# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 23:18:15 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN=C(CNc2ccccc2O)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
 1D0  1D0  '(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid'  ligand  49  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1D0
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
 1D0  N1   N  N     0  -0.405   2.6192  -3.2660   0.6275
 1D0  C2   C  CR6   0   0.318  -4.0197   1.5289   1.6753
 1D0  C4   C  CR16  0  -0.255  -6.0439   0.5623   2.5344
 1D0  C5   C  CR16  0  -0.283  -6.2059  -0.1624   1.3623
 1D0  C6   C  CR16  0  -0.290  -5.2803  -0.0242   0.3341
 1D0  O    O  OH1   0  -0.630  -2.9426   2.3176   1.8418
 1D0  C3   C  CR16  0  -0.351  -4.9525   1.4061   2.6965
 1D0  C1   C  CR6   0   0.184  -4.1892   0.8228   0.4747
 1D0  N    N  NH1   0  -0.707  -3.1786   1.0159  -0.4971
 1D0  O3P  O  O     0  -0.708   4.1820   3.0341  -0.4080
 1D0  P    P  P     0   1.464   4.5959   2.0121   0.5700
 1D0  O1P  O  OH1   0  -0.728   6.1000   1.4941   0.5273
 1D0  O2P  O  OH1   0  -0.740   4.2901   2.5291   2.0497
 1D0  O4P  O  O2    0  -0.593   3.9043   0.5766   0.4341
 1D0  C5M  C  CH2   0  -0.205   2.4871   0.4867   0.3487
 1D0  C51  C  CR6   0  -0.070   2.0701  -0.9541   0.4085
 1D0  C61  C  CR16  0  -0.137   2.9763  -1.9868   0.5895
 1D0  C41  C  CR6   0   0.112   0.7197  -1.2782   0.2683
 1D0  C31  C  CR6   0   0.264   0.3634  -2.6211   0.2852
 1D0  O3   O  OH1   0  -0.619  -0.9342  -2.9326   0.1069
 1D0  C21  C  CR6   0   0.130   1.3487  -3.6003   0.4779
 1D0  C2A  C  CH3   0  -0.785   0.9834  -5.0541   0.5134
 1D0  C4A  C  CH2   0  -0.443  -0.3375  -0.2258   0.0483
 1D0  N2   N  N     0  -0.298  -0.4015   0.0538  -1.3684
 1D0  CA   C  C     0   0.128  -1.5047   0.0951  -1.9802
 1D0  C    C  C     0   0.518  -1.4525   0.4332  -3.4475
 1D0  OXT  O  OH1   0  -0.574  -0.2321   0.4170  -3.9447
 1D0  O1   O  O     0  -0.424  -2.4409   0.7013  -4.0850
 1D0  CB   C  CH2   0  -0.403  -2.8775  -0.0988  -1.3787
 1D0  H1   H  HCR6  0   0.255  -6.7631   0.4652   3.3372
 1D0  H2   H  HCR6  0   0.252  -7.0513  -0.8264   1.2411
 1D0  H3   H  HCR6  0   0.267  -5.4136  -0.5807  -0.5856
 1D0  H4   H  HOH1  0   0.464  -2.3586   2.1643   1.0804
 1D0  H5   H  HCR6  0   0.260  -4.8122   1.9567   3.6187
 1D0  H6   H  HNH1  0   0.387  -3.3320   1.8639  -1.0313
 1D0  H7   H  HOH1  0   0.506   6.7573   2.1954   0.4237
 1D0  H8   H  HOH1  0   0.497   4.5506   1.9357   2.7671
 1D0  H9   H  HCH2  0   0.259   2.0212   1.0422   1.1705
 1D0  H10  H  HCH2  0   0.264   2.1408   0.9349  -0.5871
 1D0  H11  H  HCR6  0   0.259   4.0332  -1.7880   0.7087
 1D0  H12  H  HOH1  0   0.488  -1.0754  -3.8852   0.1419
 1D0  H13  H  HCH3  0   0.258   0.2763  -5.2801   1.3158
 1D0  H14  H  HCH3  0   0.258   0.5307  -5.3851  -0.4249
 1D0  H15  H  HCH3  0   0.273   1.8738  -5.6553   0.6798
 1D0  H16  H  HCH2  0   0.268  -1.2794  -0.5306   0.5052
 1D0  H17  H  HCH2  0   0.284  -0.0507   0.7059   0.5434
 1D0  H18  H  HOH1  0   0.488  -0.2609   0.6538  -4.8839
 1D0  H19  H  HCH2  0   0.278  -2.8709  -1.0183  -0.7900
 1D0  H20  H  HCH2  0   0.269  -3.6212  -0.2404  -2.1654

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
 1D0  O3P  P    double    1.474  0.020  1.474
 1D0  C5   C4   aromatic  1.388  0.020  1.388
 1D0  C5   C6   aromatic  1.390  0.020  1.390
 1D0  P    O2P  single    1.597  0.020  1.597
 1D0  P    O4P  single    1.599  0.020  1.599
 1D0  P    O1P  single    1.591  0.020  1.591
 1D0  C5M  O4P  single    1.423  0.020  1.423
 1D0  C5M  C51  single    1.501  0.020  1.501
 1D0  C4   C3   aromatic  1.389  0.020  1.389
 1D0  C6   C1   aromatic  1.388  0.020  1.388
 1D0  C61  C51  aromatic  1.386  0.020  1.386
 1D0  C61  N1   aromatic  1.329  0.020  1.329
 1D0  C51  C41  aromatic  1.396  0.020  1.396
 1D0  C3   C2   aromatic  1.389  0.020  1.389
 1D0  C1   C2   aromatic  1.403  0.020  1.403
 1D0  C1   N    single    1.415  0.020  1.415
 1D0  N1   C21  aromatic  1.322  0.020  1.322
 1D0  C41  C4A  single    1.508  0.020  1.508
 1D0  C41  C31  aromatic  1.389  0.020  1.389
 1D0  C2   O    single    1.345  0.020  1.345
 1D0  C4A  N2   single    1.445  0.020  1.445
 1D0  N    CB   single    1.453  0.020  1.453
 1D0  CB   CA   single    1.511  0.020  1.511
 1D0  C21  C31  aromatic  1.402  0.020  1.402
 1D0  C21  C2A  single    1.499  0.020  1.499
 1D0  C31  O3   single    1.346  0.020  1.346
 1D0  N2   CA   double    1.262  0.020  1.262
 1D0  CA   C    single    1.507  0.020  1.507
 1D0  C    O1   double    1.206  0.020  1.206
 1D0  C    OXT  single    1.318  0.020  1.318
 1D0  C4   H1   single    0.930  0.020  1.080
 1D0  C5   H2   single    0.930  0.020  1.080
 1D0  C6   H3   single    0.930  0.020  1.080
 1D0  O    H4   single    0.850  0.020  0.980
 1D0  C3   H5   single    0.930  0.020  1.080
 1D0  N    H6   single    0.890  0.020  1.040
 1D0  O1P  H7   single    0.850  0.020  0.980
 1D0  O2P  H8   single    0.850  0.020  0.980
 1D0  C5M  H9   single    0.970  0.020  1.090
 1D0  C5M  H10  single    0.970  0.020  1.090
 1D0  C61  H11  single    0.930  0.020  1.080
 1D0  O3   H12  single    0.850  0.020  0.980
 1D0  C2A  H13  single    0.970  0.020  1.090
 1D0  C2A  H14  single    0.970  0.020  1.090
 1D0  C2A  H15  single    0.970  0.020  1.090
 1D0  C4A  H16  single    0.970  0.020  1.090
 1D0  C4A  H17  single    0.970  0.020  1.090
 1D0  OXT  H18  single    0.850  0.020  0.980
 1D0  CB   H19  single    0.970  0.020  1.090
 1D0  CB   H20  single    0.970  0.020  1.090

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
 1D0  C21  N1   C61  119.90  3.000
 1D0  C1   C2   C3   120.24  3.000
 1D0  C1   C2   O    119.84  3.000
 1D0  C3   C2   O    119.92  3.000
 1D0  H1   C4   C3   119.34  3.000
 1D0  H1   C4   C5   120.15  3.000
 1D0  C3   C4   C5   120.51  3.000
 1D0  H2   C5   C6   119.90  3.000
 1D0  H2   C5   C4   120.43  3.000
 1D0  C6   C5   C4   119.67  3.000
 1D0  H3   C6   C1   119.74  3.000
 1D0  H3   C6   C5   119.66  3.000
 1D0  C1   C6   C5   120.60  3.000
 1D0  H4   O    C2   106.96  3.000
 1D0  H5   C3   C4   120.66  3.000
 1D0  H5   C3   C2   119.62  3.000
 1D0  C4   C3   C2   119.72  3.000
 1D0  N    C1   C6   125.09  3.000
 1D0  N    C1   C2   115.63  3.000
 1D0  C6   C1   C2   119.25  3.000
 1D0  H6   N    CB   110.69  3.000
 1D0  H6   N    C1   111.59  3.000
 1D0  CB   N    C1   117.39  3.000
 1D0  O4P  P    O2P  106.65  3.000
 1D0  O4P  P    O1P   96.56  3.000
 1D0  O2P  P    O1P  108.13  3.000
 1D0  O1P  P    O3P  118.25  3.000
 1D0  O4P  P    O3P  116.41  3.000
 1D0  O2P  P    O3P  109.67  3.000
 1D0  H7   O1P  P    114.16  3.000
 1D0  H8   O2P  P    115.93  3.000
 1D0  C5M  O4P  P    119.51  3.000
 1D0  H10  C5M  H9   107.41  3.000
 1D0  H10  C5M  C51  109.84  3.000
 1D0  H9   C5M  C51  109.79  3.000
 1D0  H10  C5M  O4P  109.93  3.000
 1D0  H9   C5M  O4P  110.27  3.000
 1D0  C51  C5M  O4P  109.57  3.000
 1D0  C41  C51  C61  118.21  3.000
 1D0  C41  C51  C5M  119.18  3.000
 1D0  C61  C51  C5M  122.60  3.000
 1D0  H11  C61  C51  121.08  3.000
 1D0  H11  C61  N1   115.87  3.000
 1D0  C51  C61  N1   123.06  3.000
 1D0  C4A  C41  C31  119.77  3.000
 1D0  C31  C41  C51  118.12  3.000
 1D0  C4A  C41  C51  122.07  3.000
 1D0  C21  C31  O3   122.26  3.000
 1D0  O3   C31  C41  117.98  3.000
 1D0  C21  C31  C41  119.76  3.000
 1D0  H12  O3   C31  111.42  3.000
 1D0  C2A  C21  C31  120.60  3.000
 1D0  C2A  C21  N1   118.46  3.000
 1D0  C31  C21  N1   120.93  3.000
 1D0  H15  C2A  H14  107.64  3.000
 1D0  H15  C2A  H13  107.64  3.000
 1D0  H14  C2A  H13  107.43  3.000
 1D0  H15  C2A  C21  109.89  3.000
 1D0  H14  C2A  C21  111.97  3.000
 1D0  H13  C2A  C21  112.05  3.000
 1D0  H17  C4A  H16  105.96  3.000
 1D0  H17  C4A  N2   106.90  3.000
 1D0  H16  C4A  N2   115.25  3.000
 1D0  H17  C4A  C41  110.17  3.000
 1D0  H16  C4A  C41  110.45  3.000
 1D0  N2   C4A  C41  108.01  3.000
 1D0  CA   N2   C4A  121.34  3.000
 1D0  CB   CA   C    116.61  3.000
 1D0  C    CA   N2   116.69  3.000
 1D0  CB   CA   N2   126.64  3.000
 1D0  O1   C    OXT  124.20  3.000
 1D0  OXT  C    CA   113.38  3.000
 1D0  O1   C    CA   122.42  3.000
 1D0  H18  OXT  C    109.58  3.000
 1D0  H20  CB   H19  106.46  3.000
 1D0  H20  CB   CA   110.40  3.000
 1D0  H19  CB   CA   108.49  3.000
 1D0  H20  CB   N    113.30  3.000
 1D0  H19  CB   N    108.68  3.000
 1D0  CA   CB   N    109.35  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
 1D0  CONST_01  C41  C51  C61  N1      0.00   0.0  0
 1D0  CONST_02  C41  C31  C21  N1      0.00   0.0  0
 1D0  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 1D0  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 1D0  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 1D0  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 1D0  CONST_07  C3   C4   C5   C6      0.00   0.0  0
 1D0  CONST_08  C3   C2   C1   C6      0.00   0.0  0
 1D0  CONST_09  C21  N1   C61  C51     0.00   0.0  0
 1D0  CONST_10  C21  C31  C41  C51     0.00   0.0  0
 1D0  CONST_11  C31  C41  C51  C61     0.00   0.0  0
 1D0  CONST_12  C31  C21  N1   C61     0.00   0.0  0
 1D0  CONST_13  C5M  C51  C61  N1    180.00   0.0  0
 1D0  CONST_14  O3   C31  C21  N1    180.00   0.0  0
 1D0  CONST_15  O    C2   C3   C4    180.00   0.0  0
 1D0  CONST_16  N    C1   C6   C5    180.00   0.0  0
 1D0  CONST_17  O    C2   C1   C6    180.00   0.0  0
 1D0  CONST_18  N    C1   C2   C3    180.00   0.0  0
 1D0  CONST_19  C31  C41  C51  C5M   180.00   0.0  0
 1D0  CONST_20  O3   C31  C41  C51   180.00   0.0  0
 1D0  CONST_21  C4A  C41  C51  C61   180.00   0.0  0
 1D0  CONST_22  C2A  C21  N1   C61   180.00   0.0  0
 1D0  CONST_23  C2A  C21  C31  C41   180.00   0.0  0
 1D0  CONST_24  C4A  C41  C31  C21   180.00   0.0  0
 1D0  CONST_25  H1   C4   C3   C2    180.00   0.0  0
 1D0  CONST_26  H3   C6   C1   C2    180.00   0.0  0
 1D0  CONST_27  H5   C3   C4   C5    180.00   0.0  0
 1D0  CONST_28  H2   C5   C4   C3    180.00   0.0  0
 1D0  CONST_29  H11  C61  C51  C41   180.00   0.0  0
 1D0  CONST_33  H18  OXT  C    CA    180.00   0.0  0
 1D0  Var_01    C61  C51  C5M  O4P     2.98  30.0  2
 1D0  Var_02    N2   C4A  C41  C51    85.18  30.0  2
 1D0  Var_03    H13  C2A  C21  N1    120.36  30.0  2
 1D0  Var_04    CA   CB   N    C1   -159.95  30.0  3
 1D0  Var_05    C51  C5M  O4P  P    -172.69  30.0  1
 1D0  Var_06    CB   CA   N2   C4A     1.31   0.0  2
 1D0  Var_07    N2   CA   CB   N      67.83  30.0  3
 1D0  Var_08    O1   C    CA   N2   -168.40  30.0  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
 1D0  plan-1  C2   0.020
 1D0  plan-1  C4   0.020
 1D0  plan-1  C5   0.020
 1D0  plan-1  C6   0.020
 1D0  plan-1  O    0.020
 1D0  plan-1  C3   0.020
 1D0  plan-1  C1   0.020
 1D0  plan-1  N    0.020
 1D0  plan-1  H1   0.020
 1D0  plan-1  H2   0.020
 1D0  plan-1  H3   0.020
 1D0  plan-1  H5   0.020
 1D0  plan-2  N1   0.020
 1D0  plan-2  C5M  0.020
 1D0  plan-2  C51  0.020
 1D0  plan-2  C61  0.020
 1D0  plan-2  C41  0.020
 1D0  plan-2  C31  0.020
 1D0  plan-2  O3   0.020
 1D0  plan-2  C21  0.020
 1D0  plan-2  C2A  0.020
 1D0  plan-2  C4A  0.020
 1D0  plan-2  H11  0.020
 1D0  plan-3  C1   0.020
 1D0  plan-3  N    0.020
 1D0  plan-3  CB   0.020
 1D0  plan-3  H6   0.020
 1D0  plan-4  CA   0.020
 1D0  plan-4  C    0.020
 1D0  plan-4  OXT  0.020
 1D0  plan-4  O1   0.020
 1D0  plan-4  H18  0.020
 1D0  plan-5  C4A  0.020
 1D0  plan-5  N2   0.020
 1D0  plan-5  CA   0.020
 1D0  plan-5  C    0.020
 1D0  plan-5  CB   0.020

