# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 23:40:16 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-[2-oxo-2-(piperidin-1-yl)ethyl]piperazin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CN1CC[NH2+]CC1)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
 4XE  4XE  4-[2-oxo-2-(piperidin-1-yl)ethyl]piperazin-1-ium  ligand  37  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4XE
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
 4XE  C2   C  C     0   0.547  -0.5898  -0.3501  -0.6420
 4XE  C3   C  CH2   0  -0.424   0.4122   0.7326  -0.2444
 4XE  N4   N  NT    0  -0.417   1.7666   0.2386  -0.2331
 4XE  C5   C  CH2   0  -0.309   2.0586  -0.5823   0.9267
 4XE  C6   C  CH2   0  -0.328   3.4227  -1.2200   0.7892
 4XE  C8   C  CH2   0  -0.328   4.1271   0.7510  -0.5174
 4XE  C11  C  CH2   0  -0.309  -2.9370  -0.9721  -0.8980
 4XE  C12  C  CH2   0  -0.433  -3.8549  -1.0854   0.3134
 4XE  C13  C  CH2   0  -0.446  -4.4211   0.2760   0.7015
 4XE  C14  C  CH2   0  -0.428  -3.3035   1.2973   0.8814
 4XE  C15  C  CH2   0  -0.322  -2.4005   1.3337  -0.3446
 4XE  O1   O  O     0  -0.496  -0.2121  -1.4761  -0.9345
 4XE  N7   N  NT2   1  -0.642   4.4546  -0.1607   0.6124
 4XE  C9   C  CH2   0  -0.304   2.7346   1.3137  -0.3321
 4XE  N10  N  NT    0  -0.453  -1.8895   0.0072  -0.6509
 4XE  H16  H  HCH2  0   0.288   0.3494   1.5472  -0.9713
 4XE  H17  H  HCH2  0   0.246   0.1213   1.1678   0.7250
 4XE  H19  H  HCH2  0   0.227   2.0161  -0.0002   1.8634
 4XE  H18  H  HCH2  0   0.282   1.3315  -1.3869   1.0136
 4XE  H20  H  HCH2  0   0.306   3.6869  -1.7949   1.6730
 4XE  H21  H  HCH2  0   0.295   3.4723  -1.8615  -0.0881
 4XE  H25  H  HCH2  0   0.307   4.8765   1.5382  -0.5380
 4XE  H24  H  HCH2  0   0.295   4.1960   0.1633  -1.4308
 4XE  H28  H  HCH2  0   0.235  -3.5129  -0.6546  -1.7741
 4XE  H31  H  HCH2  0   0.238  -4.6601  -1.7876   0.0866
 4XE  H30  H  HCH2  0   0.224  -3.2900  -1.5076   1.1497
 4XE  H32  H  HCH2  0   0.217  -5.1015   0.6212  -0.0843
 4XE  H33  H  HCH2  0   0.239  -5.0149   0.1976   1.6143
 4XE  H35  H  HCH2  0   0.240  -3.7150   2.2948   1.0492
 4XE  H34  H  HCH2  0   0.224  -2.7025   1.0476   1.7610
 4XE  H37  H  HCH2  0   0.243  -2.9699   1.6882  -1.2106
 4XE  H36  H  HCH2  0   0.273  -1.5904   2.0429  -0.2022
 4XE  H23  H  HNT2  0   0.464   4.5416   0.3784   1.4758
 4XE  H22  H  HNT2  0   0.480   5.3698  -0.5857   0.4644
 4XE  H26  H  HCH2  0   0.280   2.5146   1.9318  -1.2036
 4XE  H27  H  HCH2  0   0.228   2.7192   1.9777   0.5478
 4XE  H29  H  HCH2  0   0.262  -2.4852  -1.9307  -1.1371

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
 4XE  C13  C12  single  1.525  0.020  1.525
 4XE  C13  C14  single  1.525  0.020  1.525
 4XE  C12  C11  single  1.524  0.020  1.524
 4XE  C14  C15  single  1.523  0.020  1.523
 4XE  C11  N10  single  1.455  0.020  1.455
 4XE  C15  N10  single  1.454  0.020  1.454
 4XE  N10  C2   single  1.348  0.020  1.348
 4XE  C2   O1   double  1.223  0.020  1.223
 4XE  C2   C3   single  1.528  0.020  1.528
 4XE  C3   N4   single  1.442  0.020  1.442
 4XE  N4   C9   single  1.450  0.020  1.450
 4XE  N4   C5   single  1.451  0.020  1.451
 4XE  C9   C8   single  1.513  0.020  1.513
 4XE  C5   C6   single  1.512  0.020  1.512
 4XE  C8   N7   single  1.488  0.020  1.488
 4XE  C6   N7   single  1.489  0.020  1.489
 4XE  C3   H16  single  0.970  0.020  1.090
 4XE  C3   H17  single  0.970  0.020  1.090
 4XE  C5   H19  single  0.970  0.020  1.090
 4XE  C5   H18  single  0.970  0.020  1.090
 4XE  C6   H20  single  0.970  0.020  1.090
 4XE  C6   H21  single  0.970  0.020  1.090
 4XE  C8   H25  single  0.970  0.020  1.090
 4XE  C8   H24  single  0.970  0.020  1.090
 4XE  C11  H29  single  0.970  0.020  1.090
 4XE  C11  H28  single  0.970  0.020  1.090
 4XE  C12  H31  single  0.970  0.020  1.090
 4XE  C12  H30  single  0.970  0.020  1.090
 4XE  C13  H32  single  0.970  0.020  1.090
 4XE  C13  H33  single  0.970  0.020  1.090
 4XE  C14  H35  single  0.970  0.020  1.090
 4XE  C14  H34  single  0.970  0.020  1.090
 4XE  C15  H37  single  0.970  0.020  1.090
 4XE  C15  H36  single  0.970  0.020  1.090
 4XE  N7   H23  single  0.890  0.020  1.040
 4XE  N7   H22  single  0.890  0.020  1.040
 4XE  C9   H26  single  0.970  0.020  1.090
 4XE  C9   H27  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
 4XE  N10  C2   O1   122.70  3.000
 4XE  O1   C2   C3   120.80  3.000
 4XE  N10  C2   C3   116.50  3.000
 4XE  H17  C3   H16  105.99  3.000
 4XE  H17  C3   N4   112.12  3.000
 4XE  H16  C3   N4   108.32  3.000
 4XE  H17  C3   C2   109.62  3.000
 4XE  H16  C3   C2   108.49  3.000
 4XE  N4   C3   C2   112.04  3.000
 4XE  C9   N4   C5   109.86  3.000
 4XE  C5   N4   C3   112.91  3.000
 4XE  C9   N4   C3   111.88  3.000
 4XE  H18  C5   H19  107.25  3.000
 4XE  H18  C5   C6   107.36  3.000
 4XE  H19  C5   C6   109.53  3.000
 4XE  H18  C5   N4   110.36  3.000
 4XE  H19  C5   N4   111.86  3.000
 4XE  C6   C5   N4   110.34  3.000
 4XE  H21  C6   H20  109.43  3.000
 4XE  H21  C6   N7   106.98  3.000
 4XE  H20  C6   N7   107.72  3.000
 4XE  H21  C6   C5   111.29  3.000
 4XE  H20  C6   C5   111.62  3.000
 4XE  N7   C6   C5   109.62  3.000
 4XE  H24  C8   H25  109.36  3.000
 4XE  H24  C8   C9   111.22  3.000
 4XE  H25  C8   C9   111.56  3.000
 4XE  H24  C8   N7   107.00  3.000
 4XE  H25  C8   N7   107.83  3.000
 4XE  C9   C8   N7   109.71  3.000
 4XE  H28  C11  H29  107.36  3.000
 4XE  H28  C11  N10  108.61  3.000
 4XE  H29  C11  N10  109.38  3.000
 4XE  H28  C11  C12  109.91  3.000
 4XE  H29  C11  C12  111.09  3.000
 4XE  N10  C11  C12  110.40  3.000
 4XE  H30  C12  H31  106.94  3.000
 4XE  H30  C12  C13  109.99  3.000
 4XE  H31  C12  C13  110.68  3.000
 4XE  H30  C12  C11  108.98  3.000
 4XE  H31  C12  C11  109.07  3.000
 4XE  C13  C12  C11  111.07  3.000
 4XE  H33  C13  H32  106.54  3.000
 4XE  H33  C13  C14  110.37  3.000
 4XE  H32  C13  C14  109.21  3.000
 4XE  H33  C13  C12  110.52  3.000
 4XE  H32  C13  C12  109.24  3.000
 4XE  C14  C13  C12  110.85  3.000
 4XE  H34  C14  H35  106.98  3.000
 4XE  H34  C14  C15  109.08  3.000
 4XE  H35  C14  C15  108.98  3.000
 4XE  H34  C14  C13  110.16  3.000
 4XE  H35  C14  C13  110.72  3.000
 4XE  C15  C14  C13  110.83  3.000
 4XE  H36  C15  H37  106.26  3.000
 4XE  H36  C15  N10  111.18  3.000
 4XE  H37  C15  N10  108.14  3.000
 4XE  H36  C15  C14  110.63  3.000
 4XE  H37  C15  C14  109.63  3.000
 4XE  N10  C15  C14  110.86  3.000
 4XE  H22  N7   H23  105.43  3.000
 4XE  H22  N7   C8   110.03  3.000
 4XE  H23  N7   C8   109.70  3.000
 4XE  H22  N7   C6   110.03  3.000
 4XE  H23  N7   C6   109.51  3.000
 4XE  C8   N7   C6   111.93  3.000
 4XE  H27  C9   H26  107.07  3.000
 4XE  H27  C9   C8   109.55  3.000
 4XE  H26  C9   C8   107.37  3.000
 4XE  H27  C9   N4   112.50  3.000
 4XE  H26  C9   N4   109.87  3.000
 4XE  C8   C9   N4   110.30  3.000
 4XE  C15  N10  C11  113.37  3.000
 4XE  C15  N10  C2   125.40  3.000
 4XE  C11  N10  C2   121.12  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
 4XE  CONST_01  C11  N10  C2   C3   180.00   0.0  0
 4XE  CONST_02  C15  N10  C2   C3     0.00   0.0  0
 4XE  CONST_03  O1   C2   N10  C11    0.00   0.0  0
 4XE  CONST_04  O1   C2   N10  C15  180.00   0.0  0
 4XE  Var_01    N7   C8   C9   N4   -57.37  30.0  1
 4XE  Var_02    N7   C6   C5   N4    57.48  30.0  1
 4XE  Var_03    C8   C9   N4   C5    61.89  30.0  1
 4XE  Var_04    C8   N7   C6   C5   -54.03  30.0  1
 4XE  Var_05    C9   N4   C5   C6   -62.01  30.0  1
 4XE  Var_06    C9   C8   N7   C6    53.98  30.0  1
 4XE  Var_07    C14  C13  C12  C11  -52.94  30.0  1
 4XE  Var_08    C14  C15  N10  C11   58.56  30.0  1
 4XE  Var_09    C15  C14  C13  C12   52.62  30.0  1
 4XE  Var_10    C15  N10  C11  C12  -58.50  30.0  1
 4XE  Var_11    N10  C11  C12  C13   54.95  30.0  1
 4XE  Var_12    N10  C15  C14  C13  -54.68  30.0  1
 4XE  Var_13    N10  C2   C3   N4   178.48  30.0  1

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
 4XE  plan-1  C2   0.020
 4XE  plan-1  C3   0.020
 4XE  plan-1  C11  0.020
 4XE  plan-1  C15  0.020
 4XE  plan-1  O1   0.020
 4XE  plan-1  N10  0.020

