# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:35:03 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  23  15  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   NR6   0  -0.520  -0.6045  -0.4914   0.7175
 BWD  C2    C   CR6   0   0.743  -1.8914  -0.0203   0.5503
 BWD  O2    O   OC    0  -0.466  -2.6629   0.1178   1.4737
 BWD  N3    N   NR16  0  -0.733  -2.2267   0.2789  -0.7444
 BWD  C4    C   CR6   0   0.598  -1.4402   0.1912  -1.8787
 BWD  O4    O   OC    0  -0.431  -1.8675   0.5016  -2.9696
 BWD  C5    C   CR6   0  -0.369  -0.1062  -0.2993  -1.5966
 BWD  BR5   BR  BR    0   0.009   1.0763  -0.4793  -3.0274
 BWD  C6    C   CR16  0   0.109   0.2480  -0.6124  -0.3367
 BWD  C7    C   CH2   0  -0.339  -0.1449  -0.7962   2.0660
 BWD  C8    C   CH1   0  -0.229   0.3310   0.4788   2.7971
 BWD  N8    N   NH2   0  -0.780   1.3546   1.2284   2.1230
 BWD  C9    C   C     0   0.554   0.8090   0.0888   4.1856
 BWD  O91   O   O     0  -0.425   1.9299   0.2415   4.5925
 BWD  O92   O   OH1   0  -0.595  -0.1667  -0.4626   4.8953
 BWD  H3    H   HNR6  0   0.436  -3.1713   0.6210  -0.8781
 BWD  H6    H   HCR6  0   0.339   1.2316  -0.9906  -0.0956
 BWD  H71   H   HCH2  0   0.295   0.6784  -1.5051   1.9747
 BWD  H72   H   HCH2  0   0.295  -0.9483  -1.2943   2.6030
 BWD  H8    H   HCH1  0   0.300  -0.5345   1.1354   2.9314
 BWD  H81   H   HNH2  0   0.352   2.1521   0.6559   1.8783
 BWD  H82   H   HNH2  0   0.365   1.0035   1.6585   1.2790
 BWD  H92O  H   HOH1  0   0.492   0.1614  -0.7320   5.7668

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  1.381  0.020  1.381
 BWD  N1   C6    aromatic  1.361  0.020  1.361
 BWD  N1   C7    single    1.457  0.020  1.457
 BWD  C2   O2    double    1.211  0.020  1.211
 BWD  C2   N3    aromatic  1.370  0.020  1.370
 BWD  N3   C4    aromatic  1.383  0.020  1.383
 BWD  N3   H3    single    0.860  0.020  1.020
 BWD  C4   O4    double    1.212  0.020  1.212
 BWD  C4   C5    aromatic  1.449  0.020  1.449
 BWD  C5   BR5   single    1.865  0.020  1.865
 BWD  C5   C6    aromatic  1.346  0.020  1.346
 BWD  C6   H6    single    0.930  0.020  1.080
 BWD  C7   C8    single    1.545  0.020  1.545
 BWD  C7   H71   single    0.970  0.020  1.090
 BWD  C7   H72   single    0.970  0.020  1.090
 BWD  C8   N8    single    1.437  0.020  1.437
 BWD  C8   C9    single    1.519  0.020  1.519
 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   double    1.202  0.020  1.202
 BWD  C9   O92   single    1.327  0.020  1.327
 BWD  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
 BWD  C7    N1   C6   120.05  3.000
 BWD  C7    N1   C2   118.52  3.000
 BWD  C6    N1   C2   121.35  3.000
 BWD  N3    C2   O2   122.65  3.000
 BWD  N3    C2   N1   114.65  3.000
 BWD  O2    C2   N1   122.70  3.000
 BWD  H3    N3   C4   116.31  3.000
 BWD  H3    N3   C2   115.24  3.000
 BWD  C4    N3   C2   128.44  3.000
 BWD  C5    C4   O4   125.91  3.000
 BWD  C5    C4   N3   112.67  3.000
 BWD  O4    C4   N3   121.43  3.000
 BWD  C6    C5   BR5  121.94  3.000
 BWD  C6    C5   C4   120.22  3.000
 BWD  BR5   C5   C4   117.84  3.000
 BWD  H6    C6   C5   121.99  3.000
 BWD  H6    C6   N1   115.35  3.000
 BWD  C5    C6   N1   122.66  3.000
 BWD  H72   C7   H71  107.54  3.000
 BWD  H72   C7   C8   111.84  3.000
 BWD  H71   C7   C8   110.10  3.000
 BWD  H72   C7   N1   108.66  3.000
 BWD  H71   C7   N1   107.26  3.000
 BWD  C8    C7   N1   111.26  3.000
 BWD  H8    C8   C9   106.90  3.000
 BWD  H8    C8   N8   107.93  3.000
 BWD  C9    C8   N8   109.79  3.000
 BWD  H8    C8   C7   108.03  3.000
 BWD  C9    C8   C7   108.51  3.000
 BWD  N8    C8   C7   115.34  3.000
 BWD  H82   N8   H81  108.23  3.000
 BWD  H82   N8   C8   111.50  3.000
 BWD  H81   N8   C8   112.32  3.000
 BWD  O92   C9   O91  123.89  3.000
 BWD  O92   C9   C8   111.36  3.000
 BWD  O91   C9   C8   124.75  3.000
 BWD  H92O  O92  C9   110.33  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  CONST_18  H92O  O92  C9  C8  180.00   0.0  0
 BWD  Var_01    C8    C7   N1  C2  -82.26  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
 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
 BWD  plan-2  H92O  0.020

