# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 17:48:34 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: 5,6-dimethyl-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=NC(=O)NC(=C1C)C(O)=O
#
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
 TJ4  TJ4  '5,6-dimethyl-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid'  ligand  19  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TJ4
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
 TJ4  O3  O  O      0  -0.509  38.0572  -26.9393  -13.1712
 TJ4  C9  C  CR6    0   0.531  37.4320  -27.1528  -14.2017
 TJ4  N2  N  NR16   0  -0.671  37.1928  -28.4351  -14.6298
 TJ4  N1  N  N      0  -0.487  36.9322  -26.1574  -14.9893
 TJ4  C4  C  CR6    0   0.271  36.2785  -26.4505  -16.0818
 TJ4  C5  C  CH3    0  -0.739  35.7521  -25.2940  -16.8719
 TJ4  C3  C  CR6    0  -0.070  36.0443  -27.7804  -16.5572
 TJ4  C6  C  CH3    0  -0.752  35.2746  -27.9721  -17.8297
 TJ4  C2  C  CR6    0   0.211  36.5420  -28.7787  -15.7625
 TJ4  C1  C  C      0   0.410  36.4832  -30.3113  -15.9629
 TJ4  O1  O  O      0  -0.543  36.1383  -30.7310  -17.0733
 TJ4  O2  O  OC    -1  -0.575  36.8200  -30.9620  -14.9586
 TJ4  H1  H  HCH3   0   0.259  36.0241  -24.3538  -16.3986
 TJ4  H2  H  HCH3   0   0.257  36.1450  -25.3036  -17.8903
 TJ4  H3  H  HCH3   0   0.258  34.6651  -25.3434  -16.9562
 TJ4  H5  H  HCH3   0   0.273  35.1233  -29.0213  -18.0480
 TJ4  H6  H  HCH3   0   0.234  34.2987  -27.4867  -17.7702
 TJ4  H7  H  HCH3   0   0.236  35.7971  -27.5226  -18.6770
 TJ4  H9  H  HNR6   0   0.406  37.4975  -29.2165  -14.0573

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
 TJ4  C6  C3  single  1.499  0.020  1.499
 TJ4  C5  C4  single  1.496  0.020  1.496
 TJ4  O1  C1  deloc   1.236  0.020  1.236
 TJ4  C3  C4  single  1.432  0.020  1.432
 TJ4  C3  C2  double  1.370  0.020  1.370
 TJ4  C4  N1  double  1.306  0.020  1.306
 TJ4  C1  C2  single  1.547  0.020  1.547
 TJ4  C1  O2  deloc   1.243  0.020  1.243
 TJ4  C2  N2  single  1.351  0.020  1.351
 TJ4  N1  C9  single  1.364  0.020  1.364
 TJ4  N2  C9  single  1.373  0.020  1.373
 TJ4  C9  O3  double  1.224  0.020  1.224
 TJ4  C5  H1  single  0.970  0.020  1.090
 TJ4  C5  H2  single  0.970  0.020  1.090
 TJ4  C5  H3  single  0.970  0.020  1.090
 TJ4  C6  H5  single  0.970  0.020  1.090
 TJ4  C6  H6  single  0.970  0.020  1.090
 TJ4  C6  H7  single  0.970  0.020  1.090
 TJ4  N2  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
 TJ4  N1  C9  N2  115.95  3.000
 TJ4  N2  C9  O3  120.96  3.000
 TJ4  N1  C9  O3  123.09  3.000
 TJ4  H9  N2  C2  114.94  3.000
 TJ4  H9  N2  C9  119.38  3.000
 TJ4  C2  N2  C9  125.66  3.000
 TJ4  C4  N1  C9  120.16  3.000
 TJ4  C3  C4  C5  119.02  3.000
 TJ4  C3  C4  N1  124.60  3.000
 TJ4  C5  C4  N1  116.37  3.000
 TJ4  H3  C5  H2  106.62  3.000
 TJ4  H3  C5  H1  108.78  3.000
 TJ4  H2  C5  H1  108.89  3.000
 TJ4  H3  C5  C4  110.87  3.000
 TJ4  H2  C5  C4  111.05  3.000
 TJ4  H1  C5  C4  110.52  3.000
 TJ4  C2  C3  C6  125.86  3.000
 TJ4  C2  C3  C4  115.15  3.000
 TJ4  C6  C3  C4  118.98  3.000
 TJ4  H7  C6  H6  106.68  3.000
 TJ4  H7  C6  H5  108.02  3.000
 TJ4  H6  C6  H5  108.48  3.000
 TJ4  H7  C6  C3  111.11  3.000
 TJ4  H6  C6  C3  110.85  3.000
 TJ4  H5  C6  C3  111.52  3.000
 TJ4  C1  C2  C3  129.29  3.000
 TJ4  C1  C2  N2  112.27  3.000
 TJ4  C3  C2  N2  118.44  3.000
 TJ4  O2  C1  O1  128.58  3.000
 TJ4  O2  C1  C2  113.81  3.000
 TJ4  O1  C1  C2  117.60  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
 TJ4  CONST_01  C4  N1  C9  N2     0.00   0.0  0
 TJ4  CONST_02  C2  N2  C9  N1     0.00   0.0  0
 TJ4  CONST_03  C4  N1  C9  O3   180.00   0.0  0
 TJ4  CONST_04  C2  N2  C9  O3   180.00   0.0  0
 TJ4  CONST_05  H9  N2  C9  N1   180.00   0.0  0
 TJ4  Var_01    O1  C1  C2  N2  -166.82  30.0  2
 TJ4  Var_02    H1  C5  C4  N1     1.00  30.0  3
 TJ4  Var_03    H5  C6  C3  C4  -176.97  30.0  3

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
 TJ4  plan-1  O3  0.020
 TJ4  plan-1  C9  0.020
 TJ4  plan-1  N2  0.020
 TJ4  plan-1  N1  0.020
 TJ4  plan-1  C4  0.020
 TJ4  plan-1  C5  0.020
 TJ4  plan-1  C3  0.020
 TJ4  plan-1  C6  0.020
 TJ4  plan-1  C2  0.020
 TJ4  plan-1  C1  0.020
 TJ4  plan-1  H9  0.020
 TJ4  plan-2  C2  0.020
 TJ4  plan-2  C1  0.020
 TJ4  plan-2  O1  0.020
 TJ4  plan-2  O2  0.020

