# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 23:04:49 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 2-[4-(3-chlorophenyl)piperazin-1-ium-1-yl]ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(c1)N2CC[NH+](CC2)CC#N
#
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
 A6Z  A6Z  2-[4-(3-chlorophenyl)piperazin-1-ium-1-yl]ethanenitrile  ligand  31  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A6Z
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
 A6Z  C12  C   CSP   0   0.115  -5.4108   0.2221  -0.2404
 A6Z  C11  C   CH2   0  -0.365  -4.3148   1.1773  -0.2898
 A6Z  C10  C   CH2   0  -0.338  -0.6888   1.0122   0.7644
 A6Z  C9   C   CH2   0  -0.327  -1.9721   1.6178   0.2464
 A6Z  C8   C   CH2   0  -0.326  -2.6069  -0.5978  -0.5917
 A6Z  C7   C   CH2   0  -0.340  -1.3022  -1.1471  -0.0576
 A6Z  C4   C   CR16  0  -0.284   2.0500   0.4558  -0.2033
 A6Z  C5   C   CR6   0  -0.025   3.3796   0.0816  -0.1937
 A6Z  C6   C   CR16  0  -0.246   3.7759  -1.2357  -0.0154
 A6Z  C3   C   CR6   0   0.375   1.0526  -0.5085  -0.0105
 A6Z  C2   C   CR16  0  -0.347   1.4409  -1.8371   0.1789
 A6Z  C1   C   CR16  0  -0.246   2.7843  -2.1856   0.1643
 A6Z  N1   N   NT    0  -0.522  -0.2886  -0.1185  -0.0521
 A6Z  N2   N   NT1   1  -0.545  -3.0527   0.5812   0.2144
 A6Z  N3   N   NS    0  -0.209  -6.2849  -0.5211  -0.2012
 A6Z  H1   H   HCH2  0   0.374  -4.1599   1.5087  -1.3162
 A6Z  H2   H   HCH2  0   0.381  -4.5619   2.0426   0.3246
 A6Z  H3   H   HCH2  0   0.303   0.0591   1.8006   0.7376
 A6Z  H4   H   HCH2  0   0.263  -0.8092   0.7224   1.8179
 A6Z  H5   H   HCH2  0   0.328  -2.3084   2.4246   0.8941
 A6Z  H6   H   HCH2  0   0.316  -1.8568   1.9902  -0.7706
 A6Z  H7   H   HCH2  0   0.317  -2.5027  -0.2548  -1.6203
 A6Z  H8   H   HCH2  0   0.325  -3.3809  -1.3607  -0.5402
 A6Z  H9   H   HCH2  0   0.258  -1.4620  -1.5890   0.9370
 A6Z  H10  H   HCH2  0   0.302  -1.0208  -1.9550  -0.7321
 A6Z  H11  H   HCR6  0   0.287   1.7893   1.4894  -0.3866
 A6Z  H12  H   HCR6  0   0.277   4.8215  -1.5096  -0.0152
 A6Z  H13  H   HCR6  0   0.279   0.7097  -2.6142   0.3495
 A6Z  H14  H   HCR6  0   0.270   3.0608  -3.2211   0.3124
 A6Z  H15  H   HNT1  0   0.478  -3.2132   0.2736   1.1783
 A6Z  CL1  CL  CL    0  -0.129   4.5893   1.3019  -0.4375

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
 A6Z  C6   C1   aromatic  1.385  0.020  1.385
 A6Z  C6   C5   aromatic  1.387  0.020  1.387
 A6Z  C1   C2   aromatic  1.388  0.020  1.388
 A6Z  CL1  C5   single    1.736  0.020  1.736
 A6Z  C5   C4   aromatic  1.381  0.020  1.381
 A6Z  C2   C3   aromatic  1.397  0.020  1.397
 A6Z  C4   C3   aromatic  1.401  0.020  1.401
 A6Z  C3   N1   single    1.397  0.020  1.397
 A6Z  C7   N1   single    1.444  0.020  1.444
 A6Z  C7   C8   single    1.513  0.020  1.513
 A6Z  N1   C10  single    1.451  0.020  1.451
 A6Z  C8   N2   single    1.496  0.020  1.496
 A6Z  C10  C9   single    1.511  0.020  1.511
 A6Z  C9   N2   single    1.498  0.020  1.498
 A6Z  N2   C11  single    1.484  0.020  1.484
 A6Z  C11  C12  single    1.455  0.020  1.455
 A6Z  C12  N3   triple    1.148  0.020  1.148
 A6Z  C11  H1   single    0.970  0.020  1.090
 A6Z  C11  H2   single    0.970  0.020  1.090
 A6Z  C10  H3   single    0.970  0.020  1.090
 A6Z  C10  H4   single    0.970  0.020  1.090
 A6Z  C9   H5   single    0.970  0.020  1.090
 A6Z  C9   H6   single    0.970  0.020  1.090
 A6Z  C8   H7   single    0.970  0.020  1.090
 A6Z  C8   H8   single    0.970  0.020  1.090
 A6Z  C7   H9   single    0.970  0.020  1.090
 A6Z  C7   H10  single    0.970  0.020  1.090
 A6Z  C4   H11  single    0.930  0.020  1.080
 A6Z  C6   H12  single    0.930  0.020  1.080
 A6Z  C2   H13  single    0.930  0.020  1.080
 A6Z  C1   H14  single    0.930  0.020  1.080
 A6Z  N2   H15  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
 A6Z  N3   C12  C11  180.00  3.000
 A6Z  H2   C11  H1   108.77  3.000
 A6Z  H2   C11  N2   108.68  3.000
 A6Z  H1   C11  N2   108.75  3.000
 A6Z  H2   C11  C12  109.35  3.000
 A6Z  H1   C11  C12  109.80  3.000
 A6Z  N2   C11  C12  111.44  3.000
 A6Z  H4   C10  H3   106.87  3.000
 A6Z  H4   C10  N1   111.35  3.000
 A6Z  H3   C10  N1   111.20  3.000
 A6Z  H4   C10  C9   109.95  3.000
 A6Z  H3   C10  C9   106.58  3.000
 A6Z  N1   C10  C9   110.72  3.000
 A6Z  H6   C9   H5   109.57  3.000
 A6Z  H6   C9   N2   107.04  3.000
 A6Z  H5   C9   N2   107.64  3.000
 A6Z  H6   C9   C10  111.55  3.000
 A6Z  H5   C9   C10  110.84  3.000
 A6Z  N2   C9   C10  110.05  3.000
 A6Z  H8   C8   H7   109.48  3.000
 A6Z  H8   C8   N2   108.36  3.000
 A6Z  H7   C8   N2   106.80  3.000
 A6Z  H8   C8   C7   110.01  3.000
 A6Z  H7   C8   C7   111.43  3.000
 A6Z  N2   C8   C7   110.66  3.000
 A6Z  H10  C7   H9   107.42  3.000
 A6Z  H10  C7   N1   110.44  3.000
 A6Z  H9   C7   N1   112.62  3.000
 A6Z  H10  C7   C8   105.87  3.000
 A6Z  H9   C7   C8   109.87  3.000
 A6Z  N1   C7   C8   110.37  3.000
 A6Z  H11  C4   C3   120.64  3.000
 A6Z  H11  C4   C5   119.47  3.000
 A6Z  C3   C4   C5   119.87  3.000
 A6Z  CL1  C5   C6   119.12  3.000
 A6Z  CL1  C5   C4   118.65  3.000
 A6Z  C6   C5   C4   122.22  3.000
 A6Z  H12  C6   C1   121.25  3.000
 A6Z  H12  C6   C5   121.13  3.000
 A6Z  C1   C6   C5   117.61  3.000
 A6Z  N1   C3   C2   122.43  3.000
 A6Z  N1   C3   C4   119.16  3.000
 A6Z  C2   C3   C4   118.39  3.000
 A6Z  H13  C2   C1   118.43  3.000
 A6Z  H13  C2   C3   121.14  3.000
 A6Z  C1   C2   C3   120.43  3.000
 A6Z  H14  C1   C2   119.09  3.000
 A6Z  H14  C1   C6   119.42  3.000
 A6Z  C2   C1   C6   121.48  3.000
 A6Z  C3   N1   C7   118.36  3.000
 A6Z  C7   N1   C10  111.32  3.000
 A6Z  C3   N1   C10  117.74  3.000
 A6Z  H15  N2   C8   108.48  3.000
 A6Z  H15  N2   C9   107.50  3.000
 A6Z  C8   N2   C9   109.99  3.000
 A6Z  H15  N2   C11  107.88  3.000
 A6Z  C9   N2   C11  110.05  3.000
 A6Z  C8   N2   C11  112.76  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
 A6Z  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 A6Z  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 A6Z  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 A6Z  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 A6Z  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 A6Z  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 A6Z  CONST_07  N1   C3   C4   C5   180.00   0.0  0
 A6Z  CONST_08  N1   C3   C2   C1   180.00   0.0  0
 A6Z  CONST_09  CL1  C5   C4   C3   180.00   0.0  0
 A6Z  CONST_10  CL1  C5   C6   C1   180.00   0.0  0
 A6Z  CONST_11  H12  C6   C5   C4   180.00   0.0  0
 A6Z  CONST_12  H13  C2   C3   C4   180.00   0.0  0
 A6Z  CONST_13  H14  C1   C6   C5   180.00   0.0  0
 A6Z  CONST_14  H11  C4   C5   C6   180.00   0.0  0
 A6Z  Var_01    C2   C3   N1   C10  131.18  30.0  3
 A6Z  Var_02    C8   C7   N1   C10   59.09  30.0  1
 A6Z  Var_03    C3   N1   C10  C9   158.99  30.0  1
 A6Z  Var_04    N2   C8   C7   N1   -57.07  30.0  1
 A6Z  Var_05    N2   C9   C10  N1    57.38  30.0  1
 A6Z  Var_06    H1   C11  C12  N3   -82.40  30.0  2

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
 A6Z  chir_01  N2  C8  C9  C11  negativ

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
 A6Z  plan-1  C4   0.020
 A6Z  plan-1  C5   0.020
 A6Z  plan-1  C6   0.020
 A6Z  plan-1  C3   0.020
 A6Z  plan-1  C2   0.020
 A6Z  plan-1  C1   0.020
 A6Z  plan-1  N1   0.020
 A6Z  plan-1  H11  0.020
 A6Z  plan-1  H12  0.020
 A6Z  plan-1  H13  0.020
 A6Z  plan-1  H14  0.020
 A6Z  plan-1  CL1  0.020

