# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:42:08 2021
#   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  20  12  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.495  38.5005  -26.7970  -13.4850
 TJ4  C9  C  CR6   0   0.557  37.7184  -27.0552  -14.3844
 TJ4  N2  N  NR16  0  -0.694  37.3876  -28.3555  -14.6824
 TJ4  N1  N  N     0  -0.470  37.1111  -26.0922  -15.1416
 TJ4  C4  C  CR6   0   0.291  36.3113  -26.4122  -16.1152
 TJ4  C5  C  CH3   0  -0.750  35.6956  -25.2838  -16.8772
 TJ4  C3  C  CR6   0  -0.044  35.9860  -27.7687  -16.4812
 TJ4  C6  C  CH3   0  -0.737  35.1032  -28.0225  -17.6666
 TJ4  C2  C  CR6   0   0.305  36.5474  -28.7180  -15.6818
 TJ4  C1  C  C     0   0.507  36.3675  -30.2049  -15.7599
 TJ4  O1  O  O     0  -0.420  37.1803  -30.9593  -15.2909
 TJ4  O2  O  OH1   0  -0.567  35.2443  -30.5649  -16.3346
 TJ4  H1  H  HCH3  0   0.270  35.9508  -24.3344  -16.4149
 TJ4  H2  H  HCH3  0   0.270  36.0513  -25.2751  -17.9092
 TJ4  H3  H  HCH3  0   0.266  34.6101  -25.3831  -16.9172
 TJ4  H5  H  HCH3  0   0.265  35.2708  -28.9955  -18.1146
 TJ4  H6  H  HCH3  0   0.261  34.0471  -27.9537  -17.3987
 TJ4  H7  H  HCH3  0   0.256  35.2883  -27.2796  -18.4402
 TJ4  H8  H  HOH1  0   0.502  35.1703  -31.5325  -16.3588
 TJ4  H9  H  HNR6  0   0.427  37.8096  -29.0846  -14.1199

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  1.500  0.020  1.500
 TJ4  C5  C4  single  1.494  0.020  1.494
 TJ4  O1  C1  double  1.204  0.020  1.204
 TJ4  C3  C4  single  1.442  0.020  1.442
 TJ4  C3  C2  double  1.362  0.020  1.362
 TJ4  C4  N1  double  1.300  0.020  1.300
 TJ4  C1  C2  single  1.500  0.020  1.500
 TJ4  C1  O2  single  1.312  0.020  1.312
 TJ4  C2  N2  single  1.355  0.020  1.355
 TJ4  N1  C9  single  1.367  0.020  1.367
 TJ4  N2  C9  single  1.374  0.020  1.374
 TJ4  C9  O3  double  1.220  0.020  1.220
 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  O2  H8  single  0.850  0.020  0.980
 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  116.06  3.000
 TJ4  N2  C9  O3  120.97  3.000
 TJ4  N1  C9  O3  122.97  3.000
 TJ4  H9  N2  C2  118.38  3.000
 TJ4  H9  N2  C9  117.41  3.000
 TJ4  C2  N2  C9  124.21  3.000
 TJ4  C4  N1  C9  120.97  3.000
 TJ4  C3  C4  C5  119.20  3.000
 TJ4  C3  C4  N1  124.08  3.000
 TJ4  C5  C4  N1  116.71  3.000
 TJ4  H3  C5  H2  106.88  3.000
 TJ4  H3  C5  H1  109.20  3.000
 TJ4  H2  C5  H1  108.59  3.000
 TJ4  H3  C5  C4  111.10  3.000
 TJ4  H2  C5  C4  110.72  3.000
 TJ4  H1  C5  C4  110.25  3.000
 TJ4  C2  C3  C6  126.05  3.000
 TJ4  C2  C3  C4  114.44  3.000
 TJ4  C6  C3  C4  119.51  3.000
 TJ4  H7  C6  H6  107.21  3.000
 TJ4  H7  C6  H5  107.01  3.000
 TJ4  H6  C6  H5  107.90  3.000
 TJ4  H7  C6  C3  110.26  3.000
 TJ4  H6  C6  C3  111.40  3.000
 TJ4  H5  C6  C3  112.80  3.000
 TJ4  C1  C2  C3  127.66  3.000
 TJ4  C1  C2  N2  112.21  3.000
 TJ4  C3  C2  N2  120.13  3.000
 TJ4  O2  C1  O1  125.21  3.000
 TJ4  O2  C1  C2  113.42  3.000
 TJ4  O1  C1  C2  121.33  3.000
 TJ4  H8  O2  C1  110.47  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  CONST_06  H8  O2  C1  C2  180.00   0.0  0
 TJ4  Var_01    O1  C1  C2  N2  -21.71  30.0  2
 TJ4  Var_02    H1  C5  C4  N1   -5.68  30.0  3
 TJ4  Var_03    H5  C6  C3  C4  154.35  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
 TJ4  plan-2  H8  0.020

