# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 20:44:09 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: {[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]oxy}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNOCC(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
 IK2  IK2  '{[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]oxy}acetic acid'  ligand  36  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IK2
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
 IK2  N1    N  N     0  -0.407   2.8285   0.3587   2.1492
 IK2  C2    C  CR6   0   0.136   3.2665   0.4534   0.9059
 IK2  C2A   C  CH3   0  -0.721   4.7162   0.7510   0.6771
 IK2  C3    C  CR6   0   0.274   2.3993   0.2727  -0.1821
 IK2  O3    O  OH1   0  -0.641   2.9149   0.3775  -1.4174
 IK2  C4    C  CR6   0   0.013   1.0561  -0.0239   0.0480
 IK2  C4A   C  CH2   0  -0.349   0.1414  -0.2961  -1.1213
 IK2  N4A   N  NH1   0  -0.381   0.3563   0.7170  -2.1513
 IK2  OX    O  O2    0  -0.391  -0.4631   0.4306  -3.2497
 IK2  C1'   C  CH2   0  -0.237   0.3347   0.2461  -4.3908
 IK2  C2'   C  C     0   0.498  -0.5833  -0.0584  -5.5470
 IK2  O1'   O  O     0  -0.430  -1.7809  -0.1269  -5.4765
 IK2  O2'   O  OH1   0  -0.592   0.1163  -0.2368  -6.6579
 IK2  C5    C  CR6   0  -0.072   0.6172  -0.1065   1.3729
 IK2  C6    C  CR16  0  -0.139   1.5466   0.0933   2.3808
 IK2  C5A   C  CH2   0  -0.214  -0.8230  -0.4257   1.6683
 IK2  O4P   O  O2    0  -0.592  -1.0189  -0.4689   3.0762
 IK2  P     P  P     0   1.461  -2.5002  -0.4132   3.6748
 IK2  O1P   O  O     0  -0.707  -3.4644  -1.3933   3.1440
 IK2  O2P   O  OH1   0  -0.728  -2.0813  -0.5272   5.2060
 IK2  O3P   O  OH1   0  -0.739  -3.0398   1.0672   3.4146
 IK2  H2A1  H  HCH3  0   0.248   5.2244  -0.0796   0.1830
 IK2  H2A2  H  HCH3  0   0.246   4.8515   1.6281   0.0423
 IK2  H2A3  H  HCH3  0   0.246   5.2123   0.9343   1.6280
 IK2  HO3   H  HOH1  0   0.474   2.1716   0.5468  -2.0398
 IK2  H4A1  H  HCH2  0   0.284   0.3969  -1.2694  -1.5503
 IK2  H4A2  H  HCH2  0   0.266  -0.9067  -0.3445  -0.8178
 IK2  HNA   H  HNH1  0   0.393   0.0373   1.6195  -1.8098
 IK2  H1'1  H  HCH2  0   0.267   0.9195   1.1427  -4.6280
 IK2  H1'2  H  HCH2  0   0.263   1.0434  -0.5824  -4.2689
 IK2  HO2   H  HOH1  0   0.488  -0.4769  -0.4225  -7.4015
 IK2  H6    H  HCR6  0   0.257   1.2566   0.0410   3.4218
 IK2  H5A1  H  HCH2  0   0.256  -1.4688   0.3329   1.2121
 IK2  H5A2  H  HCH2  0   0.267  -1.0954  -1.3912   1.2334
 IK2  HOP2  H  HOH1  0   0.506  -2.8200  -0.6999   5.8050
 IK2  HOP3  H  HOH1  0   0.497  -2.5000   1.7832   3.7754

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
 IK2  N1   C2    aromatic  1.322  0.020  1.322
 IK2  N1   C6    aromatic  1.329  0.020  1.329
 IK2  C2   C2A   single    1.498  0.020  1.498
 IK2  C2   C3    aromatic  1.403  0.020  1.403
 IK2  C2A  H2A1  single    0.970  0.020  1.090
 IK2  C2A  H2A2  single    0.970  0.020  1.090
 IK2  C2A  H2A3  single    0.970  0.020  1.090
 IK2  C3   O3    single    1.343  0.020  1.343
 IK2  C3   C4    aromatic  1.395  0.020  1.395
 IK2  O3   HO3   single    0.850  0.020  0.980
 IK2  C4   C4A   single    1.509  0.020  1.509
 IK2  C4   C5    aromatic  1.398  0.020  1.398
 IK2  C4A  N4A   single    1.461  0.020  1.461
 IK2  C4A  H4A1  single    0.970  0.020  1.090
 IK2  C4A  H4A2  single    0.970  0.020  1.090
 IK2  N4A  OX    single    1.400  0.020  1.400
 IK2  N4A  HNA   single    0.890  0.020  1.040
 IK2  OX   C1'   single    1.405  0.020  1.405
 IK2  C1'  C2'   single    1.507  0.020  1.507
 IK2  C1'  H1'1  single    0.970  0.020  1.090
 IK2  C1'  H1'2  single    0.970  0.020  1.090
 IK2  C2'  O1'   double    1.202  0.020  1.202
 IK2  C2'  O2'   single    1.325  0.020  1.325
 IK2  O2'  HO2   single    0.850  0.020  0.980
 IK2  C5   C6    aromatic  1.385  0.020  1.385
 IK2  C5   C5A   single    1.504  0.020  1.504
 IK2  C6   H6    single    0.930  0.020  1.080
 IK2  C5A  O4P   single    1.422  0.020  1.422
 IK2  C5A  H5A1  single    0.970  0.020  1.090
 IK2  C5A  H5A2  single    0.970  0.020  1.090
 IK2  O4P  P     single    1.599  0.020  1.599
 IK2  P    O1P   double    1.474  0.020  1.474
 IK2  P    O2P   single    1.592  0.020  1.592
 IK2  P    O3P   single    1.597  0.020  1.597
 IK2  O2P  HOP2  single    0.850  0.020  0.980
 IK2  O3P  HOP3  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
 IK2  C6    N1   C2    119.85  3.000
 IK2  C3    C2   C2A   120.36  3.000
 IK2  C3    C2   N1    121.03  3.000
 IK2  C2A   C2   N1    118.61  3.000
 IK2  H2A3  C2A  H2A2  108.45  3.000
 IK2  H2A3  C2A  H2A1  108.14  3.000
 IK2  H2A2  C2A  H2A1  106.88  3.000
 IK2  H2A3  C2A  C2    109.96  3.000
 IK2  H2A2  C2A  C2    111.64  3.000
 IK2  H2A1  C2A  C2    111.62  3.000
 IK2  C4    C3   O3    122.56  3.000
 IK2  C4    C3   C2    119.65  3.000
 IK2  O3    C3   C2    117.78  3.000
 IK2  HO3   O3   C3    107.78  3.000
 IK2  C5    C4   C4A   122.23  3.000
 IK2  C5    C4   C3    118.11  3.000
 IK2  C4A   C4   C3    119.62  3.000
 IK2  H4A2  C4A  H4A1  107.08  3.000
 IK2  H4A2  C4A  N4A   111.58  3.000
 IK2  H4A1  C4A  N4A   107.83  3.000
 IK2  H4A2  C4A  C4    111.98  3.000
 IK2  H4A1  C4A  C4    108.83  3.000
 IK2  N4A   C4A  C4    109.39  3.000
 IK2  HNA   N4A  OX    105.16  3.000
 IK2  HNA   N4A  C4A   109.44  3.000
 IK2  OX    N4A  C4A   108.98  3.000
 IK2  C1'   OX   N4A   109.38  3.000
 IK2  H1'2  C1'  H1'1  107.28  3.000
 IK2  H1'2  C1'  C2'   109.03  3.000
 IK2  H1'1  C1'  C2'   108.91  3.000
 IK2  H1'2  C1'  OX    112.08  3.000
 IK2  H1'1  C1'  OX    111.79  3.000
 IK2  C2'   C1'  OX    107.69  3.000
 IK2  O2'   C2'  O1'   124.60  3.000
 IK2  O2'   C2'  C1'   110.41  3.000
 IK2  O1'   C2'  C1'   124.99  3.000
 IK2  HO2   O2'  C2'   110.24  3.000
 IK2  C5A   C5   C6    122.00  3.000
 IK2  C5A   C5   C4    119.94  3.000
 IK2  C6    C5   C4    118.06  3.000
 IK2  H6    C6   C5    120.88  3.000
 IK2  H6    C6   N1    115.83  3.000
 IK2  C5    C6   N1    123.29  3.000
 IK2  H5A2  C5A  H5A1  107.39  3.000
 IK2  H5A2  C5A  O4P   109.42  3.000
 IK2  H5A1  C5A  O4P   110.61  3.000
 IK2  H5A2  C5A  C5    110.35  3.000
 IK2  H5A1  C5A  C5    109.61  3.000
 IK2  O4P   C5A  C5    109.43  3.000
 IK2  P     O4P  C5A   119.82  3.000
 IK2  O3P   P    O2P   108.18  3.000
 IK2  O3P   P    O1P   109.68  3.000
 IK2  O2P   P    O1P   118.11  3.000
 IK2  O3P   P    O4P   106.52  3.000
 IK2  O2P   P    O4P    96.53  3.000
 IK2  O1P   P    O4P   116.63  3.000
 IK2  HOP2  O2P  P     114.07  3.000
 IK2  HOP3  O3P  P     115.92  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
 IK2  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 IK2  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 IK2  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 IK2  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 IK2  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 IK2  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 IK2  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 IK2  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 IK2  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 IK2  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 IK2  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 IK2  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 IK2  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 IK2  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 IK2  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 IK2  CONST_16  HO2   O2'  C2'  C1'   180.00   0.0  0
 IK2  Var_01    N4A   C4A  C4   C3    -46.00  30.0  2
 IK2  Var_02    O4P   C5A  C5   C4    179.33  30.0  2
 IK2  Var_03    H2A1  C2A  C2   N1    115.32  30.0  2
 IK2  Var_04    OX    N4A  C4A  C4    178.02  30.0  3
 IK2  Var_05    C2'   C1'  OX   N4A  -179.97  30.0  3
 IK2  Var_06    O1'   C2'  C1'  OX     -0.11  30.0  3
 IK2  Var_07    O1P   P    O4P  C5A    52.78  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
 IK2  plan-1  N1   0.020
 IK2  plan-1  C2   0.020
 IK2  plan-1  C2A  0.020
 IK2  plan-1  C3   0.020
 IK2  plan-1  O3   0.020
 IK2  plan-1  C4   0.020
 IK2  plan-1  C4A  0.020
 IK2  plan-1  C5   0.020
 IK2  plan-1  C6   0.020
 IK2  plan-1  C5A  0.020
 IK2  plan-1  H6   0.020
 IK2  plan-2  C1'  0.020
 IK2  plan-2  C2'  0.020
 IK2  plan-2  O1'  0.020
 IK2  plan-2  O2'  0.020
 IK2  plan-2  HO2  0.020

