# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 01:14:08 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: ~{N}4-methyl-6-piperidin-1-yl-pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(nc(N)n1)N2CCCCC2
#
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
 CJU  CJU  ~{N}4-methyl-6-piperidin-1-yl-pyrimidine-2,4-diamine  ligand  32  15  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CJU
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
 CJU  C11  C  CH3   0  -0.527  26.7724   7.1791  -18.6282
 CJU  C13  C  CH2   0  -0.307  31.0906   9.1100  -13.9931
 CJU  C15  C  CH2   0  -0.444  33.2705   8.8058  -15.2080
 CJU  C16  C  CH2   0  -0.429  32.4889   8.1826  -16.3578
 CJU  C17  C  CH2   0  -0.304  31.1886   7.5625  -15.8614
 CJU  C03  C  CR16  0  -0.577  28.3970   8.2110  -16.4639
 CJU  C04  C  CR6   0   0.580  29.0919   8.7971  -15.3932
 CJU  N05  N  N     0  -0.551  28.4796   9.6668  -14.5776
 CJU  C06  C  CR6   0   0.518  27.2044   9.9444  -14.8289
 CJU  N07  N  NH2   0  -0.825  26.6197  10.8665  -14.0176
 CJU  N08  N  N     0  -0.540  26.4503   9.4499  -15.8026
 CJU  C09  C  CR6   0   0.523  27.0603   8.5803  -16.6221
 CJU  N10  N  NH1   0  -0.650  26.2973   8.0772  -17.6118
 CJU  N12  N  NT    0  -0.499  30.3951   8.5301  -15.1292
 CJU  C14  C  CH2   0  -0.434  32.3893   9.7752  -14.4306
 CJU  H1   H  HCH3  0   0.261  25.9522   6.9581  -19.3059
 CJU  H2   H  HCH3  0   0.229  27.5877   7.6112  -19.2151
 CJU  H3   H  HCH3  0   0.231  27.1246   6.2334  -18.2092
 CJU  H4   H  HCH2  0   0.268  30.4342   9.8227  -13.5050
 CJU  H5   H  HCH2  0   0.218  31.3097   8.3172  -13.2656
 CJU  H6   H  HCH2  0   0.214  33.6201   8.0120  -14.5390
 CJU  H7   H  HCH2  0   0.236  34.1625   9.3132  -15.5813
 CJU  H8   H  HCH2  0   0.235  33.0819   7.4123  -16.8555
 CJU  H9   H  HCH2  0   0.221  32.2587   8.9440  -17.1091
 CJU  H10  H  HCH2  0   0.262  30.6309   7.1629  -16.7020
 CJU  H11  H  HCH2  0   0.227  31.4158   6.7147  -15.2025
 CJU  H12  H  HCR6  0   0.264  28.8526   7.5093  -17.1423
 CJU  H13  H  HNH2  0   0.381  25.6147  10.8998  -14.0102
 CJU  H14  H  HNH2  0   0.382  27.0669  11.0530  -13.1365
 CJU  H15  H  HNH1  0   0.384  25.3583   8.4302  -17.6780
 CJU  H16  H  HCH2  0   0.233  32.9113  10.1497  -13.5471
 CJU  H17  H  HCH2  0   0.220  32.1515  10.6430  -15.0534

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
 CJU  C11  N10  single    1.437  0.020  1.437
 CJU  N10  C09  single    1.347  0.020  1.347
 CJU  C09  C03  aromatic  1.396  0.020  1.396
 CJU  C09  N08  aromatic  1.342  0.020  1.342
 CJU  C03  C04  aromatic  1.405  0.020  1.405
 CJU  C16  C17  single    1.524  0.020  1.524
 CJU  C16  C15  single    1.524  0.020  1.524
 CJU  C17  N12  single    1.450  0.020  1.450
 CJU  N08  C06  aromatic  1.327  0.020  1.327
 CJU  C04  N12  single    1.356  0.020  1.356
 CJU  C04  N05  aromatic  1.340  0.020  1.340
 CJU  N12  C13  single    1.453  0.020  1.453
 CJU  C15  C14  single    1.523  0.020  1.523
 CJU  C06  N05  aromatic  1.329  0.020  1.329
 CJU  C06  N07  single    1.360  0.020  1.360
 CJU  C14  C13  single    1.523  0.020  1.523
 CJU  C11  H1   single    0.970  0.020  1.090
 CJU  C11  H2   single    0.970  0.020  1.090
 CJU  C11  H3   single    0.970  0.020  1.090
 CJU  C13  H4   single    0.970  0.020  1.090
 CJU  C13  H5   single    0.970  0.020  1.090
 CJU  C15  H6   single    0.970  0.020  1.090
 CJU  C15  H7   single    0.970  0.020  1.090
 CJU  C16  H8   single    0.970  0.020  1.090
 CJU  C16  H9   single    0.970  0.020  1.090
 CJU  C17  H10  single    0.970  0.020  1.090
 CJU  C17  H11  single    0.970  0.020  1.090
 CJU  C03  H12  single    0.930  0.020  1.080
 CJU  N07  H13  single    0.890  0.020  1.040
 CJU  N07  H14  single    0.890  0.020  1.040
 CJU  N10  H15  single    0.860  0.020  1.020
 CJU  C14  H16  single    0.970  0.020  1.090
 CJU  C14  H17  single    0.970  0.020  1.090

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
 CJU  H3   C11  H2   107.91  3.000
 CJU  H3   C11  H1   107.85  3.000
 CJU  H2   C11  H1   107.97  3.000
 CJU  H3   C11  N10  112.10  3.000
 CJU  H2   C11  N10  112.27  3.000
 CJU  H1   C11  N10  108.58  3.000
 CJU  H5   C13  H4   107.28  3.000
 CJU  H5   C13  C14  109.60  3.000
 CJU  H4   C13  C14  110.98  3.000
 CJU  H5   C13  N12  108.99  3.000
 CJU  H4   C13  N12  108.93  3.000
 CJU  C14  C13  N12  110.97  3.000
 CJU  H7   C15  H6   106.55  3.000
 CJU  H7   C15  C14  110.57  3.000
 CJU  H6   C15  C14  109.52  3.000
 CJU  H7   C15  C16  110.55  3.000
 CJU  H6   C15  C16  109.16  3.000
 CJU  C14  C15  C16  110.41  3.000
 CJU  H9   C16  H8   106.99  3.000
 CJU  H9   C16  C17  109.11  3.000
 CJU  H8   C16  C17  108.95  3.000
 CJU  H9   C16  C15  109.97  3.000
 CJU  H8   C16  C15  110.72  3.000
 CJU  C17  C16  C15  111.00  3.000
 CJU  H11  C17  H10  106.69  3.000
 CJU  H11  C17  N12  109.00  3.000
 CJU  H10  C17  N12  110.84  3.000
 CJU  H11  C17  C16  109.47  3.000
 CJU  H10  C17  C16  109.64  3.000
 CJU  N12  C17  C16  111.09  3.000
 CJU  H12  C03  C09  120.40  3.000
 CJU  H12  C03  C04  122.87  3.000
 CJU  C09  C03  C04  116.73  3.000
 CJU  N12  C04  N05  116.63  3.000
 CJU  N05  C04  C03  120.57  3.000
 CJU  N12  C04  C03  122.80  3.000
 CJU  C06  N05  C04  117.32  3.000
 CJU  N08  C06  N07  116.48  3.000
 CJU  N07  C06  N05  116.19  3.000
 CJU  N08  C06  N05  127.30  3.000
 CJU  H14  N07  H13  115.58  3.000
 CJU  H14  N07  C06  117.20  3.000
 CJU  H13  N07  C06  117.16  3.000
 CJU  C09  N08  C06  115.55  3.000
 CJU  N10  C09  N08  115.68  3.000
 CJU  N08  C09  C03  122.53  3.000
 CJU  N10  C09  C03  121.79  3.000
 CJU  H15  N10  C09  116.50  3.000
 CJU  H15  N10  C11  118.79  3.000
 CJU  C09  N10  C11  124.45  3.000
 CJU  C04  N12  C17  123.98  3.000
 CJU  C04  N12  C13  122.26  3.000
 CJU  C17  N12  C13  113.54  3.000
 CJU  H17  C14  H16  106.99  3.000
 CJU  H17  C14  C15  109.87  3.000
 CJU  H16  C14  C15  110.76  3.000
 CJU  H17  C14  C13  108.94  3.000
 CJU  H16  C14  C13  108.96  3.000
 CJU  C15  C14  C13  111.21  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
 CJU  CONST_01  C06  N08  C09  C03     0.00   0.0  0
 CJU  CONST_02  C06  N05  C04  C03     0.00   0.0  0
 CJU  CONST_03  N08  C09  C03  C04     0.00   0.0  0
 CJU  CONST_04  N08  C06  N05  C04     0.00   0.0  0
 CJU  CONST_05  C09  C03  C04  N05     0.00   0.0  0
 CJU  CONST_06  C09  N08  C06  N05     0.00   0.0  0
 CJU  CONST_07  N12  C04  N05  C06   180.00   0.0  0
 CJU  CONST_08  N12  C04  C03  C09   180.00   0.0  0
 CJU  CONST_09  N10  C09  C03  C04   180.00   0.0  0
 CJU  CONST_10  N07  C06  N05  C04   180.00   0.0  0
 CJU  CONST_11  N10  C09  N08  C06   180.00   0.0  0
 CJU  CONST_12  C09  N08  C06  N07   180.00   0.0  0
 CJU  CONST_13  H12  C03  C04  N05   180.00   0.0  0
 CJU  CONST_14  C03  C09  N10  C11     0.00   0.0  0
 CJU  CONST_15  N08  C09  N10  C11   180.00   0.0  0
 CJU  CONST_16  H15  N10  C09  C03   180.00   0.0  0
 CJU  Var_01    C16  C17  N12  C13   -57.47  30.0  1
 CJU  Var_02    C03  C04  N12  C13  -177.98  30.0  2
 CJU  Var_03    C16  C15  C14  C13    53.04  30.0  1
 CJU  Var_04    N12  C17  C16  C15    54.77  30.0  1
 CJU  Var_05    N12  C13  C14  C15   -54.49  30.0  1
 CJU  Var_06    C14  C15  C16  C17   -53.06  30.0  1
 CJU  Var_07    C14  C13  N12  C17    57.25  30.0  1
 CJU  Var_08    H1   C11  N10  C09  -178.56  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
 CJU  plan-1  C03  0.020
 CJU  plan-1  C04  0.020
 CJU  plan-1  N05  0.020
 CJU  plan-1  C06  0.020
 CJU  plan-1  N07  0.020
 CJU  plan-1  N08  0.020
 CJU  plan-1  C09  0.020
 CJU  plan-1  N10  0.020
 CJU  plan-1  N12  0.020
 CJU  plan-1  H12  0.020
 CJU  plan-2  C06  0.020
 CJU  plan-2  N07  0.020
 CJU  plan-2  H13  0.020
 CJU  plan-2  H14  0.020
 CJU  plan-3  C11  0.020
 CJU  plan-3  C09  0.020
 CJU  plan-3  N10  0.020
 CJU  plan-3  H15  0.020

