# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 07:37:41 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: N-(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carbonyl)-beta-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCNC(=O)C1=CC(=O)NC(=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
 P1J  P1J  N-(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carbonyl)-beta-alanine  ligand  25  16  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P1J
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
 P1J  C1  C  CH2   0  -0.595  -3.2893  -0.5428  -0.1096
 P1J  C2  C  CH2   0  -0.273  -2.4065   0.5537   0.4668
 P1J  C4  C  CR6   0   0.355   1.3247   0.1918  -0.0597
 P1J  C5  C  CR16  0  -0.518   1.5631  -1.1259   0.0692
 P1J  C6  C  CR6   0   0.595   2.9301  -1.6055   0.0924
 P1J  C7  C  CR6   0   0.676   3.6647   0.7388  -0.1737
 P1J  N   N  NH1   0  -0.643  -1.0186   0.1412   0.4669
 P1J  C   C  C     0   0.556  -4.7441  -0.1643  -0.1018
 P1J  O   O  OH1   0  -0.593  -5.5080  -1.1324  -0.5924
 P1J  C3  C  C     0   0.531  -0.0436   0.8154  -0.1431
 P1J  N1  N  NR16  0  -0.718   3.8830  -0.6084  -0.0277
 P1J  N2  N  NR16  0  -0.721   2.3407   1.0871  -0.1818
 P1J  O1  O  O     0  -0.443  -5.1793   0.8872   0.2966
 P1J  O2  O  O     0  -0.470  -0.1756   1.8709  -0.7412
 P1J  O3  O  O     0  -0.454   3.2580  -2.7707   0.2038
 P1J  O4  O  O     0  -0.468   4.5612   1.5470  -0.2815
 P1J  H1  H  HCH2  0   0.294  -2.9915  -0.7705  -1.1369
 P1J  H2  H  HCH2  0   0.290  -3.1716  -1.4731   0.4541
 P1J  H3  H  HCH2  0   0.268  -2.4913   1.4633  -0.1226
 P1J  H4  H  HCH2  0   0.266  -2.7066   0.7945   1.4878
 P1J  H5  H  HCR6  0   0.296   0.7675  -1.8530   0.1259
 P1J  H7  H  HNH1  0   0.421  -0.7789  -0.6610   1.0286
 P1J  H8  H  HOH1  0   0.481  -6.4385  -0.8619  -0.5762
 P1J  H9  H  HNR6  0   0.431   4.8538  -0.8979  -0.0163
 P1J  H6  H  HNR6  0   0.434   2.1184   2.0658  -0.3128

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
 P1J  O3  C6  double  1.216  0.020  1.216
 P1J  C6  C5  single  1.449  0.020  1.449
 P1J  C6  N1  single  1.385  0.020  1.385
 P1J  C5  C4  double  1.345  0.020  1.345
 P1J  N1  C7  single  1.372  0.020  1.372
 P1J  C4  C3  single  1.506  0.020  1.506
 P1J  C4  N2  single  1.360  0.020  1.360
 P1J  O2  C3  double  1.220  0.020  1.220
 P1J  C7  N2  single  1.369  0.020  1.369
 P1J  C7  O4  double  1.212  0.020  1.212
 P1J  C3  N   single  1.333  0.020  1.333
 P1J  N   C2  single  1.448  0.020  1.448
 P1J  O1  C   double  1.206  0.020  1.206
 P1J  C1  C   single  1.503  0.020  1.503
 P1J  C1  C2  single  1.521  0.020  1.521
 P1J  C   O   single  1.327  0.020  1.327
 P1J  C1  H1  single  0.970  0.020  1.090
 P1J  C1  H2  single  0.970  0.020  1.090
 P1J  C2  H3  single  0.970  0.020  1.090
 P1J  C2  H4  single  0.970  0.020  1.090
 P1J  C5  H5  single  0.930  0.020  1.080
 P1J  N   H7  single  0.860  0.020  1.020
 P1J  O   H8  single  0.850  0.020  0.980
 P1J  N1  H9  single  0.860  0.020  1.020
 P1J  N2  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
 P1J  H2  C1  H1  106.12  3.000
 P1J  H2  C1  C   108.39  3.000
 P1J  H1  C1  C   108.72  3.000
 P1J  H2  C1  C2  110.81  3.000
 P1J  H1  C1  C2  110.36  3.000
 P1J  C   C1  C2  112.22  3.000
 P1J  H4  C2  H3  107.54  3.000
 P1J  H4  C2  N   109.06  3.000
 P1J  H3  C2  N   108.25  3.000
 P1J  H4  C2  C1  110.73  3.000
 P1J  H3  C2  C1  110.63  3.000
 P1J  N   C2  C1  110.54  3.000
 P1J  N2  C4  C3  113.65  3.000
 P1J  N2  C4  C5  121.41  3.000
 P1J  C3  C4  C5  124.88  3.000
 P1J  H5  C5  C6  118.14  3.000
 P1J  H5  C5  C4  122.29  3.000
 P1J  C6  C5  C4  119.54  3.000
 P1J  O3  C6  N1  120.84  3.000
 P1J  N1  C6  C5  114.18  3.000
 P1J  O3  C6  C5  124.98  3.000
 P1J  O4  C7  N2  123.04  3.000
 P1J  O4  C7  N1  123.12  3.000
 P1J  N2  C7  N1  113.84  3.000
 P1J  H7  N   C3  118.91  3.000
 P1J  H7  N   C2  117.05  3.000
 P1J  C3  N   C2  123.84  3.000
 P1J  O1  C   O   123.40  3.000
 P1J  O   C   C1  111.80  3.000
 P1J  O1  C   C1  124.79  3.000
 P1J  H8  O   C   110.06  3.000
 P1J  O2  C3  N   125.63  3.000
 P1J  N   C3  C4  115.45  3.000
 P1J  O2  C3  C4  118.92  3.000
 P1J  H9  N1  C7  115.73  3.000
 P1J  H9  N1  C6  116.92  3.000
 P1J  C7  N1  C6  127.35  3.000
 P1J  H6  N2  C7  117.34  3.000
 P1J  H6  N2  C4  118.96  3.000
 P1J  C7  N2  C4  123.68  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
 P1J  CONST_01  N1  C7  N2  C4     0.00   0.0  0
 P1J  CONST_02  C7  N1  C6  C5     0.00   0.0  0
 P1J  CONST_03  N2  C7  N1  C6     0.00   0.0  0
 P1J  CONST_04  O4  C7  N2  C4   180.00   0.0  0
 P1J  CONST_05  O4  C7  N1  C6   180.00   0.0  0
 P1J  CONST_06  O3  C6  N1  C7   180.00   0.0  0
 P1J  CONST_07  H9  N1  C6  C5   180.00   0.0  0
 P1J  CONST_08  H6  N2  C7  N1   180.00   0.0  0
 P1J  CONST_09  C4  C3  N   C2   180.00   0.0  0
 P1J  CONST_10  H7  N   C3  C4     0.00   0.0  0
 P1J  CONST_11  O2  C3  N   C2     0.00   0.0  0
 P1J  CONST_12  H8  O   C   C1   180.00   0.0  0
 P1J  Var_01    O2  C3  C4  C5  -152.47  30.0  2
 P1J  Var_02    C3  N   C2  C1   122.70  30.0  1
 P1J  Var_03    O1  C   C1  C2     0.80  30.0  3
 P1J  Var_04    C   C1  C2  N    178.84  30.0  1

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
 P1J  plan-1  C4  0.020
 P1J  plan-1  C5  0.020
 P1J  plan-1  C6  0.020
 P1J  plan-1  C7  0.020
 P1J  plan-1  C3  0.020
 P1J  plan-1  N1  0.020
 P1J  plan-1  N2  0.020
 P1J  plan-1  O3  0.020
 P1J  plan-1  O4  0.020
 P1J  plan-1  H5  0.020
 P1J  plan-1  H9  0.020
 P1J  plan-1  H6  0.020
 P1J  plan-2  C2  0.020
 P1J  plan-2  C4  0.020
 P1J  plan-2  N   0.020
 P1J  plan-2  C3  0.020
 P1J  plan-2  O2  0.020
 P1J  plan-2  H7  0.020
 P1J  plan-3  C1  0.020
 P1J  plan-3  C   0.020
 P1J  plan-3  O   0.020
 P1J  plan-3  O1  0.020
 P1J  plan-3  H8  0.020

