# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 05:58:03 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 5-(2-bromoethyl)-5-ethyl-1,3-diazinane-2,4,6-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC1(CCBr)C(=O)NC(=O)NC1=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
 6JW  6JW  5-(2-bromoethyl)-5-ethyl-1,3-diazinane-2,4,6-trione  ligand  25  14  .  2021-08-05  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6JW
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
 6JW  C    C   CH3   0  -0.691   3.0873   2.1385   0.0632
 6JW  O    O   O     0  -0.408   0.9040   0.3923   2.3810
 6JW  N    N   NH1   0  -0.705   2.1010  -1.0408   1.1411
 6JW  BR   BR  BR    0  -0.117  -3.3681   0.0936  -0.0490
 6JW  C1   C   CH2   0  -0.403   1.5665   2.1752   0.0712
 6JW  C2   C   CT    0  -0.432   0.8731   0.7867   0.0279
 6JW  C3   C   CH2   0  -0.391  -0.6533   1.0099   0.0285
 6JW  C4   C   CH2   0  -0.533  -1.4409  -0.2829  -0.0567
 6JW  C5   C   C     0   0.623   1.2723   0.0383   1.2861
 6JW  C6   C   C     0   0.699   2.5526  -1.5896  -0.0354
 6JW  C7   C   C     0   0.622   1.2841   0.1153  -1.2696
 6JW  O2   O   O     0  -0.409   0.9276   0.5366  -2.3444
 6JW  N1   N   NH1   0  -0.704   2.1057  -0.9751  -1.1811
 6JW  O1   O   O     0  -0.434   3.2830  -2.5483  -0.0615
 6JW  H1   H   HCH3  0   0.259   3.4746   3.1559   0.0998
 6JW  H2   H   HCH3  0   0.236   3.4973   1.6084   0.9236
 6JW  H3   H   HCH3  0   0.236   3.4873   1.6763  -0.8402
 6JW  H4   H   HNH1  0   0.437   2.3990  -1.5121   1.9877
 6JW  H5   H   HCH2  0   0.264   1.2086   2.6891   0.9646
 6JW  H6   H   HCH2  0   0.264   1.2011   2.7440  -0.7846
 6JW  H7   H   HCH2  0   0.278  -0.9139   1.5482   0.9397
 6JW  H8   H   HCH2  0   0.277  -0.8991   1.6580  -0.8128
 6JW  H9   H   HCH2  0   0.297  -1.2629  -0.9426   0.7923
 6JW  H10  H   HCH2  0   0.298  -1.2475  -0.8334  -0.9765
 6JW  H11  H   HNH1  0   0.437   2.4034  -1.4013  -2.0511

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
 6JW  BR  C4   single  1.964  0.020  1.964
 6JW  C4  C3   single  1.516  0.020  1.516
 6JW  O   C5   double  1.208  0.020  1.208
 6JW  C   C1   single  1.521  0.020  1.521
 6JW  C3  C2   single  1.543  0.020  1.543
 6JW  C5  C2   single  1.517  0.020  1.517
 6JW  C5  N    single  1.368  0.020  1.368
 6JW  C1  C2   single  1.553  0.020  1.553
 6JW  C2  C7   single  1.518  0.020  1.518
 6JW  N   C6   single  1.374  0.020  1.374
 6JW  C7  O2   double  1.208  0.020  1.208
 6JW  C7  N1   single  1.368  0.020  1.368
 6JW  C6  N1   single  1.375  0.020  1.375
 6JW  C6  O1   double  1.206  0.020  1.206
 6JW  C   H1   single  0.970  0.020  1.090
 6JW  C   H2   single  0.970  0.020  1.090
 6JW  C   H3   single  0.970  0.020  1.090
 6JW  N   H4   single  0.860  0.020  1.020
 6JW  C1  H5   single  0.970  0.020  1.090
 6JW  C1  H6   single  0.970  0.020  1.090
 6JW  C3  H7   single  0.970  0.020  1.090
 6JW  C3  H8   single  0.970  0.020  1.090
 6JW  C4  H9   single  0.970  0.020  1.090
 6JW  C4  H10  single  0.970  0.020  1.090
 6JW  N1  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
 6JW  H3   C   H2  108.03  3.000
 6JW  H3   C   H1  107.05  3.000
 6JW  H2   C   H1  107.09  3.000
 6JW  H3   C   C1  112.41  3.000
 6JW  H2   C   C1  112.55  3.000
 6JW  H1   C   C1  109.43  3.000
 6JW  H4   N   C6  115.63  3.000
 6JW  H4   N   C5  117.14  3.000
 6JW  C6   N   C5  127.20  3.000
 6JW  H6   C1  H5  106.68  3.000
 6JW  H6   C1  C2  107.15  3.000
 6JW  H5   C1  C2  107.31  3.000
 6JW  H6   C1  C   110.08  3.000
 6JW  H5   C1  C   110.09  3.000
 6JW  C2   C1  C   115.13  3.000
 6JW  C7   C2  C5  114.80  3.000
 6JW  C7   C2  C3  109.41  3.000
 6JW  C5   C2  C3  109.35  3.000
 6JW  C7   C2  C1  107.37  3.000
 6JW  C5   C2  C1  107.49  3.000
 6JW  C3   C2  C1  108.21  3.000
 6JW  H8   C3  H7  107.32  3.000
 6JW  H8   C3  C4  110.27  3.000
 6JW  H7   C3  C4  110.12  3.000
 6JW  H8   C3  C2  107.99  3.000
 6JW  H7   C3  C2  107.96  3.000
 6JW  C4   C3  C2  112.99  3.000
 6JW  H10  C4  H9  108.84  3.000
 6JW  H10  C4  C3  112.72  3.000
 6JW  H9   C4  C3  112.80  3.000
 6JW  H10  C4  BR  105.93  3.000
 6JW  H9   C4  BR  105.87  3.000
 6JW  C3   C4  BR  110.25  3.000
 6JW  C2   C5  N   117.41  3.000
 6JW  N    C5  O   120.78  3.000
 6JW  C2   C5  O   121.78  3.000
 6JW  O1   C6  N1  122.30  3.000
 6JW  O1   C6  N   122.36  3.000
 6JW  N1   C6  N   115.34  3.000
 6JW  N1   C7  O2  120.84  3.000
 6JW  N1   C7  C2  117.38  3.000
 6JW  O2   C7  C2  121.76  3.000
 6JW  H11  N1  C7  117.13  3.000
 6JW  H11  N1  C6  115.59  3.000
 6JW  C7   N1  C6  127.25  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
 6JW  CONST_01  C7   N1  C6  N      0.00   0.0  0
 6JW  CONST_02  C6   N   C5  C2     0.00   0.0  0
 6JW  CONST_03  N1   C6  N   C5     0.00   0.0  0
 6JW  CONST_04  C6   N   C5  O    180.00   0.0  0
 6JW  CONST_05  O1   C6  N   C5   180.00   0.0  0
 6JW  CONST_06  O1   C6  N1  C7   180.00   0.0  0
 6JW  CONST_07  H11  N1  C6  N    180.00   0.0  0
 6JW  CONST_08  H4   N   C5  C2   180.00   0.0  0
 6JW  Var_01    O2   C7  N1  C6  -177.61  30.0  1
 6JW  Var_02    C2   C3  C4  BR   179.96  30.0  3
 6JW  Var_03    H1   C   C1  C2  -179.76  30.0  3

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
 6JW  chir_01  C2  C5  C1  C7  negativ

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
 6JW  plan-1  C2   0.020
 6JW  plan-1  C7   0.020
 6JW  plan-1  O2   0.020
 6JW  plan-1  N1   0.020
 6JW  plan-2  O    0.020
 6JW  plan-2  N    0.020
 6JW  plan-2  C2   0.020
 6JW  plan-2  C5   0.020
 6JW  plan-2  C6   0.020
 6JW  plan-2  C7   0.020
 6JW  plan-2  N1   0.020
 6JW  plan-2  O1   0.020
 6JW  plan-2  H4   0.020
 6JW  plan-2  H11  0.020

