# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:44:22 2021
#   Inital geometry file: a 99 line input string
#   Ligand name: ~{N}4-cyclopropyl-5-ethyl-6-(4-methylpiperazin-1-yl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(NC2CC2)nc(N)nc1N3CCN(C)CC3
#
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
 CG0  CG0  ~{N}4-cyclopropyl-5-ethyl-6-(4-methylpiperazin-1-yl)pyrimidine-2,4-diamine  ligand  44  20  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CG0
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
 CG0  C13  C  CR6   0   0.459  26.7596   9.1327  -17.2720
 CG0  C15  C  CH1   0  -0.111  26.1950   7.0369  -18.4494
 CG0  C16  C  CH2   0  -0.479  26.4190   6.0252  -17.3684
 CG0  C17  C  CH2   0  -0.500  25.1259   6.0427  -18.1225
 CG0  C03  C  CH2   0  -0.278  31.9321   7.8494  -15.5834
 CG0  C04  C  CH2   0  -0.329  30.4349   8.0275  -15.4399
 CG0  C06  C  CH2   0  -0.291  30.7489  10.3468  -14.9178
 CG0  C07  C  CH2   0  -0.281  32.2481  10.1506  -15.0624
 CG0  C08  C  CR6   0   0.470  28.7434   9.6392  -16.1118
 CG0  C10  C  CR6   0   0.518  26.8317  10.7939  -15.7299
 CG0  C18  C  CR6   0  -0.108  28.1482   8.9408  -17.1760
 CG0  C19  C  CH2   0  -0.529  28.9656   8.2401  -18.2335
 CG0  C20  C  CH3   0  -0.662  28.7719   8.8444  -19.6250
 CG0  N02  N  NT    0  -0.413  32.6369   8.7928  -14.7396
 CG0  N05  N  NT    0  -0.500  30.0594   9.3960  -15.7687
 CG0  N09  N  N     0  -0.518  28.1033  10.5724  -15.4101
 CG0  N11  N  NH2   0  -0.826  26.2202  11.8507  -15.1304
 CG0  N12  N  N     0  -0.520  26.1101  10.0705  -16.5730
 CG0  N14  N  NH1   0  -0.649  25.9647   8.4024  -18.1036
 CG0  H1   H  HCH1  0   0.259  26.7273   6.8703  -19.3816
 CG0  H2   H  HCH2  0   0.256  26.4128   6.3797  -16.3455
 CG0  H3   H  HCH2  0   0.254  27.1251   5.2281  -17.5621
 CG0  H4   H  HCH2  0   0.257  24.9331   5.2590  -18.8434
 CG0  H5   H  HCH2  0   0.256  24.2451   6.4022  -17.6044
 CG0  H6   H  HCH3  0   0.233  34.3353   7.5950  -14.5429
 CG0  H7   H  HCH3  0   0.192  34.4764   8.8115  -15.8217
 CG0  H8   H  HCH3  0   0.233  34.5671   9.2908  -14.1191
 CG0  H9   H  HCH2  0   0.193  32.2095   7.9617  -16.6473
 CG0  H10  H  HCH2  0   0.238  32.2010   6.8332  -15.2854
 CG0  H11  H  HCH2  0   0.232  30.1399   7.7978  -14.4059
 CG0  H12  H  HCH2  0   0.269  29.9161   7.3203  -16.0835
 CG0  H13  H  HCH2  0   0.209  30.4611  10.2335  -13.8636
 CG0  H14  H  HCH2  0   0.247  30.4907  11.3606  -15.2181
 CG0  H15  H  HCH2  0   0.190  32.5478  10.4257  -16.0891
 CG0  H16  H  HCH2  0   0.237  32.7587  10.8386  -14.3841
 CG0  H17  H  HCH2  0   0.240  28.7830   7.1638  -18.2680
 CG0  H18  H  HCH2  0   0.254  30.0212   8.3517  -17.9838
 CG0  H19  H  HCH3  0   0.226  29.4016   8.3306  -20.3529
 CG0  H20  H  HCH3  0   0.227  27.7425   8.7784  -19.9758
 CG0  H21  H  HCH3  0   0.222  29.0530   9.8984  -19.6272
 CG0  H23  H  HNH2  0   0.383  25.2142  11.8578  -15.1329
 CG0  H24  H  HNH2  0   0.383  26.6486  12.2063  -14.2927
 CG0  H25  H  HNH1  0   0.377  25.0019   8.7030  -18.1021
 CG0  C01  C  CH3   0  -0.518  34.0684   8.6166  -14.8173

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
 CG0  C17  C16  single    1.497  0.020  1.497
 CG0  C17  C15  single    1.496  0.020  1.496
 CG0  C16  C15  single    1.497  0.020  1.497
 CG0  C20  C19  single    1.529  0.020  1.529
 CG0  C15  N14  single    1.427  0.020  1.427
 CG0  C19  C18  single    1.509  0.020  1.509
 CG0  N14  C13  single    1.363  0.020  1.363
 CG0  C18  C13  aromatic  1.405  0.020  1.405
 CG0  C18  C08  aromatic  1.405  0.020  1.405
 CG0  C06  C07  single    1.519  0.020  1.519
 CG0  C06  N05  single    1.450  0.020  1.450
 CG0  C13  N12  aromatic  1.338  0.020  1.338
 CG0  C07  N02  single    1.449  0.020  1.449
 CG0  N05  C08  single    1.382  0.020  1.382
 CG0  N05  C04  single    1.457  0.020  1.457
 CG0  C08  N09  aromatic  1.332  0.020  1.332
 CG0  N12  C10  aromatic  1.325  0.020  1.325
 CG0  N09  C10  aromatic  1.330  0.020  1.330
 CG0  C10  N11  single    1.360  0.020  1.360
 CG0  N02  C03  single    1.449  0.020  1.449
 CG0  N02  C01  single    1.444  0.020  1.444
 CG0  C04  C03  single    1.515  0.020  1.515
 CG0  C15  H1   single    0.970  0.020  1.090
 CG0  C16  H2   single    0.970  0.020  1.090
 CG0  C16  H3   single    0.970  0.020  1.090
 CG0  C17  H4   single    0.970  0.020  1.090
 CG0  C17  H5   single    0.970  0.020  1.090
 CG0  C01  H6   single    0.970  0.020  1.090
 CG0  C01  H7   single    0.970  0.020  1.090
 CG0  C01  H8   single    0.970  0.020  1.090
 CG0  C03  H9   single    0.970  0.020  1.090
 CG0  C03  H10  single    0.970  0.020  1.090
 CG0  C04  H11  single    0.970  0.020  1.090
 CG0  C04  H12  single    0.970  0.020  1.090
 CG0  C06  H13  single    0.970  0.020  1.090
 CG0  C06  H14  single    0.970  0.020  1.090
 CG0  C07  H15  single    0.970  0.020  1.090
 CG0  C07  H16  single    0.970  0.020  1.090
 CG0  C19  H17  single    0.970  0.020  1.090
 CG0  C19  H18  single    0.970  0.020  1.090
 CG0  C20  H19  single    0.970  0.020  1.090
 CG0  C20  H20  single    0.970  0.020  1.090
 CG0  C20  H21  single    0.970  0.020  1.090
 CG0  N11  H23  single    0.890  0.020  1.040
 CG0  N11  H24  single    0.890  0.020  1.040
 CG0  N14  H25  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
 CG0  N14  C13  N12  114.29  3.000
 CG0  N12  C13  C18  122.67  3.000
 CG0  N14  C13  C18  123.02  3.000
 CG0  H1   C15  N14  115.70  3.000
 CG0  H1   C15  C17  115.83  3.000
 CG0  N14  C15  C17  117.88  3.000
 CG0  H1   C15  C16  116.27  3.000
 CG0  N14  C15  C16  119.71  3.000
 CG0  C17  C15  C16   60.01  3.000
 CG0  H3   C16  H2   114.45  3.000
 CG0  H3   C16  C17  118.81  3.000
 CG0  H2   C16  C17  117.85  3.000
 CG0  H3   C16  C15  117.78  3.000
 CG0  H2   C16  C15  117.39  3.000
 CG0  C17  C16  C15   59.95  3.000
 CG0  H5   C17  H4   114.46  3.000
 CG0  H5   C17  C16  117.73  3.000
 CG0  H4   C17  C16  118.75  3.000
 CG0  H5   C17  C15  117.71  3.000
 CG0  H4   C17  C15  117.58  3.000
 CG0  C16  C17  C15   60.04  3.000
 CG0  H10  C03  H9   107.17  3.000
 CG0  H10  C03  N02  109.09  3.000
 CG0  H9   C03  N02  111.87  3.000
 CG0  H10  C03  C04  109.08  3.000
 CG0  H9   C03  C04  109.11  3.000
 CG0  N02  C03  C04  110.44  3.000
 CG0  H12  C04  H11  107.01  3.000
 CG0  H12  C04  N05  110.75  3.000
 CG0  H11  C04  N05  109.84  3.000
 CG0  H12  C04  C03  109.81  3.000
 CG0  H11  C04  C03  109.25  3.000
 CG0  N05  C04  C03  110.11  3.000
 CG0  H14  C06  H13  107.38  3.000
 CG0  H14  C06  N05  109.63  3.000
 CG0  H13  C06  N05  111.77  3.000
 CG0  H14  C06  C07  109.16  3.000
 CG0  H13  C06  C07  109.67  3.000
 CG0  N05  C06  C07  109.19  3.000
 CG0  H16  C07  H15  107.07  3.000
 CG0  H16  C07  N02  109.04  3.000
 CG0  H15  C07  N02  111.58  3.000
 CG0  H16  C07  C06  108.71  3.000
 CG0  H15  C07  C06  108.92  3.000
 CG0  N02  C07  C06  111.39  3.000
 CG0  N09  C08  N05  116.77  3.000
 CG0  N09  C08  C18  122.95  3.000
 CG0  N05  C08  C18  120.27  3.000
 CG0  N12  C10  N11  117.38  3.000
 CG0  N11  C10  N09  116.96  3.000
 CG0  N12  C10  N09  125.66  3.000
 CG0  C19  C18  C08  122.15  3.000
 CG0  C08  C18  C13  113.73  3.000
 CG0  C19  C18  C13  123.42  3.000
 CG0  H18  C19  H17  105.66  3.000
 CG0  H18  C19  C20  106.89  3.000
 CG0  H17  C19  C20  109.84  3.000
 CG0  H18  C19  C18  108.44  3.000
 CG0  H17  C19  C18  112.90  3.000
 CG0  C20  C19  C18  112.67  3.000
 CG0  H21  C20  H20  107.54  3.000
 CG0  H21  C20  H19  107.76  3.000
 CG0  H20  C20  H19  107.57  3.000
 CG0  H21  C20  C19  110.55  3.000
 CG0  H20  C20  C19  112.87  3.000
 CG0  H19  C20  C19  110.35  3.000
 CG0  C07  N02  C03  110.48  3.000
 CG0  C03  N02  C01  111.80  3.000
 CG0  C07  N02  C01  111.61  3.000
 CG0  C08  N05  C06  118.89  3.000
 CG0  C08  N05  C04  117.84  3.000
 CG0  C06  N05  C04  111.15  3.000
 CG0  C10  N09  C08  116.72  3.000
 CG0  H24  N11  H23  115.18  3.000
 CG0  H24  N11  C10  116.75  3.000
 CG0  H23  N11  C10  117.00  3.000
 CG0  C10  N12  C13  116.80  3.000
 CG0  H25  N14  C15  116.07  3.000
 CG0  H25  N14  C13  113.34  3.000
 CG0  C15  N14  C13  124.50  3.000
 CG0  H8   C01  H7   107.75  3.000
 CG0  H8   C01  H6   107.81  3.000
 CG0  H7   C01  H6   107.73  3.000
 CG0  H8   C01  N02  110.07  3.000
 CG0  H7   C01  N02  113.24  3.000
 CG0  H6   C01  N02  110.07  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
 CG0  CONST_01  N09  C08  C18  C13     0.00   0.0  0
 CG0  CONST_02  N09  C10  N12  C13     0.00   0.0  0
 CG0  CONST_03  N12  C13  C18  C08     0.00   0.0  0
 CG0  CONST_04  N12  C10  N09  C08     0.00   0.0  0
 CG0  CONST_05  C18  C13  N12  C10     0.00   0.0  0
 CG0  CONST_06  C18  C08  N09  C10     0.00   0.0  0
 CG0  CONST_07  N05  C08  C18  C13   180.00   0.0  0
 CG0  CONST_08  N05  C08  N09  C10   180.00   0.0  0
 CG0  CONST_09  N11  C10  N12  C13   180.00   0.0  0
 CG0  CONST_10  N14  C13  C18  C08   180.00   0.0  0
 CG0  CONST_11  N11  C10  N09  C08   180.00   0.0  0
 CG0  CONST_12  N14  C13  N12  C10   180.00   0.0  0
 CG0  CONST_18  H25  N14  C13  C18   180.00   0.0  0
 CG0  Var_01    C06  C07  N02  C03    57.53  30.0  1
 CG0  Var_02    C06  N05  C04  C03   -58.21  30.0  1
 CG0  Var_03    C07  C06  N05  C04    57.53  30.0  1
 CG0  Var_04    C18  C08  N05  C04   -56.44  30.0  2
 CG0  Var_05    C07  N02  C03  C04   -57.12  30.0  1
 CG0  Var_06    N05  C06  C07  N02   -57.23  30.0  1
 CG0  Var_07    N05  C04  C03  N02    57.33  30.0  1
 CG0  Var_08    C17  C15  N14  C13   120.96  30.0  1
 CG0  Var_09    N14  C15  C17  C16  -110.01  30.0  1
 CG0  Var_10    H2   C16  C17  C15   107.18  30.0  1
 CG0  Var_11    C20  C19  C18  C13    53.91  30.0  3
 CG0  Var_12    H6   C01  N02  C03   -57.26  30.0  3
 CG0  Var_13    H19  C20  C19  C18   178.27  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
 CG0  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
 CG0  plan-1  C10  0.020
 CG0  plan-1  N11  0.020
 CG0  plan-1  H23  0.020
 CG0  plan-1  H24  0.020
 CG0  plan-2  C13  0.020
 CG0  plan-2  C08  0.020
 CG0  plan-2  C10  0.020
 CG0  plan-2  C18  0.020
 CG0  plan-2  C19  0.020
 CG0  plan-2  N05  0.020
 CG0  plan-2  N09  0.020
 CG0  plan-2  N11  0.020
 CG0  plan-2  N12  0.020
 CG0  plan-2  N14  0.020
 CG0  plan-3  C13  0.020
 CG0  plan-3  C15  0.020
 CG0  plan-3  N14  0.020
 CG0  plan-3  H25  0.020

