# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 12:04:11 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-(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)NC1=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
 HWD  HWD  3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine  ligand  22  14  .  2022-07-25  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_HWD
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
 HWD  N1   N  N      0  -0.517  -0.0135  -0.5443  -0.5225
 HWD  C2   C  C      0   0.728  -1.1088  -0.0231  -1.1762
 HWD  O2   O  OC     0  -0.480  -2.1723   0.1770  -0.6264
 HWD  N3   N  NC1    0  -0.730  -0.9094   0.2508  -2.5050
 HWD  C4   C  C      0   0.562   0.2493   0.0837  -3.2490
 HWD  O4   O  OC     0  -0.471   0.2736   0.3814  -4.4303
 HWD  C5   C  C1     0  -0.509   1.3432  -0.4567  -2.4848
 HWD  C6   C  C1     0   0.078   1.1625  -0.7384  -1.1814
 HWD  C7   C  CH2    0  -0.324  -0.1122  -0.8230   0.9086
 HWD  C8   C  CH1    0  -0.226   0.1396   0.4182   1.7821
 HWD  N8   N  NH2    0  -0.786   1.3877   1.0999   1.5224
 HWD  C9   C  C      0   0.410   0.0311  -0.0458   3.2563
 HWD  O91  O  O      0  -0.594   1.0631  -0.0088   3.9482
 HWD  O92  O  OC    -1  -0.615  -1.0956  -0.4515   3.6049
 HWD  H3   H  HNC1   0   0.424  -1.7143   0.6253  -2.9922
 HWD  H5   H  H      0   0.290   2.2949  -0.6394  -2.9588
 HWD  H6   H  H      0   0.320   1.9626  -1.1552  -0.5860
 HWD  H71  H  HCH2   0   0.262   0.6299  -1.5923   1.1290
 HWD  H72  H  HCH2   0   0.269  -1.0924  -1.2432   1.1164
 HWD  H8   H  HCH1   0   0.235  -0.6751   1.1253   1.5960
 HWD  H81  H  HNH2   0   0.334   2.1720   0.5038   1.7521
 HWD  H82  H  HNH2   0   0.339   1.4734   1.3622   0.5489

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
 HWD  N1  C2   aromatic  1.378  0.020  1.378
 HWD  N1  C6   aromatic  1.362  0.020  1.362
 HWD  N1  C7   single    1.461  0.020  1.461
 HWD  C2  O2   double    1.214  0.020  1.214
 HWD  C2  N3   aromatic  1.371  0.020  1.371
 HWD  N3  C4   aromatic  1.387  0.020  1.387
 HWD  N3  H3   single    0.860  0.020  1.020
 HWD  C4  O4   double    1.218  0.020  1.218
 HWD  C4  C5   aromatic  1.440  0.020  1.440
 HWD  C5  C6   aromatic  1.346  0.020  1.346
 HWD  C5  H5   single    0.930  0.020  1.080
 HWD  C6  H6   single    0.930  0.020  1.080
 HWD  C7  C8   single    1.538  0.020  1.538
 HWD  C7  H71  single    0.970  0.020  1.090
 HWD  C7  H72  single    0.970  0.020  1.090
 HWD  C8  N8   single    1.446  0.020  1.446
 HWD  C8  C9   single    1.549  0.020  1.549
 HWD  C8  H8   single    0.970  0.020  1.090
 HWD  N8  H81  single    0.890  0.020  1.040
 HWD  N8  H82  single    0.890  0.020  1.040
 HWD  C9  O91  deloc     1.243  0.020  1.243
 HWD  C9  O92  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
 HWD  C7   N1  C6   120.33  3.000
 HWD  C7   N1  C2   118.88  3.000
 HWD  C6   N1  C2   120.72  3.000
 HWD  N3   C2  O2   122.24  3.000
 HWD  N3   C2  N1   114.81  3.000
 HWD  O2   C2  N1   122.95  3.000
 HWD  H3   N3  C4   116.77  3.000
 HWD  H3   N3  C2   115.12  3.000
 HWD  C4   N3  C2   128.11  3.000
 HWD  C5   C4  O4   126.24  3.000
 HWD  C5   C4  N3   113.28  3.000
 HWD  O4   C4  N3   120.48  3.000
 HWD  H5   C5  C6   120.57  3.000
 HWD  H5   C5  C4   120.04  3.000
 HWD  C6   C5  C4   119.39  3.000
 HWD  H6   C6  C5   120.99  3.000
 HWD  H6   C6  N1   115.31  3.000
 HWD  C5   C6  N1   123.69  3.000
 HWD  H72  C7  H71  107.59  3.000
 HWD  H72  C7  C8   110.55  3.000
 HWD  H71  C7  C8   110.04  3.000
 HWD  H72  C7  N1   108.79  3.000
 HWD  H71  C7  N1   106.64  3.000
 HWD  C8   C7  N1   113.02  3.000
 HWD  H8   C8  C9   107.64  3.000
 HWD  H8   C8  N8   107.91  3.000
 HWD  C9   C8  N8   111.87  3.000
 HWD  H8   C8  C7   107.63  3.000
 HWD  C9   C8  C7   106.69  3.000
 HWD  N8   C8  C7   114.82  3.000
 HWD  H82  N8  H81  107.79  3.000
 HWD  H82  N8  C8   111.60  3.000
 HWD  H81  N8  C8   110.53  3.000
 HWD  O92  C9  O91  127.17  3.000
 HWD  O92  C9  C8   115.25  3.000
 HWD  O91  C9  C8   117.56  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
 HWD  CONST_01  C4  N3  C2  N1    0.00   0.0  0
 HWD  CONST_02  C4  C5  C6  N1    0.00   0.0  0
 HWD  CONST_03  C5  C6  N1  C2    0.00   0.0  0
 HWD  CONST_04  C5  C4  N3  C2    0.00   0.0  0
 HWD  CONST_05  C6  N1  C2  N3    0.00   0.0  0
 HWD  CONST_06  C6  C5  C4  N3    0.00   0.0  0
 HWD  CONST_07  O4  C4  N3  C2  180.00   0.0  0
 HWD  CONST_08  C6  N1  C2  O2  180.00   0.0  0
 HWD  CONST_09  C4  N3  C2  O2  180.00   0.0  0
 HWD  CONST_10  C7  N1  C2  N3  180.00   0.0  0
 HWD  CONST_11  C6  C5  C4  O4  180.00   0.0  0
 HWD  CONST_12  C7  N1  C6  C5  180.00   0.0  0
 HWD  CONST_13  H3  N3  C2  N1  180.00   0.0  0
 HWD  CONST_14  H5  C5  C6  N1  180.00   0.0  0
 HWD  CONST_15  H6  C6  N1  C2  180.00   0.0  0
 HWD  CONST_16  C7  N1  C2  O2    0.00   0.0  0
 HWD  Var_01    C8  C7  N1  C2  -83.26  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
 HWD  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
 HWD  plan-1  N1   0.020
 HWD  plan-1  C2   0.020
 HWD  plan-1  O2   0.020
 HWD  plan-1  N3   0.020
 HWD  plan-1  C4   0.020
 HWD  plan-1  O4   0.020
 HWD  plan-1  C5   0.020
 HWD  plan-1  C6   0.020
 HWD  plan-1  C7   0.020
 HWD  plan-1  H3   0.020
 HWD  plan-1  H5   0.020
 HWD  plan-1  H6   0.020
 HWD  plan-2  C8   0.020
 HWD  plan-2  C9   0.020
 HWD  plan-2  O91  0.020
 HWD  plan-2  O92  0.020

