# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:02:44 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=CNC(=O)NC1=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
 5CU  5CU  '2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid'  ligand  15  11  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5CU
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
 5CU  O53  O  O     0  -0.453   2.5716  -1.5154  0.0627
 5CU  C51  C  C     0   0.551   2.0582  -0.4190  0.0409
 5CU  O52  O  OH1   0  -0.583   2.7564   0.7028  0.0206
 5CU  C5   C  CR6   0  -0.380   0.5998  -0.2188  0.0319
 5CU  C4   C  CR6   0   0.593  -0.0624   1.0786  0.0237
 5CU  O4   O  O     0  -0.430   0.4635   2.1703  0.0267
 5CU  N3   N  NR16  0  -0.720  -1.4516   0.9940  0.0129
 5CU  C2   C  CR6   0   0.697  -2.2371  -0.1239  0.0111
 5CU  O2   O  O     0  -0.455  -3.4455  -0.1011  0.0016
 5CU  N1   N  NR16  0  -0.664  -1.5132  -1.2982  0.0219
 5CU  C6   C  CR16  0   0.140  -0.1743  -1.3357  0.0318
 5CU  H1   H  HOH1  0   0.485   3.7012   0.4874  0.0274
 5CU  H3   H  HNR6  0   0.433  -1.9480   1.8771  0.0069
 5CU  H4   H  HCR6  0   0.338   0.2599  -2.3252  0.0396
 5CU  H2   H  HNR6  0   0.449  -2.0353  -2.1636  0.0215

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
 5CU  N1   C6   single  1.339  0.020  1.339
 5CU  N1   C2   single  1.380  0.020  1.380
 5CU  O2   C2   double  1.209  0.020  1.209
 5CU  C6   C5   double  1.359  0.020  1.359
 5CU  C2   N3   single  1.366  0.020  1.366
 5CU  O53  C51  double  1.211  0.020  1.211
 5CU  C5   C51  single  1.472  0.020  1.472
 5CU  C5   C4   single  1.457  0.020  1.457
 5CU  N3   C4   single  1.392  0.020  1.392
 5CU  C51  O52  single  1.322  0.020  1.322
 5CU  C4   O4   double  1.212  0.020  1.212
 5CU  O52  H1   single  0.850  0.020  0.980
 5CU  N3   H3   single  0.860  0.020  1.020
 5CU  C6   H4   single  0.930  0.020  1.080
 5CU  N1   H2   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
 5CU  C5   C51  O52  114.07  3.000
 5CU  O52  C51  O53  123.01  3.000
 5CU  C5   C51  O53  122.91  3.000
 5CU  H1   O52  C51  109.05  3.000
 5CU  C6   C5   C4   118.23  3.000
 5CU  C4   C5   C51  124.86  3.000
 5CU  C6   C5   C51  116.91  3.000
 5CU  N3   C4   O4   119.21  3.000
 5CU  O4   C4   C5   127.23  3.000
 5CU  N3   C4   C5   113.56  3.000
 5CU  H3   N3   C2   115.57  3.000
 5CU  H3   N3   C4   115.85  3.000
 5CU  C2   N3   C4   128.58  3.000
 5CU  N1   C2   O2   122.74  3.000
 5CU  O2   C2   N3   124.01  3.000
 5CU  N1   C2   N3   113.26  3.000
 5CU  H2   N1   C6   119.50  3.000
 5CU  H2   N1   C2   117.24  3.000
 5CU  C6   N1   C2   123.25  3.000
 5CU  H4   C6   N1   115.29  3.000
 5CU  H4   C6   C5   121.58  3.000
 5CU  N1   C6   C5   123.12  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
 5CU  CONST_01  C2  N3   C4   C5     0.00   0.0  0
 5CU  CONST_02  N1  C2   N3   C4     0.00   0.0  0
 5CU  CONST_03  C6  N1   C2   N3     0.00   0.0  0
 5CU  CONST_04  O2  C2   N3   C4   180.00   0.0  0
 5CU  CONST_05  C2  N3   C4   O4   180.00   0.0  0
 5CU  CONST_06  C6  N1   C2   O2   180.00   0.0  0
 5CU  CONST_07  H3  N3   C4   C5   180.00   0.0  0
 5CU  CONST_08  H2  N1   C2   N3   180.00   0.0  0
 5CU  CONST_09  H1  O52  C51  C5   180.00   0.0  0
 5CU  Var_01    C6  C5   C51  O53   -0.83  30.0  2

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
 5CU  plan-1  C51  0.020
 5CU  plan-1  C5   0.020
 5CU  plan-1  C4   0.020
 5CU  plan-1  O4   0.020
 5CU  plan-1  N3   0.020
 5CU  plan-1  C2   0.020
 5CU  plan-1  O2   0.020
 5CU  plan-1  N1   0.020
 5CU  plan-1  C6   0.020
 5CU  plan-1  H3   0.020
 5CU  plan-1  H4   0.020
 5CU  plan-1  H2   0.020
 5CU  plan-2  O53  0.020
 5CU  plan-2  C51  0.020
 5CU  plan-2  O52  0.020
 5CU  plan-2  C5   0.020
 5CU  plan-2  H1   0.020

