# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:07:03 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 4-[(5-bromopyridin-2-yl)amino]-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)Nc1ccc(Br)cn1
#
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
 SX2  SX2  '4-[(5-bromopyridin-2-yl)amino]-4-oxobutanoic acid'  ligand  23  15  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SX2
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
 SX2  BR1  BR  BR     0  -0.032  -4.7790  -0.1079   0.1249
 SX2  C8   C   CR6    0  -0.202  -2.9149  -0.3557   0.0920
 SX2  C9   C   CR16   0  -0.043  -2.0640   0.7308   0.1773
 SX2  N2   N   N      0  -0.420  -0.7425   0.6133   0.1579
 SX2  C7   C   CR16   0  -0.111  -2.3653  -1.6281  -0.0190
 SX2  C6   C   CR16   0  -0.397  -0.9944  -1.7506  -0.0415
 SX2  C5   C   CR6    0   0.536  -0.2101  -0.5919   0.0489
 SX2  N1   N   NH1    0  -0.733   1.1656  -0.7453   0.0287
 SX2  C4   C   C      0   0.554   2.1581   0.2072   0.0285
 SX2  O3   O   O      0  -0.441   1.9456   1.3991   0.0388
 SX2  C3   C   CH2    0  -0.599   3.5426  -0.4038   0.0133
 SX2  C2   C   CH2    0  -0.582   4.6617   0.6186   0.0015
 SX2  C1   C   C      0   0.419   6.0800   0.0173  -0.0151
 SX2  O2   O   OC    -1  -0.629   7.0148   0.8444  -0.0182
 SX2  O1   O   O      0  -0.606   6.1894  -1.2244  -0.0260
 SX2  H9   H   HCR6   0   0.280  -2.4537   1.7390   0.2658
 SX2  H7   H   HCR6   0   0.296  -2.9883  -2.5095  -0.0897
 SX2  H6   H   HCR6   0   0.290  -0.5363  -2.7271  -0.1304
 SX2  HN1  H   HNH1   0   0.423   1.4834  -1.7027  -0.0100
 SX2  H3   H   HCH2   0   0.267   3.6335  -1.0630   0.8819
 SX2  H3A  H   HCH2   0   0.266   3.6179  -1.0646  -0.8553
 SX2  H2   H   HCH2   0   0.232   4.5616   1.2777  -0.8660
 SX2  H2A  H   HCH2   0   0.232   4.5804   1.2763   0.8719

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
 SX2  BR1  C8   single    1.881  0.020  1.881
 SX2  C8   C7   aromatic  1.391  0.020  1.391
 SX2  C8   C9   aromatic  1.383  0.020  1.383
 SX2  C9   N2   aromatic  1.327  0.020  1.327
 SX2  C9   H9   single    0.930  0.020  1.080
 SX2  N2   C5   aromatic  1.322  0.020  1.322
 SX2  C7   C6   aromatic  1.377  0.020  1.377
 SX2  C7   H7   single    0.930  0.020  1.080
 SX2  C6   C5   aromatic  1.402  0.020  1.402
 SX2  C6   H6   single    0.930  0.020  1.080
 SX2  C5   N1   single    1.384  0.020  1.384
 SX2  C4   N1   single    1.376  0.020  1.376
 SX2  N1   HN1  single    0.860  0.020  1.020
 SX2  O3   C4   double    1.211  0.020  1.211
 SX2  C4   C3   single    1.513  0.020  1.513
 SX2  C3   C2   single    1.516  0.020  1.516
 SX2  C3   H3   single    0.970  0.020  1.090
 SX2  C3   H3A  single    0.970  0.020  1.090
 SX2  C1   C2   single    1.541  0.020  1.541
 SX2  C2   H2   single    0.970  0.020  1.090
 SX2  C2   H2A  single    0.970  0.020  1.090
 SX2  O1   C1   deloc     1.246  0.020  1.246
 SX2  C1   O2   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
 SX2  C7   C8  C9   118.73  3.000
 SX2  C9   C8  BR1  120.36  3.000
 SX2  C7   C8  BR1  120.91  3.000
 SX2  H9   C9  N2   116.20  3.000
 SX2  H9   C9  C8   120.95  3.000
 SX2  N2   C9  C8   122.85  3.000
 SX2  C5   N2  C9   118.88  3.000
 SX2  H7   C7  C6   120.01  3.000
 SX2  H7   C7  C8   121.55  3.000
 SX2  C6   C7  C8   118.45  3.000
 SX2  H6   C6  C5   120.94  3.000
 SX2  H6   C6  C7   120.21  3.000
 SX2  C5   C6  C7   118.85  3.000
 SX2  N1   C5  C6   117.60  3.000
 SX2  N1   C5  N2   120.16  3.000
 SX2  C6   C5  N2   122.24  3.000
 SX2  HN1  N1  C4   115.43  3.000
 SX2  HN1  N1  C5   114.74  3.000
 SX2  C4   N1  C5   129.81  3.000
 SX2  C3   C4  O3   123.92  3.000
 SX2  C3   C4  N1   112.37  3.000
 SX2  O3   C4  N1   123.71  3.000
 SX2  H3A  C3  H3   105.11  3.000
 SX2  H3A  C3  C2   110.51  3.000
 SX2  H3   C3  C2   110.56  3.000
 SX2  H3A  C3  C4   108.35  3.000
 SX2  H3   C3  C4   108.14  3.000
 SX2  C2   C3  C4   113.78  3.000
 SX2  H2A  C2  H2   105.18  3.000
 SX2  H2A  C2  C1   108.16  3.000
 SX2  H2   C2  C1   108.11  3.000
 SX2  H2A  C2  C3   110.15  3.000
 SX2  H2   C2  C3   110.18  3.000
 SX2  C1   C2  C3   114.61  3.000
 SX2  O1   C1  O2   126.46  3.000
 SX2  O2   C1  C2   115.52  3.000
 SX2  O1   C1  C2   118.02  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
 SX2  CONST_01  C5   C6  C7  C8      0.00   0.0  0
 SX2  CONST_02  C5   N2  C9  C8      0.00   0.0  0
 SX2  CONST_03  C6   C7  C8  C9      0.00   0.0  0
 SX2  CONST_04  C6   C5  N2  C9      0.00   0.0  0
 SX2  CONST_05  C7   C8  C9  N2      0.00   0.0  0
 SX2  CONST_06  C7   C6  C5  N2      0.00   0.0  0
 SX2  CONST_07  C6   C7  C8  BR1   180.00   0.0  0
 SX2  CONST_08  N2   C9  C8  BR1   180.00   0.0  0
 SX2  CONST_09  N1   C5  N2  C9    180.00   0.0  0
 SX2  CONST_10  N1   C5  C6  C7    180.00   0.0  0
 SX2  CONST_11  H6   C6  C7  C8    180.00   0.0  0
 SX2  CONST_12  H7   C7  C8  C9    180.00   0.0  0
 SX2  CONST_13  H9   C9  C8  C7    180.00   0.0  0
 SX2  CONST_14  C4   N1  C5  N2      0.00   0.0  0
 SX2  CONST_15  C4   N1  C5  C6    180.00   0.0  0
 SX2  CONST_16  HN1  N1  C5  N2    180.00   0.0  0
 SX2  CONST_17  O3   C4  N1  C5      0.00   0.0  0
 SX2  CONST_18  C3   C4  N1  C5    180.00   0.0  0
 SX2  Var_01    C2   C3  C4  N1    179.54  30.0  3
 SX2  Var_02    C1   C2  C3  C4   -179.95  30.0  3
 SX2  Var_03    O1   C1  C2  C3      0.45  30.0  3

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
 SX2  plan-1  BR1  0.020
 SX2  plan-1  C8   0.020
 SX2  plan-1  C9   0.020
 SX2  plan-1  N2   0.020
 SX2  plan-1  C7   0.020
 SX2  plan-1  C6   0.020
 SX2  plan-1  C5   0.020
 SX2  plan-1  N1   0.020
 SX2  plan-1  H9   0.020
 SX2  plan-1  H7   0.020
 SX2  plan-1  H6   0.020
 SX2  plan-2  C5   0.020
 SX2  plan-2  N1   0.020
 SX2  plan-2  C4   0.020
 SX2  plan-2  O3   0.020
 SX2  plan-2  C3   0.020
 SX2  plan-2  HN1  0.020
 SX2  plan-3  C2   0.020
 SX2  plan-3  C1   0.020
 SX2  plan-3  O2   0.020
 SX2  plan-3  O1   0.020

