# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 18:47:33 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  33  19  .  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_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  -0.924  41.2386  19.3430   9.9098
 C6M  PAL  P  P      0   1.187  40.9737  17.8929  10.3670
 C6M  OAO  O  OP    -1  -0.918  39.5144  17.4674  10.1380
 C6M  OAM  O  OP    -1  -0.934  41.9635  16.8891   9.7433
 C6M  CAK  C  CH1    0  -0.738  41.3076  17.8322  12.2097
 C6M  PAP  P  P      0   1.168  39.8835  18.0951  13.3750
 C6M  OAR  O  OP    -1  -0.925  38.9235  16.9060  13.2116
 C6M  OAS  O  O      0  -0.934  39.2639  19.4616  13.0365
 C6M  OAQ  O  OP    -1  -0.904  40.5246  18.0955  14.7897
 C6M  CAJ  C  CH2    0  -0.529  42.4540  18.7980  12.5619
 C6M  CAF  C  CR6    0   0.359  43.8180  18.2982  12.2168
 C6M  CAE  C  CR16   0  -0.382  44.4987  18.7144  11.1144
 C6M  CAD  C  CR16   0  -0.275  45.7886  18.2243  10.7784
 C6M  CAC  C  CR16   0  -0.359  46.3447  17.2623  11.6430
 C6M  CAB  C  CR16   0  -0.066  45.6584  16.8398  12.7409
 C6M  NAA  N  NR6    0  -0.502  44.3850  17.3163  13.0380
 C6M  CAG  C  CH2    0  -0.347  43.8418  17.0172  14.3482
 C6M  CAH  C  CH2    0  -0.417  44.3554  17.9382  15.4522
 C6M  CAI  C  CH3    0  -0.680  43.6141  17.6834  16.7564
 C6M  H3   H  HCH1   0   0.157  41.6507  16.8077  12.4092
 C6M  H6   H  HCH2   0   0.218  42.4132  19.0413  13.6271
 C6M  H7   H  HCH2   0   0.216  42.2901  19.7278  12.0200
 C6M  H8   H  HCR6   0   0.221  43.9858  19.4152  10.4683
 C6M  H9   H  HCR6   0   0.214  46.3169  18.5724   9.9022
 C6M  H10  H  HCR6   0   0.234  47.3232  16.8380  11.4547
 C6M  H11  H  HCR6   0   0.251  46.0525  16.0993  13.4233
 C6M  H12  H  HCH2   0   0.284  42.7532  17.0815  14.3206
 C6M  H13  H  HCH2   0   0.228  44.0946  15.9801  14.5890
 C6M  H14  H  HCH2   0   0.213  45.4333  17.8046  15.5849
 C6M  H15  H  HCH2   0   0.215  44.2040  18.9768  15.1443
 C6M  H16  H  HCH3   0   0.222  43.9562  18.3472  17.5511
 C6M  H17  H  HCH3   0   0.234  42.5449  17.8440  16.6092
 C6M  H18  H  HCH3   0   0.211  43.7558  16.6571  17.1024

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  deloc     1.543  0.020  1.543
 C6M  CAD  CAE  aromatic  1.420  0.020  1.420
 C6M  CAD  CAC  aromatic  1.408  0.020  1.408
 C6M  CAE  CAF  aromatic  1.361  0.020  1.361
 C6M  PAL  OAM  deloc     1.542  0.020  1.542
 C6M  PAL  OAO  deloc     1.537  0.020  1.537
 C6M  PAL  CAK  single    1.874  0.020  1.874
 C6M  OAS  PAP  deloc     1.538  0.020  1.538
 C6M  CAC  CAB  aromatic  1.362  0.020  1.362
 C6M  CAF  CAJ  single    1.493  0.020  1.493
 C6M  CAF  NAA  aromatic  1.400  0.020  1.400
 C6M  CAJ  CAK  single    1.540  0.020  1.540
 C6M  CAK  PAP  single    1.859  0.020  1.859
 C6M  CAB  NAA  aromatic  1.392  0.020  1.392
 C6M  PAP  OAR  deloc     1.537  0.020  1.537
 C6M  PAP  OAQ  deloc     1.553  0.020  1.553
 C6M  NAA  CAG  single    1.449  0.020  1.449
 C6M  CAG  CAH  single    1.527  0.020  1.527
 C6M  CAH  CAI  single    1.522  0.020  1.522
 C6M  CAK  H3   single    0.970  0.020  1.090
 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  105.21  3.000
 C6M  CAK  PAL  OAO  107.86  3.000
 C6M  OAM  PAL  OAO  111.65  3.000
 C6M  CAK  PAL  OAN  106.93  3.000
 C6M  OAO  PAL  OAN  112.26  3.000
 C6M  OAM  PAL  OAN  112.44  3.000
 C6M  H3   CAK  CAJ  108.11  3.000
 C6M  H3   CAK  PAP  104.91  3.000
 C6M  CAJ  CAK  PAP  109.77  3.000
 C6M  H3   CAK  PAL  105.33  3.000
 C6M  PAP  CAK  PAL  118.39  3.000
 C6M  CAJ  CAK  PAL  109.71  3.000
 C6M  OAQ  PAP  OAS  111.50  3.000
 C6M  OAQ  PAP  OAR  110.78  3.000
 C6M  OAS  PAP  OAR  114.35  3.000
 C6M  OAQ  PAP  CAK  104.76  3.000
 C6M  OAR  PAP  CAK  107.61  3.000
 C6M  OAS  PAP  CAK  107.24  3.000
 C6M  H7   CAJ  H6   106.82  3.000
 C6M  H7   CAJ  CAF  107.96  3.000
 C6M  H6   CAJ  CAF  109.49  3.000
 C6M  H7   CAJ  CAK  108.05  3.000
 C6M  H6   CAJ  CAK  109.55  3.000
 C6M  CAF  CAJ  CAK  114.66  3.000
 C6M  NAA  CAF  CAE  119.15  3.000
 C6M  NAA  CAF  CAJ  117.99  3.000
 C6M  CAE  CAF  CAJ  122.80  3.000
 C6M  H8   CAE  CAD  120.83  3.000
 C6M  H8   CAE  CAF  116.40  3.000
 C6M  CAD  CAE  CAF  122.71  3.000
 C6M  H9   CAD  CAC  121.66  3.000
 C6M  H9   CAD  CAE  121.65  3.000
 C6M  CAC  CAD  CAE  116.69  3.000
 C6M  H10  CAC  CAB  118.29  3.000
 C6M  H10  CAC  CAD  121.18  3.000
 C6M  CAB  CAC  CAD  120.53  3.000
 C6M  H11  CAB  NAA  115.67  3.000
 C6M  H11  CAB  CAC  122.51  3.000
 C6M  NAA  CAB  CAC  121.80  3.000
 C6M  CAG  NAA  CAB  117.73  3.000
 C6M  CAG  NAA  CAF  121.54  3.000
 C6M  CAB  NAA  CAF  119.04  3.000
 C6M  H13  CAG  H12  106.97  3.000
 C6M  H13  CAG  CAH  109.57  3.000
 C6M  H12  CAG  CAH  108.57  3.000
 C6M  H13  CAG  NAA  107.93  3.000
 C6M  H12  CAG  NAA  109.82  3.000
 C6M  CAH  CAG  NAA  113.77  3.000
 C6M  H15  CAH  H14  106.64  3.000
 C6M  H15  CAH  CAI  109.44  3.000
 C6M  H14  CAH  CAI  110.82  3.000
 C6M  H15  CAH  CAG  108.83  3.000
 C6M  H14  CAH  CAG  110.21  3.000
 C6M  CAI  CAH  CAG  110.79  3.000
 C6M  H18  CAI  H17  107.95  3.000
 C6M  H18  CAI  H16  107.48  3.000
 C6M  H17  CAI  H16  108.43  3.000
 C6M  H18  CAI  CAH  111.45  3.000
 C6M  H17  CAI  CAH  109.70  3.000
 C6M  H16  CAI  CAH  111.70  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_09  CAG  NAA  CAF  CAE   180.00   0.0  0
 C6M  CONST_10  CAG  NAA  CAB  CAC   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   101.55  30.0  3
 C6M  Var_02    CAH  CAG  NAA  CAF   -84.59  30.0  2
 C6M  Var_03    CAF  CAJ  CAK  PAL   -76.87  30.0  3
 C6M  Var_04    CAI  CAH  CAG  NAA   172.77  30.0  3
 C6M  Var_05    CAJ  CAK  PAL  OAN   -33.89  30.0  3
 C6M  Var_06    OAS  PAP  CAK  PAL   -56.98  30.0  3
 C6M  Var_07    H16  CAI  CAH  CAG  -178.90  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

