# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:25:21 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-[(3-chlorophenyl)methyl]piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(CN2CCNCC2)c1
#
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
 GNW  GNW  1-[(3-chlorophenyl)methyl]piperazine  ligand  29  14  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GNW
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
 GNW  C4   C   CH2   0  -0.299   4.2109   0.4320   0.1416
 GNW  C5   C   CH2   0  -0.314   0.7340   0.6515  -1.2145
 GNW  C6   C   CR6   0   0.080  -0.5986   0.7347  -0.5128
 GNW  C11  C   CR16  0  -0.275  -1.7399   0.2186  -1.1155
 GNW  C7   C   CR16  0  -0.273  -0.7120   1.3595   0.7271
 GNW  C8   C   CR16  0  -0.246  -1.9459   1.4695   1.3487
 GNW  C9   C   CR16  0  -0.234  -3.0912   0.9618   0.7485
 GNW  C10  C   CR6   0  -0.021  -2.9681   0.3410  -0.4829
 GNW  N1   N   NT    0  -0.419   1.8193   0.3687  -0.3044
 GNW  N2   N   NH1   0  -0.600   4.1540  -0.9333   0.6293
 GNW  C3   C   CH2   0  -0.276   3.1179   0.6457  -0.8897
 GNW  C1   C   CH2   0  -0.274   1.7671  -0.9870   0.2128
 GNW  C2   C   CH2   0  -0.298   2.8648  -1.2024   1.2382
 GNW  CL1  CL  CL    0  -0.135  -4.3817  -0.3125  -1.2511
 GNW  H1   H   HCH2  0   0.191   4.0822   1.1755   0.9439
 GNW  H2   H   HCH2  0   0.232   5.1840   0.6128  -0.3193
 GNW  H3   H   HCH2  0   0.215   0.6718  -0.0816  -2.0363
 GNW  H4   H   HCH2  0   0.256   0.9339   1.6186  -1.6876
 GNW  H5   H   HCR6  0   0.271  -1.6711  -0.2819  -2.0736
 GNW  H6   H   HCR6  0   0.252   0.1770   1.7481   1.2063
 GNW  H7   H   HCR6  0   0.264  -2.0254   1.9566   2.3119
 GNW  H8   H   HCR6  0   0.277  -4.0542   1.0475   1.2330
 GNW  H10  H   HNH1  0   0.353   4.8906  -1.0864   1.3053
 GNW  H12  H   HCH2  0   0.234   3.1397   1.6830  -1.2322
 GNW  H13  H   HCH2  0   0.189   3.3192   0.0084  -1.7681
 GNW  H14  H   HCH2  0   0.237   0.7967  -1.1590   0.6825
 GNW  H15  H   HCH2  0   0.192   1.8741  -1.7289  -0.5979
 GNW  H16  H   HCH2  0   0.231   2.8362  -2.2371   1.5852
 GNW  H17  H   HCH2  0   0.191   2.6603  -0.5582   2.1082

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
 GNW  CL1  C10  single    1.736  0.020  1.736
 GNW  C11  C10  aromatic  1.387  0.020  1.387
 GNW  C11  C6   aromatic  1.390  0.020  1.390
 GNW  C10  C9   aromatic  1.385  0.020  1.385
 GNW  C5   C6   single    1.508  0.020  1.508
 GNW  C5   N1   single    1.444  0.020  1.444
 GNW  C6   C7   aromatic  1.393  0.020  1.393
 GNW  C9   C8   aromatic  1.389  0.020  1.389
 GNW  C7   C8   aromatic  1.386  0.020  1.386
 GNW  C1   N1   single    1.452  0.020  1.452
 GNW  C1   C2   single    1.518  0.020  1.518
 GNW  N1   C3   single    1.451  0.020  1.451
 GNW  C3   C4   single    1.518  0.020  1.518
 GNW  C2   N2   single    1.451  0.020  1.451
 GNW  N2   C4   single    1.451  0.020  1.451
 GNW  C4   H1   single    0.970  0.020  1.090
 GNW  C4   H2   single    0.970  0.020  1.090
 GNW  C5   H3   single    0.970  0.020  1.090
 GNW  C5   H4   single    0.970  0.020  1.090
 GNW  C11  H5   single    0.930  0.020  1.080
 GNW  C7   H6   single    0.930  0.020  1.080
 GNW  C8   H7   single    0.930  0.020  1.080
 GNW  C9   H8   single    0.930  0.020  1.080
 GNW  N2   H10  single    0.890  0.020  1.040
 GNW  C3   H12  single    0.970  0.020  1.090
 GNW  C3   H13  single    0.970  0.020  1.090
 GNW  C1   H14  single    0.970  0.020  1.090
 GNW  C1   H15  single    0.970  0.020  1.090
 GNW  C2   H16  single    0.970  0.020  1.090
 GNW  C2   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
 GNW  H2   C4   H1   107.45  3.000
 GNW  H2   C4   C3   109.37  3.000
 GNW  H1   C4   C3   108.41  3.000
 GNW  H2   C4   N2   109.43  3.000
 GNW  H1   C4   N2   112.69  3.000
 GNW  C3   C4   N2   109.43  3.000
 GNW  H4   C5   H3   105.99  3.000
 GNW  H4   C5   N1   107.94  3.000
 GNW  H3   C5   N1   112.44  3.000
 GNW  H4   C5   C6   108.27  3.000
 GNW  H3   C5   C6   109.48  3.000
 GNW  N1   C5   C6   112.42  3.000
 GNW  C7   C6   C11  119.06  3.000
 GNW  C7   C6   C5   120.71  3.000
 GNW  C11  C6   C5   120.21  3.000
 GNW  H5   C11  C10  120.03  3.000
 GNW  H5   C11  C6   120.20  3.000
 GNW  C10  C11  C6   119.77  3.000
 GNW  H6   C7   C8   120.28  3.000
 GNW  H6   C7   C6   119.23  3.000
 GNW  C8   C7   C6   120.48  3.000
 GNW  H7   C8   C9   119.24  3.000
 GNW  H7   C8   C7   120.02  3.000
 GNW  C9   C8   C7   120.74  3.000
 GNW  H8   C9   C10  120.87  3.000
 GNW  H8   C9   C8   120.78  3.000
 GNW  C10  C9   C8   118.35  3.000
 GNW  CL1  C10  C9   119.33  3.000
 GNW  C9   C10  C11  121.60  3.000
 GNW  CL1  C10  C11  119.07  3.000
 GNW  C1   N1   C3   110.74  3.000
 GNW  C3   N1   C5   112.39  3.000
 GNW  C1   N1   C5   112.35  3.000
 GNW  H10  N2   C2   109.79  3.000
 GNW  H10  N2   C4   109.79  3.000
 GNW  C2   N2   C4   110.52  3.000
 GNW  H13  C3   H12  107.17  3.000
 GNW  H13  C3   N1   111.96  3.000
 GNW  H12  C3   N1   109.00  3.000
 GNW  H13  C3   C4   109.15  3.000
 GNW  H12  C3   C4   109.41  3.000
 GNW  N1   C3   C4   110.09  3.000
 GNW  H15  C1   H14  107.23  3.000
 GNW  H15  C1   C2   109.31  3.000
 GNW  H14  C1   C2   109.26  3.000
 GNW  H15  C1   N1   111.25  3.000
 GNW  H14  C1   N1   109.41  3.000
 GNW  C2   C1   N1   110.32  3.000
 GNW  H17  C2   H16  107.36  3.000
 GNW  H17  C2   C1   108.44  3.000
 GNW  H16  C2   C1   109.29  3.000
 GNW  H17  C2   N2   112.82  3.000
 GNW  H16  C2   N2   109.42  3.000
 GNW  C1   C2   N2   109.44  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
 GNW  CONST_01  C9   C10  C11  C6      0.00   0.0  0
 GNW  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 GNW  CONST_03  C8   C9   C10  C11     0.00   0.0  0
 GNW  CONST_04  C8   C7   C6   C11     0.00   0.0  0
 GNW  CONST_05  C10  C11  C6   C7      0.00   0.0  0
 GNW  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 GNW  CONST_07  C10  C11  C6   C5    180.00   0.0  0
 GNW  CONST_08  C8   C7   C6   C5    180.00   0.0  0
 GNW  CONST_09  CL1  C10  C11  C6    180.00   0.0  0
 GNW  CONST_10  CL1  C10  C9   C8    180.00   0.0  0
 GNW  CONST_11  H7   C8   C7   C6    180.00   0.0  0
 GNW  CONST_12  H8   C9   C10  C11   180.00   0.0  0
 GNW  CONST_13  H6   C7   C6   C11   180.00   0.0  0
 GNW  CONST_14  H5   C11  C6   C7    180.00   0.0  0
 GNW  Var_01    C1   N1   C3   C4    -57.71  30.0  1
 GNW  Var_02    C1   C2   N2   C4     59.45  30.0  1
 GNW  Var_03    N2   C2   C1   N1    -57.88  30.0  1
 GNW  Var_04    N2   C4   C3   N1     58.36  30.0  1
 GNW  Var_05    C2   C1   N1   C3     57.55  30.0  1
 GNW  Var_06    C2   N2   C4   C3    -59.74  30.0  1
 GNW  Var_07    N1   C5   C6   C11  -141.54  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
 GNW  plan-1  C5   0.020
 GNW  plan-1  C6   0.020
 GNW  plan-1  C11  0.020
 GNW  plan-1  C7   0.020
 GNW  plan-1  C8   0.020
 GNW  plan-1  C9   0.020
 GNW  plan-1  C10  0.020
 GNW  plan-1  CL1  0.020
 GNW  plan-1  H5   0.020
 GNW  plan-1  H6   0.020
 GNW  plan-1  H7   0.020
 GNW  plan-1  H8   0.020

