# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 14:45:36 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-(5-bromo-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=C(Br)C(=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
 BWD  BWD  3-(5-bromo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine  ligand  22  15  .  2022-07-24  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_BWD
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
 BWD  N1   N   N      0  -0.516  -0.6044  -0.4997   0.6872
 BWD  C2   C   C      0   0.737  -1.8953  -0.0543   0.4960
 BWD  O2   O   OC     0  -0.469  -2.7026   0.0369   1.3949
 BWD  N3   N   NC1    0  -0.732  -2.2008   0.2778  -0.8003
 BWD  C4   C   C      0   0.594  -1.3827   0.2415  -1.9144
 BWD  O4   O   OC     0  -0.438  -1.7878   0.5768  -3.0079
 BWD  C5   C   C      0  -0.372  -0.0489  -0.2284  -1.6082
 BWD  BR5  BR  BR     0   0.001   1.1805  -0.3409  -3.0071
 BWD  C6   C   C1     0   0.105   0.2756  -0.5688  -0.3456
 BWD  C7   C   CH2    0  -0.327  -0.1527  -0.8021   2.0467
 BWD  C8   C   CH1    0  -0.230   0.3030   0.4531   2.8109
 BWD  N8   N   NH2    0  -0.784   1.2848   1.2591   2.1219
 BWD  C9   C   C      0   0.413   0.8052  -0.0196   4.1993
 BWD  O91  O   O      0  -0.591   1.9871   0.2187   4.4980
 BWD  O92  O   OC    -1  -0.615  -0.0389  -0.6287   4.8869
 BWD  H3   H   HNC1   0   0.433  -3.1495   0.6005  -0.9507
 BWD  H6   H   H      0   0.335   1.2620  -0.9286  -0.0876
 BWD  H71  H   HCH2   0   0.267   0.6734  -1.5084   1.9504
 BWD  H72  H   HCH2   0   0.273  -0.9557  -1.3076   2.5755
 BWD  H8   H   HCH1   0   0.240  -0.5813   1.0781   2.9750
 BWD  H81  H   HNH2   0   0.335   2.1390   0.7389   1.9697
 BWD  H82  H   HNH2   0   0.341   0.9470   1.5662   1.2191

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
 BWD  N1  C2   aromatic  1.379  0.020  1.379
 BWD  N1  C6   aromatic  1.359  0.020  1.359
 BWD  N1  C7   single    1.464  0.020  1.464
 BWD  C2  O2   double    1.212  0.020  1.212
 BWD  C2  N3   aromatic  1.373  0.020  1.373
 BWD  N3  C4   aromatic  1.383  0.020  1.383
 BWD  N3  H3   single    0.860  0.020  1.020
 BWD  C4  O4   double    1.213  0.020  1.213
 BWD  C4  C5   aromatic  1.447  0.020  1.447
 BWD  C5  BR5  single    1.866  0.020  1.866
 BWD  C5  C6   aromatic  1.347  0.020  1.347
 BWD  C6  H6   single    0.930  0.020  1.080
 BWD  C7  C8   single    1.539  0.020  1.539
 BWD  C7  H71  single    0.970  0.020  1.090
 BWD  C7  H72  single    0.970  0.020  1.090
 BWD  C8  N8   single    1.445  0.020  1.445
 BWD  C8  C9   single    1.550  0.020  1.550
 BWD  C8  H8   single    0.970  0.020  1.090
 BWD  N8  H81  single    0.890  0.020  1.040
 BWD  N8  H82  single    0.890  0.020  1.040
 BWD  C9  O91  deloc     1.242  0.020  1.242
 BWD  C9  O92  deloc     1.248  0.020  1.248

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
 BWD  C7   N1  C6   119.71  3.000
 BWD  C7   N1  C2   118.97  3.000
 BWD  C6   N1  C2   121.15  3.000
 BWD  N3   C2  O2   122.29  3.000
 BWD  N3   C2  N1   114.68  3.000
 BWD  O2   C2  N1   123.03  3.000
 BWD  H3   N3  C4   116.28  3.000
 BWD  H3   N3  C2   115.19  3.000
 BWD  C4   N3  C2   128.53  3.000
 BWD  C5   C4  O4   126.03  3.000
 BWD  C5   C4  N3   112.55  3.000
 BWD  O4   C4  N3   121.43  3.000
 BWD  C6   C5  BR5  121.92  3.000
 BWD  C6   C5  C4   120.15  3.000
 BWD  BR5  C5  C4   117.93  3.000
 BWD  H6   C6  C5   121.83  3.000
 BWD  H6   C6  N1   115.25  3.000
 BWD  C5   C6  N1   122.93  3.000
 BWD  H72  C7  H71  107.54  3.000
 BWD  H72  C7  C8   110.91  3.000
 BWD  H71  C7  C8   110.35  3.000
 BWD  H72  C7  N1   108.67  3.000
 BWD  H71  C7  N1   106.58  3.000
 BWD  C8   C7  N1   112.59  3.000
 BWD  H8   C8  C9   107.54  3.000
 BWD  H8   C8  N8   107.56  3.000
 BWD  C9   C8  N8   112.15  3.000
 BWD  H8   C8  C7   107.50  3.000
 BWD  C9   C8  C7   106.98  3.000
 BWD  N8   C8  C7   114.80  3.000
 BWD  H82  N8  H81  107.68  3.000
 BWD  H82  N8  C8   111.59  3.000
 BWD  H81  N8  C8   111.01  3.000
 BWD  O92  C9  O91  127.22  3.000
 BWD  O92  C9  C8   115.05  3.000
 BWD  O91  C9  C8   117.72  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
 BWD  CONST_01  C4   N3  C2  N1    0.00   0.0  0
 BWD  CONST_02  C4   C5  C6  N1    0.00   0.0  0
 BWD  CONST_03  C5   C6  N1  C2    0.00   0.0  0
 BWD  CONST_04  C5   C4  N3  C2    0.00   0.0  0
 BWD  CONST_05  C6   N1  C2  N3    0.00   0.0  0
 BWD  CONST_06  C6   C5  C4  N3    0.00   0.0  0
 BWD  CONST_07  BR5  C5  C6  N1  180.00   0.0  0
 BWD  CONST_08  O4   C4  N3  C2  180.00   0.0  0
 BWD  CONST_09  C6   N1  C2  O2  180.00   0.0  0
 BWD  CONST_10  C4   N3  C2  O2  180.00   0.0  0
 BWD  CONST_11  C7   N1  C2  N3  180.00   0.0  0
 BWD  CONST_12  BR5  C5  C4  N3  180.00   0.0  0
 BWD  CONST_13  C6   C5  C4  O4  180.00   0.0  0
 BWD  CONST_14  C7   N1  C6  C5  180.00   0.0  0
 BWD  CONST_15  H3   N3  C2  N1  180.00   0.0  0
 BWD  CONST_16  H6   C6  N1  C2  180.00   0.0  0
 BWD  CONST_17  C7   N1  C2  O2    0.00   0.0  0
 BWD  Var_01    C8   C7  N1  C2  -82.65  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
 BWD  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
 BWD  plan-1  N1   0.020
 BWD  plan-1  C2   0.020
 BWD  plan-1  O2   0.020
 BWD  plan-1  N3   0.020
 BWD  plan-1  C4   0.020
 BWD  plan-1  O4   0.020
 BWD  plan-1  C5   0.020
 BWD  plan-1  BR5  0.020
 BWD  plan-1  C6   0.020
 BWD  plan-1  C7   0.020
 BWD  plan-1  H3   0.020
 BWD  plan-1  H6   0.020
 BWD  plan-2  C8   0.020
 BWD  plan-2  C9   0.020
 BWD  plan-2  O91  0.020
 BWD  plan-2  O92  0.020

