# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 17:34:42 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: {[(5-chloropyridin-2-yl)amino]methanediyl}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C(Nc1ccc(Cl)cn1)[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
 CBQ  CBQ  '{[(5-chloropyridin-2-yl)amino]methanediyl}bis(phosphonic acid)'  ligand  26  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 OK
;

data_comp_CBQ
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
 CBQ  O1   O   OH1   0  -0.752   0.5388   0.8329   3.7209
 CBQ  P1   P   P     0   1.410   1.3253   0.0473   2.5666
 CBQ  O2   O   O     0  -0.686   1.7110  -1.3542   2.8258
 CBQ  O3   O   OH1   0  -0.729   2.6155   0.9098   2.1880
 CBQ  C1   C   CH1   0  -0.668   0.1419   0.2680   1.1845
 CBQ  N1   N   NH1   0  -0.676   0.6104  -0.5603   0.1108
 CBQ  C2   C   CR6   0   0.521   0.4132  -0.2982  -1.2180
 CBQ  N2   N   N     0  -0.457   0.7155  -1.3023  -2.0364
 CBQ  C3   C   CR16  0  -0.033   0.6048  -1.1309  -3.3443
 CBQ  C4   C   CR6   0  -0.138   0.1829   0.0591  -3.9071
 CBQ  CL1  CL  CL    0  -0.132   0.0586   0.2205  -5.6243
 CBQ  C5   C   CR16  0  -0.098  -0.1434   1.1130  -3.0639
 CBQ  C6   C   CR16  0  -0.387  -0.0355   0.9397  -1.7015
 CBQ  P2   P   P     0   1.377  -1.6243  -0.0757   1.5572
 CBQ  O4   O   O     0  -0.683  -2.4680  -0.1745   0.3471
 CBQ  O5   O   OH1   0  -0.738  -1.4787  -1.4053   2.4378
 CBQ  O6   O   OH1   0  -0.739  -2.1464   1.0964   2.5136
 CBQ  HO1  H   HOH1  0   0.511   0.9122   0.7575   4.6115
 CBQ  HO3  H   HOH1  0   0.499   2.4884   1.8642   2.1004
 CBQ  H1   H   HCH1  0   0.347   0.1922   1.3220   0.8971
 CBQ  HN1  H   HNH1  0   0.398   0.7861  -1.5314   0.3240
 CBQ  H3   H   HCR6  0   0.282   0.8622  -1.9776  -3.9710
 CBQ  H5   H   HCR6  0   0.293  -0.4858   2.0581  -3.4631
 CBQ  H6   H   HCR6  0   0.283  -0.2968   1.7555  -1.0439
 CBQ  HO5  H   HOH1  0   0.502  -2.3083  -1.8807   2.5901
 CBQ  HO6  H   HOH1  0   0.494  -1.6508   1.2136   3.3368

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
 CBQ  O1  P1   single    1.603  0.020  1.603
 CBQ  O1  HO1  single    0.850  0.020  0.980
 CBQ  P1  O2   double    1.477  0.020  1.477
 CBQ  P1  O3   single    1.597  0.020  1.597
 CBQ  P1  C1   single    1.833  0.020  1.833
 CBQ  O3  HO3  single    0.850  0.020  0.980
 CBQ  C1  N1   single    1.435  0.020  1.435
 CBQ  C1  P2   single    1.838  0.020  1.838
 CBQ  C1  H1   single    0.970  0.020  1.090
 CBQ  N1  C2   single    1.369  0.020  1.369
 CBQ  N1  HN1  single    0.890  0.020  1.040
 CBQ  C2  N2   aromatic  1.330  0.020  1.330
 CBQ  C2  C6   aromatic  1.403  0.020  1.403
 CBQ  N2  C3   aromatic  1.324  0.020  1.324
 CBQ  C3  C4   aromatic  1.382  0.020  1.382
 CBQ  C3  H3   single    0.930  0.020  1.080
 CBQ  C4  CL1  single    1.729  0.020  1.729
 CBQ  C4  C5   aromatic  1.389  0.020  1.389
 CBQ  C5  C6   aromatic  1.378  0.020  1.378
 CBQ  C5  H5   single    0.930  0.020  1.080
 CBQ  C6  H6   single    0.930  0.020  1.080
 CBQ  P2  O4   double    1.478  0.020  1.478
 CBQ  P2  O5   single    1.601  0.020  1.601
 CBQ  P2  O6   single    1.600  0.020  1.600
 CBQ  O5  HO5  single    0.850  0.020  0.980
 CBQ  O6  HO6  single    0.850  0.020  0.980

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
 CBQ  HO1  O1  P1   115.78  3.000
 CBQ  C1   P1  O3   106.13  3.000
 CBQ  C1   P1  O2   114.54  3.000
 CBQ  O3   P1  O2   110.07  3.000
 CBQ  C1   P1  O1    99.63  3.000
 CBQ  O3   P1  O1   107.60  3.000
 CBQ  O2   P1  O1   117.84  3.000
 CBQ  HO3  O3  P1   116.63  3.000
 CBQ  H1   C1  P2   106.13  3.000
 CBQ  H1   C1  N1   110.16  3.000
 CBQ  P2   C1  N1   110.96  3.000
 CBQ  H1   C1  P1   106.53  3.000
 CBQ  P2   C1  P1   116.43  3.000
 CBQ  N1   C1  P1   106.49  3.000
 CBQ  HN1  N1  C2   114.48  3.000
 CBQ  HN1  N1  C1   117.01  3.000
 CBQ  C2   N1  C1   124.67  3.000
 CBQ  C6   C2  N2   121.79  3.000
 CBQ  C6   C2  N1   123.35  3.000
 CBQ  N2   C2  N1   114.83  3.000
 CBQ  C3   N2  C2   119.42  3.000
 CBQ  H3   C3  C4   120.62  3.000
 CBQ  H3   C3  N2   116.75  3.000
 CBQ  C4   C3  N2   122.64  3.000
 CBQ  C5   C4  CL1  121.01  3.000
 CBQ  C5   C4  C3   118.54  3.000
 CBQ  CL1  C4  C3   120.44  3.000
 CBQ  H5   C5  C6   119.98  3.000
 CBQ  H5   C5  C4   120.89  3.000
 CBQ  C6   C5  C4   119.12  3.000
 CBQ  H6   C6  C5   119.22  3.000
 CBQ  H6   C6  C2   122.29  3.000
 CBQ  C5   C6  C2   118.49  3.000
 CBQ  O6   P2  O5   108.01  3.000
 CBQ  O6   P2  O4   110.60  3.000
 CBQ  O5   P2  O4   116.52  3.000
 CBQ  O6   P2  C1   107.33  3.000
 CBQ  O5   P2  C1   100.34  3.000
 CBQ  O4   P2  C1   113.27  3.000
 CBQ  HO5  O5  P2   114.60  3.000
 CBQ  HO6  O6  P2   115.46  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
 CBQ  CONST_01  C4   C3  N2  C2      0.00   0.0  0
 CBQ  CONST_02  C4   C5  C6  C2      0.00   0.0  0
 CBQ  CONST_03  C5   C6  C2  N2      0.00   0.0  0
 CBQ  CONST_04  C5   C4  C3  N2      0.00   0.0  0
 CBQ  CONST_05  C6   C2  N2  C3      0.00   0.0  0
 CBQ  CONST_06  C6   C5  C4  C3      0.00   0.0  0
 CBQ  CONST_07  C3   N2  C2  N1    180.00   0.0  0
 CBQ  CONST_08  C5   C6  C2  N1    180.00   0.0  0
 CBQ  CONST_09  CL1  C4  C3  N2    180.00   0.0  0
 CBQ  CONST_10  C6   C5  C4  CL1   180.00   0.0  0
 CBQ  CONST_11  H3   C3  N2  C2    180.00   0.0  0
 CBQ  CONST_12  H5   C5  C6  C2    180.00   0.0  0
 CBQ  CONST_13  H6   C6  C2  N2    180.00   0.0  0
 CBQ  CONST_14  N2   C2  N1  C1    180.00   0.0  0
 CBQ  CONST_15  C6   C2  N1  C1      0.00   0.0  0
 CBQ  CONST_16  HN1  N1  C2  N2      0.00   0.0  0
 CBQ  Var_01    C2   N1  C1  P1   -150.55  30.0  3
 CBQ  Var_02    N1   C1  P1  O1   -171.45  30.0  3
 CBQ  Var_03    O4   P2  C1  P1   -167.06  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
 CBQ  plan-1  N1   0.020
 CBQ  plan-1  C2   0.020
 CBQ  plan-1  N2   0.020
 CBQ  plan-1  C3   0.020
 CBQ  plan-1  C4   0.020
 CBQ  plan-1  CL1  0.020
 CBQ  plan-1  C5   0.020
 CBQ  plan-1  C6   0.020
 CBQ  plan-1  H3   0.020
 CBQ  plan-1  H5   0.020
 CBQ  plan-1  H6   0.020
 CBQ  plan-2  C1   0.020
 CBQ  plan-2  N1   0.020
 CBQ  plan-2  C2   0.020
 CBQ  plan-2  HN1  0.020

