# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:39:55 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=NC(=C)CCC(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
 5JV  5JV  '4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-4-enoic acid'  ligand  40  23  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5JV
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
 5JV  OA   O  O     0  -0.441  -2.4520   4.2815  -0.4832
 5JV  CA   C  C     0   0.558  -2.5643   3.6217   0.5194
 5JV  OB   O  OH1   0  -0.594  -2.3400   4.1032   1.7368
 5JV  CB   C  CH2   0  -0.582  -2.9686   2.1730   0.5608
 5JV  CG   C  CH2   0  -0.560  -3.2587   1.5972  -0.8229
 5JV  CD   C  C     0   0.344  -3.6521   0.1460  -0.7574
 5JV  CE   C  C2    0  -0.589  -4.9148  -0.2543  -0.9308
 5JV  N2   N  N     0  -0.518  -2.7064  -0.8458  -0.4781
 5JV  C4A  C  C1    0   0.040  -1.4509  -0.6080  -0.4374
 5JV  C4   C  CR6   0  -0.010  -0.4987  -1.6658  -0.1341
 5JV  C3   C  CR6   0   0.298  -0.9438  -2.9699   0.1225
 5JV  O3   O  OH1   0  -0.622  -2.2254  -3.3113   0.0965
 5JV  C2   C  CR6   0   0.133   0.0016  -3.9711   0.4232
 5JV  C2A  C  CH3   0  -0.721  -0.4500  -5.3707   0.6998
 5JV  N1   N  N     0  -0.397   1.2883  -3.6970   0.4676
 5JV  C6   C  CR16  0  -0.143   1.7247  -2.4583   0.2266
 5JV  C5   C  CR6   0  -0.067   0.8845  -1.4083  -0.0779
 5JV  C5A  C  CH2   0  -0.219   1.4018  -0.0213  -0.3419
 5JV  O4P  O  O2    0  -0.591   2.8213  -0.0268  -0.2902
 5JV  P    P  P     0   1.462   3.6058   1.3643  -0.1831
 5JV  O3P  O  O     0  -0.706   3.2166   2.4084  -1.1475
 5JV  O1P  O  OH1   0  -0.738   3.3850   1.8967   1.3059
 5JV  O2P  O  OH1   0  -0.727   5.0719   0.7545  -0.2798
 5JV  H1   H  HOH1  0   0.481  -2.0878   5.0371   1.6824
 5JV  H2   H  HCH2  0   0.283  -2.1843   1.6180   1.0835
 5JV  H3   H  HCH2  0   0.298  -3.8538   2.0822   1.1966
 5JV  H4   H  HCH2  0   0.279  -4.0789   2.1521  -1.2780
 5JV  H5   H  HCH2  0   0.264  -2.3995   1.7384  -1.4839
 5JV  H6   H  H     0   0.259  -5.1873  -1.2985  -0.8542
 5JV  H7   H  H     0   0.258  -5.6997   0.4535  -1.1568
 5JV  H8   H  H     0   0.255  -1.0527   0.3857  -0.6385
 5JV  H9   H  HOH1  0   0.478  -2.7506  -2.4952  -0.1270
 5JV  H10  H  HCH3  0   0.249  -0.9784  -5.7987  -0.1541
 5JV  H11  H  HCH3  0   0.249   0.4098  -5.9994   0.9210
 5JV  H12  H  HCH3  0   0.249  -1.1336  -5.4121   1.5496
 5JV  H13  H  HCR6  0   0.262   2.7954  -2.3183   0.2844
 5JV  H14  H  HCH2  0   0.269   1.0763   0.3279  -1.3262
 5JV  H15  H  HCH2  0   0.255   0.9933   0.6692   0.4043
 5JV  H16  H  HOH1  0   0.498   3.6446   1.2923   2.0145
 5JV  H17  H  HOH1  0   0.507   5.7689   1.4154  -0.3896

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
 5JV  CE   CD   double    1.336  0.020  1.336
 5JV  OA   CA   double    1.205  0.020  1.205
 5JV  CB   CA   single    1.505  0.020  1.505
 5JV  CB   CG   single    1.527  0.020  1.527
 5JV  CA   OB   single    1.328  0.020  1.328
 5JV  CD   CG   single    1.505  0.020  1.505
 5JV  CD   N2   single    1.399  0.020  1.399
 5JV  N2   C4A  double    1.278  0.020  1.278
 5JV  O3   C3   single    1.327  0.020  1.327
 5JV  C4A  C4   single    1.455  0.020  1.455
 5JV  C3   C4   aromatic  1.402  0.020  1.402
 5JV  C3   C2   aromatic  1.410  0.020  1.410
 5JV  C2A  C2   single    1.496  0.020  1.496
 5JV  C4   C5   aromatic  1.408  0.020  1.408
 5JV  C2   N1   aromatic  1.316  0.020  1.316
 5JV  O3P  P    double    1.474  0.020  1.474
 5JV  C5   C5A  single    1.504  0.020  1.504
 5JV  C5   C6   aromatic  1.379  0.020  1.379
 5JV  N1   C6   aromatic  1.335  0.020  1.335
 5JV  O4P  C5A  single    1.420  0.020  1.420
 5JV  O4P  P    single    1.601  0.020  1.601
 5JV  P    O1P  single    1.597  0.020  1.597
 5JV  P    O2P  single    1.591  0.020  1.591
 5JV  OB   H1   single    0.850  0.020  0.980
 5JV  CB   H2   single    0.970  0.020  1.090
 5JV  CB   H3   single    0.970  0.020  1.090
 5JV  CG   H4   single    0.970  0.020  1.090
 5JV  CG   H5   single    0.970  0.020  1.090
 5JV  CE   H6   single    0.930  0.020  1.080
 5JV  CE   H7   single    0.930  0.020  1.080
 5JV  C4A  H8   single    0.930  0.020  1.080
 5JV  O3   H9   single    0.850  0.020  0.980
 5JV  C2A  H10  single    0.970  0.020  1.090
 5JV  C2A  H11  single    0.970  0.020  1.090
 5JV  C2A  H12  single    0.970  0.020  1.090
 5JV  C6   H13  single    0.930  0.020  1.080
 5JV  C5A  H14  single    0.970  0.020  1.090
 5JV  C5A  H15  single    0.970  0.020  1.090
 5JV  O1P  H16  single    0.850  0.020  0.980
 5JV  O2P  H17  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
 5JV  CB   CA   OB   111.66  3.000
 5JV  OB   CA   OA   123.25  3.000
 5JV  CB   CA   OA   125.09  3.000
 5JV  H1   OB   CA   109.99  3.000
 5JV  H3   CB   H2   105.10  3.000
 5JV  H3   CB   CG   109.99  3.000
 5JV  H2   CB   CG   112.21  3.000
 5JV  H3   CB   CA   108.27  3.000
 5JV  H2   CB   CA   108.00  3.000
 5JV  CG   CB   CA   112.91  3.000
 5JV  H5   CG   H4   105.86  3.000
 5JV  H5   CG   CD   110.87  3.000
 5JV  H4   CG   CD   108.21  3.000
 5JV  H5   CG   CB   110.49  3.000
 5JV  H4   CG   CB   109.23  3.000
 5JV  CD   CG   CB   111.96  3.000
 5JV  N2   CD   CE   116.91  3.000
 5JV  N2   CD   CG   121.04  3.000
 5JV  CE   CD   CG   122.03  3.000
 5JV  H7   CE   H6   117.64  3.000
 5JV  H7   CE   CD   121.15  3.000
 5JV  H6   CE   CD   121.21  3.000
 5JV  C4A  N2   CD   122.58  3.000
 5JV  H8   C4A  C4   117.55  3.000
 5JV  H8   C4A  N2   121.52  3.000
 5JV  C4   C4A  N2   120.93  3.000
 5JV  C5   C4   C3   118.35  3.000
 5JV  C5   C4   C4A  121.21  3.000
 5JV  C3   C4   C4A  120.44  3.000
 5JV  C2   C3   O3   117.99  3.000
 5JV  C2   C3   C4   119.14  3.000
 5JV  O3   C3   C4   122.87  3.000
 5JV  H9   O3   C3   107.63  3.000
 5JV  N1   C2   C2A  118.92  3.000
 5JV  N1   C2   C3   120.99  3.000
 5JV  C2A  C2   C3   120.09  3.000
 5JV  H12  C2A  H11  108.35  3.000
 5JV  H12  C2A  H10  106.93  3.000
 5JV  H11  C2A  H10  108.36  3.000
 5JV  H12  C2A  C2   111.62  3.000
 5JV  H11  C2A  C2   109.85  3.000
 5JV  H10  C2A  C2   111.60  3.000
 5JV  C6   N1   C2   120.43  3.000
 5JV  H13  C6   C5   121.11  3.000
 5JV  H13  C6   N1   115.72  3.000
 5JV  C5   C6   N1   123.17  3.000
 5JV  C5A  C5   C6   122.11  3.000
 5JV  C6   C5   C4   117.91  3.000
 5JV  C5A  C5   C4   119.98  3.000
 5JV  H15  C5A  H14  107.50  3.000
 5JV  H15  C5A  O4P  110.51  3.000
 5JV  H14  C5A  O4P  109.35  3.000
 5JV  H15  C5A  C5   109.47  3.000
 5JV  H14  C5A  C5   110.49  3.000
 5JV  O4P  C5A  C5   109.50  3.000
 5JV  P    O4P  C5A  119.26  3.000
 5JV  O2P  P    O1P  108.18  3.000
 5JV  O2P  P    O3P  118.37  3.000
 5JV  O1P  P    O3P  109.73  3.000
 5JV  O2P  P    O4P   96.57  3.000
 5JV  O1P  P    O4P  106.53  3.000
 5JV  O3P  P    O4P  116.26  3.000
 5JV  H16  O1P  P    115.97  3.000
 5JV  H17  O2P  P    114.16  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
 5JV  CONST_01  N1   C2   C3   C4      0.00   0.0  0
 5JV  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 5JV  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 5JV  CONST_04  C6   N1   C2   C3      0.00   0.0  0
 5JV  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 5JV  CONST_06  C5   C6   N1   C2      0.00   0.0  0
 5JV  CONST_07  C2   C3   C4   C4A   180.00   0.0  0
 5JV  CONST_08  C6   C5   C4   C4A   180.00   0.0  0
 5JV  CONST_09  C2A  C2   C3   C4    180.00   0.0  0
 5JV  CONST_10  C5A  C5   C4   C3    180.00   0.0  0
 5JV  CONST_11  C5   C4   C3   O3    180.00   0.0  0
 5JV  CONST_12  N1   C2   C3   O3    180.00   0.0  0
 5JV  CONST_13  C6   N1   C2   C2A   180.00   0.0  0
 5JV  CONST_14  C5A  C5   C6   N1    180.00   0.0  0
 5JV  CONST_15  H13  C6   C5   C4    180.00   0.0  0
 5JV  CONST_16  H1   OB   CA   OA      0.00   0.0  0
 5JV  Var_01    C3   C4   C4A  N2     -0.13  30.0  2
 5JV  Var_02    O4P  C5A  C5   C4   -177.27  30.0  2
 5JV  Var_03    H10  C2A  C2   C3     60.38  30.0  2
 5JV  Var_04    C4   C4A  N2   CD    179.58   0.0  2
 5JV  Var_05    CG   CB   CA   OA     -1.06  30.0  2
 5JV  Var_06    CD   CG   CB   CA    179.63  30.0  3
 5JV  Var_07    CE   CD   CG   CB    105.64  30.0  2
 5JV  Var_08    O3P  P    O4P  C5A   -49.62  30.0  3
 5JV  Var_09    H6   CE   CD   CG   -178.32   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
 5JV  plan-1  C4A  0.020
 5JV  plan-1  C4   0.020
 5JV  plan-1  C3   0.020
 5JV  plan-1  O3   0.020
 5JV  plan-1  C2   0.020
 5JV  plan-1  C2A  0.020
 5JV  plan-1  N1   0.020
 5JV  plan-1  C6   0.020
 5JV  plan-1  C5   0.020
 5JV  plan-1  C5A  0.020
 5JV  plan-1  H13  0.020
 5JV  plan-2  OA   0.020
 5JV  plan-2  CA   0.020
 5JV  plan-2  OB   0.020
 5JV  plan-2  CB   0.020
 5JV  plan-2  H1   0.020
 5JV  plan-3  CG   0.020
 5JV  plan-3  CD   0.020
 5JV  plan-3  CE   0.020
 5JV  plan-3  N2   0.020
 5JV  plan-3  H6   0.020
 5JV  plan-3  H7   0.020
 5JV  plan-4  CD   0.020
 5JV  plan-4  N2   0.020
 5JV  plan-4  C4A  0.020
 5JV  plan-4  C4   0.020
 5JV  plan-4  H8   0.020

