# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 03:12:08 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 3-[3-(2-carboxyethyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CN1C=CC(=O)N(CCC(O)=O)C1=O)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
 UBP  UBP  3-[3-(2-carboxyethyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl]-L-alanine  ligand  30  19  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UBP
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
 UBP  N1    N  NR6    0  -0.535  -1.0124  -0.6819   0.4058
 UBP  C2    C  CR6    0   0.755   0.1058   0.0615   0.0926
 UBP  O2    O  O      0  -0.487   0.1112   1.2750   0.1654
 UBP  N3    N  NR6    0  -0.593   1.2193  -0.6523  -0.3050
 UBP  C4    C  CR6    0   0.593   1.3001  -2.0431  -0.3630
 UBP  O4    O  O      0  -0.481   2.3393  -2.5965  -0.6823
 UBP  C5    C  CR16   0  -0.509   0.0873  -2.7390  -0.0199
 UBP  C6    C  CR16   0   0.092  -0.9974  -2.0396   0.3448
 UBP  C7    C  CH2    0  -0.337  -2.2563  -0.0119   0.7872
 UBP  C8    C  CH1    0  -0.230  -3.2860   0.0140  -0.3555
 UBP  N8    N  NH2    0  -0.782  -2.8042   0.5734  -1.5987
 UBP  C9    C  C      0   0.412  -4.5320   0.7621   0.1799
 UBP  O91   O  O      0  -0.593  -4.8334   1.8397  -0.3606
 UBP  O92   O  OC    -1  -0.617  -5.1045   0.2164   1.1448
 UBP  C1    C  CH2    0  -0.295   2.4315   0.1205  -0.6055
 UBP  C3    C  CH2    0  -0.593   3.2767   0.3562   0.6349
 UBP  C10   C  C      0   0.419   4.5680   1.1522   0.3718
 UBP  O3    O  OC    -1  -0.625   5.2656   1.4055   1.3741
 UBP  O1    O  O      0  -0.607   4.8163   1.4708  -0.8078
 UBP  H5    H  HCR6   0   0.284   0.0712  -3.8173  -0.0460
 UBP  H6    H  HCR6   0   0.317  -1.9218  -2.5277   0.6218
 UBP  H7    H  HCH2   0   0.265  -2.6623  -0.5363   1.6510
 UBP  H7A   H  HCH2   0   0.272  -2.0079   0.9995   1.1003
 UBP  H8    H  HCH1   0   0.229  -3.5866  -1.0217  -0.5550
 UBP  HN8   H  HNH2   0   0.333  -2.5492   1.5437  -1.4695
 UBP  HN8A  H  HNH2   0   0.337  -1.9742   0.0869  -1.9134
 UBP  H1    H  HCH2   0   0.251   2.9914  -0.4272  -1.3576
 UBP  H1A   H  HCH2   0   0.253   2.1273   1.0607  -1.0556
 UBP  H3    H  HCH2   0   0.234   2.6881   0.8823   1.3922
 UBP  H3A   H  HCH2   0   0.236   3.5501  -0.6037   1.0842

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
 UBP  C6   N1    single  1.359  0.020  1.359
 UBP  N1   C7    single  1.463  0.020  1.463
 UBP  N1   C2    single  1.379  0.020  1.379
 UBP  N3   C2    single  1.381  0.020  1.381
 UBP  C2   O2    double  1.216  0.020  1.216
 UBP  C4   N3    single  1.394  0.020  1.394
 UBP  N3   C1    single  1.469  0.020  1.469
 UBP  C5   C4    single  1.440  0.020  1.440
 UBP  O4   C4    double  1.220  0.020  1.220
 UBP  C5   C6    double  1.341  0.020  1.341
 UBP  C5   H5    single  0.930  0.020  1.080
 UBP  C6   H6    single  0.930  0.020  1.080
 UBP  C7   C8    single  1.538  0.020  1.538
 UBP  C7   H7    single  0.970  0.020  1.090
 UBP  C7   H7A   single  0.970  0.020  1.090
 UBP  N8   C8    single  1.446  0.020  1.446
 UBP  C8   C9    single  1.549  0.020  1.549
 UBP  C8   H8    single  0.970  0.020  1.090
 UBP  N8   HN8   single  0.890  0.020  1.040
 UBP  N8   HN8A  single  0.890  0.020  1.040
 UBP  O91  C9    deloc   1.243  0.020  1.243
 UBP  C9   O92   deloc   1.248  0.020  1.248
 UBP  C3   C1    single  1.519  0.020  1.519
 UBP  C1   H1    single  0.970  0.020  1.090
 UBP  C1   H1A   single  0.970  0.020  1.090
 UBP  C3   C10   single  1.540  0.020  1.540
 UBP  C3   H3    single  0.970  0.020  1.090
 UBP  C3   H3A   single  0.970  0.020  1.090
 UBP  C10  O1    deloc   1.247  0.020  1.247
 UBP  C10  O3    deloc   1.247  0.020  1.247

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
 UBP  C7    N1   C6   118.58  3.000
 UBP  C7    N1   C2   120.11  3.000
 UBP  C6    N1   C2   121.30  3.000
 UBP  N3    C2   O2   121.97  3.000
 UBP  O2    C2   N1   121.89  3.000
 UBP  N3    C2   N1   116.14  3.000
 UBP  C1    N3   C4   117.94  3.000
 UBP  C1    N3   C2   116.89  3.000
 UBP  C4    N3   C2   125.05  3.000
 UBP  C5    C4   O4   124.11  3.000
 UBP  O4    C4   N3   120.85  3.000
 UBP  C5    C4   N3   115.04  3.000
 UBP  H5    C5   C6   121.05  3.000
 UBP  H5    C5   C4   119.33  3.000
 UBP  C6    C5   C4   119.61  3.000
 UBP  H6    C6   C5   121.71  3.000
 UBP  H6    C6   N1   115.46  3.000
 UBP  C5    C6   N1   122.82  3.000
 UBP  H7A   C7   H7   107.73  3.000
 UBP  H7A   C7   C8   110.55  3.000
 UBP  H7    C7   C8   110.35  3.000
 UBP  H7A   C7   N1   107.86  3.000
 UBP  H7    C7   N1   107.65  3.000
 UBP  C8    C7   N1   112.52  3.000
 UBP  H8    C8   C9   107.37  3.000
 UBP  H8    C8   N8   107.47  3.000
 UBP  C9    C8   N8   112.24  3.000
 UBP  H8    C8   C7   107.62  3.000
 UBP  C9    C8   C7   106.85  3.000
 UBP  N8    C8   C7   114.97  3.000
 UBP  HN8A  N8   HN8  107.10  3.000
 UBP  HN8A  N8   C8   110.77  3.000
 UBP  HN8   N8   C8   110.19  3.000
 UBP  O92   C9   O91  127.19  3.000
 UBP  O92   C9   C8   115.16  3.000
 UBP  O91   C9   C8   117.62  3.000
 UBP  H1A   C1   H1   107.10  3.000
 UBP  H1A   C1   C3   111.09  3.000
 UBP  H1    C1   C3   110.90  3.000
 UBP  H1A   C1   N3   108.02  3.000
 UBP  H1    C1   N3   107.58  3.000
 UBP  C3    C1   N3   111.94  3.000
 UBP  H3A   C3   H3   105.78  3.000
 UBP  H3A   C3   C10  108.30  3.000
 UBP  H3    C3   C10  108.72  3.000
 UBP  H3A   C3   C1   109.76  3.000
 UBP  H3    C3   C1   109.91  3.000
 UBP  C10   C3   C1   114.03  3.000
 UBP  O1    C10  O3   126.66  3.000
 UBP  O3    C10  C3   115.90  3.000
 UBP  O1    C10  C3   117.44  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
 UBP  CONST_01  C4   N3   C2  N1    0.00   0.0  0
 UBP  CONST_02  C5   C4   N3  C2    0.00   0.0  0
 UBP  CONST_03  C6   N1   C2  N3    0.00   0.0  0
 UBP  CONST_04  C1   N3   C2  N1  180.00   0.0  0
 UBP  CONST_05  O4   C4   N3  C2  180.00   0.0  0
 UBP  CONST_06  C6   N1   C2  O2  180.00   0.0  0
 UBP  CONST_07  C4   N3   C2  O2  180.00   0.0  0
 UBP  CONST_08  C7   N1   C2  N3  180.00   0.0  0
 UBP  CONST_09  C1   N3   C4  C5  180.00   0.0  0
 UBP  CONST_10  C7   N1   C2  O2    0.00   0.0  0
 UBP  CONST_11  C1   N3   C2  O2    0.00   0.0  0
 UBP  CONST_12  C1   N3   C4  O4    0.00   0.0  0
 UBP  Var_01    C8   C7   N1  C2  102.49  30.0  3
 UBP  Var_02    C3   C1   N3  C2   87.53  30.0  3
 UBP  Var_03    C10  C3   C1  N3  179.47  30.0  1
 UBP  Var_04    O1   C10  C3  C1   -2.76  30.0  3

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
 UBP  chir_01  C8  C7  N8  C9  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
 UBP  plan-1  N1   0.020
 UBP  plan-1  C2   0.020
 UBP  plan-1  O2   0.020
 UBP  plan-1  N3   0.020
 UBP  plan-1  C4   0.020
 UBP  plan-1  O4   0.020
 UBP  plan-1  C5   0.020
 UBP  plan-1  C6   0.020
 UBP  plan-1  C7   0.020
 UBP  plan-1  C1   0.020
 UBP  plan-1  H5   0.020
 UBP  plan-1  H6   0.020
 UBP  plan-2  C8   0.020
 UBP  plan-2  C9   0.020
 UBP  plan-2  O91  0.020
 UBP  plan-2  O92  0.020
 UBP  plan-3  C3   0.020
 UBP  plan-3  C10  0.020
 UBP  plan-3  O3   0.020
 UBP  plan-3  O1   0.020

