# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 19:50:17 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: 2-aminopteridine-4,7(3H,8H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N=CC(=O)N2)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
 7PD  7PD  2-aminopteridine-4,7(3H,8H)-dione  ligand  18  13  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7PD
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
 7PD  C1   C  CR16  0  -0.237  -22.3307  -6.5756  -10.0852
 7PD  C2   C  CR66  0  -0.071  -22.4185  -4.2957  -10.1272
 7PD  C3   C  CR66  0   0.549  -22.9360  -4.2757  -11.4198
 7PD  C4   C  CR6   0   0.492  -22.8646  -6.6916  -11.4402
 7PD  C5   C  CR6   0   0.534  -22.1894  -3.0360   -9.4656
 7PD  C6   C  CR6   0   0.727  -23.0430  -2.0307  -11.5111
 7PD  N7   N  N     0  -0.328  -22.1288  -5.4535   -9.4893
 7PD  N8   N  N     0  -0.515  -23.2507  -3.1828  -12.1144
 7PD  N9   N  NR16  0  -0.690  -23.1383  -5.4735  -12.0232
 7PD  N10  N  NR16  0  -0.718  -22.5358  -1.9430  -10.2552
 7PD  N11  N  NH2   0  -0.814  -23.3359  -0.9024  -12.1416
 7PD  O12  O  O     0  -0.462  -23.0593  -7.7436  -12.0231
 7PD  O13  O  O     0  -0.454  -21.7455  -2.8727   -8.3460
 7PD  H1   H  HCR6  0   0.277  -22.0968  -7.4979   -9.5652
 7PD  H2   H  HNR6  0   0.424  -23.5164  -5.4684  -12.9640
 7PD  H3   H  HNR6  0   0.433  -22.3914  -1.0286   -9.8450
 7PD  H4   H  HNH2  0   0.425  -23.7151  -0.9426  -13.0725
 7PD  H5   H  HNH2  0   0.428  -23.1969   0.0025  -11.7259

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
 7PD  N11  C6   single  1.325  0.020  1.325
 7PD  N8   C6   double  1.317  0.020  1.317
 7PD  N8   C3   single  1.333  0.020  1.333
 7PD  N9   C4   single  1.378  0.020  1.378
 7PD  N9   C3   single  1.356  0.020  1.356
 7PD  O12  C4   double  1.218  0.020  1.218
 7PD  C6   N10  single  1.357  0.020  1.357
 7PD  C4   C1   single  1.461  0.020  1.461
 7PD  C3   C2   double  1.393  0.020  1.393
 7PD  N10  C5   single  1.392  0.020  1.392
 7PD  C2   C5   single  1.441  0.020  1.441
 7PD  C2   N7   single  1.353  0.020  1.353
 7PD  C1   N7   double  1.286  0.020  1.286
 7PD  C5   O13  double  1.215  0.020  1.215
 7PD  C1   H1   single  0.930  0.020  1.080
 7PD  N9   H2   single  0.860  0.020  1.020
 7PD  N10  H3   single  0.860  0.020  1.020
 7PD  N11  H4   single  0.860  0.020  1.020
 7PD  N11  H5   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
 7PD  H1   C1   N7   119.08  3.000
 7PD  H1   C1   C4   117.13  3.000
 7PD  N7   C1   C4   123.79  3.000
 7PD  N7   C2   C5   119.83  3.000
 7PD  N7   C2   C3   121.96  3.000
 7PD  C5   C2   C3   118.21  3.000
 7PD  N9   C3   N8   117.20  3.000
 7PD  N9   C3   C2   117.11  3.000
 7PD  N8   C3   C2   125.69  3.000
 7PD  O12  C4   N9   121.95  3.000
 7PD  O12  C4   C1   124.79  3.000
 7PD  N9   C4   C1   113.25  3.000
 7PD  O13  C5   N10  120.52  3.000
 7PD  O13  C5   C2   126.76  3.000
 7PD  N10  C5   C2   112.73  3.000
 7PD  N11  C6   N10  117.89  3.000
 7PD  N10  C6   N8   122.64  3.000
 7PD  N11  C6   N8   119.47  3.000
 7PD  C2   N7   C1   119.63  3.000
 7PD  C6   N8   C3   116.19  3.000
 7PD  H2   N9   C4   118.10  3.000
 7PD  H2   N9   C3   117.64  3.000
 7PD  C4   N9   C3   124.25  3.000
 7PD  H3   N10  C6   119.12  3.000
 7PD  H3   N10  C5   116.34  3.000
 7PD  C6   N10  C5   124.54  3.000
 7PD  H5   N11  H4   118.07  3.000
 7PD  H5   N11  C6   122.61  3.000
 7PD  H4   N11  C6   119.31  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
 7PD  CONST_01  C3   N9   C4   C1    0.00  0.0  0
 7PD  CONST_02  C6   N8   C3   C2    0.00  0.0  0
 7PD  CONST_03  C4   N9   C3   C2    0.00  0.0  0
 7PD  CONST_04  C6   N10  C5   C2    0.00  0.0  0
 7PD  CONST_05  N10  C6   N8   C3    0.00  0.0  0
 7PD  CONST_06  N8   C3   N9   C4  180.00  0.0  0
 7PD  CONST_07  N8   C6   N10  C5    0.00  0.0  0
 7PD  CONST_08  N9   C3   N8   C6  180.00  0.0  0
 7PD  CONST_09  N11  C6   N8   C3  180.00  0.0  0
 7PD  CONST_10  O12  C4   N9   C3  180.00  0.0  0
 7PD  CONST_11  N11  C6   N10  C5  180.00  0.0  0
 7PD  CONST_12  O13  C5   N10  C6  180.00  0.0  0
 7PD  CONST_13  H2   N9   C4   C1  180.00  0.0  0
 7PD  CONST_14  H3   N10  C5   C2  180.00  0.0  0
 7PD  CONST_15  H4   N11  C6   N8    0.00  0.0  0
 7PD  CONST_16  H5   N11  C6   N8  180.00  0.0  0

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
 7PD  plan-1  C1   0.020
 7PD  plan-1  C2   0.020
 7PD  plan-1  C3   0.020
 7PD  plan-1  C4   0.020
 7PD  plan-1  C5   0.020
 7PD  plan-1  C6   0.020
 7PD  plan-1  N7   0.020
 7PD  plan-1  N8   0.020
 7PD  plan-1  N9   0.020
 7PD  plan-1  N10  0.020
 7PD  plan-1  N11  0.020
 7PD  plan-1  O12  0.020
 7PD  plan-1  O13  0.020
 7PD  plan-1  H1   0.020
 7PD  plan-1  H2   0.020
 7PD  plan-1  H3   0.020
 7PD  plan-1  H4   0.020
 7PD  plan-1  H5   0.020

