# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 12:47:09 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  23  14  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  NR6   0  -0.521  -0.0081  -0.5438  -0.4778
 HWD  C2    C  CR6   0   0.734  -1.0996  -0.0015  -1.1246
 HWD  O2    O  OC    0  -0.476  -2.1474   0.2307  -0.5583
 HWD  N3    N  NR16  0  -0.731  -0.9098   0.2510  -2.4570
 HWD  C4    C  CR6   0   0.566   0.2379   0.0487  -3.2105
 HWD  O4    O  OC    0  -0.465   0.2570   0.3311  -4.3943
 HWD  C5    C  CR16  0  -0.506   1.3296  -0.5075  -2.4515
 HWD  C6    C  CR16  0   0.084   1.1597  -0.7722  -1.1450
 HWD  C7    C  CH2   0  -0.334  -0.1123  -0.8205   0.9465
 HWD  C8    C  CH1   0  -0.229   0.1604   0.4441   1.7903
 HWD  N8    N  NH2   0  -0.782   1.4417   1.0624   1.5762
 HWD  C9    C  C     0   0.553   0.0002   0.0863   3.2572
 HWD  O91   O  O     0  -0.427   0.8912   0.0908   4.0647
 HWD  O92   O  OH1   0  -0.592  -1.2506  -0.2558   3.5386
 HWD  H3    H  HNR6  0   0.427  -1.7103   0.6408  -2.9396
 HWD  H5    H  HCR6  0   0.294   2.2710  -0.7158  -2.9355
 HWD  H6    H  HCR6  0   0.325   1.9549  -1.2021  -0.5526
 HWD  H71   H  HCH2  0   0.289   0.6220  -1.5911   1.1817
 HWD  H72   H  HCH2  0   0.290  -1.0973  -1.2329   1.1518
 HWD  H8    H  HCH1  0   0.297  -0.6141   1.1803   1.5563
 HWD  H81   H  HNH2  0   0.353   2.2020   0.3997   1.6631
 HWD  H82   H  HNH2  0   0.365   1.4941   1.4764   0.6561
 HWD  H92O  H  HOH1  0   0.485  -1.3273  -0.5118   4.4702

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  1.380  0.020  1.380
 HWD  N1   C6    aromatic  1.364  0.020  1.364
 HWD  N1   C7    single    1.455  0.020  1.455
 HWD  C2   O2    double    1.213  0.020  1.213
 HWD  C2   N3    aromatic  1.369  0.020  1.369
 HWD  N3   C4    aromatic  1.388  0.020  1.388
 HWD  N3   H3    single    0.860  0.020  1.020
 HWD  C4   O4    double    1.217  0.020  1.217
 HWD  C4   C5    aromatic  1.441  0.020  1.441
 HWD  C5   C6    aromatic  1.344  0.020  1.344
 HWD  C5   H5    single    0.930  0.020  1.080
 HWD  C6   H6    single    0.930  0.020  1.080
 HWD  C7   C8    single    1.544  0.020  1.544
 HWD  C7   H71   single    0.970  0.020  1.090
 HWD  C7   H72   single    0.970  0.020  1.090
 HWD  C8   N8    single    1.439  0.020  1.439
 HWD  C8   C9    single    1.518  0.020  1.518
 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   double    1.203  0.020  1.203
 HWD  C9   O92   single    1.327  0.020  1.327
 HWD  O92  H92O  single    0.850  0.020  0.980

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   120.55  3.000
 HWD  C7    N1   C2   118.50  3.000
 HWD  C6    N1   C2   120.91  3.000
 HWD  N3    C2   O2   122.58  3.000
 HWD  N3    C2   N1   114.77  3.000
 HWD  O2    C2   N1   122.65  3.000
 HWD  H3    N3   C4   116.81  3.000
 HWD  H3    N3   C2   115.16  3.000
 HWD  C4    N3   C2   128.03  3.000
 HWD  C5    C4   O4   126.14  3.000
 HWD  C5    C4   N3   113.38  3.000
 HWD  O4    C4   N3   120.49  3.000
 HWD  H5    C5   C6   120.56  3.000
 HWD  H5    C5   C4   119.95  3.000
 HWD  C6    C5   C4   119.49  3.000
 HWD  H6    C6   C5   121.21  3.000
 HWD  H6    C6   N1   115.36  3.000
 HWD  C5    C6   N1   123.41  3.000
 HWD  H72   C7   H71  107.54  3.000
 HWD  H72   C7   C8   111.55  3.000
 HWD  H71   C7   C8   110.00  3.000
 HWD  H72   C7   N1   108.77  3.000
 HWD  H71   C7   N1   107.31  3.000
 HWD  C8    C7   N1   111.51  3.000
 HWD  H8    C8   C9   106.89  3.000
 HWD  H8    C8   N8   108.03  3.000
 HWD  C9    C8   N8   109.81  3.000
 HWD  H8    C8   C7   108.01  3.000
 HWD  C9    C8   C7   108.44  3.000
 HWD  N8    C8   C7   115.33  3.000
 HWD  H82   N8   H81  107.90  3.000
 HWD  H82   N8   C8   110.97  3.000
 HWD  H81   N8   C8   112.01  3.000
 HWD  O92   C9   O91  123.85  3.000
 HWD  O92   C9   C8   111.41  3.000
 HWD  O91   C9   C8   124.73  3.000
 HWD  H92O  O92  C9   110.28  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
 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  CONST_17  H92O  O92  C9  C8  180.00   0.0  0
 HWD  Var_01    C8    C7   N1  C2  -82.91  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
 HWD  plan-2  H92O  0.020

