# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 18:23:19 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (6~{R})-6-(4-methoxyphenyl)-2-oxidanylidene-5,6-dihydro-1~{H}-pyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@H]2CC(=NC(=O)N2)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
 AWA  AWA  '(6~{R})-6-(4-methoxyphenyl)-2-oxidanylidene-5,6-dihydro-1~{H}-pyrimidine-4-carboxylic acid'  ligand  29  18  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AWA
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
 AWA  N1   N  N      0  -0.444  -3.0739   0.9177  -0.0877
 AWA  C4   C  C1     0  -0.284   1.6835   0.5542   0.6578
 AWA  C5   C  C      0   0.095   1.0570   0.0587  -0.4788
 AWA  C6   C  C1     0  -0.302   1.8324  -0.6332  -1.4055
 AWA  C7   C  C1     0  -0.328   3.1870  -0.8286  -1.2064
 AWA  C8   C  CH1    0  -0.109  -0.4232   0.2257  -0.7021
 AWA  C10  C  C      0   0.128  -2.6924  -0.2820   0.1168
 AWA  C1   C  CH3    0  -0.437   5.8084  -0.0352   1.1795
 AWA  C2   C  C      0   0.372   3.8073  -0.3222  -0.0632
 AWA  C3   C  C1     0  -0.368   3.0440   0.3745   0.8721
 AWA  C9   C  CH2    0  -0.517  -1.2494  -0.6732   0.2061
 AWA  C11  C  C      0   0.570  -2.1142   1.9420  -0.1958
 AWA  O2   O  O      0  -0.492  -2.4645   3.1034  -0.0671
 AWA  N2   N  NH1    0  -0.644  -0.8360   1.5918  -0.4480
 AWA  C12  C  C      0   0.385  -3.7549  -1.3565   0.3552
 AWA  O3   O  OC    -1  -0.574  -4.8176  -1.2508  -0.2697
 AWA  O4   O  O      0  -0.582  -3.4128  -2.2186   1.1834
 AWA  H1   H  H      0   0.258   1.1131   1.0994   1.4007
 AWA  H2   H  H      0   0.255   1.3712  -1.0256  -2.3040
 AWA  H3   H  H      0   0.263   3.7742  -1.3674  -1.9396
 AWA  H4   H  HCH1   0   0.267  -0.6421  -0.0438  -1.7438
 AWA  H5   H  HCH3   0   0.260   6.8541  -0.3083   1.0616
 AWA  H6   H  HCH3   0   0.229   5.7352   1.0535   1.2419
 AWA  H7   H  HCH3   0   0.229   5.4359  -0.4680   2.1115
 AWA  H8   H  H      0   0.280   3.4868   0.7852   1.7690
 AWA  H9   H  HCH2   0   0.279  -1.1115  -1.7184  -0.0658
 AWA  H10  H  HCH2   0   0.283  -0.9216  -0.5714   1.2466
 AWA  H11  H  HNH1   0   0.399  -0.1974   2.3376  -0.6825
 AWA  O1   O  O2     0  -0.470   5.1297  -0.5467   0.0497

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
 AWA  O2   C11  double    1.220  0.020  1.220
 AWA  C11  N2   single    1.349  0.020  1.349
 AWA  C11  N1   single    1.408  0.020  1.408
 AWA  N2   C8   single    1.450  0.020  1.450
 AWA  N1   C10  double    1.275  0.020  1.275
 AWA  C8   C9   single    1.522  0.020  1.522
 AWA  C8   C5   single    1.506  0.020  1.506
 AWA  C10  C9   single    1.498  0.020  1.498
 AWA  C10  C12  single    1.530  0.020  1.530
 AWA  O4   C12  deloc     1.243  0.020  1.243
 AWA  C12  O3   deloc     1.237  0.020  1.237
 AWA  C5   C6   aromatic  1.392  0.020  1.392
 AWA  C5   C4   aromatic  1.389  0.020  1.389
 AWA  C6   C7   aromatic  1.383  0.020  1.383
 AWA  C4   C3   aromatic  1.389  0.020  1.389
 AWA  C7   C2   aromatic  1.396  0.020  1.396
 AWA  C3   C2   aromatic  1.394  0.020  1.394
 AWA  C2   O1   single    1.346  0.020  1.346
 AWA  O1   C1   single    1.414  0.020  1.414
 AWA  C4   H1   single    0.930  0.020  1.080
 AWA  C6   H2   single    0.930  0.020  1.080
 AWA  C7   H3   single    0.930  0.020  1.080
 AWA  C8   H4   single    0.970  0.020  1.090
 AWA  C1   H5   single    0.970  0.020  1.090
 AWA  C1   H6   single    0.970  0.020  1.090
 AWA  C1   H7   single    0.970  0.020  1.090
 AWA  C3   H8   single    0.930  0.020  1.080
 AWA  C9   H9   single    0.970  0.020  1.090
 AWA  C9   H10  single    0.970  0.020  1.090
 AWA  N2   H11  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
 AWA  C11  N1   C10  119.52  3.000
 AWA  H1   C4   C3   118.35  3.000
 AWA  H1   C4   C5   120.20  3.000
 AWA  C3   C4   C5   121.45  3.000
 AWA  C8   C5   C6   120.25  3.000
 AWA  C6   C5   C4   118.08  3.000
 AWA  C8   C5   C4   121.66  3.000
 AWA  H2   C6   C7   119.02  3.000
 AWA  H2   C6   C5   119.66  3.000
 AWA  C7   C6   C5   121.32  3.000
 AWA  H3   C7   C2   119.61  3.000
 AWA  H3   C7   C6   120.25  3.000
 AWA  C2   C7   C6   120.13  3.000
 AWA  H4   C8   N2   109.93  3.000
 AWA  H4   C8   C9   108.24  3.000
 AWA  N2   C8   C9   107.31  3.000
 AWA  H4   C8   C5   108.02  3.000
 AWA  C9   C8   C5   112.31  3.000
 AWA  N2   C8   C5   111.00  3.000
 AWA  C12  C10  C9   118.45  3.000
 AWA  C12  C10  N1   118.55  3.000
 AWA  C9   C10  N1   122.92  3.000
 AWA  H7   C1   H6   108.83  3.000
 AWA  H7   C1   H5   108.71  3.000
 AWA  H6   C1   H5   108.71  3.000
 AWA  H7   C1   O1   112.00  3.000
 AWA  H6   C1   O1   111.96  3.000
 AWA  H5   C1   O1   106.51  3.000
 AWA  C3   C2   O1   124.40  3.000
 AWA  O1   C2   C7   116.41  3.000
 AWA  C3   C2   C7   119.19  3.000
 AWA  H8   C3   C2   121.48  3.000
 AWA  H8   C3   C4   118.68  3.000
 AWA  C2   C3   C4   119.84  3.000
 AWA  H10  C9   H9   106.77  3.000
 AWA  H10  C9   C10  108.70  3.000
 AWA  H9   C9   C10  110.97  3.000
 AWA  H10  C9   C8   110.45  3.000
 AWA  H9   C9   C8   110.45  3.000
 AWA  C10  C9   C8   109.47  3.000
 AWA  N2   C11  O2   122.61  3.000
 AWA  N2   C11  N1   118.13  3.000
 AWA  O2   C11  N1   119.26  3.000
 AWA  H11  N2   C11  116.81  3.000
 AWA  H11  N2   C8   118.38  3.000
 AWA  C11  N2   C8   123.18  3.000
 AWA  O4   C12  O3   129.19  3.000
 AWA  O3   C12  C10  117.24  3.000
 AWA  O4   C12  C10  113.56  3.000
 AWA  C2   O1   C1   118.58  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
 AWA  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 AWA  CONST_02  C7   C2   C3   C4     0.00   0.0  0
 AWA  CONST_03  C2   C7   C6   C5     0.00   0.0  0
 AWA  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 AWA  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 AWA  CONST_06  C3   C2   C7   C6     0.00   0.0  0
 AWA  CONST_07  C8   C5   C6   C7   180.00   0.0  0
 AWA  CONST_08  C3   C4   C5   C8   180.00   0.0  0
 AWA  CONST_09  C8   N2   C11  N1     0.00   0.0  0
 AWA  CONST_11  O1   C2   C3   C4   180.00   0.0  0
 AWA  CONST_12  O1   C2   C7   C6   180.00   0.0  0
 AWA  CONST_13  O2   C11  N2   C8   180.00   0.0  0
 AWA  CONST_15  H2   C6   C5   C4   180.00   0.0  0
 AWA  CONST_16  H3   C7   C6   C5   180.00   0.0  0
 AWA  CONST_17  H8   C3   C4   C5   180.00   0.0  0
 AWA  CONST_18  H1   C4   C5   C6   180.00   0.0  0
 AWA  CONST_19  H11  N2   C11  N1   180.00   0.0  0
 AWA  Var_01    C8   C9   C10  N1   -32.15  30.0  1
 AWA  Var_02    O4   C12  C10  N1  -143.85  30.0  2
 AWA  Var_03    C3   C2   O1   C1    -0.76  30.0  2
 AWA  Var_04    H5   C1   O1   C2  -178.81  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
 AWA  chir_01  C8  N2  C9  C5  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
 AWA  plan-1  C4   0.020
 AWA  plan-1  C5   0.020
 AWA  plan-1  C6   0.020
 AWA  plan-1  C7   0.020
 AWA  plan-1  C8   0.020
 AWA  plan-1  C2   0.020
 AWA  plan-1  C3   0.020
 AWA  plan-1  H1   0.020
 AWA  plan-1  H2   0.020
 AWA  plan-1  H3   0.020
 AWA  plan-1  H8   0.020
 AWA  plan-1  O1   0.020
 AWA  plan-2  N1   0.020
 AWA  plan-2  C8   0.020
 AWA  plan-2  C10  0.020
 AWA  plan-2  C11  0.020
 AWA  plan-2  O2   0.020
 AWA  plan-2  N2   0.020
 AWA  plan-2  H11  0.020
 AWA  plan-3  C10  0.020
 AWA  plan-3  C12  0.020
 AWA  plan-3  O3   0.020
 AWA  plan-3  O4   0.020

