# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 15 18:46:53 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  24  16  .  2021-08-19  2021-08-19  
;
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  -0.647  -3.3863  -0.6417  -0.0102
 P1J  C2  C  CH2    0  -0.238  -2.4064   0.5135  -0.0015
 P1J  C4  C  CR6    0   0.366   1.3793   0.1917   0.0088
 P1J  C5  C  CR16   0  -0.524   1.6512  -1.1263   0.0224
 P1J  C6  C  CR6    0   0.597   3.0290  -1.5736   0.0140
 P1J  C7  C  CR6    0   0.676   3.7096   0.7996  -0.0173
 P1J  N   N  NH1    0  -0.658  -1.0388   0.0132  -0.0133
 P1J  C   C  C      0   0.426  -4.8651  -0.2091   0.0127
 P1J  O   O  OC    -1  -0.622  -5.7003  -1.1344   0.0136
 P1J  C3  C  C      0   0.549   0.0088   0.8265   0.0150
 P1J  N1  N  NR16   0  -0.719   3.9599  -0.5497  -0.0083
 P1J  N2  N  NR16   0  -0.722   2.3787   1.1134  -0.0082
 P1J  O1  O  O      0  -0.604  -5.1048   1.0134   0.0281
 P1J  O2  O  O      0  -0.484  -0.0680   2.0472   0.0452
 P1J  O3  O  O      0  -0.456   3.3824  -2.7371   0.0248
 P1J  O4  O  O      0  -0.470   4.5874   1.6357  -0.0317
 P1J  H1  H  HCH2   0   0.241  -3.2237  -1.2649  -0.8966
 P1J  H2  H  HCH2   0   0.241  -3.2039  -1.2955   0.8495
 P1J  H3  H  HCH2   0   0.239  -2.5612   1.1571  -0.8695
 P1J  H4  H  HCH2   0   0.239  -2.5524   1.1340   0.8842
 P1J  H5  H  HCR6   0   0.290   0.8856  -1.8860   0.0413
 P1J  H7  H  HNH1   0   0.419  -0.9078  -0.9842  -0.0501
 P1J  H9  H  HNR6   0   0.430   4.9368  -0.8176  -0.0146
 P1J  H6  H  HNR6   0   0.432   2.1194   2.0928  -0.0101

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  1.384  0.020  1.384
 P1J  C5  C4  double  1.346  0.020  1.346
 P1J  N1  C7  single  1.372  0.020  1.372
 P1J  C4  C3  single  1.510  0.020  1.510
 P1J  C4  N2  single  1.360  0.020  1.360
 P1J  O2  C3  double  1.223  0.020  1.223
 P1J  C7  N2  single  1.367  0.020  1.367
 P1J  C7  O4  double  1.212  0.020  1.212
 P1J  C3  N   single  1.327  0.020  1.327
 P1J  N   C2  single  1.456  0.020  1.456
 P1J  O1  C   deloc   1.246  0.020  1.246
 P1J  C1  C   single  1.541  0.020  1.541
 P1J  C1  C2  single  1.515  0.020  1.515
 P1J  C   O   deloc   1.247  0.020  1.247
 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  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  105.71  3.000
 P1J  H2  C1  C   108.41  3.000
 P1J  H1  C1  C   108.31  3.000
 P1J  H2  C1  C2  110.05  3.000
 P1J  H1  C1  C2  110.02  3.000
 P1J  C   C1  C2  113.99  3.000
 P1J  H4  C2  H3  106.93  3.000
 P1J  H4  C2  N   109.12  3.000
 P1J  H3  C2  N   109.23  3.000
 P1J  H4  C2  C1  110.59  3.000
 P1J  H3  C2  C1  110.69  3.000
 P1J  N   C2  C1  110.21  3.000
 P1J  N2  C4  C3  112.46  3.000
 P1J  N2  C4  C5  121.03  3.000
 P1J  C3  C4  C5  126.51  3.000
 P1J  H5  C5  C6  117.24  3.000
 P1J  H5  C5  C4  123.13  3.000
 P1J  C6  C5  C4  119.64  3.000
 P1J  O3  C6  N1  120.83  3.000
 P1J  N1  C6  C5  114.29  3.000
 P1J  O3  C6  C5  124.87  3.000
 P1J  O4  C7  N2  123.13  3.000
 P1J  O4  C7  N1  123.10  3.000
 P1J  N2  C7  N1  113.77  3.000
 P1J  H7  N   C3  120.37  3.000
 P1J  H7  N   C2  117.57  3.000
 P1J  C3  N   C2  122.06  3.000
 P1J  O1  C   O   126.83  3.000
 P1J  O   C   C1  115.76  3.000
 P1J  O1  C   C1  117.41  3.000
 P1J  O2  C3  N   124.25  3.000
 P1J  N   C3  C4  117.31  3.000
 P1J  O2  C3  C4  118.45  3.000
 P1J  H9  N1  C7  115.84  3.000
 P1J  H9  N1  C6  116.94  3.000
 P1J  C7  N1  C6  127.22  3.000
 P1J  H6  N2  C7  118.09  3.000
 P1J  H6  N2  C4  117.86  3.000
 P1J  C7  N2  C4  124.05  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  Var_01    O2  C3  C4  C5   177.62  30.0  2
 P1J  Var_02    C3  N   C2  C1  -178.79  30.0  2
 P1J  Var_03    O1  C   C1  C2     0.38  30.0  3
 P1J  Var_04    C   C1  C2  N    179.54  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
 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

