# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 17:47:14 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: 5-bromo-6-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)ccc1Br
#
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
 4JO  4JO  5-bromo-6-methylpyridin-2-amine  ligand  16  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4JO
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
 4JO  BR  BR  BR    0  -0.059  -1.9829   0.2346  -0.1046
 4JO  C5  C   CR6   0  -0.237  -0.0949   0.2209  -0.0683
 4JO  C1  C   CR6   0   0.277   0.6163  -0.9744  -0.0250
 4JO  C   C   CH3   0  -0.731  -0.0531  -2.3139  -0.0019
 4JO  C4  C   CR16  0  -0.110   0.5962   1.4283  -0.0802
 4JO  C3  C   CR16  0  -0.387   1.9706   1.4179  -0.0532
 4JO  C2  C   CR6   0   0.454   2.6233   0.1748  -0.0135
 4JO  N   N   N     0  -0.478   1.9471  -0.9714   0.0018
 4JO  N1  N   NH2   0  -0.831   3.9806   0.0925  -0.0312
 4JO  H1  H   HCH3  0   0.254  -0.6740  -2.4665  -0.8861
 4JO  H2  H   HCH3  0   0.256   0.6966  -3.1006   0.0316
 4JO  H3  H   HCH3  0   0.254  -0.7034  -2.4211   0.8679
 4JO  H4  H   HCR6  0   0.285   0.0672   2.3721  -0.1099
 4JO  H5  H   HCR6  0   0.275   2.5324   2.3426  -0.0618
 4JO  H6  H   HNH2  0   0.394   4.5073   0.9045   0.2425
 4JO  H7  H   HNH2  0   0.385   4.3854  -0.7849   0.2509

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
 4JO  C   C1  single    1.498  0.020  1.498
 4JO  N   C1  aromatic  1.331  0.020  1.331
 4JO  N   C2  aromatic  1.331  0.020  1.331
 4JO  C1  C5  aromatic  1.392  0.020  1.392
 4JO  N1  C2  single    1.360  0.020  1.360
 4JO  C2  C3  aromatic  1.405  0.020  1.405
 4JO  C5  BR  single    1.888  0.020  1.888
 4JO  C5  C4  aromatic  1.391  0.020  1.391
 4JO  C3  C4  aromatic  1.375  0.020  1.375
 4JO  C   H1  single    0.970  0.020  1.090
 4JO  C   H2  single    0.970  0.020  1.090
 4JO  C   H3  single    0.970  0.020  1.090
 4JO  C4  H4  single    0.930  0.020  1.080
 4JO  C3  H5  single    0.930  0.020  1.080
 4JO  N1  H6  single    0.890  0.020  1.040
 4JO  N1  H7  single    0.890  0.020  1.040

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
 4JO  C4  C5  C1  119.46  3.000
 4JO  C4  C5  BR  119.36  3.000
 4JO  C1  C5  BR  121.19  3.000
 4JO  N   C1  C   116.65  3.000
 4JO  N   C1  C5  120.64  3.000
 4JO  C   C1  C5  122.70  3.000
 4JO  H3  C   H2  108.38  3.000
 4JO  H3  C   H1  107.04  3.000
 4JO  H2  C   H1  108.42  3.000
 4JO  H3  C   C1  111.50  3.000
 4JO  H2  C   C1  109.84  3.000
 4JO  H1  C   C1  111.53  3.000
 4JO  H4  C4  C3  119.72  3.000
 4JO  H4  C4  C5  120.94  3.000
 4JO  C3  C4  C5  119.34  3.000
 4JO  H5  C3  C2  121.02  3.000
 4JO  H5  C3  C4  120.83  3.000
 4JO  C2  C3  C4  118.15  3.000
 4JO  N1  C2  N   117.07  3.000
 4JO  N1  C2  C3  121.14  3.000
 4JO  N   C2  C3  121.76  3.000
 4JO  C2  N   C1  120.64  3.000
 4JO  H7  N1  H6  114.63  3.000
 4JO  H7  N1  C2  116.78  3.000
 4JO  H6  N1  C2  118.05  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
 4JO  CONST_01  C2  N   C1  C5    0.00   0.0  0
 4JO  CONST_02  C2  C3  C4  C5    0.00   0.0  0
 4JO  CONST_03  C3  C2  N   C1    0.00   0.0  0
 4JO  CONST_04  C3  C4  C5  C1    0.00   0.0  0
 4JO  CONST_05  N   C1  C5  C4    0.00   0.0  0
 4JO  CONST_06  N   C2  C3  C4    0.00   0.0  0
 4JO  CONST_07  N   C1  C5  BR  180.00   0.0  0
 4JO  CONST_08  C3  C4  C5  BR  180.00   0.0  0
 4JO  CONST_09  N1  C2  N   C1  180.00   0.0  0
 4JO  CONST_10  C2  N   C1  C   180.00   0.0  0
 4JO  CONST_11  C4  C5  C1  C   180.00   0.0  0
 4JO  CONST_12  N1  C2  C3  C4  180.00   0.0  0
 4JO  CONST_13  H5  C3  C4  C5  180.00   0.0  0
 4JO  CONST_14  H4  C4  C5  C1  180.00   0.0  0
 4JO  Var_01    H1  C   C1  C5   59.77  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
 4JO  plan-1  BR  0.020
 4JO  plan-1  C5  0.020
 4JO  plan-1  C1  0.020
 4JO  plan-1  C   0.020
 4JO  plan-1  C4  0.020
 4JO  plan-1  C3  0.020
 4JO  plan-1  C2  0.020
 4JO  plan-1  N   0.020
 4JO  plan-1  N1  0.020
 4JO  plan-1  H4  0.020
 4JO  plan-1  H5  0.020
 4JO  plan-2  C2  0.020
 4JO  plan-2  N1  0.020
 4JO  plan-2  H6  0.020
 4JO  plan-2  H7  0.020

