# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:12:50 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: 1-[(oxan-4-yl)methyl]piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCN1)CC2CCOCC2
#
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
 WLA  WLA  1-[(oxan-4-yl)methyl]piperazine  ligand  33  13  .  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_WLA
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
 WLA  C10  C  C     0  -0.331  -32.4673  -6.1577  -20.6288
 WLA  C13  C  C     0  -0.317  -31.0461  -7.5167  -18.8437
 WLA  C01  C  CH2   0  -0.301  -29.6266  -8.6273  -20.4900
 WLA  C02  C  CH1   0  -0.259  -28.3660  -7.7349  -20.5013
 WLA  C03  C  CH2   0  -0.457  -27.2127  -8.3583  -19.7154
 WLA  C04  C  CH2   0  -0.177  -25.9726  -7.4826  -19.7931
 WLA  C06  C  CH2   0  -0.177  -26.5899  -6.6084  -21.8760
 WLA  C07  C  CH2   0  -0.455  -27.8676  -7.4304  -21.9153
 WLA  C09  C  C     0  -0.261  -31.2705  -6.9565  -21.1592
 WLA  C12  C  C     0  -0.270  -32.5396  -7.3281  -18.5417
 WLA  N08  N  NR6   0  -0.409  -30.8881  -7.9808  -20.2039
 WLA  N11  N  NR16  0  -0.600  -33.2627  -7.0067  -19.7670
 WLA  O05  O  O2    0  -0.486  -25.5750  -7.2407  -21.1260
 WLA  H1   H  H     0   0.197  -32.1095  -5.2498  -20.1190
 WLA  H2   H  H     0   0.242  -33.0769  -5.8159  -21.4667
 WLA  H3   H  H     0   0.241  -30.6309  -8.2607  -18.1606
 WLA  H4   H  H     0   0.199  -30.4960  -6.5825  -18.6440
 WLA  H5   H  HCH2  0   0.226  -29.7175  -9.1343  -21.4578
 WLA  H6   H  HCH2  0   0.231  -29.4998  -9.4202  -19.7464
 WLA  H7   H  HCH1  0   0.227  -28.6121  -6.7805  -20.0153
 WLA  H8   H  HCH2  0   0.233  -27.4916  -8.4914  -18.6664
 WLA  H9   H  HCH2  0   0.222  -26.9880  -9.3541  -20.1140
 WLA  H10  H  HCH2  0   0.231  -25.1266  -7.9554  -19.2908
 WLA  H11  H  HCH2  0   0.191  -26.1710  -6.5303  -19.2774
 WLA  H12  H  HCH2  0   0.231  -26.1927  -6.4566  -22.8816
 WLA  H13  H  HCH2  0   0.192  -26.8099  -5.6143  -21.4573
 WLA  H14  H  HCH2  0   0.237  -28.6207  -6.8903  -22.4947
 WLA  H15  H  HCH2  0   0.221  -27.6801  -8.3723  -22.4425
 WLA  H16  H  H     0   0.218  -31.5183  -7.4415  -22.1090
 WLA  H17  H  H     0   0.196  -30.4590  -6.2427  -21.3685
 WLA  H18  H  H     0   0.198  -32.6415  -6.5536  -17.7695
 WLA  H19  H  H     0   0.215  -32.9519  -8.2502  -18.1231
 WLA  H21  H  HNR6  0   0.351  -34.1333  -6.5480  -19.5364

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
 WLA  C06  C07  single  1.520  0.020  1.520
 WLA  C06  O05  single  1.412  0.020  1.412
 WLA  C07  C02  single  1.530  0.020  1.530
 WLA  O05  C04  single  1.412  0.020  1.412
 WLA  C10  C09  single  1.534  0.020  1.534
 WLA  C10  N11  single  1.448  0.020  1.448
 WLA  C09  N08  single  1.452  0.020  1.452
 WLA  C02  C01  single  1.545  0.020  1.545
 WLA  C02  C03  single  1.529  0.020  1.529
 WLA  C04  C03  single  1.520  0.020  1.520
 WLA  N11  C12  single  1.459  0.020  1.459
 WLA  C01  N08  single  1.446  0.020  1.446
 WLA  N08  C13  single  1.446  0.020  1.446
 WLA  C12  C13  single  1.535  0.020  1.535
 WLA  C10  H1   single  0.970  0.020  1.090
 WLA  C10  H2   single  0.970  0.020  1.090
 WLA  C13  H3   single  0.970  0.020  1.090
 WLA  C13  H4   single  0.970  0.020  1.090
 WLA  C01  H5   single  0.970  0.020  1.090
 WLA  C01  H6   single  0.970  0.020  1.090
 WLA  C02  H7   single  0.970  0.020  1.090
 WLA  C03  H8   single  0.970  0.020  1.090
 WLA  C03  H9   single  0.970  0.020  1.090
 WLA  C04  H10  single  0.970  0.020  1.090
 WLA  C04  H11  single  0.970  0.020  1.090
 WLA  C06  H12  single  0.970  0.020  1.090
 WLA  C06  H13  single  0.970  0.020  1.090
 WLA  C07  H14  single  0.970  0.020  1.090
 WLA  C07  H15  single  0.970  0.020  1.090
 WLA  C09  H16  single  0.970  0.020  1.090
 WLA  C09  H17  single  0.970  0.020  1.090
 WLA  C12  H18  single  0.970  0.020  1.090
 WLA  C12  H19  single  0.970  0.020  1.090
 WLA  N11  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
 WLA  H2   C10  H1   106.19  3.000
 WLA  H2   C10  N11  109.51  3.000
 WLA  H1   C10  N11  112.73  3.000
 WLA  H2   C10  C09  109.49  3.000
 WLA  H1   C10  C09  109.64  3.000
 WLA  N11  C10  C09  109.22  3.000
 WLA  H4   C13  H3   105.93  3.000
 WLA  H4   C13  N08  112.83  3.000
 WLA  H3   C13  N08  109.17  3.000
 WLA  H4   C13  C12  110.22  3.000
 WLA  H3   C13  C12  109.30  3.000
 WLA  N08  C13  C12  109.31  3.000
 WLA  H6   C01  H5   105.92  3.000
 WLA  H6   C01  N08  106.89  3.000
 WLA  H5   C01  N08  108.00  3.000
 WLA  H6   C01  C02  109.21  3.000
 WLA  H5   C01  C02  109.17  3.000
 WLA  N08  C01  C02  117.08  3.000
 WLA  H7   C02  C07  107.99  3.000
 WLA  H7   C02  C03  107.21  3.000
 WLA  C07  C02  C03  108.10  3.000
 WLA  H7   C02  C01  108.40  3.000
 WLA  C03  C02  C01  112.11  3.000
 WLA  C07  C02  C01  112.81  3.000
 WLA  H9   C03  H8   106.89  3.000
 WLA  H9   C03  C04  109.73  3.000
 WLA  H8   C03  C04  109.10  3.000
 WLA  H9   C03  C02  109.77  3.000
 WLA  H8   C03  C02  110.51  3.000
 WLA  C04  C03  C02  110.75  3.000
 WLA  H11  C04  H10  107.38  3.000
 WLA  H11  C04  O05  110.16  3.000
 WLA  H10  C04  O05  106.88  3.000
 WLA  H11  C04  C03  109.11  3.000
 WLA  H10  C04  C03  111.06  3.000
 WLA  O05  C04  C03  112.13  3.000
 WLA  H13  C06  H12  107.30  3.000
 WLA  H13  C06  O05  110.25  3.000
 WLA  H12  C06  O05  106.86  3.000
 WLA  H13  C06  C07  109.28  3.000
 WLA  H12  C06  C07  110.94  3.000
 WLA  O05  C06  C07  112.08  3.000
 WLA  H15  C07  H14  106.72  3.000
 WLA  H15  C07  C06  109.49  3.000
 WLA  H14  C07  C06  109.01  3.000
 WLA  H15  C07  C02  109.23  3.000
 WLA  H14  C07  C02  111.34  3.000
 WLA  C06  C07  C02  110.96  3.000
 WLA  H17  C09  H16  106.81  3.000
 WLA  H17  C09  N08  112.86  3.000
 WLA  H16  C09  N08  108.54  3.000
 WLA  H17  C09  C10  107.66  3.000
 WLA  H16  C09  C10  110.74  3.000
 WLA  N08  C09  C10  110.21  3.000
 WLA  H19  C12  H18  106.89  3.000
 WLA  H19  C12  N11  108.69  3.000
 WLA  H18  C12  N11  112.90  3.000
 WLA  H19  C12  C13  109.79  3.000
 WLA  H18  C12  C13  108.37  3.000
 WLA  N11  C12  C13  110.13  3.000
 WLA  C09  N08  C01  114.51  3.000
 WLA  C01  N08  C13  115.14  3.000
 WLA  C09  N08  C13  111.33  3.000
 WLA  H21  N11  C12  109.60  3.000
 WLA  H21  N11  C10  110.05  3.000
 WLA  C12  N11  C10  110.91  3.000
 WLA  C06  O05  C04  112.08  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
 WLA  Var_01  C13  N08  C09  C10  -36.41  30.0  1
 WLA  Var_02  C13  C12  N11  C10  -36.81  30.0  1
 WLA  Var_03  O05  C06  C07  C02   56.27  30.0  1
 WLA  Var_04  O05  C04  C03  C02  -56.64  30.0  1
 WLA  Var_05  C07  C06  O05  C04  -58.68  30.0  1
 WLA  Var_06  C12  N11  C10  C09   68.12  30.0  1
 WLA  Var_07  N11  C10  C09  N08  -29.09  30.0  1
 WLA  Var_08  N11  C12  C13  N08  -28.44  30.0  1
 WLA  Var_09  C02  C01  N08  C13  -69.46  30.0  1

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
 WLA  chir_01  C02  C07  C01  C03  negativ

