# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:33:01 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=NC(=C)C(O)=O)c1O
#
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
 0JO  0JO  '2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid'  ligand  34  21  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0JO
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
 0JO  O    O  O     0  -0.430   2.1310  -2.8405  -0.9428
 0JO  C    C  C     0   0.512   3.0215  -2.7804  -0.1318
 0JO  OXT  O  OH1   0  -0.584   3.6520  -3.8366   0.3508
 0JO  CA   C  C     0   0.194   3.5570  -1.4923   0.4109
 0JO  CB   C  C2    0  -0.528   4.7707  -1.4189   0.9637
 0JO  N    N  N     0  -0.532   2.8203  -0.3192   0.2489
 0JO  C4A  C  C1    0   0.065   1.5431  -0.2860   0.2425
 0JO  C4   C  CR6   0  -0.022   0.8394   0.9788   0.0844
 0JO  C3   C  CR6   0   0.302   1.5493   2.1765  -0.0740
 0JO  O3   O  OH1   0  -0.619   2.8741   2.2339  -0.0885
 0JO  C2   C  CR6   0   0.133   0.8348   3.3831  -0.2238
 0JO  C2A  C  CH3   0  -0.720   1.5717   4.6744  -0.3916
 0JO  N1   N  N     0  -0.396  -0.4808   3.3952  -0.2219
 0JO  C6   C  CR16  0  -0.142  -1.1690   2.2597  -0.0758
 0JO  C5   C  CR6   0  -0.063  -0.5683   1.0290   0.0814
 0JO  C5A  C  CH2   0  -0.222  -1.3654  -0.2349   0.2524
 0JO  OP4  O  O2    0  -0.592  -2.7523   0.0743   0.2678
 0JO  P    P  P     0   1.459  -3.8095  -1.0890  -0.0353
 0JO  OP3  O  O     0  -0.705  -3.6067  -2.3554   0.6905
 0JO  OP1  O  OH1   0  -0.727  -5.1163  -0.2380   0.2797
 0JO  OP2  O  OH1   0  -0.737  -3.7545  -1.3537  -1.6087
 0JO  H1   H  HOH1  0   0.491   3.3196  -4.6435  -0.0713
 0JO  H2   H  H     0   0.281   5.1656  -0.4627   1.2788
 0JO  H3   H  H     0   0.283   5.3917  -2.2875   1.1171
 0JO  H4   H  H     0   0.269   0.9416  -1.1813   0.3758
 0JO  H5   H  HOH1  0   0.481   3.2180   1.3094   0.0398
 0JO  H6   H  HCH3  0   0.251   2.1736   4.6753  -1.3026
 0JO  H7   H  HCH3  0   0.250   0.8656   5.4997  -0.4479
 0JO  H8   H  HCH3  0   0.249   2.2543   4.8594   0.4395
 0JO  H9   H  HCR6  0   0.263  -2.2458   2.3583  -0.0867
 0JO  H10  H  HCH2  0   0.258  -1.1311  -0.9292  -0.5619
 0JO  H11  H  HCH2  0   0.271  -1.0963  -0.7284   1.1902
 0JO  H12  H  HOH1  0   0.507  -5.9330  -0.7558   0.2833
 0JO  H13  H  HOH1  0   0.498  -3.9323  -0.5881  -2.1720

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
 0JO  O    C    double    1.206  0.020  1.206
 0JO  OXT  C    single    1.321  0.020  1.321
 0JO  C    CA   single    1.497  0.020  1.497
 0JO  CA   CB   double    1.336  0.020  1.336
 0JO  CA   N    single    1.395  0.020  1.395
 0JO  O3   C3   single    1.326  0.020  1.326
 0JO  N    C4A  double    1.278  0.020  1.278
 0JO  C4A  C4   single    1.456  0.020  1.456
 0JO  C3   C4   aromatic  1.401  0.020  1.401
 0JO  C3   C2   aromatic  1.410  0.020  1.410
 0JO  C2A  C2   single    1.496  0.020  1.496
 0JO  C4   C5   aromatic  1.409  0.020  1.409
 0JO  C2   N1   aromatic  1.316  0.020  1.316
 0JO  OP3  P    double    1.474  0.020  1.474
 0JO  C5   C5A  single    1.504  0.020  1.504
 0JO  C5   C6   aromatic  1.378  0.020  1.378
 0JO  N1   C6   aromatic  1.336  0.020  1.336
 0JO  OP4  C5A  single    1.421  0.020  1.421
 0JO  OP4  P    single    1.601  0.020  1.601
 0JO  OP1  P    single    1.591  0.020  1.591
 0JO  P    OP2  single    1.596  0.020  1.596
 0JO  OXT  H1   single    0.850  0.020  0.980
 0JO  CB   H2   single    0.930  0.020  1.080
 0JO  CB   H3   single    0.930  0.020  1.080
 0JO  C4A  H4   single    0.930  0.020  1.080
 0JO  O3   H5   single    0.850  0.020  0.980
 0JO  C2A  H6   single    0.970  0.020  1.090
 0JO  C2A  H7   single    0.970  0.020  1.090
 0JO  C2A  H8   single    0.970  0.020  1.090
 0JO  C6   H9   single    0.930  0.020  1.080
 0JO  C5A  H10  single    0.970  0.020  1.090
 0JO  C5A  H11  single    0.970  0.020  1.090
 0JO  OP1  H12  single    0.850  0.020  0.980
 0JO  OP2  H13  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
 0JO  CA   C    OXT  112.63  3.000
 0JO  CA   C    O    123.43  3.000
 0JO  OXT  C    O    123.92  3.000
 0JO  H1   OXT  C    110.04  3.000
 0JO  N    CA   CB   118.80  3.000
 0JO  N    CA   C    119.52  3.000
 0JO  CB   CA   C    121.50  3.000
 0JO  H3   CB   H2   117.40  3.000
 0JO  H3   CB   CA   122.53  3.000
 0JO  H2   CB   CA   120.07  3.000
 0JO  C4A  N    CA   123.40  3.000
 0JO  H4   C4A  C4   117.48  3.000
 0JO  H4   C4A  N    122.09  3.000
 0JO  C4   C4A  N    120.41  3.000
 0JO  C5   C4   C3   118.40  3.000
 0JO  C5   C4   C4A  120.94  3.000
 0JO  C3   C4   C4A  120.66  3.000
 0JO  C2   C3   O3   117.90  3.000
 0JO  C2   C3   C4   119.12  3.000
 0JO  O3   C3   C4   122.98  3.000
 0JO  H5   O3   C3   107.68  3.000
 0JO  N1   C2   C2A  119.00  3.000
 0JO  N1   C2   C3   120.95  3.000
 0JO  C2A  C2   C3   120.05  3.000
 0JO  H8   C2A  H7   108.47  3.000
 0JO  H8   C2A  H6   106.89  3.000
 0JO  H7   C2A  H6   108.31  3.000
 0JO  H8   C2A  C2   111.65  3.000
 0JO  H7   C2A  C2   109.93  3.000
 0JO  H6   C2A  C2   111.46  3.000
 0JO  C6   N1   C2   120.50  3.000
 0JO  H9   C6   C5   121.10  3.000
 0JO  H9   C6   N1   115.75  3.000
 0JO  C5   C6   N1   123.16  3.000
 0JO  C5A  C5   C6   122.16  3.000
 0JO  C6   C5   C4   117.88  3.000
 0JO  C5A  C5   C4   119.97  3.000
 0JO  H11  C5A  H10  107.39  3.000
 0JO  H11  C5A  OP4  109.21  3.000
 0JO  H10  C5A  OP4  110.77  3.000
 0JO  H11  C5A  C5   110.27  3.000
 0JO  H10  C5A  C5   109.56  3.000
 0JO  OP4  C5A  C5   109.61  3.000
 0JO  P    OP4  C5A  118.97  3.000
 0JO  OP2  P    OP1  108.19  3.000
 0JO  OP2  P    OP3  109.77  3.000
 0JO  OP1  P    OP3  118.37  3.000
 0JO  OP2  P    OP4  106.52  3.000
 0JO  OP1  P    OP4   96.68  3.000
 0JO  OP3  P    OP4  116.12  3.000
 0JO  H12  OP1  P    114.08  3.000
 0JO  H13  OP2  P    115.88  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
 0JO  CONST_01  N1   C2   C3   C4      0.00   0.0  0
 0JO  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 0JO  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 0JO  CONST_04  C6   N1   C2   C3      0.00   0.0  0
 0JO  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 0JO  CONST_06  C5   C6   N1   C2      0.00   0.0  0
 0JO  CONST_07  C2   C3   C4   C4A   180.00   0.0  0
 0JO  CONST_08  C6   C5   C4   C4A   180.00   0.0  0
 0JO  CONST_09  C2A  C2   C3   C4    180.00   0.0  0
 0JO  CONST_10  C5A  C5   C4   C3    180.00   0.0  0
 0JO  CONST_11  C5   C4   C3   O3    180.00   0.0  0
 0JO  CONST_12  N1   C2   C3   O3    180.00   0.0  0
 0JO  CONST_13  C6   N1   C2   C2A   180.00   0.0  0
 0JO  CONST_14  C5A  C5   C6   N1    180.00   0.0  0
 0JO  CONST_15  H9   C6   C5   C4    180.00   0.0  0
 0JO  CONST_16  H1   OXT  C    O       0.00   0.0  0
 0JO  Var_01    C3   C4   C4A  N       0.53  30.0  2
 0JO  Var_02    OP4  C5A  C5   C4    177.75  30.0  2
 0JO  Var_03    H6   C2A  C2   C3     62.40  30.0  2
 0JO  Var_04    C4   C4A  N    CA    179.26   0.0  2
 0JO  Var_05    CB   CA   C    O    -158.98  30.0  2
 0JO  Var_06    OP3  P    OP4  C5A    47.65  30.0  3
 0JO  Var_07    H2   CB   CA   C     175.25   0.0  2

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
 0JO  plan-1  C4A  0.020
 0JO  plan-1  C4   0.020
 0JO  plan-1  C3   0.020
 0JO  plan-1  O3   0.020
 0JO  plan-1  C2   0.020
 0JO  plan-1  C2A  0.020
 0JO  plan-1  N1   0.020
 0JO  plan-1  C6   0.020
 0JO  plan-1  C5   0.020
 0JO  plan-1  C5A  0.020
 0JO  plan-1  H9   0.020
 0JO  plan-2  O    0.020
 0JO  plan-2  C    0.020
 0JO  plan-2  OXT  0.020
 0JO  plan-2  CA   0.020
 0JO  plan-2  H1   0.020
 0JO  plan-3  C    0.020
 0JO  plan-3  CA   0.020
 0JO  plan-3  CB   0.020
 0JO  plan-3  N    0.020
 0JO  plan-3  H2   0.020
 0JO  plan-3  H3   0.020
 0JO  plan-4  CA   0.020
 0JO  plan-4  N    0.020
 0JO  plan-4  C4A  0.020
 0JO  plan-4  C4   0.020
 0JO  plan-4  H4   0.020

