# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 16:14:22 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2-amino-4-formyl-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)c(CO[P](O)(O)=O)c(C=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
 X04  X04  '(2-amino-4-formyl-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate'  ligand  28  17  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X04
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
 X04  P     P  P     0   1.467   0.2754  -0.2662  -2.9799
 X04  OP1   O  O     0  -0.705   1.7400  -0.1051  -2.8446
 X04  OP2   O  OH1   0  -0.725  -0.2866  -1.7088  -3.3438
 X04  OP3   O  OH1   0  -0.733  -0.2659   0.7694  -4.0659
 X04  OP4   O  O2    0  -0.579  -0.5685  -0.0591  -1.6430
 X04  C5A   C  CH2   0  -0.343  -0.2704   1.0391  -0.7554
 X04  C5    C  CR6   0  -0.015   0.1069   0.5166   0.5956
 X04  C6    C  CR6   0   0.375   1.4508   0.3533   0.9424
 X04  N2    N  NH2   0  -0.863   2.4806   0.6456   0.0796
 X04  N1    N  N     0  -0.443   1.8131  -0.0364   2.1691
 X04  C2    C  CR6   0   0.154   0.9221  -0.3148   3.0970
 X04  C2A   C  CH3   0  -0.721   1.4070  -0.7354   4.4482
 X04  C3    C  CR6   0   0.270  -0.4554  -0.2398   2.8320
 X04  O3    O  OH1   0  -0.622  -1.2972  -0.5779   3.8137
 X04  C4    C  CR6   0  -0.065  -0.8593   0.1787   1.5613
 X04  C4A   C  C1    0   0.161  -2.2924   0.2394   1.2565
 X04  O1    O  O     0  -0.412  -3.1601  -0.0319   2.0681
 X04  HP2   H  HOH1  0   0.507   0.1141  -2.1086  -4.1277
 X04  HP3   H  HOH1  0   0.499  -1.2103   0.7134  -4.2664
 X04  H5A1  H  HCH2  0   0.278  -1.1556   1.6715  -0.7192
 X04  H5A2  H  HCH2  0   0.274   0.5346   1.6632  -1.1481
 X04  HN21  H  HNH2  0   0.378   3.3804   0.3449   0.4197
 X04  HN22  H  HNH2  0   0.392   2.3500   0.4206  -0.8976
 X04  H2A1  H  HCH3  0   0.253   1.0017  -0.0977   5.2353
 X04  H2A2  H  HCH3  0   0.254   1.1010  -1.7578   4.6773
 X04  H2A3  H  HCH3  0   0.253   2.4926  -0.6858   4.4875
 X04  HO3   H  HOH1  0   0.477  -2.2121  -0.4737   3.4867
 X04  H4A   H  H     0   0.235  -2.5849   0.5283   0.2400

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
 X04  P    OP1   double    1.480  0.020  1.480
 X04  P    OP2   single    1.590  0.020  1.590
 X04  P    OP3   single    1.595  0.020  1.595
 X04  P    OP4   single    1.595  0.020  1.595
 X04  OP2  HP2   single    0.850  0.020  0.980
 X04  OP3  HP3   single    0.850  0.020  0.980
 X04  OP4  C5A   single    1.443  0.020  1.443
 X04  C5A  C5    single    1.497  0.020  1.497
 X04  C5A  H5A1  single    0.970  0.020  1.090
 X04  C5A  H5A2  single    0.970  0.020  1.090
 X04  C5   C6    aromatic  1.398  0.020  1.398
 X04  C5   C4    aromatic  1.407  0.020  1.407
 X04  C6   N2    single    1.375  0.020  1.375
 X04  C6   N1    aromatic  1.337  0.020  1.337
 X04  N2   HN21  single    0.890  0.020  1.040
 X04  N2   HN22  single    0.890  0.020  1.040
 X04  N1   C2    aromatic  1.316  0.020  1.316
 X04  C2   C2A   single    1.496  0.020  1.496
 X04  C2   C3    aromatic  1.405  0.020  1.405
 X04  C2A  H2A1  single    0.970  0.020  1.090
 X04  C2A  H2A2  single    0.970  0.020  1.090
 X04  C2A  H2A3  single    0.970  0.020  1.090
 X04  C3   O3    single    1.337  0.020  1.337
 X04  C3   C4    aromatic  1.397  0.020  1.397
 X04  O3   HO3   single    0.850  0.020  0.980
 X04  C4   C4A   single    1.466  0.020  1.466
 X04  C4A  O1    double    1.219  0.020  1.219
 X04  C4A  H4A   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
 X04  OP4   P    OP3   107.87  3.000
 X04  OP4   P    OP2    97.04  3.000
 X04  OP3   P    OP2   108.25  3.000
 X04  OP4   P    OP1   115.67  3.000
 X04  OP3   P    OP1   109.11  3.000
 X04  OP2   P    OP1   118.00  3.000
 X04  HP2   OP2  P     114.47  3.000
 X04  HP3   OP3  P     115.78  3.000
 X04  C5A   OP4  P     120.34  3.000
 X04  H5A2  C5A  H5A1  106.23  3.000
 X04  H5A2  C5A  C5    109.78  3.000
 X04  H5A1  C5A  C5    112.20  3.000
 X04  H5A2  C5A  OP4   111.48  3.000
 X04  H5A1  C5A  OP4   107.13  3.000
 X04  C5    C5A  OP4   109.97  3.000
 X04  C4    C5   C6    117.51  3.000
 X04  C4    C5   C5A   122.02  3.000
 X04  C6    C5   C5A   120.48  3.000
 X04  N1    C6   N2    115.77  3.000
 X04  N1    C6   C5    121.49  3.000
 X04  N2    C6   C5    122.66  3.000
 X04  HN22  N2   HN21  112.02  3.000
 X04  HN22  N2   C6    117.54  3.000
 X04  HN21  N2   C6    113.17  3.000
 X04  C2    N1   C6    121.66  3.000
 X04  C3    C2   C2A   120.22  3.000
 X04  C3    C2   N1    121.30  3.000
 X04  C2A   C2   N1    118.48  3.000
 X04  H2A3  C2A  H2A2  108.37  3.000
 X04  H2A3  C2A  H2A1  108.55  3.000
 X04  H2A2  C2A  H2A1  106.97  3.000
 X04  H2A3  C2A  C2    110.09  3.000
 X04  H2A2  C2A  C2    111.23  3.000
 X04  H2A1  C2A  C2    111.52  3.000
 X04  C4    C3   O3    124.16  3.000
 X04  C4    C3   C2    118.10  3.000
 X04  O3    C3   C2    117.74  3.000
 X04  HO3   O3   C3    108.48  3.000
 X04  C4A   C4   C3    118.94  3.000
 X04  C4A   C4   C5    121.23  3.000
 X04  C3    C4   C5    119.83  3.000
 X04  H4A   C4A  O1    119.08  3.000
 X04  H4A   C4A  C4    117.66  3.000
 X04  O1    C4A  C4    123.24  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
 X04  CONST_01  C2    N1   C6   C5      0.00   0.0  0
 X04  CONST_02  C2    C3   C4   C5      0.00   0.0  0
 X04  CONST_03  C3    C4   C5   C6      0.00   0.0  0
 X04  CONST_04  C3    C2   N1   C6      0.00   0.0  0
 X04  CONST_05  C4    C5   C6   N1      0.00   0.0  0
 X04  CONST_06  C4    C3   C2   N1      0.00   0.0  0
 X04  CONST_07  N1    C6   C5   C5A   180.00   0.0  0
 X04  CONST_08  C3    C4   C5   C5A   180.00   0.0  0
 X04  CONST_09  O3    C3   C4   C5    180.00   0.0  0
 X04  CONST_10  C4A   C4   C5   C6    180.00   0.0  0
 X04  CONST_11  C2A   C2   N1   C6    180.00   0.0  0
 X04  CONST_12  C4    C5   C6   N2    180.00   0.0  0
 X04  CONST_13  C2    N1   C6   N2    180.00   0.0  0
 X04  CONST_14  O3    C3   C2   N1    180.00   0.0  0
 X04  CONST_15  C4A   C4   C3   C2    180.00   0.0  0
 X04  CONST_16  C4    C3   C2   C2A   180.00   0.0  0
 X04  CONST_17  HN21  N2   C6   C5    180.00   0.0  0
 X04  Var_01    C6    C5   C5A  OP4    96.32  30.0  2
 X04  Var_02    O1    C4A  C4   C5   -179.24  30.0  2
 X04  Var_03    H2A1  C2A  C2   N1    124.36  30.0  2
 X04  Var_04    C5    C5A  OP4  P    -119.99  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
 X04  plan-1  C5A   0.020
 X04  plan-1  C5    0.020
 X04  plan-1  C6    0.020
 X04  plan-1  N2    0.020
 X04  plan-1  N1    0.020
 X04  plan-1  C2    0.020
 X04  plan-1  C2A   0.020
 X04  plan-1  C3    0.020
 X04  plan-1  O3    0.020
 X04  plan-1  C4    0.020
 X04  plan-1  C4A   0.020
 X04  plan-2  C6    0.020
 X04  plan-2  N2    0.020
 X04  plan-2  HN21  0.020
 X04  plan-2  HN22  0.020
 X04  plan-3  C4    0.020
 X04  plan-3  C4A   0.020
 X04  plan-3  O1    0.020
 X04  plan-3  H4A   0.020

