# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 13:18:02 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  17  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 PERFECT
;

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  -0.485   1.5800  -1.4771   4.2435
 UAA  N3    N  NH1    0  -0.716   3.2511  -0.2624   3.2948
 UAA  C4    C  C      0   0.571   3.7802   0.5875   2.3314
 UAA  C5    C  C1     0  -0.552   2.8330   1.0106   1.3364
 UAA  C6    C  C      0   0.485   1.5507   0.5829   1.3804
 UAA  C7    C  CH2    0  -0.708   0.5195   0.9726   0.3852
 UAA  C8    C  C      0   0.438   0.1310  -0.1737  -0.5958
 UAA  O8A   O  O      0  -0.587   0.6406  -1.2873  -0.3928
 UAA  O8B   O  OC    -1  -0.604  -0.6644   0.1560  -1.4901
 UAA  O4    O  O      0  -0.480   4.9558   0.9113   2.3836
 UAA  C2    C  C      0   0.662   1.9632  -0.7201   3.3732
 UAA  N1    N  NH1    0  -0.697   1.1454  -0.2457   2.3856
 UAA  H3    H  HNH1   0   0.422   3.8826  -0.5933   4.0129
 UAA  H5    H  H      0   0.276   3.1611   1.6753   0.5516
 UAA  H7C1  H  HCH2   0   0.274   0.8798   1.8287  -0.1860
 UAA  H7C2  H  HCH2   0   0.275  -0.3852   1.3042   0.9046
 UAA  H1    H  HNH1   0   0.426   0.1948  -0.5866   2.3892

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  1.215  0.020  1.215
 UAA  N3  C4    single  1.389  0.020  1.389
 UAA  N3  C2    single  1.369  0.020  1.369
 UAA  N3  H3    single  0.860  0.020  1.020
 UAA  C4  C5    single  1.437  0.020  1.437
 UAA  C4  O4    double  1.221  0.020  1.221
 UAA  C5  C6    double  1.352  0.020  1.352
 UAA  C5  H5    single  0.930  0.020  1.080
 UAA  C6  C7    single  1.485  0.020  1.485
 UAA  C6  N1    single  1.364  0.020  1.364
 UAA  C7  C8    single  1.558  0.020  1.558
 UAA  C7  H7C1  single  0.970  0.020  1.090
 UAA  C7  H7C2  single  0.970  0.020  1.090
 UAA  C8  O8A   deloc   1.241  0.020  1.241
 UAA  C8  O8B   deloc   1.241  0.020  1.241
 UAA  C2  N1    single  1.367  0.020  1.367
 UAA  N1  H1    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
 UAA  H3    N3  C2    115.92  3.000
 UAA  H3    N3  C4    117.03  3.000
 UAA  C2    N3  C4    127.04  3.000
 UAA  O4    C4  C5    125.89  3.000
 UAA  O4    C4  N3    119.96  3.000
 UAA  C5    C4  N3    114.15  3.000
 UAA  H5    C5  C6    120.43  3.000
 UAA  H5    C5  C4    118.95  3.000
 UAA  C6    C5  C4    120.61  3.000
 UAA  N1    C6  C7    116.54  3.000
 UAA  N1    C6  C5    119.85  3.000
 UAA  C7    C6  C5    123.61  3.000
 UAA  H7C2  C7  H7C1  106.49  3.000
 UAA  H7C2  C7  C8    108.39  3.000
 UAA  H7C1  C7  C8    109.28  3.000
 UAA  H7C2  C7  C6    109.59  3.000
 UAA  H7C1  C7  C6    109.12  3.000
 UAA  C8    C7  C6    113.71  3.000
 UAA  O8B   C8  O8A   128.24  3.000
 UAA  O8B   C8  C7    114.71  3.000
 UAA  O8A   C8  C7    117.05  3.000
 UAA  N1    C2  N3    113.92  3.000
 UAA  N1    C2  O2    123.01  3.000
 UAA  N3    C2  O2    123.08  3.000
 UAA  H1    N1  C2    116.32  3.000
 UAA  H1    N1  C6    119.16  3.000
 UAA  C2    N1  C6    124.42  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  Var_01    C8   C7  C6  C5  107.25  30.0  3
 UAA  Var_02    O8A  C8  C7  C6    4.67  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

