# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 09:14:43 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-amino-4-[(3,5-dibromophenyl)amino]-6-methylpyrimidin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Nc2cc(Br)cc(Br)c2)nc(N)[nH+]1
#
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
 DY7  DY7  2-amino-4-[(3,5-dibromophenyl)amino]-6-methylpyrimidin-1-ium  ligand  28  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DY7
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
 DY7  C15   C   CR6   0   0.442  -4.8949   1.4458   0.1797
 DY7  C11   C   CR6   0  -0.094   1.3793  -1.0775  -0.2108
 DY7  C10   C   CR16  0  -0.230   2.5024  -0.3333   0.1103
 DY7  C14   C   CR16  0  -0.494  -3.6343   1.8575   0.4541
 DY7  N17   N   NR16  1  -0.693  -5.0679   0.1967  -0.3347
 DY7  C02   C   CR6   0   0.756  -4.0188  -0.6215  -0.5779
 DY7  N03   N   N     0  -0.526  -2.7765  -0.2481  -0.3221
 DY7  C04   C   CR6   0   0.638  -2.5688   0.9554   0.1840
 DY7  N05   N   NH1   0  -0.775  -1.3201   1.3660   0.4612
 DY7  C06   C   CR6   0   0.392  -0.0841   0.7367   0.3151
 DY7  C07   C   CR16  0  -0.329   1.0299   1.5132   0.6460
 DY7  C08   C   CR6   0  -0.095   2.2948   0.9698   0.5402
 DY7  BR9   BR  BR    0  -0.013   3.7851   2.0297   0.9901
 DY7  C13   C   CR16  0  -0.271   0.0899  -0.5767  -0.1190
 DY7  C16   C   CH3   0  -0.731  -6.1164   2.2627   0.3890
 DY7  H101  H   HCR6  0   0.303   3.4973  -0.7476   0.0286
 DY7  H141  H   HCR6  0   0.311  -3.4513   2.8402   0.8630
 DY7  H011  H   HNH2  0   0.434  -5.1724  -2.1605  -1.2835
 DY7  H012  H   HNH2  0   0.434  -3.4684  -2.4295  -1.2714
 DY7  H051  H   HNH1  0   0.440  -1.2634   2.3010   0.8376
 DY7  H071  H   HCR6  0   0.306   0.8945   2.5345   0.9799
 DY7  H131  H   HCR6  0   0.319  -0.7605  -1.1855  -0.3758
 DY7  H162  H   HCH3  0   0.286  -6.6109   2.4535  -0.5648
 DY7  H161  H   HCH3  0   0.284  -6.8250   1.7398   1.0324
 DY7  H163  H   HCH3  0   0.280  -5.8658   3.2147   0.8477
 DY7  H171  H   HNR6  0   0.451  -6.0065  -0.1217  -0.5385
 DY7  N01   N   NH2   0  -0.811  -4.2469  -1.8199  -1.0827
 DY7  BR2   BR  BR    0  -0.017   1.6107  -2.8547  -0.7964

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
 DY7  BR2  C11   single    1.885  0.020  1.885
 DY7  BR9  C08   single    1.883  0.020  1.883
 DY7  C10  C11   aromatic  1.385  0.020  1.385
 DY7  C10  C08   aromatic  1.388  0.020  1.388
 DY7  C11  C13   aromatic  1.386  0.020  1.386
 DY7  C08  C07   aromatic  1.381  0.020  1.381
 DY7  C13  C06   aromatic  1.394  0.020  1.394
 DY7  C07  C06   aromatic  1.398  0.020  1.398
 DY7  C06  N05   single    1.395  0.020  1.395
 DY7  N05  C04   single    1.343  0.020  1.343
 DY7  N03  C04   aromatic  1.322  0.020  1.322
 DY7  N03  C02   aromatic  1.322  0.020  1.322
 DY7  C04  C14   aromatic  1.422  0.020  1.422
 DY7  N01  C02   single    1.320  0.020  1.320
 DY7  C02  N17   aromatic  1.353  0.020  1.353
 DY7  C14  C15   aromatic  1.354  0.020  1.354
 DY7  N17  C15   aromatic  1.362  0.020  1.362
 DY7  C15  C16   single    1.484  0.020  1.484
 DY7  C10  H101  single    0.930  0.020  1.080
 DY7  C14  H141  single    0.930  0.020  1.080
 DY7  N01  H011  single    0.860  0.020  1.020
 DY7  N01  H012  single    0.860  0.020  1.020
 DY7  N05  H051  single    0.860  0.020  1.020
 DY7  C07  H071  single    0.930  0.020  1.080
 DY7  C13  H131  single    0.930  0.020  1.080
 DY7  C16  H162  single    0.970  0.020  1.090
 DY7  C16  H161  single    0.970  0.020  1.090
 DY7  C16  H163  single    0.970  0.020  1.090
 DY7  N17  H171  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
 DY7  C16   C15  N17   116.96  3.000
 DY7  C16   C15  C14   124.76  3.000
 DY7  N17   C15  C14   118.27  3.000
 DY7  C13   C11  BR2   118.37  3.000
 DY7  C13   C11  C10   123.01  3.000
 DY7  BR2   C11  C10   118.62  3.000
 DY7  H101  C10  C08   121.40  3.000
 DY7  H101  C10  C11   121.53  3.000
 DY7  C08   C10  C11   117.07  3.000
 DY7  H141  C14  C04   121.48  3.000
 DY7  H141  C14  C15   120.74  3.000
 DY7  C04   C14  C15   117.78  3.000
 DY7  H171  N17  C02   119.53  3.000
 DY7  H171  N17  C15   118.85  3.000
 DY7  C02   N17  C15   121.61  3.000
 DY7  N03   C02  N01   119.51  3.000
 DY7  N01   C02  N17   118.94  3.000
 DY7  N03   C02  N17   121.55  3.000
 DY7  C04   N03  C02   118.60  3.000
 DY7  N05   C04  N03   120.21  3.000
 DY7  N03   C04  C14   122.18  3.000
 DY7  N05   C04  C14   117.61  3.000
 DY7  H051  N05  C06   114.03  3.000
 DY7  H051  N05  C04   114.35  3.000
 DY7  C06   N05  C04   131.63  3.000
 DY7  C13   C06  C07   119.85  3.000
 DY7  C07   C06  N05   115.52  3.000
 DY7  C13   C06  N05   124.63  3.000
 DY7  H071  C07  C08   120.62  3.000
 DY7  H071  C07  C06   119.82  3.000
 DY7  C08   C07  C06   119.56  3.000
 DY7  BR9   C08  C07   119.02  3.000
 DY7  C07   C08  C10   122.03  3.000
 DY7  BR9   C08  C10   118.95  3.000
 DY7  H131  C13  C06   120.55  3.000
 DY7  H131  C13  C11   120.96  3.000
 DY7  C06   C13  C11   118.49  3.000
 DY7  H163  C16  H161  108.72  3.000
 DY7  H163  C16  H162  108.69  3.000
 DY7  H161  C16  H162  107.76  3.000
 DY7  H163  C16  C15   110.62  3.000
 DY7  H161  C16  C15   110.73  3.000
 DY7  H162  C16  C15   110.24  3.000
 DY7  H012  N01  H011  117.96  3.000
 DY7  H012  N01  C02   119.20  3.000
 DY7  H011  N01  C02   122.84  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
 DY7  CONST_01  N03   C04  C14  C15     0.00   0.0  0
 DY7  CONST_02  N03   C02  N17  C15     0.00   0.0  0
 DY7  CONST_03  C07   C08  C10  C11     0.00   0.0  0
 DY7  CONST_04  C07   C06  C13  C11     0.00   0.0  0
 DY7  CONST_05  C06   C13  C11  C10     0.00   0.0  0
 DY7  CONST_06  C06   C07  C08  C10     0.00   0.0  0
 DY7  CONST_07  C02   N03  C04  C14     0.00   0.0  0
 DY7  CONST_08  C02   N17  C15  C14     0.00   0.0  0
 DY7  CONST_09  C04   N03  C02  N17     0.00   0.0  0
 DY7  CONST_10  C04   C14  C15  N17     0.00   0.0  0
 DY7  CONST_11  C13   C11  C10  C08     0.00   0.0  0
 DY7  CONST_12  C13   C06  C07  C08     0.00   0.0  0
 DY7  CONST_13  N05   C04  C14  C15   180.00   0.0  0
 DY7  CONST_14  N01   C02  N17  C15   180.00   0.0  0
 DY7  CONST_15  BR9   C08  C10  C11   180.00   0.0  0
 DY7  CONST_16  N05   C06  C13  C11   180.00   0.0  0
 DY7  CONST_17  C04   N03  C02  N01   180.00   0.0  0
 DY7  CONST_18  N05   C04  N03  C02   180.00   0.0  0
 DY7  CONST_19  C16   C15  N17  C02   180.00   0.0  0
 DY7  CONST_20  C16   C15  C14  C04   180.00   0.0  0
 DY7  CONST_21  C08   C07  C06  N05   180.00   0.0  0
 DY7  CONST_22  BR2   C11  C13  C06   180.00   0.0  0
 DY7  CONST_23  BR9   C08  C07  C06   180.00   0.0  0
 DY7  CONST_24  BR2   C11  C10  C08   180.00   0.0  0
 DY7  CONST_25  H131  C13  C11  C10   180.00   0.0  0
 DY7  CONST_26  H071  C07  C08  C10   180.00   0.0  0
 DY7  CONST_27  H171  N17  C15  C14   180.00   0.0  0
 DY7  CONST_28  H141  C14  C15  N17   180.00   0.0  0
 DY7  CONST_29  H101  C10  C08  C07   180.00   0.0  0
 DY7  CONST_30  H011  N01  C02  N17     0.00   0.0  0
 DY7  CONST_31  H012  N01  C02  N17   180.00   0.0  0
 DY7  Var_01    C06   N05  C04  C14  -179.92  30.0  2
 DY7  Var_02    C13   C06  N05  C04    -3.87  30.0  2
 DY7  Var_03    H162  C16  C15  C14   116.88  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
 DY7  plan-1  C11   0.020
 DY7  plan-1  C10   0.020
 DY7  plan-1  N05   0.020
 DY7  plan-1  C06   0.020
 DY7  plan-1  C07   0.020
 DY7  plan-1  C08   0.020
 DY7  plan-1  BR9   0.020
 DY7  plan-1  C13   0.020
 DY7  plan-1  H101  0.020
 DY7  plan-1  H071  0.020
 DY7  plan-1  H131  0.020
 DY7  plan-1  BR2   0.020
 DY7  plan-2  C15   0.020
 DY7  plan-2  C14   0.020
 DY7  plan-2  N17   0.020
 DY7  plan-2  C02   0.020
 DY7  plan-2  N03   0.020
 DY7  plan-2  C04   0.020
 DY7  plan-2  N05   0.020
 DY7  plan-2  C16   0.020
 DY7  plan-2  H141  0.020
 DY7  plan-2  H171  0.020
 DY7  plan-2  N01   0.020
 DY7  plan-3  C02   0.020
 DY7  plan-3  H011  0.020
 DY7  plan-3  H012  0.020
 DY7  plan-3  N01   0.020

