# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:41:14 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: [1-phosphono-2-(1-propylpyridin-2-yl)ethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[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
 C6M  C6M  '[1-phosphono-2-(1-propylpyridin-2-yl)ethyl]phosphonic acid'  ligand  37  19  .  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_C6M
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
 C6M  OAN  O  O     0  -0.689  41.3887  18.9499   9.7171
 C6M  PAL  P  P     0   1.403  41.2341  17.7291  10.5388
 C6M  OAO  O  OH1   0  -0.754  39.8529  16.9237  10.3848
 C6M  OAM  O  OH1   0  -0.735  42.3009  16.5659  10.2402
 C6M  CAK  C  CH1   0  -0.848  41.2578  18.0009  12.3411
 C6M  PAP  P  P     0   1.391  39.6605  18.6352  12.9537
 C6M  OAR  O  OH1   0  -0.741  38.6654  17.3834  12.9980
 C6M  OAS  O  O     0  -0.697  39.2082  19.8453  12.2294
 C6M  OAQ  O  OH1   0  -0.737  39.8627  18.7945  14.5353
 C6M  CAJ  C  CH2   0  -0.566  42.4172  18.9610  12.7021
 C6M  CAF  C  CR6   0   0.305  43.7463  18.3661  12.3603
 C6M  CAE  C  CR16  0  -0.384  44.4570  18.7661  11.2622
 C6M  CAD  C  CR16  0  -0.265  45.6123  18.0890  10.8254
 C6M  CAC  C  CR16  0  -0.346  46.0080  16.9555  11.5751
 C6M  CAB  C  CR16  0  -0.040  45.3100  16.5797  12.6758
 C6M  NAA  N  NR6   0  -0.493  44.1728  17.2556  13.0996
 C6M  CAG  C  CH2   0  -0.327  43.7601  17.0679  14.4807
 C6M  CAH  C  CH2   0  -0.429  44.4811  17.9878  15.4600
 C6M  CAI  C  CH3   0  -0.666  44.0216  17.7474  16.8902
 C6M  H1   H  HOH1  0   0.507  39.5006  16.8834   9.4840
 C6M  H2   H  HOH1  0   0.495  43.2064  16.8905  10.1233
 C6M  H3   H  HCH1  0   0.343  41.4218  17.0264  12.8133
 C6M  H4   H  HOH1  0   0.496  38.5543  16.9506  12.1388
 C6M  H5   H  HOH1  0   0.501  40.0065  19.7065  14.8199
 C6M  H6   H  HCH2  0   0.282  42.3569  19.2165  13.7622
 C6M  H7   H  HCH2  0   0.299  42.2998  19.8990  12.1603
 C6M  H8   H  HCR6  0   0.265  44.0797  19.6114  10.7005
 C6M  H9   H  HCR6  0   0.245  46.1664  18.4228   9.9611
 C6M  H10  H  HCR6  0   0.257  46.8674  16.3664  11.2837
 C6M  H11  H  HCR6  0   0.278  45.5903  15.7223  13.2720
 C6M  H12  H  HCH2  0   0.246  42.6799  17.2008  14.5708
 C6M  H13  H  HCH2  0   0.261  43.9523  16.0252  14.7410
 C6M  H14  H  HCH2  0   0.233  45.5590  17.8255  15.3763
 C6M  H15  H  HCH2  0   0.229  44.3006  19.0308  15.1833
 C6M  H16  H  HCH3  0   0.237  44.5449  18.4007  17.5879
 C6M  H17  H  HCH3  0   0.222  42.9525  17.9386  16.9996
 C6M  H18  H  HCH3  0   0.224  44.2060  16.7172  17.1997

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
 C6M  OAN  PAL  double    1.480  0.020  1.480
 C6M  CAD  CAE  aromatic  1.409  0.020  1.409
 C6M  CAD  CAC  aromatic  1.415  0.020  1.415
 C6M  CAE  CAF  aromatic  1.368  0.020  1.368
 C6M  PAL  OAM  single    1.606  0.020  1.606
 C6M  PAL  OAO  single    1.606  0.020  1.606
 C6M  PAL  CAK  single    1.823  0.020  1.823
 C6M  OAS  PAP  double    1.481  0.020  1.481
 C6M  CAC  CAB  aromatic  1.356  0.020  1.356
 C6M  CAF  CAJ  single    1.496  0.020  1.496
 C6M  CAF  NAA  aromatic  1.401  0.020  1.401
 C6M  CAJ  CAK  single    1.548  0.020  1.548
 C6M  CAK  PAP  single    1.825  0.020  1.825
 C6M  CAB  NAA  aromatic  1.389  0.020  1.389
 C6M  PAP  OAR  single    1.600  0.020  1.600
 C6M  PAP  OAQ  single    1.602  0.020  1.602
 C6M  NAA  CAG  single    1.454  0.020  1.454
 C6M  CAG  CAH  single    1.525  0.020  1.525
 C6M  CAH  CAI  single    1.521  0.020  1.521
 C6M  OAO  H1   single    0.850  0.020  0.980
 C6M  OAM  H2   single    0.850  0.020  0.980
 C6M  CAK  H3   single    0.970  0.020  1.090
 C6M  OAR  H4   single    0.850  0.020  0.980
 C6M  OAQ  H5   single    0.850  0.020  0.980
 C6M  CAJ  H6   single    0.970  0.020  1.090
 C6M  CAJ  H7   single    0.970  0.020  1.090
 C6M  CAE  H8   single    0.930  0.020  1.080
 C6M  CAD  H9   single    0.930  0.020  1.080
 C6M  CAC  H10  single    0.930  0.020  1.080
 C6M  CAB  H11  single    0.930  0.020  1.080
 C6M  CAG  H12  single    0.970  0.020  1.090
 C6M  CAG  H13  single    0.970  0.020  1.090
 C6M  CAH  H14  single    0.970  0.020  1.090
 C6M  CAH  H15  single    0.970  0.020  1.090
 C6M  CAI  H16  single    0.970  0.020  1.090
 C6M  CAI  H17  single    0.970  0.020  1.090
 C6M  CAI  H18  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
 C6M  CAK  PAL  OAM  106.45  3.000
 C6M  CAK  PAL  OAO  100.41  3.000
 C6M  OAM  PAL  OAO  100.97  3.000
 C6M  CAK  PAL  OAN  115.13  3.000
 C6M  OAO  PAL  OAN  116.77  3.000
 C6M  OAM  PAL  OAN  115.14  3.000
 C6M  H1   OAO  PAL  115.02  3.000
 C6M  H2   OAM  PAL  113.61  3.000
 C6M  H3   CAK  CAJ  109.83  3.000
 C6M  H3   CAK  PAP  107.20  3.000
 C6M  CAJ  CAK  PAP  111.21  3.000
 C6M  H3   CAK  PAL  107.18  3.000
 C6M  PAP  CAK  PAL  111.86  3.000
 C6M  CAJ  CAK  PAL  109.44  3.000
 C6M  OAQ  PAP  OAS  116.10  3.000
 C6M  OAQ  PAP  OAR   97.41  3.000
 C6M  OAS  PAP  OAR  117.58  3.000
 C6M  OAQ  PAP  CAK  104.80  3.000
 C6M  OAR  PAP  CAK  106.37  3.000
 C6M  OAS  PAP  CAK  112.78  3.000
 C6M  H4   OAR  PAP  113.36  3.000
 C6M  H5   OAQ  PAP  113.79  3.000
 C6M  H7   CAJ  H6   105.98  3.000
 C6M  H7   CAJ  CAF  108.93  3.000
 C6M  H6   CAJ  CAF  111.34  3.000
 C6M  H7   CAJ  CAK  109.71  3.000
 C6M  H6   CAJ  CAK  109.28  3.000
 C6M  CAF  CAJ  CAK  111.45  3.000
 C6M  NAA  CAF  CAE  119.82  3.000
 C6M  NAA  CAF  CAJ  117.73  3.000
 C6M  CAE  CAF  CAJ  121.93  3.000
 C6M  H8   CAE  CAD  120.02  3.000
 C6M  H8   CAE  CAF  117.62  3.000
 C6M  CAD  CAE  CAF  122.32  3.000
 C6M  H9   CAD  CAC  121.88  3.000
 C6M  H9   CAD  CAE  121.37  3.000
 C6M  CAC  CAD  CAE  116.75  3.000
 C6M  H10  CAC  CAB  118.46  3.000
 C6M  H10  CAC  CAD  121.03  3.000
 C6M  CAB  CAC  CAD  120.51  3.000
 C6M  H11  CAB  NAA  115.46  3.000
 C6M  H11  CAB  CAC  122.25  3.000
 C6M  NAA  CAB  CAC  122.28  3.000
 C6M  CAG  NAA  CAB  117.36  3.000
 C6M  CAG  NAA  CAF  121.16  3.000
 C6M  CAB  NAA  CAF  118.30  3.000
 C6M  H13  CAG  H12  105.70  3.000
 C6M  H13  CAG  CAH  109.87  3.000
 C6M  H12  CAG  CAH  109.96  3.000
 C6M  H13  CAG  NAA  107.45  3.000
 C6M  H12  CAG  NAA  110.09  3.000
 C6M  CAH  CAG  NAA  113.46  3.000
 C6M  H15  CAH  H14  106.55  3.000
 C6M  H15  CAH  CAI  109.79  3.000
 C6M  H14  CAH  CAI  110.26  3.000
 C6M  H15  CAH  CAG  109.55  3.000
 C6M  H14  CAH  CAG  109.11  3.000
 C6M  CAI  CAH  CAG  111.45  3.000
 C6M  H18  CAI  H17  107.60  3.000
 C6M  H18  CAI  H16  107.65  3.000
 C6M  H17  CAI  H16  107.53  3.000
 C6M  H18  CAI  CAH  111.39  3.000
 C6M  H17  CAI  CAH  111.25  3.000
 C6M  H16  CAI  CAH  111.23  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
 C6M  CONST_01  CAC  CAD  CAE  CAF     0.00   0.0  0
 C6M  CONST_02  CAC  CAB  NAA  CAF     0.00   0.0  0
 C6M  CONST_03  CAB  CAC  CAD  CAE     0.00   0.0  0
 C6M  CONST_04  CAB  NAA  CAF  CAE     0.00   0.0  0
 C6M  CONST_05  NAA  CAF  CAE  CAD     0.00   0.0  0
 C6M  CONST_06  NAA  CAB  CAC  CAD     0.00   0.0  0
 C6M  CONST_07  CAD  CAE  CAF  CAJ   180.00   0.0  0
 C6M  CONST_08  CAB  NAA  CAF  CAJ   180.00   0.0  0
 C6M  CONST_11  H9   CAD  CAE  CAF   180.00   0.0  0
 C6M  CONST_12  H11  CAB  NAA  CAF   180.00   0.0  0
 C6M  CONST_13  H10  CAC  CAD  CAE   180.00   0.0  0
 C6M  CONST_14  H8   CAE  CAD  CAC   180.00   0.0  0
 C6M  Var_01    CAE  CAF  CAJ  CAK   103.91  30.0  2
 C6M  Var_02    CAH  CAG  NAA  CAF   -75.14  30.0  2
 C6M  Var_03    CAF  CAJ  CAK  PAL   -63.23  30.0  2
 C6M  Var_04    CAI  CAH  CAG  NAA  -179.64  30.0  3
 C6M  Var_05    CAJ  CAK  PAL  OAN   -45.18  30.0  3
 C6M  Var_06    OAS  PAP  CAK  PAL   -53.43  30.0  3
 C6M  Var_07    H16  CAI  CAH  CAG   179.53  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
 C6M  plan-1  CAJ  0.020
 C6M  plan-1  CAF  0.020
 C6M  plan-1  CAE  0.020
 C6M  plan-1  CAD  0.020
 C6M  plan-1  CAC  0.020
 C6M  plan-1  CAB  0.020
 C6M  plan-1  NAA  0.020
 C6M  plan-1  CAG  0.020
 C6M  plan-1  H8   0.020
 C6M  plan-1  H9   0.020
 C6M  plan-1  H10  0.020
 C6M  plan-1  H11  0.020

