# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 11:41:01 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (5Z)-5-(3-bromobenzylidene)imidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1cccc(c1)\C=C2/NC(=O)NC2=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
 B5H  B5H  (5Z)-5-(3-bromobenzylidene)imidazolidine-2,4-dione  ligand  22  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B5H
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
 B5H  N10  N   NR15  0  -0.746   2.0036   0.9000  -0.3325
 B5H  CA   C   CR5   0   0.254   2.2696  -0.3975   0.0636
 B5H  CB   C   C1    0  -0.353   1.4677  -1.4561   0.2203
 B5H  CG   C   CR6   0   0.160   0.0231  -1.5312   0.0423
 B5H  CD1  C   CR16  0  -0.292  -0.5405  -2.7586  -0.3182
 B5H  CE1  C   CR16  0  -0.235  -1.9056  -2.8794  -0.5096
 B5H  CZ   C   CR16  0  -0.238  -2.7453  -1.7881  -0.3305
 B5H  CE2  C   CR6   0  -0.087  -2.1863  -0.5781   0.0538
 B5H  CD2  C   CR16  0  -0.308  -0.8218  -0.4356   0.2447
 B5H  C    C   CR5   0   0.532   3.7406  -0.4442   0.2926
 B5H  N11  N   NR15  0  -0.719   4.1752   0.8165  -0.0092
 B5H  C2   C   CR5   0   0.666   3.1462   1.6484  -0.4195
 B5H  BR1  BR  BR    0  -0.036  -3.3129   0.9100   0.3395
 B5H  O2   O   O     0  -0.445   3.2469   2.7961  -0.7760
 B5H  O3   O   O     0  -0.415   4.4081  -1.3782   0.6662
 B5H  H10  H   HNR5  0   0.429   1.1303   1.2343  -0.7085
 B5H  HB   H   H     0   0.285   1.9676  -2.3819   0.4803
 B5H  HD1  H   HCR6  0   0.269   0.1016  -3.6189  -0.4576
 B5H  HD2  H   HCR6  0   0.280  -0.4269   0.5082   0.5959
 B5H  HE1  H   HCR6  0   0.276  -2.3282  -3.8318  -0.7995
 B5H  HZ   H   HCR6  0   0.286  -3.8114  -1.8917  -0.4789
 B5H  H11  H   HNR5  0   0.436   5.1386   1.1176   0.0379

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
 B5H  N10  CA   single    1.382  0.020  1.382
 B5H  N10  C2   single    1.369  0.020  1.369
 B5H  CA   CB   double    1.337  0.020  1.337
 B5H  CA   C    single    1.489  0.020  1.489
 B5H  CB   CG   single    1.457  0.020  1.457
 B5H  CG   CD1  aromatic  1.398  0.020  1.398
 B5H  CG   CD2  aromatic  1.398  0.020  1.398
 B5H  CD1  CE1  aromatic  1.384  0.020  1.384
 B5H  CE1  CZ   aromatic  1.389  0.020  1.389
 B5H  CZ   CE2  aromatic  1.387  0.020  1.387
 B5H  CE2  CD2  aromatic  1.385  0.020  1.385
 B5H  CE2  BR1  single    1.888  0.020  1.888
 B5H  C    N11  single    1.367  0.020  1.367
 B5H  C    O3   double    1.207  0.020  1.207
 B5H  N11  C2   single    1.385  0.020  1.385
 B5H  C2   O2   double    1.206  0.020  1.206
 B5H  N10  H10  single    0.860  0.020  1.020
 B5H  CB   HB   single    0.930  0.020  1.080
 B5H  CD1  HD1  single    0.930  0.020  1.080
 B5H  CD2  HD2  single    0.930  0.020  1.080
 B5H  CE1  HE1  single    0.930  0.020  1.080
 B5H  CZ   HZ   single    0.930  0.020  1.080
 B5H  N11  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
 B5H  H10  N10  C2   121.21  3.000
 B5H  H10  N10  CA   125.80  3.000
 B5H  C2   N10  CA   111.76  3.000
 B5H  C    CA   CB   123.32  3.000
 B5H  C    CA   N10  105.28  3.000
 B5H  CB   CA   N10  131.39  3.000
 B5H  HB   CB   CG   116.26  3.000
 B5H  HB   CB   CA   115.32  3.000
 B5H  CG   CB   CA   128.38  3.000
 B5H  CD2  CG   CD1  118.80  3.000
 B5H  CD2  CG   CB   122.74  3.000
 B5H  CD1  CG   CB   118.45  3.000
 B5H  HD1  CD1  CE1  119.86  3.000
 B5H  HD1  CD1  CG   119.47  3.000
 B5H  CE1  CD1  CG   120.67  3.000
 B5H  HE1  CE1  CZ   119.37  3.000
 B5H  HE1  CE1  CD1  119.96  3.000
 B5H  CZ   CE1  CD1  120.67  3.000
 B5H  HZ   CZ   CE2  121.26  3.000
 B5H  HZ   CZ   CE1  120.21  3.000
 B5H  CE2  CZ   CE1  118.53  3.000
 B5H  BR1  CE2  CD2  119.06  3.000
 B5H  BR1  CE2  CZ   119.27  3.000
 B5H  CD2  CE2  CZ   121.66  3.000
 B5H  HD2  CD2  CE2  119.61  3.000
 B5H  HD2  CD2  CG   120.67  3.000
 B5H  CE2  CD2  CG   119.65  3.000
 B5H  O3   C    N11  127.29  3.000
 B5H  O3   C    CA   128.17  3.000
 B5H  N11  C    CA   104.54  3.000
 B5H  H11  N11  C2   122.89  3.000
 B5H  H11  N11  C    124.58  3.000
 B5H  C2   N11  C    112.52  3.000
 B5H  O2   C2   N11  126.66  3.000
 B5H  O2   C2   N10  127.51  3.000
 B5H  N11  C2   N10  105.83  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
 B5H  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 B5H  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 B5H  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 B5H  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 B5H  CONST_05  CD2  CG   CD1  CE1    0.00   0.0  0
 B5H  CONST_06  CD2  CE2  CZ   CE1    0.00   0.0  0
 B5H  CONST_07  N11  C    CA   N10    0.00   0.0  0
 B5H  CONST_08  C    N11  C2   N10    0.00   0.0  0
 B5H  CONST_09  N11  C2   N10  CA     0.00   0.0  0
 B5H  CONST_10  C2   N11  C    CA     0.00   0.0  0
 B5H  CONST_11  C2   N10  CA   C      0.00   0.0  0
 B5H  CONST_12  CE1  CD1  CG   CB   180.00   0.0  0
 B5H  CONST_13  CE2  CD2  CG   CB   180.00   0.0  0
 B5H  CONST_14  BR1  CE2  CD2  CG   180.00   0.0  0
 B5H  CONST_15  BR1  CE2  CZ   CE1  180.00   0.0  0
 B5H  CONST_16  O2   C2   N10  CA   180.00   0.0  0
 B5H  CONST_17  O2   C2   N11  C    180.00   0.0  0
 B5H  CONST_18  O3   C    N11  C2   180.00   0.0  0
 B5H  CONST_19  HE1  CE1  CD1  CG   180.00   0.0  0
 B5H  CONST_20  HD2  CD2  CG   CD1  180.00   0.0  0
 B5H  CONST_21  HZ   CZ   CE1  CD1  180.00   0.0  0
 B5H  CONST_22  HD1  CD1  CE1  CZ   180.00   0.0  0
 B5H  CONST_23  H11  N11  C2   N10  180.00   0.0  0
 B5H  CONST_24  H10  N10  CA   C    180.00   0.0  0
 B5H  Var_01    CG   CB   CA   N10   -1.80  30.0  2
 B5H  Var_02    CD1  CG   CB   CA   152.41  30.0  2

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
 B5H  plan-1  N10  0.020
 B5H  plan-1  CA   0.020
 B5H  plan-1  CB   0.020
 B5H  plan-1  C    0.020
 B5H  plan-1  N11  0.020
 B5H  plan-1  C2   0.020
 B5H  plan-1  O2   0.020
 B5H  plan-1  O3   0.020
 B5H  plan-1  H10  0.020
 B5H  plan-1  H11  0.020
 B5H  plan-2  CB   0.020
 B5H  plan-2  CG   0.020
 B5H  plan-2  CD1  0.020
 B5H  plan-2  CE1  0.020
 B5H  plan-2  CZ   0.020
 B5H  plan-2  CE2  0.020
 B5H  plan-2  CD2  0.020
 B5H  plan-2  BR1  0.020
 B5H  plan-2  HD1  0.020
 B5H  plan-2  HD2  0.020
 B5H  plan-2  HE1  0.020
 B5H  plan-2  HZ   0.020

