# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:35:19 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: {[(3-methylpyridin-2-yl)amino]methanediyl}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccnc1NC([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
 3YQ  3YQ  '{[(3-methylpyridin-2-yl)amino]methanediyl}bis(phosphonic acid)'  ligand  29  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3YQ
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
 3YQ  O5   O  OH1   0  -0.738  -1.8893  -2.5462  -0.1066
 3YQ  P1   P  P     0   1.378  -0.9511  -1.5578   0.7299
 3YQ  O6   O  OH1   0  -0.759  -1.8606  -0.8697   1.8670
 3YQ  O2   O  O     0  -0.681   0.2560  -2.2618   1.2101
 3YQ  C6   C  CH1   0  -0.672  -0.6069  -0.0942  -0.3205
 3YQ  P2   P  P     0   1.402  -1.9873   1.0537  -0.6528
 3YQ  O3   O  O     0  -0.685  -1.7392   2.0355  -1.7280
 3YQ  O1   O  OH1   0  -0.756  -3.1628  -0.0123  -0.8965
 3YQ  O4   O  OH1   0  -0.744  -2.2947   1.8105   0.7238
 3YQ  N1   N  NH1   0  -0.696   0.4923   0.6658   0.2041
 3YQ  C1   C  CR6   0   0.509   1.7891   0.3954  -0.1706
 3YQ  N2   N  N     0  -0.470   1.9682  -0.4065  -1.2060
 3YQ  C5   C  CR16  0  -0.066   3.2088  -0.6550  -1.6186
 3YQ  C4   C  CR16  0  -0.358   4.3267  -0.1225  -1.0136
 3YQ  C3   C  CR16  0  -0.188   4.1269   0.7213   0.0785
 3YQ  C2   C  CR6   0  -0.027   2.8539   1.0065   0.5273
 3YQ  C7   C  CH3   0  -0.760   2.6018   1.9180   1.6884
 3YQ  H1   H  HOH1  0   0.494  -2.6931  -2.1476  -0.4715
 3YQ  H2   H  HOH1  0   0.506  -2.0526  -1.4231   2.6381
 3YQ  H3   H  HCH1  0   0.358  -0.3008  -0.4926  -1.2936
 3YQ  H4   H  HOH1  0   0.509  -3.9851   0.3416  -1.2659
 3YQ  H5   H  HOH1  0   0.494  -2.4945   1.2339   1.4762
 3YQ  H6   H  HNH1  0   0.406   0.3573   1.1039   1.1010
 3YQ  H7   H  HCR6  0   0.257   3.3029  -1.3152  -2.4735
 3YQ  H8   H  HCR6  0   0.260   5.3185  -0.3510  -1.3767
 3YQ  H9   H  HCR6  0   0.262   4.9767   1.1639   0.5845
 3YQ  H10  H  HCH3  0   0.248   2.0600   1.4162   2.4942
 3YQ  H11  H  HCH3  0   0.264   3.5398   2.2792   2.1059
 3YQ  H12  H  HCH3  0   0.253   2.0132   2.7913   1.3971

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
 3YQ  O2  P1   double    1.478  0.020  1.478
 3YQ  O6  P1   single    1.610  0.020  1.610
 3YQ  P1  O5   single    1.599  0.020  1.599
 3YQ  P1  C6   single    1.834  0.020  1.834
 3YQ  C6  N1   single    1.436  0.020  1.436
 3YQ  C6  P2   single    1.826  0.020  1.826
 3YQ  N1  C1   single    1.377  0.020  1.377
 3YQ  C7  C2   single    1.497  0.020  1.497
 3YQ  O3  P2   double    1.477  0.020  1.477
 3YQ  O4  P2   single    1.601  0.020  1.601
 3YQ  P2  O1   single    1.605  0.020  1.605
 3YQ  C1  C2   aromatic  1.412  0.020  1.412
 3YQ  C1  N2   aromatic  1.322  0.020  1.322
 3YQ  C2  C3   aromatic  1.380  0.020  1.380
 3YQ  N2  C5   aromatic  1.331  0.020  1.331
 3YQ  C3  C4   aromatic  1.395  0.020  1.395
 3YQ  C5  C4   aromatic  1.378  0.020  1.378
 3YQ  O5  H1   single    0.850  0.020  0.980
 3YQ  O6  H2   single    0.850  0.020  0.980
 3YQ  C6  H3   single    0.970  0.020  1.090
 3YQ  O1  H4   single    0.850  0.020  0.980
 3YQ  O4  H5   single    0.850  0.020  0.980
 3YQ  N1  H6   single    0.890  0.020  1.040
 3YQ  C5  H7   single    0.930  0.020  1.080
 3YQ  C4  H8   single    0.930  0.020  1.080
 3YQ  C3  H9   single    0.930  0.020  1.080
 3YQ  C7  H10  single    0.970  0.020  1.090
 3YQ  C7  H11  single    0.970  0.020  1.090
 3YQ  C7  H12  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
 3YQ  H1   O5  P1   115.45  3.000
 3YQ  C6   P1  O2   114.40  3.000
 3YQ  C6   P1  O6    99.75  3.000
 3YQ  O2   P1  O6   115.81  3.000
 3YQ  C6   P1  O5   107.68  3.000
 3YQ  O6   P1  O5   107.58  3.000
 3YQ  O2   P1  O5   110.78  3.000
 3YQ  H2   O6  P1   115.47  3.000
 3YQ  H3   C6  N1   107.65  3.000
 3YQ  H3   C6  P2   106.17  3.000
 3YQ  N1   C6  P2   108.21  3.000
 3YQ  H3   C6  P1   105.73  3.000
 3YQ  P2   C6  P1   117.65  3.000
 3YQ  N1   C6  P1   110.90  3.000
 3YQ  O4   P2  O1   107.69  3.000
 3YQ  O1   P2  O3   116.99  3.000
 3YQ  O4   P2  O3   110.13  3.000
 3YQ  O1   P2  C6    99.42  3.000
 3YQ  O4   P2  C6   106.61  3.000
 3YQ  O3   P2  C6   115.05  3.000
 3YQ  H4   O1  P2   115.91  3.000
 3YQ  H5   O4  P2   115.22  3.000
 3YQ  H6   N1  C1   117.01  3.000
 3YQ  H6   N1  C6   116.93  3.000
 3YQ  C1   N1  C6   121.19  3.000
 3YQ  C2   C1  N2   123.20  3.000
 3YQ  N2   C1  N1   117.38  3.000
 3YQ  C2   C1  N1   119.39  3.000
 3YQ  C5   N2  C1   118.84  3.000
 3YQ  H7   C5  C4   120.73  3.000
 3YQ  H7   C5  N2   116.04  3.000
 3YQ  C4   C5  N2   123.23  3.000
 3YQ  H8   C4  C3   121.50  3.000
 3YQ  H8   C4  C5   121.02  3.000
 3YQ  C3   C4  C5   117.48  3.000
 3YQ  H9   C3  C2   119.16  3.000
 3YQ  H9   C3  C4   120.04  3.000
 3YQ  C2   C3  C4   120.80  3.000
 3YQ  C7   C2  C3   122.23  3.000
 3YQ  C3   C2  C1   116.45  3.000
 3YQ  C7   C2  C1   121.31  3.000
 3YQ  H12  C7  H11  107.54  3.000
 3YQ  H12  C7  H10  107.24  3.000
 3YQ  H11  C7  H10  107.26  3.000
 3YQ  H12  C7  C2   111.74  3.000
 3YQ  H11  C7  C2   110.76  3.000
 3YQ  H10  C7  C2   112.06  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
 3YQ  CONST_01  C4   C3  C2  C1     0.00   0.0  0
 3YQ  CONST_02  C4   C5  N2  C1     0.00   0.0  0
 3YQ  CONST_03  C3   C2  C1  N2     0.00   0.0  0
 3YQ  CONST_04  C3   C4  C5  N2     0.00   0.0  0
 3YQ  CONST_05  C2   C1  N2  C5     0.00   0.0  0
 3YQ  CONST_06  C2   C3  C4  C5     0.00   0.0  0
 3YQ  CONST_07  C3   C2  C1  N1   180.00   0.0  0
 3YQ  CONST_08  C5   N2  C1  N1   180.00   0.0  0
 3YQ  CONST_09  C7   C2  C1  N2   180.00   0.0  0
 3YQ  CONST_10  C7   C2  C3  C4   180.00   0.0  0
 3YQ  CONST_11  H9   C3  C2  C1   180.00   0.0  0
 3YQ  CONST_12  H7   C5  N2  C1   180.00   0.0  0
 3YQ  CONST_13  H8   C4  C5  N2   180.00   0.0  0
 3YQ  CONST_14  C2   C1  N1  C6   180.00   0.0  0
 3YQ  CONST_15  N2   C1  N1  C6     0.00   0.0  0
 3YQ  CONST_16  H6   N1  C1  N2   180.00   0.0  0
 3YQ  Var_01    H10  C7  C2  C1    59.39  30.0  2
 3YQ  Var_02    C1   N1  C6  P1    89.37  30.0  3
 3YQ  Var_03    N1   C6  P1  O5  -164.88  30.0  3
 3YQ  Var_04    O3   P2  C6  P1  -167.15  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
 3YQ  plan-1  N1  0.020
 3YQ  plan-1  C1  0.020
 3YQ  plan-1  N2  0.020
 3YQ  plan-1  C5  0.020
 3YQ  plan-1  C4  0.020
 3YQ  plan-1  C3  0.020
 3YQ  plan-1  C2  0.020
 3YQ  plan-1  C7  0.020
 3YQ  plan-1  H7  0.020
 3YQ  plan-1  H8  0.020
 3YQ  plan-1  H9  0.020
 3YQ  plan-2  C6  0.020
 3YQ  plan-2  N1  0.020
 3YQ  plan-2  C1  0.020
 3YQ  plan-2  H6  0.020

