# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 22:28:31 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (4R)-2-oxo-1,2,3,4-tetrahydropyrimidine-4,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1NC(=O)NC(=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
 OTD  OTD  '(4R)-2-oxo-1,2,3,4-tetrahydropyrimidine-4,6-dicarboxylic acid'  ligand  19  13  .  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_OTD
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
 OTD  N1    N  NH1   0  -0.640   3.8174  -2.9450   0.4518
 OTD  N3    N  NH1   0  -0.739   1.5629  -2.9177   0.8983
 OTD  C4    C  C     0   0.252   1.4694  -1.6477   0.3512
 OTD  C5    C  C1    0  -0.315   2.4705  -1.1318  -0.3610
 OTD  C6    C  CH1   0  -0.222   3.6818  -1.9787  -0.6033
 OTD  C61   C  C     0   0.558   3.5436  -2.6518  -1.9703
 OTD  O62   O  OH1   0  -0.584   3.6039  -1.7605  -2.9446
 OTD  C41   C  C     0   0.540   0.2287  -0.8575   0.5794
 OTD  O42   O  OH1   0  -0.597  -0.6537  -1.5221   1.3044
 OTD  O41   O  O     0  -0.419   0.0597   0.2514   0.1432
 OTD  C2    C  C     0   0.639   2.7648  -3.5677   1.0401
 OTD  O2    O  O     0  -0.502   2.8662  -4.5958   1.6875
 OTD  HN1   H  HNH1  0   0.412   4.6967  -3.4351   0.5144
 OTD  HN3   H  HNH1  0   0.419   0.7862  -3.3034   1.4120
 OTD  H5    H  H     0   0.298   2.4177  -0.1363  -0.7728
 OTD  H6    H  HCH1  0   0.331   4.5754  -1.3495  -0.6215
 OTD  HO62  H  HOH1  0   0.489   3.4834  -2.1875  -3.8068
 OTD  HO42  H  HOH1  0   0.499  -1.4578  -0.9963   1.4344
 OTD  O61   O  O     0  -0.421   3.3772  -3.8317  -2.1238

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
 OTD  N1   C2    single  1.357  0.020  1.357
 OTD  N1   C6    single  1.437  0.020  1.437
 OTD  N1   HN1   single  0.890  0.020  1.040
 OTD  N3   C4    single  1.386  0.020  1.386
 OTD  N3   C2    single  1.374  0.020  1.374
 OTD  N3   HN3   single  0.860  0.020  1.020
 OTD  C4   C41   single  1.489  0.020  1.489
 OTD  C4   C5    double  1.333  0.020  1.333
 OTD  C5   C6    single  1.498  0.020  1.498
 OTD  C5   H5    single  0.930  0.020  1.080
 OTD  C6   C61   single  1.530  0.020  1.530
 OTD  C6   H6    single  0.970  0.020  1.090
 OTD  O61  C61   double  1.201  0.020  1.201
 OTD  C61  O62   single  1.322  0.020  1.322
 OTD  O62  HO62  single  0.850  0.020  0.980
 OTD  C41  O41   double  1.204  0.020  1.204
 OTD  C41  O42   single  1.321  0.020  1.321
 OTD  O42  HO42  single  0.850  0.020  0.980
 OTD  C2   O2    double  1.219  0.020  1.219

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
 OTD  HN1   N1   C2   115.24  3.000
 OTD  HN1   N1   C6   117.03  3.000
 OTD  C2    N1   C6   123.61  3.000
 OTD  HN3   N3   C2   116.14  3.000
 OTD  HN3   N3   C4   119.99  3.000
 OTD  C2    N3   C4   122.23  3.000
 OTD  C41   C4   C5   120.17  3.000
 OTD  C5    C4   N3   121.00  3.000
 OTD  C41   C4   N3   118.83  3.000
 OTD  H5    C5   C6   119.98  3.000
 OTD  H5    C5   C4   121.64  3.000
 OTD  C6    C5   C4   118.37  3.000
 OTD  H6    C6   C61  108.19  3.000
 OTD  H6    C6   C5   109.78  3.000
 OTD  C61   C6   C5   108.67  3.000
 OTD  H6    C6   N1   108.79  3.000
 OTD  C61   C6   N1   111.63  3.000
 OTD  C5    C6   N1   109.74  3.000
 OTD  O62   C61  O61  125.06  3.000
 OTD  O62   C61  C6   110.96  3.000
 OTD  O61   C61  C6   123.97  3.000
 OTD  HO62  O62  C61  110.65  3.000
 OTD  O41   C41  O42  124.65  3.000
 OTD  O42   C41  C4   111.95  3.000
 OTD  O41   C41  C4   123.41  3.000
 OTD  HO42  O42  C41  110.77  3.000
 OTD  O2    C2   N3   121.78  3.000
 OTD  O2    C2   N1   123.54  3.000
 OTD  N3    C2   N1   114.63  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
 OTD  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 OTD  CONST_03  O2    C2   N3   C4   180.00   0.0  0
 OTD  CONST_05  HN3   N3   C2   N1   180.00   0.0  0
 OTD  CONST_06  HN1   N1   C2   N3   180.00   0.0  0
 OTD  CONST_07  HO42  O42  C41  C4   180.00   0.0  0
 OTD  CONST_08  HO62  O62  C61  C6   180.00   0.0  0
 OTD  Var_01    C6    C5   C4   N3     2.36  30.0  1
 OTD  Var_02    C2    N3   C4   C5    16.94  30.0  1
 OTD  Var_03    O41   C41  C4   N3  -179.98  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 OTD  chir_01  C6  N1  C5  C61  positiv

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
 OTD  plan-1  N1    0.020
 OTD  plan-1  N3    0.020
 OTD  plan-1  C4    0.020
 OTD  plan-1  C6    0.020
 OTD  plan-1  C2    0.020
 OTD  plan-1  O2    0.020
 OTD  plan-1  HN1   0.020
 OTD  plan-1  HN3   0.020
 OTD  plan-2  C6    0.020
 OTD  plan-2  C61   0.020
 OTD  plan-2  O62   0.020
 OTD  plan-2  HO62  0.020
 OTD  plan-2  O61   0.020
 OTD  plan-3  C4    0.020
 OTD  plan-3  C41   0.020
 OTD  plan-3  O42   0.020
 OTD  plan-3  O41   0.020
 OTD  plan-3  HO42  0.020

