# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:35:43 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 6-methyl-2-oxo-2,5-dihydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=NC(=O)N=C(C1)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
 TEV  TEV  '6-methyl-2-oxo-2,5-dihydropyrimidine-4-carboxylic acid'  ligand  16  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TEV
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
 TEV  O3  O  O      0  -0.409  5.6200   1.3520  -12.6359
 TEV  C9  C  CR6    0   0.491  6.4531   1.6269  -13.4666
 TEV  N2  N  N      0  -0.422  6.7804   2.9706  -13.6953
 TEV  N1  N  N      0  -0.432  7.1068   0.5948  -14.1504
 TEV  C4  C  CR6    0   0.287  7.6815   0.8763  -15.2558
 TEV  C5  C  CH3    0  -0.730  8.3716  -0.1906  -16.0293
 TEV  C3  C  C      0  -0.596  7.6952   2.2532  -15.8222
 TEV  C2  C  CR6    0   0.120  7.3429   3.2758  -14.7981
 TEV  C1  C  C      0   0.396  7.6466   4.7506  -15.1197
 TEV  O1  O  OC    -1  -0.562  7.7104   5.5261  -14.1591
 TEV  O2  O  O      0  -0.568  7.7855   4.9812  -16.3326
 TEV  H1  H  HCH3   0   0.262  8.2444  -1.1651  -15.5651
 TEV  H2  H  HCH3   0   0.265  7.9878  -0.2221  -17.0509
 TEV  H3  H  HCH3   0   0.268  9.4370   0.0372  -16.1043
 TEV  H4  H  H      0   0.303  8.6603   2.4749  -16.2822
 TEV  H5  H  H      0   0.327  6.9780   2.3045  -16.6513

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
 TEV  O2  C1  deloc   1.242  0.020  1.242
 TEV  C5  C4  single  1.488  0.020  1.488
 TEV  C3  C4  single  1.489  0.020  1.489
 TEV  C3  C2  single  1.490  0.020  1.490
 TEV  C4  N1  double  1.277  0.020  1.277
 TEV  C1  C2  single  1.540  0.020  1.540
 TEV  C1  O1  deloc   1.236  0.020  1.236
 TEV  C2  N2  double  1.275  0.020  1.275
 TEV  N1  C9  single  1.400  0.020  1.400
 TEV  N2  C9  single  1.402  0.020  1.402
 TEV  C9  O3  double  1.208  0.020  1.208
 TEV  C5  H1  single  0.970  0.020  1.090
 TEV  C5  H2  single  0.970  0.020  1.090
 TEV  C5  H3  single  0.970  0.020  1.090
 TEV  C3  H4  single  0.970  0.020  1.090
 TEV  C3  H5  single  0.970  0.020  1.090

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
 TEV  N1  C9  N2  121.19  3.000
 TEV  N2  C9  O3  119.43  3.000
 TEV  N1  C9  O3  119.34  3.000
 TEV  C2  N2  C9  118.27  3.000
 TEV  C4  N1  C9  118.05  3.000
 TEV  C3  C4  C5  117.46  3.000
 TEV  C3  C4  N1  122.49  3.000
 TEV  C5  C4  N1  120.05  3.000
 TEV  H3  C5  H2  106.54  3.000
 TEV  H3  C5  H1  109.30  3.000
 TEV  H2  C5  H1  109.43  3.000
 TEV  H3  C5  C4  109.80  3.000
 TEV  H2  C5  C4  110.13  3.000
 TEV  H1  C5  C4  111.51  3.000
 TEV  H5  C3  H4  104.48  3.000
 TEV  H5  C3  C2  109.43  3.000
 TEV  H4  C3  C2  111.06  3.000
 TEV  H5  C3  C4  108.94  3.000
 TEV  H4  C3  C4  110.86  3.000
 TEV  C2  C3  C4  111.79  3.000
 TEV  C1  C2  C3  117.86  3.000
 TEV  C1  C2  N2  119.80  3.000
 TEV  C3  C2  N2  122.32  3.000
 TEV  O2  C1  O1  129.52  3.000
 TEV  O1  C1  C2  116.67  3.000
 TEV  O2  C1  C2  113.81  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
 TEV  Var_01  C3  C4  N1  C9     0.92  30.0  1
 TEV  Var_02  C3  C2  N2  C9    -1.83  30.0  1
 TEV  Var_03  C4  C3  C2  N2   -16.36  30.0  1
 TEV  Var_04  C2  C3  C4  N1    16.87  30.0  1
 TEV  Var_05  O2  C1  C2  N2  -158.27  30.0  2
 TEV  Var_06  H1  C5  C4  N1     3.90  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
 TEV  plan-1  O3  0.020
 TEV  plan-1  C9  0.020
 TEV  plan-1  N2  0.020
 TEV  plan-1  N1  0.020
 TEV  plan-1  C4  0.020
 TEV  plan-1  C2  0.020
 TEV  plan-2  C2  0.020
 TEV  plan-2  C1  0.020
 TEV  plan-2  O1  0.020
 TEV  plan-2  O2  0.020

