# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 12:03:04 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 4-(2-chloro-4-nitrophenyl)-6-methylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(nc(N)n1)c2ccc(cc2Cl)[N+]([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
 4ES  4ES  4-(2-chloro-4-nitrophenyl)-6-methylpyrimidin-2-amine  ligand  27  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4ES
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
 4ES  O2   O   O     -1  -0.369   4.9135  -1.1589  -0.6837
 4ES  N4   N   N      1   0.331   4.3534  -0.2940  -0.0554
 4ES  O1   O   O      0  -0.370   4.9218   0.5799   0.5536
 4ES  C9   C   CR6    0   0.246   2.8958  -0.3068  -0.0320
 4ES  C8   C   CR16   0  -0.242   2.2142  -1.2757  -0.7480
 4ES  C7   C   CR16   0  -0.295   0.8317  -1.2646  -0.7136
 4ES  C10  C   CR16   0  -0.210   2.2348   0.6529   0.7166
 4ES  C11  C   CR6    0  -0.096   0.8515   0.6430   0.7297
 4ES  CL   CL  CL     0  -0.095   0.0472   1.8097   1.7127
 4ES  C6   C   CR6    0   0.139   0.1265  -0.3075   0.0106
 4ES  C4   C   CR6    0   0.259  -1.3551  -0.3343  -0.0126
 4ES  C3   C   CR16   0  -0.398  -2.0386  -1.4802   0.3614
 4ES  N1   N   N      0  -0.457  -1.9663   0.7642  -0.4231
 4ES  C5   C   CR6    0   0.532  -3.3018   0.7210  -0.4554
 4ES  N2   N   NH2    0  -0.825  -3.9431   1.8412  -0.8340
 4ES  N3   N   N      0  -0.471  -4.0554  -0.3320  -0.1213
 4ES  C2   C   CR6    0   0.293  -3.4286  -1.4269   0.2820
 4ES  C1   C   CH3    0  -0.724  -4.2735  -2.6079   0.6339
 4ES  H8   H   HCR6   0   0.307   2.7338  -2.0254  -1.3256
 4ES  H7   H   HCR6   0   0.288   0.2845  -2.0107  -1.2739
 4ES  H9   H   HCR6   0   0.321   2.7758   1.3957   1.2844
 4ES  H4   H   HCR6   0   0.273  -1.5247  -2.3656   0.7063
 4ES  H5   H   HNH2   0   0.397  -4.9271   1.7991  -1.0329
 4ES  H6   H   HNH2   0   0.397  -3.4176   2.5911  -1.2475
 4ES  H2   H   HCH3   0   0.263  -4.7135  -3.0337  -0.2695
 4ES  H1   H   HCH3   0   0.250  -3.6944  -3.3862   1.1261
 4ES  H3   H   HCH3   0   0.258  -5.0958  -2.3139   1.2855

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
 4ES  CL   C11  single    1.725  0.020  1.725
 4ES  N2   C5   single    1.345  0.020  1.345
 4ES  C5   N3   aromatic  1.337  0.020  1.337
 4ES  C5   N1   aromatic  1.337  0.020  1.337
 4ES  N3   C2   aromatic  1.324  0.020  1.324
 4ES  N1   C4   aromatic  1.322  0.020  1.322
 4ES  C2   C1   single    1.494  0.020  1.494
 4ES  C2   C3   aromatic  1.393  0.020  1.393
 4ES  C11  C10  aromatic  1.383  0.020  1.383
 4ES  C11  C6   aromatic  1.395  0.020  1.395
 4ES  C4   C3   aromatic  1.386  0.020  1.386
 4ES  C4   C6   single    1.482  0.020  1.482
 4ES  C10  C9   aromatic  1.385  0.020  1.385
 4ES  C6   C7   aromatic  1.392  0.020  1.392
 4ES  O2   N4   single    1.207  0.020  1.207
 4ES  C9   N4   single    1.458  0.020  1.458
 4ES  C9   C8   aromatic  1.384  0.020  1.384
 4ES  C7   C8   aromatic  1.383  0.020  1.383
 4ES  N4   O1   double    1.207  0.020  1.207
 4ES  C8   H8   single    0.930  0.020  1.080
 4ES  C7   H7   single    0.930  0.020  1.080
 4ES  C10  H9   single    0.930  0.020  1.080
 4ES  C3   H4   single    0.930  0.020  1.080
 4ES  N2   H5   single    0.890  0.020  1.040
 4ES  N2   H6   single    0.890  0.020  1.040
 4ES  C1   H2   single    0.970  0.020  1.090
 4ES  C1   H1   single    0.970  0.020  1.090
 4ES  C1   H3   single    0.970  0.020  1.090

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
 4ES  C9   N4   O1   117.97  3.000
 4ES  O1   N4   O2   124.25  3.000
 4ES  C9   N4   O2   117.78  3.000
 4ES  C10  C9   C8   121.98  3.000
 4ES  C8   C9   N4   119.35  3.000
 4ES  C10  C9   N4   118.67  3.000
 4ES  H8   C8   C7   120.00  3.000
 4ES  H8   C8   C9   121.72  3.000
 4ES  C7   C8   C9   118.28  3.000
 4ES  H7   C7   C6   119.17  3.000
 4ES  H7   C7   C8   119.16  3.000
 4ES  C6   C7   C8   121.66  3.000
 4ES  H9   C10  C11  120.05  3.000
 4ES  H9   C10  C9   121.44  3.000
 4ES  C11  C10  C9   118.51  3.000
 4ES  C6   C11  CL   120.82  3.000
 4ES  C6   C11  C10  121.31  3.000
 4ES  CL   C11  C10  117.83  3.000
 4ES  C4   C6   C11  122.68  3.000
 4ES  C4   C6   C7   119.07  3.000
 4ES  C11  C6   C7   118.25  3.000
 4ES  N1   C4   C3   122.87  3.000
 4ES  C3   C4   C6   120.25  3.000
 4ES  N1   C4   C6   116.87  3.000
 4ES  H4   C3   C2   121.61  3.000
 4ES  H4   C3   C4   121.96  3.000
 4ES  C2   C3   C4   116.43  3.000
 4ES  C5   N1   C4   116.26  3.000
 4ES  N3   C5   N2   117.22  3.000
 4ES  N3   C5   N1   125.62  3.000
 4ES  N2   C5   N1   117.14  3.000
 4ES  H6   N2   H5   117.52  3.000
 4ES  H6   N2   C5   119.21  3.000
 4ES  H5   N2   C5   119.19  3.000
 4ES  C2   N3   C5   117.41  3.000
 4ES  C1   C2   N3   117.23  3.000
 4ES  C1   C2   C3   121.36  3.000
 4ES  N3   C2   C3   121.41  3.000
 4ES  H3   C1   H1   108.92  3.000
 4ES  H3   C1   H2   107.22  3.000
 4ES  H1   C1   H2   108.06  3.000
 4ES  H3   C1   C2   110.75  3.000
 4ES  H1   C1   C2   111.79  3.000
 4ES  H2   C1   C2   109.96  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
 4ES  CONST_01  C6   C11  C10  C9      0.00   0.0  0
 4ES  CONST_02  C6   C7   C8   C9      0.00   0.0  0
 4ES  CONST_03  C11  C10  C9   C8      0.00   0.0  0
 4ES  CONST_04  C11  C6   C7   C8      0.00   0.0  0
 4ES  CONST_05  C4   C6   C7   C8    180.00   0.0  0
 4ES  CONST_06  C10  C11  C6   C7      0.00   0.0  0
 4ES  CONST_09  C10  C9   C8   C7      0.00   0.0  0
 4ES  CONST_10  C4   C6   C11  C10   180.00   0.0  0
 4ES  CONST_13  C5   N1   C4   C6    180.00   0.0  0
 4ES  CONST_14  C2   C3   C4   C6    180.00   0.0  0
 4ES  CONST_15  N3   C5   N1   C4      0.00   0.0  0
 4ES  CONST_16  N3   C2   C3   C4      0.00   0.0  0
 4ES  CONST_17  C5   N3   C2   C3      0.00   0.0  0
 4ES  CONST_18  C5   N1   C4   C3      0.00   0.0  0
 4ES  CONST_19  C2   N3   C5   N1      0.00   0.0  0
 4ES  CONST_20  C2   C3   C4   N1      0.00   0.0  0
 4ES  CONST_21  C11  C10  C9   N4    180.00   0.0  0
 4ES  CONST_22  C7   C8   C9   N4    180.00   0.0  0
 4ES  CONST_23  CL   C11  C10  C9    180.00   0.0  0
 4ES  CONST_24  CL   C11  C6   C7    180.00   0.0  0
 4ES  CONST_25  C4   C6   C11  CL      0.00   0.0  0
 4ES  CONST_26  N2   C5   N1   C4    180.00   0.0  0
 4ES  CONST_27  C1   C2   C3   C4    180.00   0.0  0
 4ES  CONST_28  C1   C2   N3   C5    180.00   0.0  0
 4ES  CONST_29  C2   N3   C5   N2    180.00   0.0  0
 4ES  CONST_30  H7   C7   C8   C9    180.00   0.0  0
 4ES  CONST_31  H9   C10  C9   C8    180.00   0.0  0
 4ES  CONST_32  H8   C8   C9   C10   180.00   0.0  0
 4ES  CONST_33  H4   C3   C4   C6      0.00   0.0  0
 4ES  CONST_34  C10  C9   N4   O2    180.00   0.0  0
 4ES  CONST_35  C8   C9   N4   O2      0.00   0.0  0
 4ES  CONST_36  C10  C9   N4   O1      0.00   0.0  0
 4ES  CONST_37  C8   C9   N4   O1    180.00   0.0  0
 4ES  CONST_38  H5   N2   C5   N1    180.00   0.0  0
 4ES  CONST_39  H6   N2   C5   N1      0.00   0.0  0
 4ES  Var_01    H2   C1   C2   C3   -108.66  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
 4ES  plan-1  N4   0.020
 4ES  plan-1  C9   0.020
 4ES  plan-1  C8   0.020
 4ES  plan-1  C7   0.020
 4ES  plan-1  C10  0.020
 4ES  plan-1  C11  0.020
 4ES  plan-1  CL   0.020
 4ES  plan-1  C6   0.020
 4ES  plan-1  C4   0.020
 4ES  plan-1  H8   0.020
 4ES  plan-1  H7   0.020
 4ES  plan-1  H9   0.020
 4ES  plan-2  C6   0.020
 4ES  plan-2  C4   0.020
 4ES  plan-2  C3   0.020
 4ES  plan-2  N1   0.020
 4ES  plan-2  C5   0.020
 4ES  plan-2  N2   0.020
 4ES  plan-2  N3   0.020
 4ES  plan-2  C2   0.020
 4ES  plan-2  C1   0.020
 4ES  plan-2  H4   0.020
 4ES  plan-3  O2   0.020
 4ES  plan-3  N4   0.020
 4ES  plan-3  O1   0.020
 4ES  plan-3  C9   0.020
 4ES  plan-4  C5   0.020
 4ES  plan-4  N2   0.020
 4ES  plan-4  H5   0.020
 4ES  plan-4  H6   0.020

