# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:16:01 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: ~{N}1-(4,6-dimethylpyrimidin-2-yl)benzene-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(Nc2ccc(N)cc2)n1
#
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
 GRY  GRY  ~{N}1-(4,6-dimethylpyrimidin-2-yl)benzene-1,4-diamine  ligand  30  16  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GRY
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
 GRY  N1   N  N     0  -0.490  -2.2784  -1.1461   0.0157
 GRY  N3   N  NH2   0  -0.863   5.4045   0.4085  -0.1184
 GRY  C4   C  CR6   0   0.291  -3.4538  -0.5366  -0.0183
 GRY  C5   C  CH3   0  -0.722  -4.6701  -1.4062  -0.0050
 GRY  C6   C  CR6   0   0.566  -1.1895  -0.3685   0.0094
 GRY  C7   C  CR6   0   0.325   1.3110  -0.6074   0.0038
 GRY  C8   C  CR16  0  -0.342   2.2922  -1.5673  -0.2595
 GRY  C10  C  CR6   0   0.280   4.0645   0.0660  -0.0404
 GRY  C1   C  CH3   0  -0.721  -2.3492   3.0649  -0.0772
 GRY  C2   C  CR6   0   0.314  -2.3617   1.5702  -0.0592
 GRY  C3   C  CR16  0  -0.431  -3.5482   0.8518  -0.0637
 GRY  N2   N  NH1   0  -0.767  -0.0155  -1.0498   0.0295
 GRY  C9   C  CR16  0  -0.312   3.6359  -1.2435  -0.2797
 GRY  C11  C  CR16  0  -0.315   3.0820   1.0212   0.2246
 GRY  C12  C  CR16  0  -0.303   1.7325   0.6990   0.2518
 GRY  N4   N  N     0  -0.487  -1.1804   0.9600  -0.0204
 GRY  H1   H  HNH2  0   0.374   6.0486  -0.3418   0.0747
 GRY  H2   H  HNH2  0   0.374   5.6593   1.2431   0.3854
 GRY  H3   H  HCH3  0   0.258  -4.7122  -1.9831   0.9200
 GRY  H4   H  HCH3  0   0.247  -5.5850  -0.8227  -0.0868
 GRY  H5   H  HCH3  0   0.257  -4.6391  -2.1196  -0.8288
 GRY  H6   H  HCR6  0   0.262   1.9987  -2.5920  -0.4583
 GRY  H7   H  HCH3  0   0.254  -1.6100   3.4351  -0.7868
 GRY  H8   H  HCH3  0   0.247  -3.3242   3.4728  -0.3361
 GRY  H9   H  HCH3  0   0.259  -2.0727   3.4478   0.9071
 GRY  H10  H  HCR6  0   0.260  -4.5067   1.3502  -0.0940
 GRY  H11  H  HNH1  0   0.400  -0.1369  -2.0508   0.0380
 GRY  H12  H  HCR6  0   0.256   4.3626  -2.0200  -0.4886
 GRY  H13  H  HCR6  0   0.253   3.3752   2.0447   0.4287
 GRY  H14  H  HCR6  0   0.277   1.0121   1.4761   0.4503

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
 GRY  C1   C2   single    1.495  0.020  1.495
 GRY  C11  C12  aromatic  1.388  0.020  1.388
 GRY  C11  C10  aromatic  1.396  0.020  1.396
 GRY  N3   C10  single    1.385  0.020  1.385
 GRY  C12  C7   aromatic  1.395  0.020  1.395
 GRY  C10  C9   aromatic  1.398  0.020  1.398
 GRY  C2   N4   aromatic  1.330  0.020  1.330
 GRY  C2   C3   aromatic  1.387  0.020  1.387
 GRY  N4   C6   aromatic  1.329  0.020  1.329
 GRY  C3   C4   aromatic  1.392  0.020  1.392
 GRY  C7   N2   single    1.399  0.020  1.399
 GRY  C7   C8   aromatic  1.398  0.020  1.398
 GRY  C9   C8   aromatic  1.382  0.020  1.382
 GRY  C6   N2   single    1.357  0.020  1.357
 GRY  C6   N1   aromatic  1.338  0.020  1.338
 GRY  C4   N1   aromatic  1.324  0.020  1.324
 GRY  C4   C5   single    1.495  0.020  1.495
 GRY  N3   H1   single    0.890  0.020  1.040
 GRY  N3   H2   single    0.890  0.020  1.040
 GRY  C5   H3   single    0.970  0.020  1.090
 GRY  C5   H4   single    0.970  0.020  1.090
 GRY  C5   H5   single    0.970  0.020  1.090
 GRY  C8   H6   single    0.930  0.020  1.080
 GRY  C1   H7   single    0.970  0.020  1.090
 GRY  C1   H8   single    0.970  0.020  1.090
 GRY  C1   H9   single    0.970  0.020  1.090
 GRY  C3   H10  single    0.930  0.020  1.080
 GRY  N2   H11  single    0.860  0.020  1.020
 GRY  C9   H12  single    0.930  0.020  1.080
 GRY  C11  H13  single    0.930  0.020  1.080
 GRY  C12  H14  single    0.930  0.020  1.080

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
 GRY  C6   N1   C4   117.04  3.000
 GRY  H2   N3   H1   111.05  3.000
 GRY  H2   N3   C10  114.92  3.000
 GRY  H1   N3   C10  115.05  3.000
 GRY  C3   C4   C5   121.67  3.000
 GRY  C5   C4   N1   117.00  3.000
 GRY  C3   C4   N1   121.32  3.000
 GRY  H5   C5   H4   108.54  3.000
 GRY  H5   C5   H3   107.21  3.000
 GRY  H4   C5   H3   108.36  3.000
 GRY  H5   C5   C4   110.53  3.000
 GRY  H4   C5   C4   111.80  3.000
 GRY  H3   C5   C4   110.26  3.000
 GRY  N4   C6   N2   119.74  3.000
 GRY  N2   C6   N1   114.34  3.000
 GRY  N4   C6   N1   125.92  3.000
 GRY  C12  C7   N2   125.42  3.000
 GRY  N2   C7   C8   116.88  3.000
 GRY  C12  C7   C8   117.68  3.000
 GRY  H6   C8   C9   118.81  3.000
 GRY  H6   C8   C7   119.57  3.000
 GRY  C9   C8   C7   121.62  3.000
 GRY  C11  C10  C9   117.23  3.000
 GRY  C9   C10  N3   121.22  3.000
 GRY  C11  C10  N3   121.49  3.000
 GRY  H9   C1   H8   108.06  3.000
 GRY  H9   C1   H7   107.23  3.000
 GRY  H8   C1   H7   109.00  3.000
 GRY  H9   C1   C2   110.00  3.000
 GRY  H8   C1   C2   111.73  3.000
 GRY  H7   C1   C2   110.69  3.000
 GRY  N4   C2   C3   121.48  3.000
 GRY  C3   C2   C1   121.67  3.000
 GRY  N4   C2   C1   116.85  3.000
 GRY  H10  C3   C2   121.33  3.000
 GRY  H10  C3   C4   121.39  3.000
 GRY  C2   C3   C4   117.28  3.000
 GRY  H11  N2   C7   115.36  3.000
 GRY  H11  N2   C6   113.21  3.000
 GRY  C7   N2   C6   131.40  3.000
 GRY  H12  C9   C10  119.89  3.000
 GRY  H12  C9   C8   119.13  3.000
 GRY  C10  C9   C8   120.98  3.000
 GRY  H13  C11  C12  118.59  3.000
 GRY  H13  C11  C10  119.44  3.000
 GRY  C12  C11  C10  121.96  3.000
 GRY  H14  C12  C11  119.09  3.000
 GRY  H14  C12  C7   120.39  3.000
 GRY  C11  C12  C7   120.52  3.000
 GRY  C2   N4   C6   116.95  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
 GRY  CONST_01  C2   N4   C6   N1      0.00   0.0  0
 GRY  CONST_02  C2   C3   C4   N1      0.00   0.0  0
 GRY  CONST_03  N4   C2   C3   C4      0.00   0.0  0
 GRY  CONST_04  N4   C6   N1   C4      0.00   0.0  0
 GRY  CONST_05  C3   C2   N4   C6      0.00   0.0  0
 GRY  CONST_06  C3   C4   N1   C6      0.00   0.0  0
 GRY  CONST_07  C10  C11  C12  C7      0.00   0.0  0
 GRY  CONST_08  C10  C9   C8   C7      0.00   0.0  0
 GRY  CONST_09  C11  C12  C7   C8      0.00   0.0  0
 GRY  CONST_10  C11  C10  C9   C8      0.00   0.0  0
 GRY  CONST_11  C12  C11  C10  C9      0.00   0.0  0
 GRY  CONST_12  C12  C7   C8   C9      0.00   0.0  0
 GRY  CONST_13  C12  C11  C10  N3    180.00   0.0  0
 GRY  CONST_14  C8   C9   C10  N3    180.00   0.0  0
 GRY  CONST_15  C1   C2   C3   C4    180.00   0.0  0
 GRY  CONST_16  N2   C6   N1   C4    180.00   0.0  0
 GRY  CONST_17  C2   C3   C4   C5    180.00   0.0  0
 GRY  CONST_18  C6   N1   C4   C5    180.00   0.0  0
 GRY  CONST_19  C1   C2   N4   C6    180.00   0.0  0
 GRY  CONST_20  N2   C6   N4   C2    180.00   0.0  0
 GRY  CONST_21  C11  C12  C7   N2    180.00   0.0  0
 GRY  CONST_22  C9   C8   C7   N2    180.00   0.0  0
 GRY  CONST_23  H10  C3   C4   N1    180.00   0.0  0
 GRY  CONST_24  H13  C11  C12  C7    180.00   0.0  0
 GRY  CONST_25  H12  C9   C8   C7    180.00   0.0  0
 GRY  CONST_26  H14  C12  C7   C8    180.00   0.0  0
 GRY  CONST_27  H6   C8   C9   C10   180.00   0.0  0
 GRY  Var_01    C7   N2   C6   N1    178.53  30.0  2
 GRY  Var_02    C12  C7   N2   C6     15.44  30.0  2
 GRY  Var_03    H3   C5   C4   N1     62.33  30.0  2
 GRY  Var_04    H7   C1   C2   C3   -135.59  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
 GRY  plan-1  N1   0.020
 GRY  plan-1  C4   0.020
 GRY  plan-1  C5   0.020
 GRY  plan-1  C6   0.020
 GRY  plan-1  C1   0.020
 GRY  plan-1  C2   0.020
 GRY  plan-1  C3   0.020
 GRY  plan-1  N2   0.020
 GRY  plan-1  N4   0.020
 GRY  plan-1  H10  0.020
 GRY  plan-2  N3   0.020
 GRY  plan-2  C7   0.020
 GRY  plan-2  C8   0.020
 GRY  plan-2  C10  0.020
 GRY  plan-2  N2   0.020
 GRY  plan-2  C9   0.020
 GRY  plan-2  C11  0.020
 GRY  plan-2  C12  0.020
 GRY  plan-2  H6   0.020
 GRY  plan-2  H12  0.020
 GRY  plan-2  H13  0.020
 GRY  plan-2  H14  0.020
 GRY  plan-3  N3   0.020
 GRY  plan-3  C10  0.020
 GRY  plan-3  H1   0.020
 GRY  plan-3  H2   0.020

