# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 03:46:22 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: [2-(pyridin-2-ylamino)ethane-1,1-diyl]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C(CNc1ccccn1)[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
 1BY  1BY  '[2-(pyridin-2-ylamino)ethane-1,1-diyl]bis(phosphonic acid)'  ligand  25  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1BY
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
 1BY  C5   C  CR16   0  -0.212   2.7815   2.8851   0.6130
 1BY  C4   C  CR16   0  -0.355   1.6519   2.1074   0.5004
 1BY  C6   C  CR16   0  -0.371   3.0841   3.5102   1.8232
 1BY  C7   C  CR16   0  -0.052   2.1974   3.3065   2.8670
 1BY  N2   N  N      0  -0.484   1.1040   2.5621   2.7957
 1BY  C3   C  CR6    0   0.462   0.8097   1.9488   1.6316
 1BY  N1   N  NH1    0  -0.688  -0.2875   1.1888   1.6094
 1BY  C2   C  CH2    0  -0.257  -0.8438   0.5958   0.4146
 1BY  C1   C  CH1    0  -0.739  -1.9952  -0.3469   0.7618
 1BY  P1   P  P      0   1.138  -3.3221   0.5682   1.6939
 1BY  O1   O  O      0  -0.833  -2.6090   1.2041   2.9214
 1BY  O2   O  OP    -1  -1.042  -4.4110  -0.4294   2.0954
 1BY  O3   O  OP    -1  -0.870  -3.8243   1.6455   0.7133
 1BY  P2   P  P      0   1.137  -1.3851  -1.9599   1.4773
 1BY  O4   O  OP    -1  -0.957  -2.5031  -2.9852   1.2205
 1BY  O5   O  OP    -1  -0.975  -0.1129  -2.2900   0.6623
 1BY  O6   O  O      0  -0.859  -1.0881  -1.7470   2.9669
 1BY  H5   H  HCR6   0   0.259   3.4307   3.0106  -0.2453
 1BY  H4   H  HCR6   0   0.267   1.4072   1.6281  -0.4374
 1BY  H6   H  HCR6   0   0.249   3.9606   4.1303   1.9474
 1BY  H7   H  HCR6   0   0.252   2.3817   3.7788   3.8283
 1BY  HN1  H  HNH1   0   0.350  -0.9876   1.2587   2.3726
 1BY  H21  H  HCH2   0   0.192  -1.1971   1.3846  -0.2666
 1BY  H22  H  HCH2   0   0.221  -0.0722   0.0306  -0.1129
 1BY  H1   H  HCH1   0   0.168  -2.4450  -0.6216  -0.2029

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
 1BY  C5  C4   aromatic  1.376  0.020  1.376
 1BY  C5  C6   aromatic  1.395  0.020  1.395
 1BY  C5  H5   single    0.930  0.020  1.080
 1BY  C4  C3   aromatic  1.419  0.020  1.419
 1BY  C4  H4   single    0.930  0.020  1.080
 1BY  C6  C7   aromatic  1.385  0.020  1.385
 1BY  C6  H6   single    0.930  0.020  1.080
 1BY  C7  N2   aromatic  1.325  0.020  1.325
 1BY  C7  H7   single    0.930  0.020  1.080
 1BY  N2  C3   aromatic  1.348  0.020  1.348
 1BY  C3  N1   single    1.335  0.020  1.335
 1BY  N1  C2   single    1.445  0.020  1.445
 1BY  N1  HN1  single    0.890  0.020  1.040
 1BY  C2  C1   single    1.528  0.020  1.528
 1BY  C2  H21  single    0.970  0.020  1.090
 1BY  C2  H22  single    0.970  0.020  1.090
 1BY  C1  P1   single    1.862  0.020  1.862
 1BY  C1  P2   single    1.867  0.020  1.867
 1BY  C1  H1   single    0.970  0.020  1.090
 1BY  P1  O1   deloc     1.556  0.020  1.556
 1BY  P1  O3   deloc     1.541  0.020  1.541
 1BY  P1  O2   deloc     1.530  0.020  1.530
 1BY  P2  O6   deloc     1.534  0.020  1.534
 1BY  P2  O5   deloc     1.547  0.020  1.547
 1BY  P2  O4   deloc     1.539  0.020  1.539

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
 1BY  H5   C5  C6   120.35  3.000
 1BY  H5   C5  C4   119.51  3.000
 1BY  C6   C5  C4   120.14  3.000
 1BY  H4   C4  C3   120.50  3.000
 1BY  H4   C4  C5   120.48  3.000
 1BY  C3   C4  C5   119.02  3.000
 1BY  H6   C6  C7   121.14  3.000
 1BY  H6   C6  C5   122.18  3.000
 1BY  C7   C6  C5   116.68  3.000
 1BY  H7   C7  N2   115.58  3.000
 1BY  H7   C7  C6   119.62  3.000
 1BY  N2   C7  C6   124.80  3.000
 1BY  C3   N2  C7   118.83  3.000
 1BY  N1   C3  N2   116.92  3.000
 1BY  N1   C3  C4   122.56  3.000
 1BY  N2   C3  C4   120.52  3.000
 1BY  HN1  N1  C2   112.08  3.000
 1BY  HN1  N1  C3   120.25  3.000
 1BY  C2   N1  C3   124.32  3.000
 1BY  H22  C2  H21  107.38  3.000
 1BY  H22  C2  C1   108.83  3.000
 1BY  H21  C2  C1   109.94  3.000
 1BY  H22  C2  N1   109.86  3.000
 1BY  H21  C2  N1   109.95  3.000
 1BY  C1   C2  N1   110.82  3.000
 1BY  H1   C1  P2   104.72  3.000
 1BY  H1   C1  P1   105.70  3.000
 1BY  P2   C1  P1   117.75  3.000
 1BY  H1   C1  C2   105.26  3.000
 1BY  P2   C1  C2   111.95  3.000
 1BY  P1   C1  C2   110.34  3.000
 1BY  O3   P1  O2   113.00  3.000
 1BY  O2   P1  O1   112.69  3.000
 1BY  O3   P1  O1   111.45  3.000
 1BY  O2   P1  C1   108.55  3.000
 1BY  O3   P1  C1   104.91  3.000
 1BY  O1   P1  C1   105.62  3.000
 1BY  O6   P2  O5   112.46  3.000
 1BY  O5   P2  O4   111.56  3.000
 1BY  O6   P2  O4   113.29  3.000
 1BY  O4   P2  C1   105.92  3.000
 1BY  O5   P2  C1   104.55  3.000
 1BY  O6   P2  C1   108.40  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
 1BY  CONST_01  N2   C3  C4  C5    0.00   0.0  0
 1BY  CONST_02  N2   C7  C6  C5    0.00   0.0  0
 1BY  CONST_03  C7   C6  C5  C4    0.00   0.0  0
 1BY  CONST_04  C7   N2  C3  C4    0.00   0.0  0
 1BY  CONST_05  C3   C4  C5  C6    0.00   0.0  0
 1BY  CONST_06  C3   N2  C7  C6    0.00   0.0  0
 1BY  CONST_07  N1   C3  C4  C5  180.00   0.0  0
 1BY  CONST_08  N1   C3  N2  C7  180.00   0.0  0
 1BY  CONST_09  H7   C7  C6  C5  180.00   0.0  0
 1BY  CONST_10  H6   C6  C5  C4  180.00   0.0  0
 1BY  CONST_11  H4   C4  C5  C6  180.00   0.0  0
 1BY  CONST_12  H5   C5  C6  C7  180.00   0.0  0
 1BY  CONST_13  C2   N1  C3  C4    0.00   0.0  0
 1BY  CONST_14  C2   N1  C3  N2  180.00   0.0  0
 1BY  CONST_15  HN1  N1  C3  C4  180.00   0.0  0
 1BY  Var_01    C1   C2  N1  C3  173.11  30.0  3
 1BY  Var_02    P1   C1  C2  N1   57.98  30.0  3
 1BY  Var_03    O1   P1  C1  C2  -55.46  30.0  3
 1BY  Var_04    O6   P2  C1  C2   81.58  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
 1BY  plan-1  C5   0.020
 1BY  plan-1  C4   0.020
 1BY  plan-1  C6   0.020
 1BY  plan-1  C7   0.020
 1BY  plan-1  N2   0.020
 1BY  plan-1  C3   0.020
 1BY  plan-1  N1   0.020
 1BY  plan-1  H5   0.020
 1BY  plan-1  H4   0.020
 1BY  plan-1  H6   0.020
 1BY  plan-1  H7   0.020
 1BY  plan-2  C3   0.020
 1BY  plan-2  N1   0.020
 1BY  plan-2  C2   0.020
 1BY  plan-2  HN1  0.020

