# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 00:55:01 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 6-(phosphonomethyl)pyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(C[P](O)(O)=O)n1
#
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
 60M  60M  '6-(phosphonomethyl)pyridine-2-carboxylic acid'  ligand  22  14  .  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_60M
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
 60M  C13  C  CR16  0  -0.052  -1.4969  -2.5197  -0.1149
 60M  C14  C  CR16  0  -0.357  -2.3689  -1.4695   0.1356
 60M  O01  O  OH1   0  -0.621  -2.1603   2.1390   0.2310
 60M  C02  C  C     0   0.515  -2.7743   0.9758   0.3321
 60M  O03  O  O     0  -0.351  -3.9365   0.8407   0.6212
 60M  C04  C  CR6   0   0.122  -1.8715  -0.1808   0.0470
 60M  N05  N  N     0  -0.413  -0.6111   0.0822  -0.2795
 60M  C06  C  CR6   0   0.235   0.2267  -0.9165  -0.5301
 60M  C07  C  CH2   0  -0.790   1.6252  -0.5403  -0.9333
 60M  P08  P  P     0   1.326   2.3074   0.7743   0.1225
 60M  O09  O  OH1   0  -0.736   3.5967   1.3373  -0.6470
 60M  O10  O  OH1   0  -0.661   1.3125   2.0078  -0.0933
 60M  O11  O  O     0  -0.799   2.5469   0.3498   1.5238
 60M  C12  C  CR16  0  -0.327  -0.1831  -2.2452  -0.4472
 60M  H1   H  HCR6  0   0.292  -1.8401  -3.5431  -0.0490
 60M  H2   H  HCR6  0   0.244  -3.4010  -1.6513   0.3969
 60M  H3   H  HOH1  0   0.493  -2.7772   2.8604   0.4272
 60M  H4   H  HCH2  0   0.305   2.2876  -1.4051  -0.8873
 60M  H5   H  HCH2  0   0.310   1.6232  -0.1915  -1.9698
 60M  H6   H  HOH1  0   0.487   4.4271   0.9860  -0.2998
 60M  H7   H  HOH1  0   0.506   0.3900   1.6615  -0.1597
 60M  H8   H  HCR6  0   0.272   0.5190  -3.0435  -0.6439

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
 60M  C13  C14  aromatic  1.388  0.020  1.388
 60M  C13  C12  aromatic  1.383  0.020  1.383
 60M  C14  C04  aromatic  1.384  0.020  1.384
 60M  C12  C06  aromatic  1.393  0.020  1.393
 60M  C04  N05  aromatic  1.328  0.020  1.328
 60M  C04  C02  single    1.495  0.020  1.495
 60M  C06  N05  aromatic  1.327  0.020  1.327
 60M  C06  C07  single    1.503  0.020  1.503
 60M  O03  C02  double    1.205  0.020  1.205
 60M  C02  O01  single    1.319  0.020  1.319
 60M  C07  P08  single    1.819  0.020  1.819
 60M  O11  P08  double    1.484  0.020  1.484
 60M  P08  O09  single    1.604  0.020  1.604
 60M  P08  O10  single    1.599  0.020  1.599
 60M  C13  H1   single    0.930  0.020  1.080
 60M  C14  H2   single    0.930  0.020  1.080
 60M  O01  H3   single    0.850  0.020  0.980
 60M  C07  H4   single    0.970  0.020  1.090
 60M  C07  H5   single    0.970  0.020  1.090
 60M  O09  H6   single    0.850  0.020  0.980
 60M  O10  H7   single    0.850  0.020  0.980
 60M  C12  H8   single    0.930  0.020  1.080

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
 60M  H1   C13  C12  120.27  3.000
 60M  H1   C13  C14  120.38  3.000
 60M  C12  C13  C14  119.35  3.000
 60M  H2   C14  C04  121.04  3.000
 60M  H2   C14  C13  121.11  3.000
 60M  C04  C14  C13  117.85  3.000
 60M  H3   O01  C02  110.15  3.000
 60M  C04  C02  O03  122.79  3.000
 60M  O03  C02  O01  124.48  3.000
 60M  C04  C02  O01  112.74  3.000
 60M  N05  C04  C02  117.83  3.000
 60M  C02  C04  C14  119.41  3.000
 60M  N05  C04  C14  122.76  3.000
 60M  C06  N05  C04  119.75  3.000
 60M  C12  C06  C07  121.90  3.000
 60M  C07  C06  N05  116.71  3.000
 60M  C12  C06  N05  121.38  3.000
 60M  H5   C07  H4   107.11  3.000
 60M  H5   C07  P08  108.68  3.000
 60M  H4   C07  P08  108.72  3.000
 60M  H5   C07  C06  109.41  3.000
 60M  H4   C07  C06  110.81  3.000
 60M  P08  C07  C06  111.97  3.000
 60M  O11  P08  O10  116.65  3.000
 60M  O10  P08  O09   99.48  3.000
 60M  O11  P08  O09  115.08  3.000
 60M  O10  P08  C07  104.23  3.000
 60M  O09  P08  C07  106.07  3.000
 60M  O11  P08  C07  113.71  3.000
 60M  H6   O09  P08  113.01  3.000
 60M  H7   O10  P08  108.64  3.000
 60M  H8   C12  C06  120.16  3.000
 60M  H8   C12  C13  120.94  3.000
 60M  C06  C12  C13  118.90  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
 60M  CONST_01  N05  C04  C14  C13    0.00   0.0  0
 60M  CONST_02  N05  C06  C12  C13    0.00   0.0  0
 60M  CONST_03  C06  C12  C13  C14    0.00   0.0  0
 60M  CONST_04  C06  N05  C04  C14    0.00   0.0  0
 60M  CONST_05  C12  C13  C14  C04    0.00   0.0  0
 60M  CONST_06  C12  C06  N05  C04    0.00   0.0  0
 60M  CONST_07  C02  C04  C14  C13  180.00   0.0  0
 60M  CONST_08  C07  C06  C12  C13  180.00   0.0  0
 60M  CONST_09  C06  N05  C04  C02  180.00   0.0  0
 60M  CONST_10  C07  C06  N05  C04  180.00   0.0  0
 60M  CONST_11  H8   C12  C13  C14  180.00   0.0  0
 60M  CONST_12  H1   C13  C14  C04  180.00   0.0  0
 60M  CONST_13  H2   C14  C04  N05  180.00   0.0  0
 60M  CONST_14  H3   O01  C02  C04  180.00   0.0  0
 60M  Var_01    O03  C02  C04  C14   -1.11  30.0  2
 60M  Var_02    P08  C07  C06  N05   45.10  30.0  2
 60M  Var_03    O11  P08  C07  C06   67.48  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
 60M  plan-1  C13  0.020
 60M  plan-1  C14  0.020
 60M  plan-1  C02  0.020
 60M  plan-1  C04  0.020
 60M  plan-1  N05  0.020
 60M  plan-1  C06  0.020
 60M  plan-1  C07  0.020
 60M  plan-1  C12  0.020
 60M  plan-1  H1   0.020
 60M  plan-1  H2   0.020
 60M  plan-1  H8   0.020
 60M  plan-2  O01  0.020
 60M  plan-2  C02  0.020
 60M  plan-2  O03  0.020
 60M  plan-2  C04  0.020
 60M  plan-2  H3   0.020

