# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:06:41 2021
#   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  17  11  .  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_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  -0.392  5.9558   1.5001  -12.3953
 TEV  C9  C  C     0   0.515  6.5828   1.7120  -13.4024
 TEV  N2  N  N     0  -0.399  6.8341   3.0567  -13.7583
 TEV  N1  N  N     0  -0.431  7.0422   0.6448  -14.1718
 TEV  C4  C  C     0   0.295  7.6437   0.8774  -15.2756
 TEV  C5  C  CH3   0  -0.730  8.1404  -0.2552  -16.0988
 TEV  C3  C  CH2   0  -0.577  7.8918   2.2487  -15.7989
 TEV  C2  C  C     0   0.158  7.4257   3.2886  -14.8538
 TEV  C1  C  C     0   0.540  7.6854   4.7235  -15.2475
 TEV  O1  O  OH1   0  -0.566  7.2422   5.5837  -14.3616
 TEV  O2  O  O     0  -0.403  8.2444   4.9968  -16.2770
 TEV  H1  H  HCH3  0   0.270  7.8560  -1.2112  -15.6679
 TEV  H2  H  HCH3  0   0.271  7.7528  -0.1834  -17.1164
 TEV  H3  H  HCH3  0   0.275  9.2285  -0.2037  -16.1753
 TEV  H4  H  HCH2  0   0.336  8.9574   2.3764  -16.0152
 TEV  H5  H  HCH2  0   0.341  7.3950   2.3685  -16.7685
 TEV  H6  H  HOH1  0   0.497  7.4146   6.4910  -14.6579

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  double  1.203  0.020  1.203
 TEV  C5  C4  single  1.486  0.020  1.486
 TEV  C3  C4  single  1.489  0.020  1.489
 TEV  C3  C2  single  1.481  0.020  1.481
 TEV  C4  N1  double  1.278  0.020  1.278
 TEV  C1  C2  single  1.510  0.020  1.510
 TEV  C1  O1  single  1.312  0.020  1.312
 TEV  C2  N2  double  1.266  0.020  1.266
 TEV  N1  C9  single  1.394  0.020  1.394
 TEV  N2  C9  single  1.414  0.020  1.414
 TEV  C9  O3  double  1.205  0.020  1.205
 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
 TEV  O1  H6  single  0.850  0.020  0.980

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  122.07  3.000
 TEV  N2  C9  O3  118.05  3.000
 TEV  N1  C9  O3  119.88  3.000
 TEV  C2  N2  C9  118.36  3.000
 TEV  C4  N1  C9  119.50  3.000
 TEV  C3  C4  C5  116.86  3.000
 TEV  C3  C4  N1  123.34  3.000
 TEV  C5  C4  N1  119.80  3.000
 TEV  H3  C5  H2  106.59  3.000
 TEV  H3  C5  H1  109.27  3.000
 TEV  H2  C5  H1  109.56  3.000
 TEV  H3  C5  C4  109.63  3.000
 TEV  H2  C5  C4  110.35  3.000
 TEV  H1  C5  C4  111.32  3.000
 TEV  H5  C3  H4  104.69  3.000
 TEV  H5  C3  C2  110.19  3.000
 TEV  H4  C3  C2  110.53  3.000
 TEV  H5  C3  C4  109.65  3.000
 TEV  H4  C3  C4  109.82  3.000
 TEV  C2  C3  C4  111.72  3.000
 TEV  C1  C2  C3  116.53  3.000
 TEV  C1  C2  N2  118.67  3.000
 TEV  C3  C2  N2  124.80  3.000
 TEV  O2  C1  O1  125.87  3.000
 TEV  O1  C1  C2  112.88  3.000
 TEV  O2  C1  C2  121.25  3.000
 TEV  H6  O1  C1  110.30  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  CONST_01  C4  N1  C9  N2    0.00   0.0  0
 TEV  CONST_02  C2  N2  C9  N1    0.00   0.0  0
 TEV  CONST_03  C4  N1  C9  O3  180.00   0.0  0
 TEV  CONST_04  C2  N2  C9  O3  180.00   0.0  0
 TEV  CONST_05  H6  O1  C1  C2  180.00   0.0  0
 TEV  Var_01    C3  C4  N1  C9    0.17  30.0  1
 TEV  Var_02    C3  C2  N2  C9   -0.56  30.0  1
 TEV  Var_03    C4  C3  C2  N2   -2.91  30.0  1
 TEV  Var_04    C2  C3  C4  N1    3.11  30.0  1
 TEV  Var_05    O2  C1  C2  N2  179.95  30.0  2
 TEV  Var_06    H1  C5  C4  N1    4.04  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
 TEV  plan-2  H6  0.020

