# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 22:35:37 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (5-hydroxy-4-{[(3-hydroxyisoxazol-4-yl)amino]methyl}-6-methylpyridin-3-yl)methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNc2conc2O)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
 PMH  PMH  '(5-hydroxy-4-{[(3-hydroxyisoxazol-4-yl)amino]methyl}-6-methylpyridin-3-yl)methyl dihydrogen phosphate'  ligand  36  22  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PMH
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
 PMH  N1    N  N     0  -0.405   3.3534   0.5616   1.6312
 PMH  C2    C  CR6   0   0.128   3.8433   0.2712   0.4390
 PMH  C2A   C  CH3   0  -0.788   5.3102   0.4760   0.2031
 PMH  C3    C  CR6   0   0.257   3.0149  -0.2128  -0.5856
 PMH  O3    O  OH1   0  -0.619   3.4942  -0.5023  -1.8099
 PMH  C4    C  CR6   0   0.067   1.6582  -0.4009  -0.3463
 PMH  C4A   C  CH2   0  -0.385   0.7380  -0.8946  -1.4306
 PMH  C5    C  CR6   0  -0.064   1.1671  -0.0846   0.9249
 PMH  C6    C  CR16  0  -0.136   2.0577   0.3926   1.8727
 PMH  C5A   C  CH2   0  -0.200  -0.2925  -0.2755   1.2207
 PMH  O4P   O  O2    0  -0.593  -0.5479   0.0330   2.5870
 PMH  P     P  P     0   1.466  -2.0511   0.0118   3.1300
 PMH  O1P   O  O     0  -0.708  -2.8263  -1.2139   2.8674
 PMH  O2P   O  OH1   0  -0.729  -1.7044   0.3711   4.6416
 PMH  O3P   O  OH1   0  -0.741  -2.7946   1.2672   2.4806
 PMH  N     N  NH1   0  -0.667  -0.1213   0.1869  -1.8757
 PMH  CA    C  CR5   0   0.065  -1.1036  -0.1515  -2.7866
 PMH  C     C  CR5   0   0.407  -2.0118   0.7560  -3.4117
 PMH  O     O  OH1   0  -0.605  -1.9651   2.0685  -3.2323
 PMH  ND    N  N     0  -0.207  -2.8694   0.1473  -4.1720
 PMH  OG    O  O     0  -0.344  -2.5775  -1.1814  -4.0743
 PMH  CB    C  CR15  0   0.037  -1.5194  -1.3497  -3.2598
 PMH  H2A1  H  HCH3  0   0.273   5.7824   0.8397   1.1125
 PMH  H2A2  H  HCH3  0   0.258   5.8153  -0.4508  -0.0814
 PMH  H2A3  H  HCH3  0   0.259   5.5012   1.2093  -0.5848
 PMH  HO3   H  HOH1  0   0.488   4.4412  -0.3337  -1.8644
 PMH  H4A1  H  HCH2  0   0.266   1.3009  -1.3466  -2.2531
 PMH  H4A2  H  HCH2  0   0.262   0.1014  -1.6888  -1.0294
 PMH  H6    H  HCR6  0   0.259   1.7254   0.6517   2.8692
 PMH  H5A1  H  HCH2  0   0.263  -0.8853   0.3646   0.5618
 PMH  H5A2  H  HCH2  0   0.257  -0.5827  -1.3115   1.0176
 PMH  H2P   H  HOH1  0   0.505  -2.4400   0.2449   5.2557
 PMH  H3P   H  HOH1  0   0.497  -2.3958   2.1307   2.6527
 PMH  HN    H  HNH1  0   0.383   0.4008   1.0073  -2.1525
 PMH  HO    H  HOH1  0   0.488  -2.6605   2.5089  -3.7386
 PMH  HB    H  HCR5  0   0.306  -1.1856  -2.3631  -3.1009

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
 PMH  N1   C2    aromatic  1.321  0.020  1.321
 PMH  N1   C6    aromatic  1.329  0.020  1.329
 PMH  C2   C2A   single    1.500  0.020  1.500
 PMH  C2   C3    aromatic  1.404  0.020  1.404
 PMH  C2A  H2A1  single    0.970  0.020  1.090
 PMH  C2A  H2A2  single    0.970  0.020  1.090
 PMH  C2A  H2A3  single    0.970  0.020  1.090
 PMH  C3   O3    single    1.346  0.020  1.346
 PMH  C3   C4    aromatic  1.390  0.020  1.390
 PMH  O3   HO3   single    0.850  0.020  0.980
 PMH  C4   C4A   single    1.505  0.020  1.505
 PMH  C4   C5    aromatic  1.399  0.020  1.399
 PMH  C4A  N     single    1.451  0.020  1.451
 PMH  C4A  H4A1  single    0.970  0.020  1.090
 PMH  C4A  H4A2  single    0.970  0.020  1.090
 PMH  C5   C6    aromatic  1.385  0.020  1.385
 PMH  C5   C5A   single    1.502  0.020  1.502
 PMH  C6   H6    single    0.930  0.020  1.080
 PMH  C5A  O4P   single    1.424  0.020  1.424
 PMH  C5A  H5A1  single    0.970  0.020  1.090
 PMH  C5A  H5A2  single    0.970  0.020  1.090
 PMH  O4P  P     single    1.598  0.020  1.598
 PMH  P    O1P   double    1.474  0.020  1.474
 PMH  P    O2P   single    1.592  0.020  1.592
 PMH  P    O3P   single    1.597  0.020  1.597
 PMH  O2P  H2P   single    0.850  0.020  0.980
 PMH  O3P  H3P   single    0.850  0.020  0.980
 PMH  N    CA    single    1.382  0.020  1.382
 PMH  N    HN    single    0.890  0.020  1.040
 PMH  CA   C     aromatic  1.428  0.020  1.428
 PMH  CA   CB    aromatic  1.354  0.020  1.354
 PMH  C    O     single    1.326  0.020  1.326
 PMH  C    ND    aromatic  1.298  0.020  1.298
 PMH  O    HO    single    0.850  0.020  0.980
 PMH  ND   OG    aromatic  1.364  0.020  1.364
 PMH  OG   CB    aromatic  1.346  0.020  1.346
 PMH  CB   HB    single    0.930  0.020  1.080

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
 PMH  C6    N1   C2    119.84  3.000
 PMH  C3    C2   C2A   120.63  3.000
 PMH  C3    C2   N1    121.04  3.000
 PMH  C2A   C2   N1    118.33  3.000
 PMH  H2A3  C2A  H2A2  107.48  3.000
 PMH  H2A3  C2A  H2A1  107.62  3.000
 PMH  H2A2  C2A  H2A1  107.49  3.000
 PMH  H2A3  C2A  C2    112.08  3.000
 PMH  H2A2  C2A  C2    112.15  3.000
 PMH  H2A1  C2A  C2    109.81  3.000
 PMH  C4    C3   O3    118.35  3.000
 PMH  C4    C3   C2    119.79  3.000
 PMH  O3    C3   C2    121.86  3.000
 PMH  HO3   O3   C3    111.33  3.000
 PMH  C5    C4   C4A   120.94  3.000
 PMH  C5    C4   C3    117.92  3.000
 PMH  C4A   C4   C3    121.12  3.000
 PMH  H4A2  C4A  H4A1  105.97  3.000
 PMH  H4A2  C4A  N     107.99  3.000
 PMH  H4A1  C4A  N     112.45  3.000
 PMH  H4A2  C4A  C4    109.25  3.000
 PMH  H4A1  C4A  C4    111.25  3.000
 PMH  N     C4A  C4    109.78  3.000
 PMH  C5A   C5   C6    122.27  3.000
 PMH  C5A   C5   C4    119.44  3.000
 PMH  C6    C5   C4    118.29  3.000
 PMH  H6    C6   C5    121.01  3.000
 PMH  H6    C6   N1    115.88  3.000
 PMH  C5    C6   N1    123.11  3.000
 PMH  H5A2  C5A  H5A1  107.37  3.000
 PMH  H5A2  C5A  O4P   109.60  3.000
 PMH  H5A1  C5A  O4P   110.74  3.000
 PMH  H5A2  C5A  C5    109.96  3.000
 PMH  H5A1  C5A  C5    109.51  3.000
 PMH  O4P   C5A  C5    109.63  3.000
 PMH  P     O4P  C5A   119.46  3.000
 PMH  O3P   P    O2P   108.07  3.000
 PMH  O3P   P    O1P   109.66  3.000
 PMH  O2P   P    O1P   118.13  3.000
 PMH  O3P   P    O4P   106.81  3.000
 PMH  O2P   P    O4P    96.59  3.000
 PMH  O1P   P    O4P   116.43  3.000
 PMH  H2P   O2P  P     114.09  3.000
 PMH  H3P   O3P  P     115.96  3.000
 PMH  HN    N    CA    112.67  3.000
 PMH  HN    N    C4A   112.51  3.000
 PMH  CA    N    C4A   116.14  3.000
 PMH  CB    CA   C     102.36  3.000
 PMH  CB    CA   N     131.73  3.000
 PMH  C     CA   N     125.81  3.000
 PMH  ND    C    O     124.54  3.000
 PMH  ND    C    CA    112.26  3.000
 PMH  O     C    CA    123.20  3.000
 PMH  HO    O    C     110.79  3.000
 PMH  OG    ND   C     105.87  3.000
 PMH  CB    OG   ND    109.48  3.000
 PMH  HB    CB   OG    116.74  3.000
 PMH  HB    CB   CA    133.23  3.000
 PMH  OG    CB   CA    110.02  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
 PMH  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PMH  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PMH  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 PMH  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PMH  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 PMH  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PMH  CONST_07  OG    ND   C    CA      0.00   0.0  0
 PMH  CONST_08  ND    OG   CB   CA      0.00   0.0  0
 PMH  CONST_09  OG    CB   CA   C       0.00   0.0  0
 PMH  CONST_10  CB    OG   ND   C       0.00   0.0  0
 PMH  CONST_11  CB    CA   C    ND      0.00   0.0  0
 PMH  CONST_12  O3    C3   C2   N1    180.00   0.0  0
 PMH  CONST_13  C5A   C5   C6   N1    180.00   0.0  0
 PMH  CONST_14  C4A   C4   C3   C2    180.00   0.0  0
 PMH  CONST_15  C6    N1   C2   C2A   180.00   0.0  0
 PMH  CONST_16  C4    C3   C2   C2A   180.00   0.0  0
 PMH  CONST_17  C5A   C5   C4   C3    180.00   0.0  0
 PMH  CONST_18  C5    C4   C3   O3    180.00   0.0  0
 PMH  CONST_19  C6    C5   C4   C4A   180.00   0.0  0
 PMH  CONST_20  ND    C    CA   N     180.00   0.0  0
 PMH  CONST_21  OG    CB   CA   N     180.00   0.0  0
 PMH  CONST_22  CB    CA   C    O     180.00   0.0  0
 PMH  CONST_23  OG    ND   C    O     180.00   0.0  0
 PMH  CONST_24  H6    C6   N1   C2    180.00   0.0  0
 PMH  CONST_25  HB    CB   CA   C     180.00   0.0  0
 PMH  CONST_26  C     CA   N    C4A   180.00   0.0  0
 PMH  CONST_27  CB    CA   N    C4A     0.00   0.0  0
 PMH  Var_01    N     C4A  C4   C3   -108.03  30.0  2
 PMH  Var_02    CA    N    C4A  C4   -174.34  30.0  3
 PMH  Var_03    O4P   C5A  C5   C4    176.61  30.0  2
 PMH  Var_04    H2A1  C2A  C2   N1      1.04  30.0  2
 PMH  Var_05    O1P   P    O4P  C5A    52.39  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
 PMH  plan-1  N    0.020
 PMH  plan-1  CA   0.020
 PMH  plan-1  C    0.020
 PMH  plan-1  O    0.020
 PMH  plan-1  ND   0.020
 PMH  plan-1  OG   0.020
 PMH  plan-1  CB   0.020
 PMH  plan-1  HB   0.020
 PMH  plan-2  N1   0.020
 PMH  plan-2  C2   0.020
 PMH  plan-2  C2A  0.020
 PMH  plan-2  C3   0.020
 PMH  plan-2  O3   0.020
 PMH  plan-2  C4   0.020
 PMH  plan-2  C4A  0.020
 PMH  plan-2  C5   0.020
 PMH  plan-2  C6   0.020
 PMH  plan-2  C5A  0.020
 PMH  plan-2  H6   0.020
 PMH  plan-3  C4A  0.020
 PMH  plan-3  N    0.020
 PMH  plan-3  CA   0.020
 PMH  plan-3  HN   0.020

