# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Nov 22 16:50:21 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN=C(C=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
 WBJ  WBJ  "(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid"  ligand  37  22  .  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_WBJ
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
 WBJ  C10  C  CH3   0  -0.718   0.4592  -32.5299  15.7101
 WBJ  C15  C  CH2   0  -0.296   0.3518  -26.8330  15.1817
 WBJ  C21  C  C     0   0.489  -4.7405  -29.2849  18.5241
 WBJ  C01  C  C2    0  -0.474  -5.2917  -26.3840  17.7179
 WBJ  C02  C  C1    0  -0.270  -4.0601  -26.8700  17.8604
 WBJ  C03  C  C     0   0.219  -3.7429  -28.2986  17.9522
 WBJ  C05  C  CH2   0  -0.342  -1.5636  -28.0729  17.0419
 WBJ  C06  C  CR6   0   0.022  -0.6063  -28.9298  16.2459
 WBJ  C07  C  CR6   0   0.260  -0.5529  -30.3213  16.3553
 WBJ  C09  C  CR6   0   0.133   0.3902  -31.0385  15.5942
 WBJ  C12  C  CR16  0  -0.149   1.1911  -29.1113  14.6714
 WBJ  C14  C  CR6   0  -0.001   0.3036  -28.3169  15.3736
 WBJ  N04  N  N     0  -0.436  -2.6532  -28.8391  17.5972
 WBJ  N11  N  N     0  -0.404   1.2334  -30.4341  14.7756
 WBJ  O16  O  O2    0  -0.582   0.8137  -26.2352  16.4032
 WBJ  O18  O  OH1   0  -0.741  -0.9947  -24.5451  16.9341
 WBJ  O19  O  OH1   0  -0.726   1.2207  -24.6630  18.1360
 WBJ  O20  O  O     0  -0.698   1.1117  -23.7339  15.6755
 WBJ  O22  O  OH1   0  -0.574  -5.4211  -28.7683  19.5295
 WBJ  O23  O  O     0  -0.407  -4.8500  -30.4103  18.1211
 WBJ  P17  P  P     0   1.457   0.5832  -24.6792  16.6778
 WBJ  H1   H  HCH3  0   0.245   1.2266  -32.9181  15.0438
 WBJ  H2   H  HCH3  0   0.246   0.6993  -32.8436  16.7278
 WBJ  H3   H  HCH3  0   0.246  -0.4917  -32.9991  15.4517
 WBJ  H4   H  HCH2  0   0.276   1.0405  -26.5837  14.3724
 WBJ  H5   H  HCH2  0   0.257  -0.6331  -26.4413  14.9077
 WBJ  H6   H  H     0   0.267  -6.1780  -27.0040  17.6927
 WBJ  H7   H  H     0   0.274  -5.4477  -25.3204  17.6016
 WBJ  H8   H  H     0   0.292  -3.2219  -26.1831  17.8519
 WBJ  H9   H  HCH2  0   0.297  -1.0169  -27.6045  17.8682
 WBJ  H10  H  HCH2  0   0.265  -1.9297  -27.2562  16.4144
 WBJ  H11  H  HCR6  0   0.254   1.9017  -28.6557  13.9890
 WBJ  H12  H  HOH1  0   0.472  -2.0380  -30.4352  17.5204
 WBJ  H13  H  HOH1  0   0.497  -1.4419  -23.9401  16.3279
 WBJ  H14  H  HOH1  0   0.502   1.3828  -23.7767  18.4869
 WBJ  H15  H  HOH1  0   0.491  -6.0371  -29.4241  19.8938
 WBJ  O08  O  OH1   0  -0.641  -1.3481  -31.0422  17.1560

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
 WBJ  C12  N11  aromatic  1.328  0.020  1.328
 WBJ  C12  C14  aromatic  1.383  0.020  1.383
 WBJ  N11  C09  aromatic  1.321  0.020  1.321
 WBJ  C15  C14  single    1.497  0.020  1.497
 WBJ  C15  O16  single    1.436  0.020  1.436
 WBJ  C14  C06  aromatic  1.402  0.020  1.402
 WBJ  O20  P17  double    1.476  0.020  1.476
 WBJ  C09  C10  single    1.498  0.020  1.498
 WBJ  C09  C07  aromatic  1.408  0.020  1.408
 WBJ  C06  C07  aromatic  1.397  0.020  1.397
 WBJ  C06  C05  single    1.511  0.020  1.511
 WBJ  O16  P17  single    1.597  0.020  1.597
 WBJ  C07  O08  single    1.339  0.020  1.339
 WBJ  P17  O18  single    1.604  0.020  1.604
 WBJ  P17  O19  single    1.592  0.020  1.592
 WBJ  C05  N04  single    1.443  0.020  1.443
 WBJ  N04  C03  double    1.267  0.020  1.267
 WBJ  C02  C03  single    1.466  0.020  1.466
 WBJ  C02  C01  double    1.332  0.020  1.332
 WBJ  C03  C21  single    1.515  0.020  1.515
 WBJ  O23  C21  double    1.200  0.020  1.200
 WBJ  C21  O22  single    1.319  0.020  1.319
 WBJ  C10  H1   single    0.970  0.020  1.090
 WBJ  C10  H2   single    0.970  0.020  1.090
 WBJ  C10  H3   single    0.970  0.020  1.090
 WBJ  C15  H4   single    0.970  0.020  1.090
 WBJ  C15  H5   single    0.970  0.020  1.090
 WBJ  C01  H6   single    0.930  0.020  1.080
 WBJ  C01  H7   single    0.930  0.020  1.080
 WBJ  C02  H8   single    0.930  0.020  1.080
 WBJ  C05  H9   single    0.970  0.020  1.090
 WBJ  C05  H10  single    0.970  0.020  1.090
 WBJ  C12  H11  single    0.930  0.020  1.080
 WBJ  O08  H12  single    0.850  0.020  0.980
 WBJ  O18  H13  single    0.850  0.020  0.980
 WBJ  O19  H14  single    0.850  0.020  0.980
 WBJ  O22  H15  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
 WBJ  H3   C10  H2   106.79  3.000
 WBJ  H3   C10  H1   108.43  3.000
 WBJ  H2   C10  H1   108.26  3.000
 WBJ  H3   C10  C09  111.69  3.000
 WBJ  H2   C10  C09  111.62  3.000
 WBJ  H1   C10  C09  109.91  3.000
 WBJ  H5   C15  H4   107.48  3.000
 WBJ  H5   C15  O16  110.68  3.000
 WBJ  H4   C15  O16  109.43  3.000
 WBJ  H5   C15  C14  110.96  3.000
 WBJ  H4   C15  C14  109.98  3.000
 WBJ  O16  C15  C14  108.30  3.000
 WBJ  O23  C21  O22  125.16  3.000
 WBJ  O22  C21  C03  111.87  3.000
 WBJ  O23  C21  C03  122.94  3.000
 WBJ  H7   C01  H6   116.29  3.000
 WBJ  H7   C01  C02  120.26  3.000
 WBJ  H6   C01  C02  123.44  3.000
 WBJ  H8   C02  C03  116.79  3.000
 WBJ  H8   C02  C01  118.89  3.000
 WBJ  C03  C02  C01  124.22  3.000
 WBJ  N04  C03  C02  125.73  3.000
 WBJ  C02  C03  C21  121.03  3.000
 WBJ  N04  C03  C21  113.23  3.000
 WBJ  H10  C05  H9   106.30  3.000
 WBJ  H10  C05  N04  111.39  3.000
 WBJ  H9   C05  N04  108.27  3.000
 WBJ  H10  C05  C06  109.48  3.000
 WBJ  H9   C05  C06  108.87  3.000
 WBJ  N04  C05  C06  112.32  3.000
 WBJ  C14  C06  C07  117.36  3.000
 WBJ  C07  C06  C05  123.22  3.000
 WBJ  C14  C06  C05  119.40  3.000
 WBJ  O08  C07  C09  116.53  3.000
 WBJ  O08  C07  C06  124.08  3.000
 WBJ  C09  C07  C06  119.38  3.000
 WBJ  N11  C09  C07  121.95  3.000
 WBJ  C07  C09  C10  119.75  3.000
 WBJ  N11  C09  C10  118.30  3.000
 WBJ  H11  C12  N11  116.53  3.000
 WBJ  H11  C12  C14  119.89  3.000
 WBJ  N11  C12  C14  123.58  3.000
 WBJ  C12  C14  C06  118.78  3.000
 WBJ  C06  C14  C15  122.29  3.000
 WBJ  C12  C14  C15  118.93  3.000
 WBJ  C05  N04  C03  122.05  3.000
 WBJ  C12  N11  C09  118.95  3.000
 WBJ  P17  O16  C15  120.36  3.000
 WBJ  H13  O18  P17  114.04  3.000
 WBJ  H14  O19  P17  114.14  3.000
 WBJ  H15  O22  C21  110.41  3.000
 WBJ  O20  P17  O19  118.19  3.000
 WBJ  O19  P17  O18  104.28  3.000
 WBJ  O20  P17  O18  114.03  3.000
 WBJ  O19  P17  O16   96.30  3.000
 WBJ  O18  P17  O16  104.53  3.000
 WBJ  O20  P17  O16  117.11  3.000
 WBJ  H12  O08  C07  107.72  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
 WBJ  CONST_01  N11  C12  C14  C06     0.00   0.0  0
 WBJ  CONST_02  N11  C09  C07  C06     0.00   0.0  0
 WBJ  CONST_03  C12  N11  C09  C07     0.00   0.0  0
 WBJ  CONST_04  C12  C14  C06  C07     0.00   0.0  0
 WBJ  CONST_05  C14  C12  N11  C09     0.00   0.0  0
 WBJ  CONST_06  C14  C06  C07  C09     0.00   0.0  0
 WBJ  CONST_07  C12  N11  C09  C10   180.00   0.0  0
 WBJ  CONST_08  C06  C07  C09  C10   180.00   0.0  0
 WBJ  CONST_09  N11  C12  C14  C15   180.00   0.0  0
 WBJ  CONST_10  C07  C06  C14  C15   180.00   0.0  0
 WBJ  CONST_11  C12  C14  C06  C05   180.00   0.0  0
 WBJ  CONST_12  C09  C07  C06  C05   180.00   0.0  0
 WBJ  CONST_13  O08  C07  C06  C14   180.00   0.0  0
 WBJ  CONST_14  O08  C07  C09  N11   180.00   0.0  0
 WBJ  CONST_15  H11  C12  C14  C06   180.00   0.0  0
 WBJ  CONST_16  H11  C12  N11  C09   180.00   0.0  0
 WBJ  CONST_17  H15  O22  C21  C03   180.00   0.0  0
 WBJ  CONST_18  H15  O22  C21  O23     0.00   0.0  0
 WBJ  Var_01    O16  C15  C14  C06    67.57  30.0  2
 WBJ  Var_02    N04  C05  C06  C07   -17.46  30.0  2
 WBJ  Var_03    O16  C15  C14  C12  -112.12  30.0  2
 WBJ  Var_04    N04  C05  C06  C14   164.17  30.0  2
 WBJ  Var_05    H4   C15  C14  C06  -172.89  30.0  2
 WBJ  Var_06    H5   C15  C14  C06   -54.10  30.0  2
 WBJ  Var_07    H1   C10  C09  C07   179.02  30.0  2
 WBJ  Var_08    H2   C10  C09  C07   -60.85  30.0  2
 WBJ  Var_09    H3   C10  C09  C07    58.62  30.0  2
 WBJ  Var_10    H9   C05  C06  C07   102.43  30.0  2
 WBJ  Var_11    H10  C05  C06  C07  -141.76  30.0  2
 WBJ  Var_12    H4   C15  C14  C12     7.43  30.0  2
 WBJ  Var_13    H5   C15  C14  C12   126.21  30.0  2
 WBJ  Var_14    H9   C05  C06  C14   -75.94  30.0  2
 WBJ  Var_15    H10  C05  C06  C14    39.87  30.0  2
 WBJ  Var_16    H1   C10  C09  N11    -1.37  30.0  2
 WBJ  Var_17    H2   C10  C09  N11   118.76  30.0  2
 WBJ  Var_18    H3   C10  C09  N11  -121.76  30.0  2
 WBJ  Var_19    C06  C05  N04  C03  -159.11  30.0  1
 WBJ  Var_20    P17  O16  C15  C14  -162.32  30.0  3
 WBJ  Var_21    C05  N04  C03  C21  -179.25   0.0  2
 WBJ  Var_22    C05  N04  C03  C02     0.01   0.0  2
 WBJ  Var_23    O20  P17  O16  C15   -56.29  30.0  3
 WBJ  Var_24    O18  P17  O16  C15    70.96  30.0  3
 WBJ  Var_25    O19  P17  O16  C15   177.53  30.0  3
 WBJ  Var_26    C01  C02  C03  C21   -28.80  30.0  2
 WBJ  Var_27    N04  C03  C02  C01   151.99  30.0  2
 WBJ  Var_28    O23  C21  C03  C02   145.47  30.0  2
 WBJ  Var_29    O22  C21  C03  C02   -36.74  30.0  2
 WBJ  Var_30    O23  C21  C03  N04   -35.23  30.0  2
 WBJ  Var_31    O22  C21  C03  N04   142.57  30.0  2
 WBJ  Var_32    H6   C01  C02  C03     2.30   0.0  2
 WBJ  Var_33    H7   C01  C02  C03  -176.59   0.0  2
 WBJ  Var_34    H8   C02  C03  C21   154.88  30.0  2
 WBJ  Var_35    H9   C05  N04  C03    80.65  30.0  1
 WBJ  Var_36    H10  C05  N04  C03   -35.88  30.0  1
 WBJ  Var_37    H8   C02  C03  N04   -24.33  30.0  2
 WBJ  Var_38    H4   C15  O16  P17    77.79  30.0  2
 WBJ  Var_39    H5   C15  O16  P17   -40.48  30.0  2
 WBJ  Var_40    H8   C02  C01  H6    178.54   0.0  2
 WBJ  Var_41    H8   C02  C01  H7     -0.35   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
 WBJ  plan-1  C10  0.020
 WBJ  plan-1  C15  0.020
 WBJ  plan-1  C05  0.020
 WBJ  plan-1  C06  0.020
 WBJ  plan-1  C07  0.020
 WBJ  plan-1  C09  0.020
 WBJ  plan-1  C12  0.020
 WBJ  plan-1  C14  0.020
 WBJ  plan-1  N11  0.020
 WBJ  plan-1  H11  0.020
 WBJ  plan-1  O08  0.020
 WBJ  plan-2  C21  0.020
 WBJ  plan-2  C03  0.020
 WBJ  plan-2  O22  0.020
 WBJ  plan-2  O23  0.020
 WBJ  plan-2  H15  0.020
 WBJ  plan-3  C21  0.020
 WBJ  plan-3  C02  0.020
 WBJ  plan-3  C03  0.020
 WBJ  plan-3  C05  0.020
 WBJ  plan-3  N04  0.020
 WBJ  plan-4  C01  0.020
 WBJ  plan-4  C02  0.020
 WBJ  plan-4  C03  0.020
 WBJ  plan-4  H6   0.020
 WBJ  plan-4  H7   0.020
 WBJ  plan-4  H8   0.020

