# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 22:46:30 2021
#   Inital geometry file: a 79 line input string
#   Ligand name: ~{N}4-methyl-6-(4-methylpiperazin-1-yl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(nc(N)n1)N2CCN(C)CC2
#
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
 CEU  CEU  ~{N}4-methyl-6-(4-methylpiperazin-1-yl)pyrimidine-2,4-diamine  ligand  34  16  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CEU
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
 CEU  C01  C  CH3   0  -0.530   4.3125   -9.4644  16.3020
 CEU  N02  N  NT    0  -0.399   3.5873   -8.6940  15.3118
 CEU  C03  C  CH2   0  -0.324   2.7713   -7.6381  15.8724
 CEU  C04  C  CH2   0  -0.307   1.5120   -8.1220  16.5854
 CEU  N05  N  NT    0  -0.502   0.7368   -9.0052  15.7309
 CEU  C06  C  CH2   0  -0.302   1.5071  -10.0599  15.0827
 CEU  C07  C  CH2   0  -0.331   2.7645   -9.4991  14.4299
 CEU  C08  C  CR6   0   0.577  -0.5927   -9.2014  15.9701
 CEU  N09  N  N     0  -0.548  -1.1851  -10.1830  15.2800
 CEU  C10  C  CR6   0   0.517  -2.4877  -10.3625  15.4784
 CEU  N11  N  NH2   0  -0.824  -3.0830  -11.3302  14.7322
 CEU  N12  N  N     0  -0.535  -3.2751   -9.6775  16.2988
 CEU  C13  C  CR6   0   0.523  -2.6810   -8.7002  16.9972
 CEU  N14  N  NH1   0  -0.649  -3.4797   -8.0079  17.8302
 CEU  C15  C  CH3   0  -0.527  -3.0406   -6.9357  18.6810
 CEU  C16  C  CR16  0  -0.565  -1.3173   -8.4161  16.8758
 CEU  H1   H  HCH3  0   0.234   4.9307   -8.7935  16.9001
 CEU  H2   H  HCH3  0   0.201   3.6915  -10.0437  16.9983
 CEU  H3   H  HCH3  0   0.234   4.9785  -10.1671  15.7983
 CEU  H5   H  HCH2  0   0.245   3.3654   -7.0460  16.5719
 CEU  H6   H  HCH2  0   0.235   2.4732   -6.9694  15.0582
 CEU  H7   H  HCH2  0   0.226   1.7665   -8.6206  17.5299
 CEU  H8   H  HCH2  0   0.256   0.9299   -7.2377  16.8370
 CEU  H9   H  HCH2  0   0.263   0.8932  -10.5325  14.3215
 CEU  H10  H  HCH2  0   0.219   1.7657  -10.8397  15.8112
 CEU  H11  H  HCH2  0   0.234   2.4712   -8.8792  13.5760
 CEU  H12  H  HCH2  0   0.243   3.3550  -10.3290  14.0354
 CEU  H13  H  HNH2  0   0.382  -2.4864  -12.0254  14.3174
 CEU  H14  H  HNH2  0   0.382  -3.9851  -11.6557  15.0347
 CEU  H15  H  HNH1  0   0.385  -4.4391   -8.3043  17.8812
 CEU  H16  H  HCH3  0   0.262  -3.9004   -6.5496  19.2213
 CEU  H17  H  HCH3  0   0.231  -2.3003   -7.2630  19.4161
 CEU  H18  H  HCH3  0   0.232  -2.6072   -6.1119  18.1091
 CEU  H19  H  HCR6  0   0.263  -0.8638   -7.6383  17.4671

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
 CEU  N11  C10  single    1.359  0.020  1.359
 CEU  C07  N02  single    1.450  0.020  1.450
 CEU  C07  C06  single    1.524  0.020  1.524
 CEU  N02  C01  single    1.449  0.020  1.449
 CEU  N02  C03  single    1.447  0.020  1.447
 CEU  C10  N09  aromatic  1.330  0.020  1.330
 CEU  C10  N12  aromatic  1.327  0.020  1.327
 CEU  N09  C08  aromatic  1.338  0.020  1.338
 CEU  C06  N05  single    1.458  0.020  1.458
 CEU  C03  C04  single    1.526  0.020  1.526
 CEU  N12  C13  aromatic  1.340  0.020  1.340
 CEU  C08  N05  single    1.365  0.020  1.365
 CEU  C08  C16  aromatic  1.401  0.020  1.401
 CEU  N05  C04  single    1.453  0.020  1.453
 CEU  C13  C16  aromatic  1.398  0.020  1.398
 CEU  C13  N14  single    1.346  0.020  1.346
 CEU  N14  C15  single    1.437  0.020  1.437
 CEU  C01  H1   single    0.970  0.020  1.090
 CEU  C01  H2   single    0.970  0.020  1.090
 CEU  C01  H3   single    0.970  0.020  1.090
 CEU  C03  H5   single    0.970  0.020  1.090
 CEU  C03  H6   single    0.970  0.020  1.090
 CEU  C04  H7   single    0.970  0.020  1.090
 CEU  C04  H8   single    0.970  0.020  1.090
 CEU  C06  H9   single    0.970  0.020  1.090
 CEU  C06  H10  single    0.970  0.020  1.090
 CEU  C07  H11  single    0.970  0.020  1.090
 CEU  C07  H12  single    0.970  0.020  1.090
 CEU  N11  H13  single    0.890  0.020  1.040
 CEU  N11  H14  single    0.890  0.020  1.040
 CEU  N14  H15  single    0.860  0.020  1.020
 CEU  C15  H16  single    0.970  0.020  1.090
 CEU  C15  H17  single    0.970  0.020  1.090
 CEU  C15  H18  single    0.970  0.020  1.090
 CEU  C16  H19  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
 CEU  H3   C01  H2   107.34  3.000
 CEU  H3   C01  H1   107.65  3.000
 CEU  H2   C01  H1   107.29  3.000
 CEU  H3   C01  N02  109.41  3.000
 CEU  H2   C01  N02  115.51  3.000
 CEU  H1   C01  N02  109.35  3.000
 CEU  C07  N02  C03  108.71  3.000
 CEU  C03  N02  C01  113.91  3.000
 CEU  C07  N02  C01  113.85  3.000
 CEU  H6   C03  H5   107.06  3.000
 CEU  H6   C03  C04  108.45  3.000
 CEU  H5   C03  C04  108.76  3.000
 CEU  H6   C03  N02  108.12  3.000
 CEU  H5   C03  N02  109.69  3.000
 CEU  C04  C03  N02  114.51  3.000
 CEU  H8   C04  H7   107.11  3.000
 CEU  H8   C04  N05  110.15  3.000
 CEU  H7   C04  N05  110.70  3.000
 CEU  H8   C04  C03  106.97  3.000
 CEU  H7   C04  C03  110.78  3.000
 CEU  N05  C04  C03  110.99  3.000
 CEU  C08  N05  C06  119.24  3.000
 CEU  C08  N05  C04  120.26  3.000
 CEU  C06  N05  C04  114.79  3.000
 CEU  H10  C06  H9   106.80  3.000
 CEU  H10  C06  C07  110.57  3.000
 CEU  H9   C06  C07  109.05  3.000
 CEU  H10  C06  N05  110.07  3.000
 CEU  H9   C06  N05  109.13  3.000
 CEU  C07  C06  N05  111.12  3.000
 CEU  H12  C07  H11  107.06  3.000
 CEU  H12  C07  C06  108.74  3.000
 CEU  H11  C07  C06  108.75  3.000
 CEU  H12  C07  N02  109.55  3.000
 CEU  H11  C07  N02  108.17  3.000
 CEU  C06  C07  N02  114.33  3.000
 CEU  C16  C08  N09  121.05  3.000
 CEU  C16  C08  N05  122.45  3.000
 CEU  N09  C08  N05  116.50  3.000
 CEU  C10  N09  C08  117.11  3.000
 CEU  N12  C10  N11  116.54  3.000
 CEU  N12  C10  N09  127.13  3.000
 CEU  N11  C10  N09  116.31  3.000
 CEU  H14  N11  H13  115.62  3.000
 CEU  H14  N11  C10  117.28  3.000
 CEU  H13  N11  C10  117.31  3.000
 CEU  C13  N12  C10  115.81  3.000
 CEU  C16  C13  N14  121.87  3.000
 CEU  N14  C13  N12  115.76  3.000
 CEU  C16  C13  N12  122.36  3.000
 CEU  H15  N14  C15  118.78  3.000
 CEU  H15  N14  C13  116.49  3.000
 CEU  C15  N14  C13  124.66  3.000
 CEU  H18  C15  H17  108.01  3.000
 CEU  H18  C15  H16  107.83  3.000
 CEU  H17  C15  H16  107.93  3.000
 CEU  H18  C15  N14  111.95  3.000
 CEU  H17  C15  N14  112.43  3.000
 CEU  H16  C15  N14  108.52  3.000
 CEU  H19  C16  C13  120.64  3.000
 CEU  H19  C16  C08  122.82  3.000
 CEU  C13  C16  C08  116.53  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
 CEU  CONST_01  N12  C10  N09  C08     0.00   0.0  0
 CEU  CONST_02  N12  C13  C16  C08     0.00   0.0  0
 CEU  CONST_03  C13  N12  C10  N09     0.00   0.0  0
 CEU  CONST_04  C13  C16  C08  N09     0.00   0.0  0
 CEU  CONST_05  C16  C08  N09  C10     0.00   0.0  0
 CEU  CONST_06  C16  C13  N12  C10     0.00   0.0  0
 CEU  CONST_07  C10  N09  C08  N05   180.00   0.0  0
 CEU  CONST_08  C13  C16  C08  N05   180.00   0.0  0
 CEU  CONST_09  N11  C10  N09  C08   180.00   0.0  0
 CEU  CONST_10  N14  C13  C16  C08   180.00   0.0  0
 CEU  CONST_11  N14  C13  N12  C10   180.00   0.0  0
 CEU  CONST_12  C13  N12  C10  N11   180.00   0.0  0
 CEU  CONST_13  H19  C16  C08  N05     0.00   0.0  0
 CEU  CONST_14  C15  N14  C13  N12   180.00   0.0  0
 CEU  CONST_15  C16  C13  N14  C15     0.00   0.0  0
 CEU  CONST_18  H15  N14  C13  N12     0.00   0.0  0
 CEU  Var_01    N05  C06  C07  N02    52.23  30.0  1
 CEU  Var_02    N05  C04  C03  N02   -52.33  30.0  1
 CEU  Var_03    C06  C07  N02  C03   -55.02  30.0  1
 CEU  Var_04    C06  N05  C04  C03    48.23  30.0  1
 CEU  Var_05    C07  N02  C03  C04    55.09  30.0  1
 CEU  Var_06    C07  C06  N05  C04   -48.33  30.0  1
 CEU  Var_07    N09  C08  N05  C04  -169.68  30.0  2
 CEU  Var_08    H1   C01  N02  C03   -56.52  30.0  3
 CEU  Var_09    H16  C15  N14  C13   178.66  30.0  3

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
 CEU  plan-1  N05  0.020
 CEU  plan-1  C08  0.020
 CEU  plan-1  N09  0.020
 CEU  plan-1  C10  0.020
 CEU  plan-1  N11  0.020
 CEU  plan-1  N12  0.020
 CEU  plan-1  C13  0.020
 CEU  plan-1  N14  0.020
 CEU  plan-1  C16  0.020
 CEU  plan-1  H19  0.020
 CEU  plan-2  C10  0.020
 CEU  plan-2  N11  0.020
 CEU  plan-2  H13  0.020
 CEU  plan-2  H14  0.020
 CEU  plan-3  C13  0.020
 CEU  plan-3  N14  0.020
 CEU  plan-3  C15  0.020
 CEU  plan-3  H15  0.020

