# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:18:15 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: (6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N[C@H](CN2)C(O)=O)C(=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
 2K8  2K8  '(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid'  ligand  23  15  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2K8
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
 2K8  O6A  O  OC    -1  -0.613  -3.3380   0.6997   1.0446
 2K8  C6A  C  C      0   0.419  -2.5273  -0.1983   0.7413
 2K8  O6B  O  O      0  -0.597  -2.0757  -1.0813   1.4928
 2K8  C6   C  CH1    0  -0.295  -2.0899  -0.2550  -0.7481
 2K8  N5   N  NH1    0  -0.648  -0.9332  -1.0988  -0.9998
 2K8  C4A  C  CR6    0  -0.004   0.2737  -0.5216  -0.5453
 2K8  C7   C  CH2    0  -0.265  -1.8118   1.1283  -1.3202
 2K8  N8   N  NH1    0  -0.660  -0.6197   1.6637  -0.7074
 2K8  C8A  C  CR6    0   0.476   0.4243   0.8490  -0.4367
 2K8  N1   N  N      0  -0.524   1.5743   1.4566  -0.0514
 2K8  C2   C  CR6    0   0.655   2.5874   0.6923   0.2370
 2K8  N2   N  NH2    0  -0.831   3.7795   1.2407   0.5659
 2K8  N3   N  NR16   0  -0.707   2.5144  -0.6563   0.1741
 2K8  C4   C  CR6    0   0.456   1.3655  -1.3510  -0.2105
 2K8  O4   O  O      0  -0.531   1.3808  -2.5853  -0.2313
 2K8  H2   H  HCH1   0   0.248  -2.9329  -0.6730  -1.3113
 2K8  H3   H  HNH1   0   0.347  -1.0680  -1.9924  -0.5439
 2K8  H4   H  HCH2   0   0.228  -1.7049   1.0626  -2.4091
 2K8  H5   H  HCH2   0   0.245  -2.6476   1.7914  -1.1120
 2K8  H6   H  HNH1   0   0.382  -0.4350   2.6512  -0.7663
 2K8  H7   H  HNH2   0   0.401   3.7617   2.2164   0.8118
 2K8  H8   H  HNH2   0   0.403   4.4490   0.6903   1.0777
 2K8  H9   H  HNR6   0   0.414   3.3245  -1.2157   0.4042

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
 2K8  C7   N8   single  1.443  0.020  1.443
 2K8  C7   C6   single  1.523  0.020  1.523
 2K8  N8   C8A  single  1.352  0.020  1.352
 2K8  C6   C6A  single  1.553  0.020  1.553
 2K8  C6   N5   single  1.454  0.020  1.454
 2K8  C8A  N1   single  1.357  0.020  1.357
 2K8  C8A  C4A  double  1.383  0.020  1.383
 2K8  O6B  C6A  deloc   1.244  0.020  1.244
 2K8  C6A  O6A  deloc   1.247  0.020  1.247
 2K8  N1   C2   double  1.301  0.020  1.301
 2K8  N5   C4A  single  1.413  0.020  1.413
 2K8  C4A  C4   single  1.411  0.020  1.411
 2K8  C2   N2   single  1.353  0.020  1.353
 2K8  C2   N3   single  1.352  0.020  1.352
 2K8  C4   N3   single  1.397  0.020  1.397
 2K8  C4   O4   double  1.235  0.020  1.235
 2K8  C6   H2   single  0.970  0.020  1.090
 2K8  N5   H3   single  0.890  0.020  1.040
 2K8  C7   H4   single  0.970  0.020  1.090
 2K8  C7   H5   single  0.970  0.020  1.090
 2K8  N8   H6   single  0.890  0.020  1.040
 2K8  N2   H7   single  0.890  0.020  1.040
 2K8  N2   H8   single  0.890  0.020  1.040
 2K8  N3   H9   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
 2K8  C6   C6A  O6B  116.81  3.000
 2K8  O6B  C6A  O6A  126.87  3.000
 2K8  C6   C6A  O6A  116.26  3.000
 2K8  H2   C6   C7   107.08  3.000
 2K8  H2   C6   N5   107.55  3.000
 2K8  C7   C6   N5   108.48  3.000
 2K8  H2   C6   C6A  106.85  3.000
 2K8  N5   C6   C6A  114.28  3.000
 2K8  C7   C6   C6A  112.25  3.000
 2K8  H3   N5   C4A  109.24  3.000
 2K8  H3   N5   C6   109.18  3.000
 2K8  C4A  N5   C6   112.76  3.000
 2K8  C4   C4A  C8A  118.65  3.000
 2K8  C4   C4A  N5   119.80  3.000
 2K8  C8A  C4A  N5   121.53  3.000
 2K8  H5   C7   H4   107.57  3.000
 2K8  H5   C7   N8   109.11  3.000
 2K8  H4   C7   N8   111.32  3.000
 2K8  H5   C7   C6   109.98  3.000
 2K8  H4   C7   C6   109.67  3.000
 2K8  N8   C7   C6   109.17  3.000
 2K8  H6   N8   C8A  117.47  3.000
 2K8  H6   N8   C7   119.39  3.000
 2K8  C8A  N8   C7   119.96  3.000
 2K8  N1   C8A  N8   116.21  3.000
 2K8  N1   C8A  C4A  123.95  3.000
 2K8  N8   C8A  C4A  119.83  3.000
 2K8  C2   N1   C8A  117.38  3.000
 2K8  N3   C2   N2   117.60  3.000
 2K8  N3   C2   N1   122.24  3.000
 2K8  N2   C2   N1   120.12  3.000
 2K8  H8   N2   H7   114.69  3.000
 2K8  H8   N2   C2   119.21  3.000
 2K8  H7   N2   C2   115.90  3.000
 2K8  H9   N3   C4   116.53  3.000
 2K8  H9   N3   C2   119.87  3.000
 2K8  C4   N3   C2   123.60  3.000
 2K8  O4   C4   N3   119.45  3.000
 2K8  O4   C4   C4A  126.38  3.000
 2K8  N3   C4   C4A  114.17  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
 2K8  CONST_01  C7   N8   C8A  C4A    0.00   0.0  0
 2K8  CONST_02  C2   N1   C8A  C4A    0.00   0.0  0
 2K8  CONST_03  C2   N3   C4   C4A    0.00   0.0  0
 2K8  CONST_04  N1   C8A  N8   C7   180.00   0.0  0
 2K8  CONST_05  C2   N1   C8A  N8   180.00   0.0  0
 2K8  CONST_06  N3   C2   N1   C8A    0.00   0.0  0
 2K8  CONST_07  C4   N3   C2   N1     0.00   0.0  0
 2K8  CONST_08  N2   C2   N1   C8A  180.00   0.0  0
 2K8  CONST_09  O4   C4   N3   C2   180.00   0.0  0
 2K8  CONST_10  C4   N3   C2   N2   180.00   0.0  0
 2K8  CONST_11  H6   N8   C8A  C4A  180.00   0.0  0
 2K8  CONST_12  H9   N3   C4   C4A  180.00   0.0  0
 2K8  Var_01    C8A  N8   C7   C6    37.90  30.0  1
 2K8  Var_02    C8A  C4A  N5   C6   -26.31  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2K8  chir_01  C6  C7  C6A  N5  positiv

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
 2K8  plan-1  N5   0.020
 2K8  plan-1  C4A  0.020
 2K8  plan-1  C7   0.020
 2K8  plan-1  N8   0.020
 2K8  plan-1  C8A  0.020
 2K8  plan-1  N1   0.020
 2K8  plan-1  C2   0.020
 2K8  plan-1  N2   0.020
 2K8  plan-1  N3   0.020
 2K8  plan-1  C4   0.020
 2K8  plan-1  O4   0.020
 2K8  plan-1  H6   0.020
 2K8  plan-1  H7   0.020
 2K8  plan-1  H8   0.020
 2K8  plan-1  H9   0.020
 2K8  plan-2  C6   0.020
 2K8  plan-2  N5   0.020
 2K8  plan-2  C4A  0.020
 2K8  plan-2  H3   0.020
 2K8  plan-3  O6A  0.020
 2K8  plan-3  C6A  0.020
 2K8  plan-3  O6B  0.020
 2K8  plan-3  C6   0.020

