 C6J  CAA  C  CR16  0  -0.045  45.9420  17.1377  12.5990
 C6J  NAF  N  NR6   0  -0.496  44.7520  17.7332  13.0035
 C6J  CAJ  C  CH3   0  -0.552  44.1689  17.2724  14.2429
 C6J  H1   H  HOH1  0   0.499  40.0068  15.8134  10.1886
 C6J  H2   H  HOH1  0   0.493  43.5912  16.4361  10.5491
 C6J  H3   H  HCH1  0   0.340  41.7625  17.2914  13.2197
 C6J  H4   H  HOH1  0   0.497  40.3274  20.7239  13.8309
 C6J  H5   H  HOH1  0   0.498  38.2421  17.7481  13.5674
 C6J  H6   H  HCH2  0   0.289  42.7549  19.5655  13.4564
 C6J  H7   H  HCH2  0   0.295  42.4922  19.8974  11.7631
 C6J  H8   H  HCR6  0   0.260  44.1016  19.4895  10.2191
 C6J  H9   H  HCR6  0   0.241  46.3064  18.5101   9.5201
 C6J  H10  H  HCR6  0   0.256  47.4390  16.9139  11.1454
 C6J  H11  H  HCR6  0   0.278  46.3941  16.4668  13.3147
 C6J  H12  H  HCH3  0   0.269  44.9630  17.0743  14.9607
 C6J  H13  H  HCH3  0   0.261  43.5222  18.0267  14.6833
 C6J  H14  H  HCH3  0   0.242  43.5953  16.3494  14.1141

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
 C6J  OAN  PAK  double    1.481  0.020  1.481
 C6J  CAC  CAD  aromatic  1.411  0.020  1.411
 C6J  CAC  CAB  aromatic  1.413  0.020  1.413
 C6J  CAD  CAE  aromatic  1.367  0.020  1.367
 C6J  PAK  OAM  single    1.610  0.020  1.610
 C6J  PAK  OAL  single    1.598  0.020  1.598
 C6J  PAK  CAH  single    1.824  0.020  1.824
 C6J  OAQ  PAI  double    1.481  0.020  1.481
 C6J  CAB  CAA  aromatic  1.357  0.020  1.357
 C6J  CAE  CAG  single    1.498  0.020  1.498
 C6J  CAE  NAF  aromatic  1.398  0.020  1.398
 C6J  CAG  CAH  single    1.550  0.020  1.550
 C6J  CAA  NAF  aromatic  1.391  0.020  1.391
 C6J  CAH  PAI  single    1.824  0.020  1.824
 C6J  PAI  OAP  single    1.597  0.020  1.597
 C6J  PAI  OAO  single    1.609  0.020  1.609
 C6J  NAF  CAJ  single    1.445  0.020  1.445
 C6J  OAL  H1   single    0.850  0.020  0.980
 C6J  OAM  H2   single    0.850  0.020  0.980
 C6J  CAH  H3   single    0.970  0.020  1.090
 C6J  OAO  H4   single    0.850  0.020  0.980
 C6J  OAP  H5   single    0.850  0.020  0.980
 C6J  CAG  H6   single    0.970  0.020  1.090
 C6J  CAG  H7   single    0.970  0.020  1.090
 C6J  CAD  H8   single    0.930  0.020  1.080
 C6J  CAC  H9   single    0.930  0.020  1.080
 C6J  CAB  H10  single    0.930  0.020  1.080
 C6J  CAA  H11  single    0.930  0.020  1.080
 C6J  CAJ  H12  single    0.970  0.020  1.090
 C6J  CAJ  H13  single    0.970  0.020  1.090
 C6J  CAJ  H14  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
 C6J  H1   OAL  PAK  114.27  3.000
 C6J  CAH  PAK  OAM  105.78  3.000
 C6J  CAH  PAK  OAN  114.84  3.000
 C6J  OAM  PAK  OAN  114.61  3.000
 C6J  CAH  PAK  OAL  101.01  3.000
 C6J  OAM  PAK  OAL  101.41  3.000
 C6J  OAN  PAK  OAL  117.32  3.000
 C6J  H2   OAM  PAK  113.26  3.000
 C6J  H3   CAH  CAG  110.21  3.000
 C6J  H3   CAH  PAI  106.92  3.000
 C6J  CAG  CAH  PAI  110.90  3.000
 C6J  H3   CAH  PAK  107.74  3.000
 C6J  PAI  CAH  PAK  111.15  3.000
 C6J  CAG  CAH  PAK  109.83  3.000
 C6J  OAP  PAI  OAQ  117.63  3.000
 C6J  OAP  PAI  OAO  101.77  3.000
 C6J  OAQ  PAI  OAO  114.40  3.000
 C6J  OAO  PAI  CAH  104.99  3.000
 C6J  OAP  PAI  CAH  101.39  3.000
 C6J  OAQ  PAI  CAH  114.79  3.000
 C6J  H4   OAO  PAI  114.02  3.000
 C6J  H5   OAP  PAI  114.03  3.000
 C6J  H7   CAG  H6   106.19  3.000
 C6J  H7   CAG  CAE  107.44  3.000
 C6J  H6   CAG  CAE  110.79  3.000
 C6J  H7   CAG  CAH  109.25  3.000
 C6J  H6   CAG  CAH  108.66  3.000
 C6J  CAE  CAG  CAH  114.20  3.000
 C6J  NAF  CAE  CAD  119.38  3.000
 C6J  NAF  CAE  CAG  119.33  3.000
 C6J  CAD  CAE  CAG  121.28  3.000
 C6J  H8   CAD  CAC  119.87  3.000
 C6J  H8   CAD  CAE  117.52  3.000
 C6J  CAC  CAD  CAE  122.59  3.000
 C6J  H9   CAC  CAB  121.96  3.000
 C6J  H9   CAC  CAD  121.38  3.000
 C6J  CAB  CAC  CAD  116.64  3.000
 C6J  H10  CAB  CAA  118.31  3.000
 C6J  H10  CAB  CAC  121.14  3.000
 C6J  CAA  CAB  CAC  120.55  3.000
 C6J  H11  CAA  NAF  115.55  3.000
 C6J  H11  CAA  CAB  122.39  3.000
 C6J  NAF  CAA  CAB  122.05  3.000
 C6J  CAJ  NAF  CAA  117.27  3.000
 C6J  CAJ  NAF  CAE  123.15  3.000
 C6J  CAA  NAF  CAE  118.62  3.000
 C6J  H14  CAJ  H13  108.74  3.000
 C6J  H14  CAJ  H12  107.85  3.000
 C6J  H13  CAJ  H12  107.05  3.000
 C6J  H14  CAJ  NAF  112.30  3.000
 C6J  H13  CAJ  NAF  111.49  3.000
 C6J  H12  CAJ  NAF  109.22  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
 C6J  CONST_01  CAB  CAC  CAD  CAE     0.00   0.0  0
 C6J  CONST_02  CAB  CAA  NAF  CAE     0.00   0.0  0
 C6J  CONST_03  CAA  CAB  CAC  CAD     0.00   0.0  0
 C6J  CONST_04  CAA  NAF  CAE  CAD     0.00   0.0  0
 C6J  CONST_05  NAF  CAE  CAD  CAC     0.00   0.0  0
 C6J  CONST_06  NAF  CAA  CAB  CAC     0.00   0.0  0
 C6J  CONST_07  CAC  CAD  CAE  CAG   180.00   0.0  0
 C6J  CONST_08  CAA  NAF  CAE  CAG   180.00   0.0  0
 C6J  CONST_09  CAJ  NAF  CAE  CAD   180.00   0.0  0
 C6J  CONST_10  CAJ  NAF  CAA  CAB   180.00   0.0  0
 C6J  CONST_11  H9   CAC  CAD  CAE   180.00   0.0  0
 C6J  CONST_12  H11  CAA  NAF  CAE   180.00   0.0  0
 C6J  CONST_13  H10  CAB  CAC  CAD   180.00   0.0  0
 C6J  CONST_14  H8   CAD  CAC  CAB   180.00   0.0  0
 C6J  Var_01    CAD  CAE  CAG  CAH   106.28  30.0  1
 C6J  Var_02    H12  CAJ  NAF  CAE  -153.37  30.0  2
 C6J  Var_03    CAE  CAG  CAH  PAK   -53.29  30.0  3
 C6J  Var_04    CAG  CAH  PAK  OAL  -175.60  30.0  3
 C6J  Var_05    OAQ  PAI  CAH  PAK   -41.02  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
 C6J  plan-1  CAG  0.020
 C6J  plan-1  CAE  0.020
 C6J  plan-1  CAD  0.020
 C6J  plan-1  CAC  0.020
 C6J  plan-1  CAB  0.020
 C6J  plan-1  CAA  0.020
 C6J  plan-1  NAF  0.020
 C6J  plan-1  CAJ  0.020
 C6J  plan-1  H8   0.020
 C6J  plan-1  H9   0.020
 C6J  plan-1  H10  0.020
 C6J  plan-1  H11  0.020

