# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 22:33:34 2021
#   Inital geometry file: a 87 line input string
#   Ligand name: ~{N}4-cyclopropyl-6-(4-methylpiperazin-1-yl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2cc(NC3CC3)nc(N)n2
#
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
 CJ6  CJ6  ~{N}4-cyclopropyl-6-(4-methylpiperazin-1-yl)pyrimidine-2,4-diamine  ligand  38  18  .  2022-07-24  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CJ6
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
 CJ6  C10  C  CR6   0   0.520  27.4087   9.7940  -14.3381
 CJ6  C13  C  CR6   0   0.517  27.0300   8.6754  -16.2635
 CJ6  C15  C  CH1   0  -0.100  26.4294   7.6180  -18.3867
 CJ6  C16  C  CH2   0  -0.484  27.1859   6.3338  -18.5566
 CJ6  C17  C  CH2   0  -0.510  25.7257   6.3943  -18.8764
 CJ6  C18  C  CR16  0  -0.559  28.3868   8.7397  -16.5829
 CJ6  N02  N  NT    0  -0.414  33.4102   9.4134  -15.9494
 CJ6  C03  C  CH2   0  -0.285  32.7339   9.8143  -14.7332
 CJ6  C04  C  CH2   0  -0.304  31.3637  10.3865  -15.0395
 CJ6  N05  N  NT    0  -0.508  30.5703   9.4432  -15.8060
 CJ6  C06  C  CH2   0  -0.301  31.2408   8.9650  -16.9965
 CJ6  C07  C  CH2   0  -0.276  32.6185   8.4262  -16.6508
 CJ6  C08  C  CR6   0   0.580  29.2210   9.3638  -15.6460
 CJ6  N09  N  N     0  -0.546  28.7195   9.9019  -14.5278
 CJ6  N11  N  NH2   0  -0.824  26.9088  10.3863  -13.2221
 CJ6  N12  N  N     0  -0.536  26.5301   9.1995  -15.1384
 CJ6  N14  N  NH1   0  -0.657  26.1290   8.0692  -17.0738
 CJ6  H1   H  HCH1  0   0.261  26.6238   8.3945  -19.1240
 CJ6  H2   H  HCH2  0   0.257  27.4839   5.8133  -17.6554
 CJ6  H3   H  HCH2  0   0.255  27.8954   6.2708  -19.3714
 CJ6  H4   H  HCH2  0   0.258  25.4201   6.3741  -19.9141
 CJ6  H5   H  HCH2  0   0.257  25.0393   5.9067  -18.1959
 CJ6  H6   H  HCR6  0   0.268  28.7457   8.3308  -17.5118
 CJ6  H7   H  HCH3  0   0.234  35.3367   9.7126  -15.2021
 CJ6  H8   H  HCH3  0   0.193  34.7644   8.0441  -15.0318
 CJ6  H9   H  HCH3  0   0.234  35.2418   8.6674  -16.6192
 CJ6  H11  H  HCH2  0   0.194  32.6259   8.9712  -14.0279
 CJ6  H12  H  HCH2  0   0.240  33.3261  10.5819  -14.2291
 CJ6  H13  H  HCH2  0   0.222  31.4774  11.3215  -15.6039
 CJ6  H14  H  HCH2  0   0.267  30.8488  10.6226  -14.1137
 CJ6  H15  H  HCH2  0   0.227  31.3318   9.7681  -17.7388
 CJ6  H16  H  HCH2  0   0.255  30.6762   8.1565  -17.4535
 CJ6  H17  H  HCH2  0   0.194  32.5031   7.5005  -16.0593
 CJ6  H18  H  HCH2  0   0.243  33.1245   8.1514  -17.5791
 CJ6  H19  H  HNH2  0   0.383  25.9892  10.1083  -12.9250
 CJ6  H20  H  HNH2  0   0.383  27.5577  10.6030  -12.4853
 CJ6  H21  H  HNH1  0   0.381  25.1612   8.2169  -16.8338
 CJ6  C01  C  CH3   0  -0.518  34.7464   8.9316  -15.6837

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
 CJ6  C17  C16  single    1.496  0.020  1.496
 CJ6  C17  C15  single    1.494  0.020  1.494
 CJ6  C16  C15  single    1.500  0.020  1.500
 CJ6  C15  N14  single    1.420  0.020  1.420
 CJ6  N14  C13  single    1.355  0.020  1.355
 CJ6  C07  C06  single    1.519  0.020  1.519
 CJ6  C07  N02  single    1.447  0.020  1.447
 CJ6  C06  N05  single    1.448  0.020  1.448
 CJ6  C01  N02  single    1.445  0.020  1.445
 CJ6  C18  C13  aromatic  1.395  0.020  1.395
 CJ6  C18  C08  aromatic  1.401  0.020  1.401
 CJ6  N02  C03  single    1.448  0.020  1.448
 CJ6  C13  N12  aromatic  1.338  0.020  1.338
 CJ6  N05  C08  single    1.361  0.020  1.361
 CJ6  N05  C04  single    1.451  0.020  1.451
 CJ6  C08  N09  aromatic  1.338  0.020  1.338
 CJ6  N12  C10  aromatic  1.329  0.020  1.329
 CJ6  C03  C04  single    1.516  0.020  1.516
 CJ6  N09  C10  aromatic  1.329  0.020  1.329
 CJ6  C10  N11  single    1.359  0.020  1.359
 CJ6  C15  H1   single    0.970  0.020  1.090
 CJ6  C16  H2   single    0.970  0.020  1.090
 CJ6  C16  H3   single    0.970  0.020  1.090
 CJ6  C17  H4   single    0.970  0.020  1.090
 CJ6  C17  H5   single    0.970  0.020  1.090
 CJ6  C18  H6   single    0.930  0.020  1.080
 CJ6  C01  H7   single    0.970  0.020  1.090
 CJ6  C01  H8   single    0.970  0.020  1.090
 CJ6  C01  H9   single    0.970  0.020  1.090
 CJ6  C03  H11  single    0.970  0.020  1.090
 CJ6  C03  H12  single    0.970  0.020  1.090
 CJ6  C04  H13  single    0.970  0.020  1.090
 CJ6  C04  H14  single    0.970  0.020  1.090
 CJ6  C06  H15  single    0.970  0.020  1.090
 CJ6  C06  H16  single    0.970  0.020  1.090
 CJ6  C07  H17  single    0.970  0.020  1.090
 CJ6  C07  H18  single    0.970  0.020  1.090
 CJ6  N11  H19  single    0.890  0.020  1.040
 CJ6  N11  H20  single    0.890  0.020  1.040
 CJ6  N14  H21  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
 CJ6  N12  C10  N11  116.52  3.000
 CJ6  N11  C10  N09  116.40  3.000
 CJ6  N12  C10  N09  127.06  3.000
 CJ6  N14  C13  N12  115.44  3.000
 CJ6  N12  C13  C18  122.53  3.000
 CJ6  N14  C13  C18  122.03  3.000
 CJ6  H1   C15  N14  115.94  3.000
 CJ6  H1   C15  C17  116.52  3.000
 CJ6  N14  C15  C17  117.61  3.000
 CJ6  H1   C15  C16  116.36  3.000
 CJ6  N14  C15  C16  118.90  3.000
 CJ6  C17  C15  C16   59.95  3.000
 CJ6  H3   C16  H2   114.73  3.000
 CJ6  H3   C16  C17  118.76  3.000
 CJ6  H2   C16  C17  117.78  3.000
 CJ6  H3   C16  C15  117.75  3.000
 CJ6  H2   C16  C15  117.14  3.000
 CJ6  C17  C16  C15   59.82  3.000
 CJ6  H5   C17  H4   114.54  3.000
 CJ6  H5   C17  C16  117.79  3.000
 CJ6  H4   C17  C16  118.69  3.000
 CJ6  H5   C17  C15  117.48  3.000
 CJ6  H4   C17  C15  117.56  3.000
 CJ6  C16  C17  C15   60.23  3.000
 CJ6  H6   C18  C08  123.21  3.000
 CJ6  H6   C18  C13  120.28  3.000
 CJ6  C08  C18  C13  116.51  3.000
 CJ6  C07  N02  C03  109.91  3.000
 CJ6  C03  N02  C01  111.70  3.000
 CJ6  C07  N02  C01  111.57  3.000
 CJ6  H12  C03  H11  107.13  3.000
 CJ6  H12  C03  C04  108.54  3.000
 CJ6  H11  C03  C04  109.19  3.000
 CJ6  H12  C03  N02  109.19  3.000
 CJ6  H11  C03  N02  111.75  3.000
 CJ6  C04  C03  N02  110.91  3.000
 CJ6  H14  C04  H13  107.60  3.000
 CJ6  H14  C04  N05  109.42  3.000
 CJ6  H13  C04  N05  109.78  3.000
 CJ6  H14  C04  C03  109.79  3.000
 CJ6  H13  C04  C03  109.37  3.000
 CJ6  N05  C04  C03  110.82  3.000
 CJ6  C08  N05  C06  122.45  3.000
 CJ6  C08  N05  C04  121.18  3.000
 CJ6  C06  N05  C04  113.32  3.000
 CJ6  H16  C06  H15  107.64  3.000
 CJ6  H16  C06  C07  107.64  3.000
 CJ6  H15  C06  C07  109.77  3.000
 CJ6  H16  C06  N05  110.55  3.000
 CJ6  H15  C06  N05  110.67  3.000
 CJ6  C07  C06  N05  110.49  3.000
 CJ6  H18  C07  H17  107.02  3.000
 CJ6  H18  C07  C06  108.42  3.000
 CJ6  H17  C07  C06  108.92  3.000
 CJ6  H18  C07  N02  109.28  3.000
 CJ6  H17  C07  N02  111.68  3.000
 CJ6  C06  C07  N02  111.38  3.000
 CJ6  N09  C08  N05  116.50  3.000
 CJ6  N09  C08  C18  120.97  3.000
 CJ6  N05  C08  C18  122.52  3.000
 CJ6  C08  N09  C10  117.14  3.000
 CJ6  H20  N11  H19  115.68  3.000
 CJ6  H20  N11  C10  117.29  3.000
 CJ6  H19  N11  C10  117.29  3.000
 CJ6  C13  N12  C10  115.76  3.000
 CJ6  H21  N14  C15  118.02  3.000
 CJ6  H21  N14  C13  115.50  3.000
 CJ6  C15  N14  C13  123.66  3.000
 CJ6  H9   C01  H8   107.75  3.000
 CJ6  H9   C01  H7   107.83  3.000
 CJ6  H8   C01  H7   107.86  3.000
 CJ6  H9   C01  N02  110.06  3.000
 CJ6  H8   C01  N02  113.11  3.000
 CJ6  H7   C01  N02  110.05  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
 CJ6  CONST_01  C18  C13  N12  C10     0.00   0.0  0
 CJ6  CONST_02  C18  C08  N09  C10     0.00   0.0  0
 CJ6  CONST_03  N09  C08  C18  C13     0.00   0.0  0
 CJ6  CONST_04  N09  C10  N12  C13     0.00   0.0  0
 CJ6  CONST_05  N12  C13  C18  C08     0.00   0.0  0
 CJ6  CONST_06  N12  C10  N09  C08     0.00   0.0  0
 CJ6  CONST_07  N05  C08  N09  C10   180.00   0.0  0
 CJ6  CONST_08  N05  C08  C18  C13   180.00   0.0  0
 CJ6  CONST_09  N14  C13  N12  C10   180.00   0.0  0
 CJ6  CONST_10  N11  C10  N12  C13   180.00   0.0  0
 CJ6  CONST_11  N14  C13  C18  C08   180.00   0.0  0
 CJ6  CONST_12  N11  C10  N09  C08   180.00   0.0  0
 CJ6  CONST_13  C18  C13  N14  C15     0.00   0.0  0
 CJ6  CONST_14  N12  C13  N14  C15   180.00   0.0  0
 CJ6  CONST_15  H6   C18  C08  N05     0.00   0.0  0
 CJ6  CONST_16  H21  N14  C13  C18   180.00   0.0  0
 CJ6  Var_01    C06  N05  C08  C18     4.04  30.0  3
 CJ6  Var_02    N05  C06  C07  N02   -55.16  30.0  1
 CJ6  Var_03    N05  C04  C03  N02    55.46  30.0  1
 CJ6  Var_04    C06  C07  N02  C03    58.71  30.0  1
 CJ6  Var_05    C07  C06  N05  C04    52.47  30.0  1
 CJ6  Var_06    C07  N02  C03  C04   -58.69  30.0  1
 CJ6  Var_07    C17  C15  N14  C13   147.02  30.0  2
 CJ6  Var_08    N14  C15  C17  C16  -109.11  30.0  1
 CJ6  Var_09    H2   C16  C17  C15   106.87  30.0  1
 CJ6  Var_10    H7   C01  N02  C03   -59.50  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 CJ6  chir_01  C15  C17  C16  N14  both

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
 CJ6  plan-1  C10  0.020
 CJ6  plan-1  C13  0.020
 CJ6  plan-1  C18  0.020
 CJ6  plan-1  N05  0.020
 CJ6  plan-1  C08  0.020
 CJ6  plan-1  N09  0.020
 CJ6  plan-1  N11  0.020
 CJ6  plan-1  N12  0.020
 CJ6  plan-1  N14  0.020
 CJ6  plan-1  H6   0.020
 CJ6  plan-2  C10  0.020
 CJ6  plan-2  N11  0.020
 CJ6  plan-2  H19  0.020
 CJ6  plan-2  H20  0.020
 CJ6  plan-3  C13  0.020
 CJ6  plan-3  C15  0.020
 CJ6  plan-3  N14  0.020
 CJ6  plan-3  H21  0.020

