# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:18:41 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: 2,4-dimethyl-6-(piperazin-1-yl)pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(nc(C)n1)N2CCNCC2
#
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
 WKS  WKS  2,4-dimethyl-6-(piperazin-1-yl)pyrimidine  ligand  30  14  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WKS
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
 WKS  C10  C  CH2   0  -0.304  -41.2314   8.8072   2.4655
 WKS  N12  N  NH1   0  -0.601  -42.7594   9.5372   4.2019
 WKS  C13  C  CH2   0  -0.291  -41.6501   9.7812   5.1021
 WKS  C02  C  CR6   0   0.263  -36.4833   9.2267   3.2738
 WKS  C03  C  CR16  0  -0.459  -37.7327   9.0975   3.8373
 WKS  C04  C  CR6   0   0.579  -38.8424   9.0658   2.9666
 WKS  C06  C  CR6   0   0.338  -37.3951   9.2694   1.2047
 WKS  C07  C  CH3   0  -0.729  -37.2086   9.3919  -0.2770
 WKS  C11  C  CH2   0  -0.297  -42.3569   9.7602   2.8265
 WKS  C14  C  CH2   0  -0.301  -40.5080   8.8295   4.7823
 WKS  N05  N  N     0  -0.497  -38.6364   9.1455   1.6449
 WKS  N08  N  N     0  -0.473  -36.2996   9.3155   1.9498
 WKS  N09  N  NT    0  -0.505  -40.1201   8.9611   3.3904
 WKS  H1   H  HCH2  0   0.230  -41.5989   7.7751   2.5126
 WKS  H2   H  HCH2  0   0.272  -40.8858   8.9945   1.4542
 WKS  H3   H  HNH1  0   0.358  -43.5306  10.1474   4.4378
 WKS  H5   H  HCH2  0   0.200  -41.2692  10.8132   5.0440
 WKS  H6   H  HCH2  0   0.242  -41.9713   9.6081   6.1307
 WKS  H7   H  HCH3  0   0.252  -34.5579   8.4860   3.8355
 WKS  H8   H  HCH3  0   0.253  -34.7349  10.2238   3.9899
 WKS  H9   H  HCH3  0   0.243  -35.4862   9.1587   5.1823
 WKS  H10  H  HCR6  0   0.268  -37.8238   9.0217   4.9095
 WKS  H11  H  HCH3  0   0.243  -38.1098   9.1058  -0.8141
 WKS  H12  H  HCH3  0   0.253  -36.9703  10.4247  -0.5392
 WKS  H13  H  HCH3  0   0.247  -36.3767   8.7760  -0.6165
 WKS  H14  H  HCH2  0   0.198  -42.0175  10.7919   2.6419
 WKS  H15  H  HCH2  0   0.240  -43.2037   9.5710   2.1644
 WKS  H16  H  HCH2  0   0.237  -40.8218   7.7981   4.9793
 WKS  H17  H  HCH2  0   0.263  -39.6759   9.0491   5.4444
 WKS  C01  C  CH3   0  -0.720  -35.2543   9.2738   4.1253

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
 WKS  C07  C06  single    1.498  0.020  1.498
 WKS  C06  N05  aromatic  1.323  0.020  1.323
 WKS  C06  N08  aromatic  1.326  0.020  1.326
 WKS  N05  C04  aromatic  1.340  0.020  1.340
 WKS  N08  C02  aromatic  1.340  0.020  1.340
 WKS  C10  C11  single    1.518  0.020  1.518
 WKS  C10  N09  single    1.454  0.020  1.454
 WKS  C04  N09  single    1.350  0.020  1.350
 WKS  C04  C03  aromatic  1.411  0.020  1.411
 WKS  C11  N12  single    1.450  0.020  1.450
 WKS  N09  C14  single    1.451  0.020  1.451
 WKS  C02  C03  aromatic  1.377  0.020  1.377
 WKS  C02  C01  single    1.496  0.020  1.496
 WKS  N12  C13  single    1.449  0.020  1.449
 WKS  C14  C13  single    1.521  0.020  1.521
 WKS  C10  H1   single    0.970  0.020  1.090
 WKS  C10  H2   single    0.970  0.020  1.090
 WKS  N12  H3   single    0.890  0.020  1.040
 WKS  C13  H5   single    0.970  0.020  1.090
 WKS  C13  H6   single    0.970  0.020  1.090
 WKS  C01  H7   single    0.970  0.020  1.090
 WKS  C01  H8   single    0.970  0.020  1.090
 WKS  C01  H9   single    0.970  0.020  1.090
 WKS  C03  H10  single    0.930  0.020  1.080
 WKS  C07  H11  single    0.970  0.020  1.090
 WKS  C07  H12  single    0.970  0.020  1.090
 WKS  C07  H13  single    0.970  0.020  1.090
 WKS  C11  H14  single    0.970  0.020  1.090
 WKS  C11  H15  single    0.970  0.020  1.090
 WKS  C14  H16  single    0.970  0.020  1.090
 WKS  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
 WKS  H2   C10  H1   108.02  3.000
 WKS  H2   C10  N09  109.34  3.000
 WKS  H1   C10  N09  109.18  3.000
 WKS  H2   C10  C11  110.45  3.000
 WKS  H1   C10  C11  109.39  3.000
 WKS  N09  C10  C11  110.42  3.000
 WKS  H3   N12  C11  109.88  3.000
 WKS  H3   N12  C13  109.71  3.000
 WKS  C11  N12  C13  110.53  3.000
 WKS  H6   C13  H5   107.46  3.000
 WKS  H6   C13  C14  108.66  3.000
 WKS  H5   C13  C14  108.39  3.000
 WKS  H6   C13  N12  109.48  3.000
 WKS  H5   C13  N12  112.93  3.000
 WKS  C14  C13  N12  109.81  3.000
 WKS  N08  C02  C03  122.36  3.000
 WKS  C03  C02  C01  121.04  3.000
 WKS  N08  C02  C01  116.60  3.000
 WKS  H10  C03  C04  123.05  3.000
 WKS  H10  C03  C02  119.35  3.000
 WKS  C04  C03  C02  117.60  3.000
 WKS  N09  C04  N05  117.37  3.000
 WKS  N09  C04  C03  123.53  3.000
 WKS  N05  C04  C03  119.11  3.000
 WKS  N08  C06  N05  126.28  3.000
 WKS  N08  C06  C07  116.75  3.000
 WKS  N05  C06  C07  116.97  3.000
 WKS  H13  C07  H12  107.06  3.000
 WKS  H13  C07  H11  109.29  3.000
 WKS  H12  C07  H11  108.12  3.000
 WKS  H13  C07  C06  110.91  3.000
 WKS  H12  C07  C06  109.99  3.000
 WKS  H11  C07  C06  111.33  3.000
 WKS  H15  C11  H14  107.45  3.000
 WKS  H15  C11  N12  109.47  3.000
 WKS  H14  C11  N12  112.85  3.000
 WKS  H15  C11  C10  108.79  3.000
 WKS  H14  C11  C10  108.64  3.000
 WKS  N12  C11  C10  109.55  3.000
 WKS  H17  C14  H16  107.47  3.000
 WKS  H17  C14  N09  111.21  3.000
 WKS  H16  C14  N09  109.53  3.000
 WKS  H17  C14  C13  108.71  3.000
 WKS  H16  C14  C13  109.64  3.000
 WKS  N09  C14  C13  110.23  3.000
 WKS  C06  N05  C04  118.56  3.000
 WKS  C06  N08  C02  116.09  3.000
 WKS  C14  N09  C04  124.13  3.000
 WKS  C14  N09  C10  113.35  3.000
 WKS  C04  N09  C10  122.12  3.000
 WKS  H9   C01  H8   108.30  3.000
 WKS  H9   C01  H7   108.52  3.000
 WKS  H8   C01  H7   106.98  3.000
 WKS  H9   C01  C02  111.99  3.000
 WKS  H8   C01  C02  110.36  3.000
 WKS  H7   C01  C02  110.52  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
 WKS  CONST_01  N05  C06  N08  C02     0.00   0.0  0
 WKS  CONST_02  N05  C04  C03  C02     0.00   0.0  0
 WKS  CONST_03  C06  N05  C04  C03     0.00   0.0  0
 WKS  CONST_04  C06  N08  C02  C03     0.00   0.0  0
 WKS  CONST_05  N08  C06  N05  C04     0.00   0.0  0
 WKS  CONST_06  N08  C02  C03  C04     0.00   0.0  0
 WKS  CONST_07  N09  C04  C03  C02   180.00   0.0  0
 WKS  CONST_08  N09  C04  N05  C06   180.00   0.0  0
 WKS  CONST_09  C06  N08  C02  C01   180.00   0.0  0
 WKS  CONST_10  C04  C03  C02  C01   180.00   0.0  0
 WKS  CONST_11  C07  C06  N08  C02   180.00   0.0  0
 WKS  CONST_12  C07  C06  N05  C04   180.00   0.0  0
 WKS  CONST_13  H10  C03  C04  N05   180.00   0.0  0
 WKS  Var_01    C13  N12  C11  C10    60.73  30.0  1
 WKS  Var_02    N05  C04  N09  C10     5.93  30.0  3
 WKS  Var_03    C13  C14  N09  C10   -53.61  30.0  1
 WKS  Var_04    N09  C10  C11  N12   -56.17  30.0  1
 WKS  Var_05    N09  C14  C13  N12    56.04  30.0  1
 WKS  Var_06    C11  C10  N09  C04  -133.06  30.0  1
 WKS  Var_07    C14  C13  N12  C11   -60.75  30.0  1
 WKS  Var_08    H7   C01  C02  C03   123.22  30.0  2
 WKS  Var_09    H11  C07  C06  N05   -14.73  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
 WKS  plan-1  C02  0.020
 WKS  plan-1  C03  0.020
 WKS  plan-1  C04  0.020
 WKS  plan-1  C06  0.020
 WKS  plan-1  C07  0.020
 WKS  plan-1  N05  0.020
 WKS  plan-1  N08  0.020
 WKS  plan-1  N09  0.020
 WKS  plan-1  H10  0.020
 WKS  plan-1  C01  0.020

