# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 22:40:03 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]cc(C(O)=O)c2C(=O)N1
#
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
 2KA  2KA  '2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid'  ligand  20  14  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2KA
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
 2KA  O7B  O  OH1   0  -0.608  -3.7378  -0.3977   0.0870
 2KA  C7A  C  C     0   0.447  -2.6542   0.3761  -0.0146
 2KA  O7A  O  O     0  -0.442  -2.7201   1.5795  -0.0991
 2KA  C7   C  CR5   0  -0.182  -1.4249  -0.4077  -0.0124
 2KA  C5   C  CR56  0  -0.187  -0.0582   0.0396  -0.0453
 2KA  C8   C  CR15  0   0.009  -1.3815  -1.7793   0.0030
 2KA  N9   N  NR15  0  -0.654  -0.0858  -2.1828  -0.0192
 2KA  C4   C  CR56  0   0.507   0.7357  -1.1040  -0.0467
 2KA  N3   N  N     0  -0.506   2.0749  -1.1963  -0.0644
 2KA  C2   C  CR6   0   0.683   2.6826  -0.0403  -0.0842
 2KA  N2   N  NH2   0  -0.831   4.0236   0.0172  -0.1494
 2KA  N1   N  NR16  0  -0.719   2.0076   1.1418  -0.0795
 2KA  C6   C  CR6   0   0.494   0.6158   1.3021  -0.0538
 2KA  O6   O  O     0  -0.464   0.1518   2.4289  -0.0401
 2KA  H1   H  HOH1  0   0.483  -4.5319   0.1553   0.0688
 2KA  H2   H  HCR5  0   0.306  -2.1803  -2.5010   0.0227
 2KA  H3   H  HNR5  0   0.422   0.2238  -3.1425  -0.0161
 2KA  H4   H  HNH2  0   0.410   4.5250  -0.8353   0.0357
 2KA  H5   H  HNH2  0   0.412   4.5079   0.8668   0.0874
 2KA  H6   H  HNR6  0   0.422   2.5403   2.0020  -0.0987

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
 2KA  N9   C8   aromatic  1.357  0.020  1.357
 2KA  N9   C4   aromatic  1.356  0.020  1.356
 2KA  C8   C7   aromatic  1.372  0.020  1.372
 2KA  C4   N3   single    1.342  0.020  1.342
 2KA  C4   C5   aromatic  1.392  0.020  1.392
 2KA  C7   C5   aromatic  1.438  0.020  1.438
 2KA  C7   C7A  single    1.458  0.020  1.458
 2KA  N3   C2   double    1.306  0.020  1.306
 2KA  O7A  C7A  double    1.208  0.020  1.208
 2KA  C5   C6   single    1.431  0.020  1.431
 2KA  C7A  O7B  single    1.335  0.020  1.335
 2KA  C2   N2   single    1.344  0.020  1.344
 2KA  C2   N1   single    1.361  0.020  1.361
 2KA  C6   N1   single    1.401  0.020  1.401
 2KA  C6   O6   double    1.219  0.020  1.219
 2KA  O7B  H1   single    0.850  0.020  0.980
 2KA  C8   H2   single    0.930  0.020  1.080
 2KA  N9   H3   single    0.860  0.020  1.020
 2KA  N2   H4   single    0.890  0.020  1.040
 2KA  N2   H5   single    0.890  0.020  1.040
 2KA  N1   H6   single    0.860  0.020  1.020

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
 2KA  H1   O7B  C7A  109.46  3.000
 2KA  C7   C7A  O7A  125.57  3.000
 2KA  O7A  C7A  O7B  122.56  3.000
 2KA  C7   C7A  O7B  111.87  3.000
 2KA  C8   C7   C5   106.32  3.000
 2KA  C5   C7   C7A  129.34  3.000
 2KA  C8   C7   C7A  124.34  3.000
 2KA  C6   C5   C4   117.14  3.000
 2KA  C6   C5   C7   136.21  3.000
 2KA  C4   C5   C7   106.64  3.000
 2KA  H2   C8   N9   120.62  3.000
 2KA  H2   C8   C7   130.28  3.000
 2KA  N9   C8   C7   109.10  3.000
 2KA  H3   N9   C4   124.83  3.000
 2KA  H3   N9   C8   125.17  3.000
 2KA  C4   N9   C8   110.01  3.000
 2KA  N3   C4   N9   123.35  3.000
 2KA  N3   C4   C5   128.71  3.000
 2KA  N9   C4   C5   107.94  3.000
 2KA  C2   N3   C4   113.80  3.000
 2KA  N1   C2   N2   117.24  3.000
 2KA  N1   C2   N3   122.53  3.000
 2KA  N2   C2   N3   120.20  3.000
 2KA  H5   N2   H4   115.61  3.000
 2KA  H5   N2   C2   120.33  3.000
 2KA  H4   N2   C2   116.87  3.000
 2KA  H6   N1   C6   115.21  3.000
 2KA  H6   N1   C2   118.50  3.000
 2KA  C6   N1   C2   126.29  3.000
 2KA  O6   C6   N1   118.96  3.000
 2KA  O6   C6   C5   129.51  3.000
 2KA  N1   C6   C5   111.53  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
 2KA  CONST_01  C4  N9   C8   C7     0.00   0.0  0
 2KA  CONST_02  N9  C4   C5   C7     0.00   0.0  0
 2KA  CONST_03  C8  N9   C4   C5     0.00   0.0  0
 2KA  CONST_04  N9  C8   C7   C5     0.00   0.0  0
 2KA  CONST_05  C4  C5   C7   C8     0.00   0.0  0
 2KA  CONST_06  C2  N1   C6   C5     0.00   0.0  0
 2KA  CONST_07  N1  C2   N3   C4     0.00   0.0  0
 2KA  CONST_08  C6  N1   C2   N3     0.00   0.0  0
 2KA  CONST_09  N9  C8   C7   C7A  180.00   0.0  0
 2KA  CONST_10  C4  C5   C7   C7A  180.00   0.0  0
 2KA  CONST_11  C6  C5   C7   C7A    0.00   0.0  0
 2KA  CONST_12  N2  C2   N3   C4   180.00   0.0  0
 2KA  CONST_13  O6  C6   N1   C2   180.00   0.0  0
 2KA  CONST_14  C6  N1   C2   N2   180.00   0.0  0
 2KA  CONST_15  H3  N9   C8   C7   180.00   0.0  0
 2KA  CONST_16  H2  C8   C7   C5   180.00   0.0  0
 2KA  CONST_17  H6  N1   C6   C5   180.00   0.0  0
 2KA  CONST_18  H4  N2   C2   N3     0.00   0.0  0
 2KA  CONST_20  H1  O7B  C7A  C7   180.00   0.0  0
 2KA  Var_01    C8  C7   C7A  O7B    4.02  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
 2KA  plan-1  C7A  0.020
 2KA  plan-1  C7   0.020
 2KA  plan-1  C5   0.020
 2KA  plan-1  C8   0.020
 2KA  plan-1  N9   0.020
 2KA  plan-1  C4   0.020
 2KA  plan-1  N3   0.020
 2KA  plan-1  C2   0.020
 2KA  plan-1  N2   0.020
 2KA  plan-1  N1   0.020
 2KA  plan-1  C6   0.020
 2KA  plan-1  O6   0.020
 2KA  plan-1  H2   0.020
 2KA  plan-1  H3   0.020
 2KA  plan-1  H4   0.020
 2KA  plan-1  H5   0.020
 2KA  plan-1  H6   0.020
 2KA  plan-2  O7B  0.020
 2KA  plan-2  C7A  0.020
 2KA  plan-2  O7A  0.020
 2KA  plan-2  C7   0.020
 2KA  plan-2  H1   0.020

