# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 20:30:53 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 6-[(~{S})-oxidanyl(phosphono)methyl]pyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](c1cccc(n1)C(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
 60N  60N  '6-[(~{S})-oxidanyl(phosphono)methyl]pyridine-2-carboxylic acid'  ligand  23  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_60N
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
 60N  C10  C  CR16  0  -0.291   2.6127   1.4379  -0.2134
 60N  C11  C  CR6   0   0.091   2.0473   0.1941   0.0288
 60N  C12  C  C     0   0.521   2.9194  -1.0191  -0.0091
 60N  O01  O  OH1   0  -0.634  -2.3333   1.8676   0.2924
 60N  C02  C  CH1   0  -0.284  -1.4868   0.8144   0.6484
 60N  P03  P  P     0   1.354  -2.0377  -0.8213  -0.0299
 60N  O04  O  O     0  -0.698  -1.6191  -2.0241   0.7208
 60N  O05  O  OH1   0  -0.742  -3.6214  -0.5519  -0.0888
 60N  O06  O  OH1   0  -0.750  -1.5444  -0.8919  -1.5591
 60N  C07  C  CR6   0   0.202  -0.0338   1.0794   0.3222
 60N  C08  C  CR16  0  -0.310   0.4343   2.3722   0.0982
 60N  C09  C  CR16  0  -0.139   1.7802   2.5452  -0.1752
 60N  O13  O  OH1   0  -0.573   2.2604  -2.1354   0.2299
 60N  O14  O  O     0  -0.430   4.1032  -0.9649  -0.2381
 60N  N15  N  N     0  -0.410   0.7589   0.0231   0.2878
 60N  H1   H  HCR6  0   0.284   3.6671   1.5401  -0.4255
 60N  H3   H  HCH1  0   0.310  -1.5739   0.7079   1.7358
 60N  H4   H  HOH1  0   0.495  -4.1407  -1.3426  -0.2909
 60N  H5   H  HOH1  0   0.490  -2.0123  -0.3244  -2.1845
 60N  H6   H  HCR6  0   0.283  -0.2300   3.2233   0.1420
 60N  H7   H  HCR6  0   0.284   2.1774   3.5347  -0.3560
 60N  H8   H  HOH1  0   0.487   2.8695  -2.8879   0.1877
 60N  H2   H  HOH1  0   0.459  -2.2632   2.0465  -0.6522

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
 60N  O04  P03  double    1.478  0.020  1.478
 60N  O05  P03  single    1.608  0.020  1.608
 60N  P03  O06  single    1.608  0.020  1.608
 60N  P03  C02  single    1.854  0.020  1.854
 60N  O01  C02  single    1.397  0.020  1.397
 60N  C02  C07  single    1.513  0.020  1.513
 60N  C08  C07  aromatic  1.393  0.020  1.393
 60N  C08  C09  aromatic  1.384  0.020  1.384
 60N  C07  N15  aromatic  1.321  0.020  1.321
 60N  C09  C10  aromatic  1.386  0.020  1.386
 60N  N15  C11  aromatic  1.325  0.020  1.325
 60N  C10  C11  aromatic  1.388  0.020  1.388
 60N  C11  C12  single    1.495  0.020  1.495
 60N  C12  O14  double    1.207  0.020  1.207
 60N  C12  O13  single    1.318  0.020  1.318
 60N  C10  H1   single    0.930  0.020  1.080
 60N  O01  H2   single    0.850  0.020  0.980
 60N  C02  H3   single    0.970  0.020  1.090
 60N  O05  H4   single    0.850  0.020  0.980
 60N  O06  H5   single    0.850  0.020  0.980
 60N  C08  H6   single    0.930  0.020  1.080
 60N  C09  H7   single    0.930  0.020  1.080
 60N  O13  H8   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
 60N  H1   C10  C09  121.07  3.000
 60N  H1   C10  C11  121.12  3.000
 60N  C09  C10  C11  117.82  3.000
 60N  N15  C11  C12  117.87  3.000
 60N  C12  C11  C10  119.04  3.000
 60N  N15  C11  C10  123.09  3.000
 60N  O14  C12  O13  124.25  3.000
 60N  O13  C12  C11  113.02  3.000
 60N  O14  C12  C11  122.73  3.000
 60N  H2   O01  C02  110.21  3.000
 60N  H3   C02  C07  107.90  3.000
 60N  H3   C02  P03  104.69  3.000
 60N  C07  C02  P03  111.16  3.000
 60N  H3   C02  O01  106.14  3.000
 60N  C07  C02  O01  113.26  3.000
 60N  P03  C02  O01  113.06  3.000
 60N  O06  P03  O05  105.95  3.000
 60N  O06  P03  O04  111.12  3.000
 60N  O05  P03  O04  115.71  3.000
 60N  O06  P03  C02  107.18  3.000
 60N  O05  P03  C02   99.11  3.000
 60N  O04  P03  C02  116.60  3.000
 60N  H4   O05  P03  113.55  3.000
 60N  H5   O06  P03  116.20  3.000
 60N  N15  C07  C08  122.42  3.000
 60N  N15  C07  C02  116.23  3.000
 60N  C08  C07  C02  121.34  3.000
 60N  H6   C08  C09  120.48  3.000
 60N  H6   C08  C07  121.19  3.000
 60N  C09  C08  C07  118.33  3.000
 60N  H7   C09  C08  120.30  3.000
 60N  H7   C09  C10  120.39  3.000
 60N  C08  C09  C10  119.31  3.000
 60N  H8   O13  C12  109.60  3.000
 60N  C07  N15  C11  119.03  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
 60N  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 60N  CONST_02  C07  N15  C11  C10    0.00   0.0  0
 60N  CONST_03  C08  C07  N15  C11    0.00   0.0  0
 60N  CONST_04  C08  C09  C10  C11    0.00   0.0  0
 60N  CONST_05  N15  C07  C08  C09    0.00   0.0  0
 60N  CONST_06  N15  C11  C10  C09    0.00   0.0  0
 60N  CONST_07  C02  C07  N15  C11  180.00   0.0  0
 60N  CONST_08  C07  N15  C11  C12  180.00   0.0  0
 60N  CONST_09  C09  C10  C11  C12  180.00   0.0  0
 60N  CONST_10  C09  C08  C07  C02  180.00   0.0  0
 60N  CONST_11  H6   C08  C09  C10  180.00   0.0  0
 60N  CONST_12  H7   C09  C10  C11  180.00   0.0  0
 60N  CONST_13  H1   C10  C09  C08  180.00   0.0  0
 60N  CONST_14  H8   O13  C12  C11  180.00   0.0  0
 60N  Var_01    O14  C12  C11  C10    0.27  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 60N  chir_01  C02  P03  O01  C07  positiv

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
 60N  plan-1  C10  0.020
 60N  plan-1  C11  0.020
 60N  plan-1  C12  0.020
 60N  plan-1  C02  0.020
 60N  plan-1  C07  0.020
 60N  plan-1  C08  0.020
 60N  plan-1  C09  0.020
 60N  plan-1  N15  0.020
 60N  plan-1  H1   0.020
 60N  plan-1  H6   0.020
 60N  plan-1  H7   0.020
 60N  plan-2  C11  0.020
 60N  plan-2  C12  0.020
 60N  plan-2  O13  0.020
 60N  plan-2  O14  0.020
 60N  plan-2  H8   0.020

