# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 17:51:03 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-({3-[(2S)-2-amino-2-carboxyethyl]-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CN1C=CC(=O)N(Cc2ccccc2C(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
 UBC  UBC  '2-({3-[(2S)-2-amino-2-carboxyethyl]-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)benzoic acid'  ligand  37  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UBC
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
 UBC  O1    O  OC    -1  -0.592  -4.4898  -2.5717   1.0448
 UBC  C10   C  C      0   0.378  -3.9164  -1.4730   1.1649
 UBC  O2    O  O      0  -0.587  -3.6589  -0.8823   2.2322
 UBC  C22   C  CR6    0  -0.122  -3.5227  -0.7666  -0.1288
 UBC  C23   C  CR16   0  -0.280  -4.2927  -1.0225  -1.2628
 UBC  C24   C  CR16   0  -0.261  -4.0550  -0.3836  -2.4694
 UBC  C25   C  CR16   0  -0.251  -3.0065   0.5181  -2.5599
 UBC  C26   C  CR16   0  -0.295  -2.2135   0.7633  -1.4484
 UBC  C21   C  CR6    0   0.087  -2.4519   0.1371  -0.2265
 UBC  C17   C  CH2    0  -0.343  -1.5616   0.4358   0.9612
 UBC  N6    N  NR6    0  -0.608  -0.2982   1.0669   0.5873
 UBC  C5    C  CR6    0   0.774   0.6714   0.2247   0.0776
 UBC  O8    O  OC     0  -0.475   0.4813  -0.9671  -0.0507
 UBC  C1    C  CR6    0   0.583  -0.1565   2.4468   0.7563
 UBC  O7    O  OC     0  -0.473  -1.0747   3.1223   1.1892
 UBC  C2    C  CR16   0  -0.506   1.1274   2.9699   0.3737
 UBC  C3    C  CR16   0   0.072   2.0648   2.1466  -0.1240
 UBC  N4    N  NR6    0  -0.530   1.8627   0.8132  -0.2864
 UBC  CB    C  CH2    0  -0.324   2.9300  -0.0371  -0.8116
 UBC  CA    C  CH1    0  -0.226   3.7487  -0.7305   0.2903
 UBC  N     N  NH2    0  -0.786   4.3147   0.1643   1.2752
 UBC  C     C  C      0   0.409   4.8381  -1.5663  -0.4263
 UBC  OXT   O  OC     0  -0.616   4.4127  -2.5027  -1.1319
 UBC  O     O  O     -1  -0.595   6.0221  -1.2203  -0.2729
 UBC  H23   H  HCR6   0   0.245  -5.1016  -1.7372  -1.1899
 UBC  H24   H  HCR6   0   0.247  -4.6784  -0.5917  -3.3298
 UBC  H25   H  HCR6   0   0.251  -2.7982   1.0291  -3.4914
 UBC  H26   H  HCR6   0   0.234  -1.3913   1.4590  -1.5555
 UBC  H171  H  HCH2   0   0.267  -1.3374  -0.4708   1.5141
 UBC  H172  H  HCH2   0   0.279  -2.0659   1.1043   1.6519
 UBC  H2    H  HCR6   0   0.286   1.3177   4.0267   0.4765
 UBC  H3    H  HCR6   0   0.319   3.0319   2.5141  -0.4367
 UBC  HB1   H  HCH2   0   0.261   3.5802   0.6095  -1.4036
 UBC  HB2   H  HCH2   0   0.268   2.4926  -0.7702  -1.4839
 UBC  HA    H  HCH1   0   0.236   3.0829  -1.4246   0.8118
 UBC  HN1   H  HNH2   0   0.333   4.9660   0.8061   0.8422
 UBC  HN2   H  HNH2   0   0.339   3.5981   0.7138   1.7315

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
 UBC  O1   C10   deloc     1.245  0.020  1.245
 UBC  C10  O2    deloc     1.247  0.020  1.247
 UBC  C10  C22   single    1.526  0.020  1.526
 UBC  C22  C23   aromatic  1.394  0.020  1.394
 UBC  C22  C21   aromatic  1.405  0.020  1.405
 UBC  C23  C24   aromatic  1.386  0.020  1.386
 UBC  C23  H23   single    0.930  0.020  1.080
 UBC  C24  C25   aromatic  1.386  0.020  1.386
 UBC  C24  H24   single    0.930  0.020  1.080
 UBC  C25  C26   aromatic  1.387  0.020  1.387
 UBC  C25  H25   single    0.930  0.020  1.080
 UBC  C26  C21   aromatic  1.394  0.020  1.394
 UBC  C26  H26   single    0.930  0.020  1.080
 UBC  C21  C17   single    1.514  0.020  1.514
 UBC  C17  N6    single    1.461  0.020  1.461
 UBC  C17  H171  single    0.970  0.020  1.090
 UBC  C17  H172  single    0.970  0.020  1.090
 UBC  N6   C5    aromatic  1.382  0.020  1.382
 UBC  N6   C1    aromatic  1.397  0.020  1.397
 UBC  C5   O8    double    1.214  0.020  1.214
 UBC  C5   N4    aromatic  1.378  0.020  1.378
 UBC  C1   O7    double    1.219  0.020  1.219
 UBC  C1   C2    aromatic  1.438  0.020  1.438
 UBC  C2   C3    aromatic  1.343  0.020  1.343
 UBC  C2   H2    single    0.930  0.020  1.080
 UBC  C3   N4    aromatic  1.358  0.020  1.358
 UBC  C3   H3    single    0.930  0.020  1.080
 UBC  N4   CB    single    1.462  0.020  1.462
 UBC  CB   CA    single    1.538  0.020  1.538
 UBC  CB   HB1   single    0.970  0.020  1.090
 UBC  CB   HB2   single    0.970  0.020  1.090
 UBC  CA   N     single    1.446  0.020  1.446
 UBC  CA   C     single    1.549  0.020  1.549
 UBC  CA   HA    single    0.970  0.020  1.090
 UBC  N    HN1   single    0.890  0.020  1.040
 UBC  N    HN2   single    0.890  0.020  1.040
 UBC  C    OXT   deloc     1.247  0.020  1.247
 UBC  C    O     deloc     1.243  0.020  1.243

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
 UBC  C22   C10  O2    116.95  3.000
 UBC  C22   C10  O1    116.46  3.000
 UBC  O2    C10  O1    126.57  3.000
 UBC  C21   C22  C23   118.85  3.000
 UBC  C21   C22  C10   123.61  3.000
 UBC  C23   C22  C10   117.52  3.000
 UBC  H23   C23  C24   119.44  3.000
 UBC  H23   C23  C22   118.64  3.000
 UBC  C24   C23  C22   121.92  3.000
 UBC  H24   C24  C25   120.58  3.000
 UBC  H24   C24  C23   120.30  3.000
 UBC  C25   C24  C23   119.12  3.000
 UBC  H25   C25  C26   119.73  3.000
 UBC  H25   C25  C24   120.59  3.000
 UBC  C26   C25  C24   119.68  3.000
 UBC  H26   C26  C21   120.37  3.000
 UBC  H26   C26  C25   117.94  3.000
 UBC  C21   C26  C25   121.69  3.000
 UBC  C17   C21  C26   119.90  3.000
 UBC  C17   C21  C22   121.38  3.000
 UBC  C26   C21  C22   118.72  3.000
 UBC  H172  C17  H171  106.63  3.000
 UBC  H172  C17  N6    107.37  3.000
 UBC  H171  C17  N6    108.22  3.000
 UBC  H172  C17  C21   110.33  3.000
 UBC  H171  C17  C21   110.87  3.000
 UBC  N6    C17  C21   113.14  3.000
 UBC  C1    N6   C5    125.12  3.000
 UBC  C1    N6   C17   118.91  3.000
 UBC  C5    N6   C17   115.97  3.000
 UBC  N4    C5   O8    121.80  3.000
 UBC  N4    C5   N6    116.36  3.000
 UBC  O8    C5   N6    121.84  3.000
 UBC  C2    C1   O7    124.42  3.000
 UBC  C2    C1   N6    114.68  3.000
 UBC  O7    C1   N6    120.90  3.000
 UBC  H2    C2   C3    120.84  3.000
 UBC  H2    C2   C1    119.24  3.000
 UBC  C3    C2   C1    119.91  3.000
 UBC  H3    C3   N4    115.62  3.000
 UBC  H3    C3   C2    121.55  3.000
 UBC  N4    C3   C2    122.83  3.000
 UBC  CB    N4   C3    120.34  3.000
 UBC  CB    N4   C5    118.54  3.000
 UBC  C3    N4   C5    121.09  3.000
 UBC  HB2   CB   HB1   107.70  3.000
 UBC  HB2   CB   CA    110.69  3.000
 UBC  HB1   CB   CA    109.79  3.000
 UBC  HB2   CB   N4    108.71  3.000
 UBC  HB1   CB   N4    106.57  3.000
 UBC  CA    CB   N4    113.17  3.000
 UBC  HA    CA   C     107.84  3.000
 UBC  HA    CA   N     107.82  3.000
 UBC  C     CA   N     111.95  3.000
 UBC  HA    CA   CB    107.67  3.000
 UBC  C     CA   CB    106.63  3.000
 UBC  N     CA   CB    114.66  3.000
 UBC  HN2   N    HN1   107.72  3.000
 UBC  HN2   N    CA    111.48  3.000
 UBC  HN1   N    CA    110.67  3.000
 UBC  O     C    OXT   127.13  3.000
 UBC  O     C    CA    117.56  3.000
 UBC  OXT   C    CA    115.28  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
 UBC  CONST_01  C25  C24  C23  C22    0.00   0.0  0
 UBC  CONST_02  C25  C26  C21  C22    0.00   0.0  0
 UBC  CONST_03  C26  C21  C22  C23    0.00   0.0  0
 UBC  CONST_04  C26  C25  C24  C23    0.00   0.0  0
 UBC  CONST_05  C21  C22  C23  C24    0.00   0.0  0
 UBC  CONST_06  C21  C26  C25  C24    0.00   0.0  0
 UBC  CONST_07  C3   N4   C5   N6     0.00   0.0  0
 UBC  CONST_08  C3   C2   C1   N6     0.00   0.0  0
 UBC  CONST_09  C2   C1   N6   C5     0.00   0.0  0
 UBC  CONST_10  C2   C3   N4   C5     0.00   0.0  0
 UBC  CONST_11  N4   C5   N6   C1     0.00   0.0  0
 UBC  CONST_12  N4   C3   C2   C1     0.00   0.0  0
 UBC  CONST_13  C24  C23  C22  C10  180.00   0.0  0
 UBC  CONST_14  C26  C21  C22  C10  180.00   0.0  0
 UBC  CONST_15  C17  C21  C22  C23  180.00   0.0  0
 UBC  CONST_16  C17  C21  C26  C25  180.00   0.0  0
 UBC  CONST_17  N4   C5   N6   C17  180.00   0.0  0
 UBC  CONST_18  C2   C1   N6   C17  180.00   0.0  0
 UBC  CONST_19  CB   N4   C5   N6   180.00   0.0  0
 UBC  CONST_20  O7   C1   N6   C5   180.00   0.0  0
 UBC  CONST_21  C1   N6   C5   O8   180.00   0.0  0
 UBC  CONST_22  C3   N4   C5   O8   180.00   0.0  0
 UBC  CONST_23  C3   C2   C1   O7   180.00   0.0  0
 UBC  CONST_24  CB   N4   C3   C2   180.00   0.0  0
 UBC  CONST_25  H24  C24  C23  C22  180.00   0.0  0
 UBC  CONST_26  H26  C26  C21  C22  180.00   0.0  0
 UBC  CONST_27  H25  C25  C24  C23  180.00   0.0  0
 UBC  CONST_28  H23  C23  C24  C25  180.00   0.0  0
 UBC  CONST_29  H2   C2   C1   N6   180.00   0.0  0
 UBC  CONST_30  H3   C3   N4   C5   180.00   0.0  0
 UBC  CONST_31  O8   C5   N6   C17    0.00   0.0  0
 UBC  CONST_32  O7   C1   N6   C17    0.00   0.0  0
 UBC  CONST_33  CB   N4   C5   O8     0.00   0.0  0
 UBC  Var_01    N6   C17  C21  C22  162.92  30.0  2
 UBC  Var_02    C5   N6   C17  C21  -78.19  30.0  2
 UBC  Var_03    C23  C22  C10  O1    28.05  30.0  2
 UBC  Var_04    CA   CB   N4   C5   -82.21  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
 UBC  chir_01  CA  CB  N  C  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
 UBC  plan-1  C10  0.020
 UBC  plan-1  C22  0.020
 UBC  plan-1  C23  0.020
 UBC  plan-1  C24  0.020
 UBC  plan-1  C25  0.020
 UBC  plan-1  C26  0.020
 UBC  plan-1  C21  0.020
 UBC  plan-1  C17  0.020
 UBC  plan-1  H23  0.020
 UBC  plan-1  H24  0.020
 UBC  plan-1  H25  0.020
 UBC  plan-1  H26  0.020
 UBC  plan-2  C17  0.020
 UBC  plan-2  N6   0.020
 UBC  plan-2  C5   0.020
 UBC  plan-2  O8   0.020
 UBC  plan-2  C1   0.020
 UBC  plan-2  O7   0.020
 UBC  plan-2  C2   0.020
 UBC  plan-2  C3   0.020
 UBC  plan-2  N4   0.020
 UBC  plan-2  CB   0.020
 UBC  plan-2  H2   0.020
 UBC  plan-2  H3   0.020
 UBC  plan-3  O1   0.020
 UBC  plan-3  C10  0.020
 UBC  plan-3  O2   0.020
 UBC  plan-3  C22  0.020
 UBC  plan-4  CA   0.020
 UBC  plan-4  C    0.020
 UBC  plan-4  OXT  0.020
 UBC  plan-4  O    0.020

