# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 15:44:23 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC1=CC(=O)NC(=O)N1
#
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
 UAA  UAA  '(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)acetic acid'  ligand  18  12  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UAA
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
 UAA  O2    O  O     0  -0.474   1.6156  -1.4798   4.2365
 UAA  N3    N  NR16  0  -0.717   3.2700  -0.2512   3.2762
 UAA  C4    C  CR6   0   0.581   3.7825   0.6160   2.3221
 UAA  C5    C  CR16  0  -0.532   2.8212   1.0375   1.3316
 UAA  C6    C  CR6   0   0.471   1.5520   0.5906   1.3879
 UAA  C7    C  CH2   0  -0.691   0.5106   0.9878   0.3963
 UAA  C8    C  C     0   0.567   0.2014  -0.1247  -0.5792
 UAA  O8A   O  O     0  -0.425   0.7106  -1.2142  -0.5564
 UAA  O8B   O  OH1   0  -0.584  -0.7026   0.2597  -1.4647
 UAA  O4    O  O     0  -0.465   4.9504   0.9573   2.3639
 UAA  C2    C  CR6   0   0.672   1.9866  -0.7216   3.3652
 UAA  N1    N  NR16  0  -0.706   1.1554  -0.2564   2.3801
 UAA  H3    H  HNR6  0   0.427   3.9092  -0.5785   3.9897
 UAA  H5    H  HCR6  0   0.290   3.1355   1.7106   0.5484
 UAA  H7C1  H  HCH2  0   0.332   0.8457   1.8652  -0.1585
 UAA  H7C2  H  HCH2  0   0.330  -0.4130   1.2813   0.9050
 UAA  H1    H  HNR6  0   0.435   0.1978  -0.5768   2.4161
 UAA  HO1   H  HOH1  0   0.488  -0.8901  -0.4598  -2.0869

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
 UAA  O2   C2    double  1.213  0.020  1.213
 UAA  N3   C4    single  1.387  0.020  1.387
 UAA  N3   C2    single  1.370  0.020  1.370
 UAA  N3   H3    single  0.860  0.020  1.020
 UAA  C4   C5    single  1.443  0.020  1.443
 UAA  C4   O4    double  1.218  0.020  1.218
 UAA  C5   C6    double  1.347  0.020  1.347
 UAA  C5   H5    single  0.930  0.020  1.080
 UAA  C6   C7    single  1.492  0.020  1.492
 UAA  C6   N1    single  1.364  0.020  1.364
 UAA  C7   C8    single  1.512  0.020  1.512
 UAA  C7   H7C1  single  0.970  0.020  1.090
 UAA  C7   H7C2  single  0.970  0.020  1.090
 UAA  C8   O8A   double  1.203  0.020  1.203
 UAA  C8   O8B   single  1.322  0.020  1.322
 UAA  C2   N1    single  1.370  0.020  1.370
 UAA  N1   H1    single  0.860  0.020  1.020
 UAA  HO1  O8B   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
 UAA  H3    N3   C2    115.76  3.000
 UAA  H3    N3   C4    116.97  3.000
 UAA  C2    N3   C4    127.26  3.000
 UAA  O4    C4   C5    125.49  3.000
 UAA  O4    C4   N3    120.40  3.000
 UAA  C5    C4   N3    114.11  3.000
 UAA  H5    C5   C6    120.77  3.000
 UAA  H5    C5   C4    119.08  3.000
 UAA  C6    C5   C4    120.14  3.000
 UAA  N1    C6   C7    116.49  3.000
 UAA  N1    C6   C5    120.71  3.000
 UAA  C7    C6   C5    122.80  3.000
 UAA  H7C2  C7   H7C1  106.26  3.000
 UAA  H7C2  C7   C8    108.95  3.000
 UAA  H7C1  C7   C8    109.06  3.000
 UAA  H7C2  C7   C6    110.58  3.000
 UAA  H7C1  C7   C6    109.74  3.000
 UAA  C8    C7   C6    112.07  3.000
 UAA  O8B   C8   O8A   124.42  3.000
 UAA  O8B   C8   C7    110.98  3.000
 UAA  O8A   C8   C7    124.60  3.000
 UAA  HO1   O8B  C8    110.26  3.000
 UAA  N1    C2   N3    113.89  3.000
 UAA  N1    C2   O2    122.89  3.000
 UAA  N3    C2   O2    123.22  3.000
 UAA  H1    N1   C2    116.21  3.000
 UAA  H1    N1   C6    119.90  3.000
 UAA  C2    N1   C6    123.89  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
 UAA  CONST_01  C6   N1   C2  N3    0.00   0.0  0
 UAA  CONST_02  N1   C2   N3  C4    0.00   0.0  0
 UAA  CONST_03  C2   N3   C4  C5    0.00   0.0  0
 UAA  CONST_04  C4   N3   C2  O2  180.00   0.0  0
 UAA  CONST_05  C6   N1   C2  O2  180.00   0.0  0
 UAA  CONST_06  C2   N3   C4  O4  180.00   0.0  0
 UAA  CONST_07  H1   N1   C2  N3  180.00   0.0  0
 UAA  CONST_08  H3   N3   C4  C5  180.00   0.0  0
 UAA  CONST_09  HO1  O8B  C8  C7  180.00   0.0  0
 UAA  Var_01    C8   C7   C6  C5  105.37  30.0  3
 UAA  Var_02    O8A  C8   C7  C6    1.19  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
 UAA  plan-1  O2   0.020
 UAA  plan-1  N3   0.020
 UAA  plan-1  C4   0.020
 UAA  plan-1  C5   0.020
 UAA  plan-1  C6   0.020
 UAA  plan-1  C7   0.020
 UAA  plan-1  O4   0.020
 UAA  plan-1  C2   0.020
 UAA  plan-1  N1   0.020
 UAA  plan-1  H3   0.020
 UAA  plan-1  H5   0.020
 UAA  plan-1  H1   0.020
 UAA  plan-2  C7   0.020
 UAA  plan-2  C8   0.020
 UAA  plan-2  O8A  0.020
 UAA  plan-2  O8B  0.020
 UAA  plan-2  HO1  0.020

