# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 13:47:23 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  27  17  .  2021-08-07  2021-08-07  
;
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  OP    -1  -0.925  40.1769  16.1530  10.9491
 C6J  PAK  P  P      0   1.180  41.5239  16.8986  10.9649
 C6J  OAN  O  O      0  -0.921  41.7028  17.8230   9.7480
 C6J  OAM  O  OP    -1  -0.922  42.7056  15.9229  11.1613
 C6J  CAH  C  CH1    0  -0.732  41.5550  17.9613  12.4881
 C6J  PAI  P  P      0   1.169  40.0146  18.8969  12.9551
 C6J  OAO  O  OP    -1  -0.938  40.4388  19.7769  14.1559
 C6J  OAQ  O  O      0  -0.933  39.6149  19.7496  11.7383
 C6J  OAP  O  OP    -1  -0.925  38.9526  17.8655  13.3663
 C6J  CAG  C  CH2    0  -0.516  42.7191  18.9611  12.4243
 C6J  CAE  C  CR6    0   0.406  44.0913  18.4893  12.0508
 C6J  CAD  C  CR16   0  -0.392  44.6789  18.8521  10.8775
 C6J  CAC  C  CR16   0  -0.272  46.0083  18.4876  10.5337
 C6J  CAB  C  CR16   0  -0.356  46.7137  17.7175  11.4749
 C6J  CAA  C  CR16   0  -0.072  46.1288  17.3633  12.6524
 C6J  NAF  N  NR6    0  -0.505  44.8380  17.7667  12.9825
 C6J  CAJ  C  CH3    0  -0.519  44.2127  17.1235  14.1121
 C6J  H3   H  HCH1   0   0.152  41.7237  17.2684  13.3202
 C6J  H6   H  HCH2   0   0.200  42.7719  19.4908  13.3823
 C6J  H7   H  HCH2   0   0.206  42.4443  19.7147  11.6851
 C6J  H8   H  HCR6   0   0.216  44.0741  19.4150  10.1803
 C6J  H9   H  HCR6   0   0.212  46.4485  18.7770   9.5900
 C6J  H10  H  HCR6   0   0.233  47.7313  17.3956  11.2906
 C6J  H11  H  HCR6   0   0.250  46.6425  16.7793  13.4030
 C6J  H12  H  HCH3   0   0.234  44.9758  16.8714  14.8478
 C6J  H13  H  HCH3   0   0.244  43.4976  17.7867  14.5925
 C6J  H14  H  HCH3   0   0.226  43.6904  16.2113  13.8139

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  deloc     1.539  0.020  1.539
 C6J  CAC  CAD  aromatic  1.421  0.020  1.421
 C6J  CAC  CAB  aromatic  1.406  0.020  1.406
 C6J  CAD  CAE  aromatic  1.361  0.020  1.361
 C6J  PAK  OAM  deloc     1.545  0.020  1.545
 C6J  PAK  OAL  deloc     1.540  0.020  1.540
 C6J  PAK  CAH  single    1.858  0.020  1.858
 C6J  OAQ  PAI  deloc     1.539  0.020  1.539
 C6J  CAB  CAA  aromatic  1.362  0.020  1.362
 C6J  CAE  CAG  single    1.498  0.020  1.498
 C6J  CAE  NAF  aromatic  1.396  0.020  1.396
 C6J  CAG  CAH  single    1.536  0.020  1.536
 C6J  CAA  NAF  aromatic  1.392  0.020  1.392
 C6J  CAH  PAI  single    1.862  0.020  1.862
 C6J  PAI  OAP  deloc     1.536  0.020  1.536
 C6J  PAI  OAO  deloc     1.548  0.020  1.548
 C6J  NAF  CAJ  single    1.442  0.020  1.442
 C6J  CAH  H3   single    0.970  0.020  1.090
 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  CAH  PAK  OAM  104.14  3.000
 C6J  CAH  PAK  OAN  107.63  3.000
 C6J  OAM  PAK  OAN  113.02  3.000
 C6J  CAH  PAK  OAL  107.46  3.000
 C6J  OAM  PAK  OAL  111.39  3.000
 C6J  OAN  PAK  OAL  112.62  3.000
 C6J  H3   CAH  CAG  109.05  3.000
 C6J  H3   CAH  PAI  104.75  3.000
 C6J  CAG  CAH  PAI  108.08  3.000
 C6J  H3   CAH  PAK  105.28  3.000
 C6J  PAI  CAH  PAK  118.64  3.000
 C6J  CAG  CAH  PAK  110.55  3.000
 C6J  OAP  PAI  OAQ  113.83  3.000
 C6J  OAP  PAI  OAO  111.32  3.000
 C6J  OAQ  PAI  OAO  111.69  3.000
 C6J  OAO  PAI  CAH  104.69  3.000
 C6J  OAP  PAI  CAH  107.56  3.000
 C6J  OAQ  PAI  CAH  107.16  3.000
 C6J  H7   CAG  H6   105.70  3.000
 C6J  H7   CAG  CAE  106.22  3.000
 C6J  H6   CAG  CAE  109.03  3.000
 C6J  H7   CAG  CAH  106.67  3.000
 C6J  H6   CAG  CAH  108.35  3.000
 C6J  CAE  CAG  CAH  119.97  3.000
 C6J  NAF  CAE  CAD  118.84  3.000
 C6J  NAF  CAE  CAG  119.12  3.000
 C6J  CAD  CAE  CAG  121.75  3.000
 C6J  H8   CAD  CAC  120.07  3.000
 C6J  H8   CAD  CAE  116.94  3.000
 C6J  CAC  CAD  CAE  122.96  3.000
 C6J  H9   CAC  CAB  121.79  3.000
 C6J  H9   CAC  CAD  121.59  3.000
 C6J  CAB  CAC  CAD  116.62  3.000
 C6J  H10  CAB  CAA  118.26  3.000
 C6J  H10  CAB  CAC  121.35  3.000
 C6J  CAA  CAB  CAC  120.39  3.000
 C6J  H11  CAA  NAF  115.63  3.000
 C6J  H11  CAA  CAB  122.47  3.000
 C6J  NAF  CAA  CAB  121.87  3.000
 C6J  CAJ  NAF  CAA  117.29  3.000
 C6J  CAJ  NAF  CAE  121.45  3.000
 C6J  CAA  NAF  CAE  119.20  3.000
 C6J  H14  CAJ  H13  108.38  3.000
 C6J  H14  CAJ  H12  109.02  3.000
 C6J  H13  CAJ  H12  107.67  3.000
 C6J  H14  CAJ  NAF  111.45  3.000
 C6J  H13  CAJ  NAF  111.05  3.000
 C6J  H12  CAJ  NAF  109.17  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   111.80  30.0  3
 C6J  Var_02    H12  CAJ  NAF  CAE  -163.84  30.0  2
 C6J  Var_03    CAE  CAG  CAH  PAK   -47.83  30.0  3
 C6J  Var_04    CAG  CAH  PAK  OAL  -167.66  30.0  3
 C6J  Var_05    OAQ  PAI  CAH  PAK   -55.31  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

