# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 13:11:12 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 4-(4-chlorophenyl)piperazine-1-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)N1CCN(CC1)c2ccc(Cl)cc2
#
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
 613  613  4-(4-chlorophenyl)piperazine-1-carboximidamide  ligand  31  16  .  2021-08-05  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_613
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
 613  C1    C   CR16  0  -0.331  -1.7146  -1.2048   0.4357
 613  N1    N   NT    0  -0.518   0.4014  -0.0422   0.2421
 613  CL1   CL  CL    0  -0.145  -5.5316  -0.0441   0.2447
 613  C2    C   CR16  0  -0.202  -3.0965  -1.2148   0.4416
 613  N2    N   NT    0  -0.474   3.2212  -0.0011  -0.0983
 613  C3    C   CR6   0  -0.071  -3.7950  -0.0349   0.2289
 613  N3    N   N     0  -0.725   5.1879   1.1964  -0.0558
 613  C4    C   CR16  0  -0.199  -3.1110   1.1455   0.0067
 613  N4    N   NH2   0  -0.848   5.2184  -1.0882  -0.6297
 613  C5    C   CR16  0  -0.363  -1.7228   1.1478  -0.0128
 613  C6    C   CR6   0   0.377  -0.9904  -0.0243   0.2076
 613  C7    C   CH2   0  -0.318   1.1096   1.2176   0.1522
 613  C8    C   CH2   0  -0.278   2.5434   1.0575   0.6215
 613  C9    C   CH2   0  -0.313   2.5086  -1.2602  -0.0551
 613  C10   C   CH2   0  -0.301   1.0781  -1.0762  -0.5246
 613  C11   C   C     0   0.575   4.5911   0.0722  -0.2254
 613  H1    H   HCR6  0   0.271  -1.1967  -2.1330   0.6376
 613  H2    H   HCR6  0   0.276  -3.6237  -2.1409   0.6281
 613  HN3   H   H     0   0.317   6.1853   1.0936  -0.1982
 613  H4    H   HCR6  0   0.276  -3.6474   2.0684  -0.1692
 613  HN4   H   HNH2  0   0.394   4.8750  -1.9646  -0.2715
 613  HN4A  H   HNH2  0   0.388   6.2235  -1.0482  -0.5753
 613  H5    H   HCR6  0   0.277  -1.2240   2.0846  -0.2176
 613  H7    H   HCH2  0   0.219   1.0991   1.6173  -0.8730
 613  H7A   H   HCH2  0   0.258   0.6342   1.9548   0.7997
 613  H8    H   HCH2  0   0.220   2.5486   0.8517   1.7006
 613  H8A   H   HCH2  0   0.265   3.0736   1.9921   0.4626
 613  H9    H   HCH2  0   0.257   2.9656  -1.9872  -0.7237
 613  H9A   H   HCH2  0   0.230   2.5057  -1.6847   0.9579
 613  H10   H   HCH2  0   0.262   0.5665  -2.0299  -0.4169
 613  H10A  H   HCH2  0   0.225   1.0777  -0.8227  -1.5949

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
 613  C1   C2    aromatic  1.382  0.020  1.382
 613  C1   C6    aromatic  1.404  0.020  1.404
 613  N1   C6    single    1.392  0.020  1.392
 613  N1   C7    single    1.448  0.020  1.448
 613  N1   C10   single    1.454  0.020  1.454
 613  CL1  C3    single    1.737  0.020  1.737
 613  C2   C3    aromatic  1.388  0.020  1.388
 613  N2   C8    single    1.449  0.020  1.449
 613  N2   C9    single    1.447  0.020  1.447
 613  N2   C11   single    1.378  0.020  1.378
 613  C3   C4    aromatic  1.382  0.020  1.382
 613  N3   C11   double    1.284  0.020  1.284
 613  C4   C5    aromatic  1.388  0.020  1.388
 613  N4   C11   single    1.380  0.020  1.380
 613  C5   C6    aromatic  1.400  0.020  1.400
 613  C7   C8    single    1.517  0.020  1.517
 613  C9   C10   single    1.517  0.020  1.517
 613  C1   H1    single    0.930  0.020  1.080
 613  C2   H2    single    0.930  0.020  1.080
 613  N3   HN3   single    0.890  0.020  1.040
 613  C4   H4    single    0.930  0.020  1.080
 613  N4   HN4   single    0.890  0.020  1.040
 613  N4   HN4A  single    0.890  0.020  1.040
 613  C5   H5    single    0.930  0.020  1.080
 613  C7   H7    single    0.970  0.020  1.090
 613  C7   H7A   single    0.970  0.020  1.090
 613  C8   H8    single    0.970  0.020  1.090
 613  C8   H8A   single    0.970  0.020  1.090
 613  C9   H9    single    0.970  0.020  1.090
 613  C9   H9A   single    0.970  0.020  1.090
 613  C10  H10   single    0.970  0.020  1.090
 613  C10  H10A  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
 613  H1    C1   C6   120.33  3.000
 613  H1    C1   C2   118.14  3.000
 613  C6    C1   C2   121.51  3.000
 613  C10   N1   C7   110.99  3.000
 613  C10   N1   C6   117.47  3.000
 613  C7    N1   C6   118.44  3.000
 613  H2    C2   C3   120.60  3.000
 613  H2    C2   C1   119.62  3.000
 613  C3    C2   C1   119.77  3.000
 613  C11   N2   C9   122.58  3.000
 613  C11   N2   C8   118.18  3.000
 613  C9    N2   C8   112.99  3.000
 613  C4    C3   C2   120.11  3.000
 613  C4    C3   CL1  120.05  3.000
 613  C2    C3   CL1  119.83  3.000
 613  HN3   N3   C11  110.51  3.000
 613  H4    C4   C5   119.48  3.000
 613  H4    C4   C3   120.62  3.000
 613  C5    C4   C3   119.90  3.000
 613  HN4A  N4   HN4  110.82  3.000
 613  HN4A  N4   C11  113.86  3.000
 613  HN4   N4   C11  118.21  3.000
 613  H5    C5   C6   120.94  3.000
 613  H5    C5   C4   117.74  3.000
 613  C6    C5   C4   121.31  3.000
 613  C5    C6   N1   122.53  3.000
 613  C5    C6   C1   117.38  3.000
 613  N1    C6   C1   120.06  3.000
 613  H7A   C7   H7   107.66  3.000
 613  H7A   C7   C8   107.44  3.000
 613  H7    C7   C8   109.61  3.000
 613  H7A   C7   N1   109.76  3.000
 613  H7    C7   N1   111.67  3.000
 613  C8    C7   N1   110.56  3.000
 613  H8A   C8   H8   107.62  3.000
 613  H8A   C8   C7   108.98  3.000
 613  H8    C8   C7   109.15  3.000
 613  H8A   C8   N2   109.13  3.000
 613  H8    C8   N2   110.42  3.000
 613  C7    C8   N2   111.44  3.000
 613  H9A   C9   H9   108.03  3.000
 613  H9A   C9   C10  109.26  3.000
 613  H9    C9   C10  106.67  3.000
 613  H9A   C9   N2   111.41  3.000
 613  H9    C9   N2   110.86  3.000
 613  C10   C9   N2   110.46  3.000
 613  H10A  C10  H10  107.35  3.000
 613  H10A  C10  C9   109.24  3.000
 613  H10   C10  C9   107.86  3.000
 613  H10A  C10  N1   110.43  3.000
 613  H10   C10  N1   110.63  3.000
 613  C9    C10  N1   111.22  3.000
 613  N4    C11  N3   124.32  3.000
 613  N4    C11  N2   115.75  3.000
 613  N3    C11  N2   119.77  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
 613  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 613  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 613  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 613  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 613  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 613  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 613  CONST_07  C2    C1   C6   N1    180.00   0.0  0
 613  CONST_08  C4    C5   C6   N1    180.00   0.0  0
 613  CONST_09  CL1   C3   C2   C1    180.00   0.0  0
 613  CONST_10  C5    C4   C3   CL1   180.00   0.0  0
 613  CONST_11  H5    C5   C6   C1    180.00   0.0  0
 613  CONST_12  H1    C1   C6   N1      0.00   0.0  0
 613  CONST_13  H4    C4   C3   C2    180.00   0.0  0
 613  CONST_14  H2    C2   C3   C4    180.00   0.0  0
 613  CONST_16  C9    N2   C11  N3    180.00   0.0  0
 613  CONST_17  C8    N2   C11  N4    180.00   0.0  0
 613  CONST_19  HN3   N3   C11  N2    180.00   0.0  0
 613  CONST_21  HN4A  N4   C11  N2    180.00   0.0  0
 613  Var_01    C7    N1   C6   C1   -173.16  30.0  2
 613  Var_02    N2    C8   C7   N1     54.63  30.0  1
 613  Var_03    N2    C9   C10  N1    -55.06  30.0  1
 613  Var_04    C8    C7   N1   C6    162.79  30.0  1
 613  Var_05    C9    C10  N1   C6   -161.65  30.0  1
 613  Var_06    C9    N2   C8   C7    -53.72  30.0  1
 613  Var_07    C10   C9   N2   C8     53.53  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
 613  plan-1  C1    0.020
 613  plan-1  N1    0.020
 613  plan-1  CL1   0.020
 613  plan-1  C2    0.020
 613  plan-1  C3    0.020
 613  plan-1  C4    0.020
 613  plan-1  C5    0.020
 613  plan-1  C6    0.020
 613  plan-1  H1    0.020
 613  plan-1  H2    0.020
 613  plan-1  H4    0.020
 613  plan-1  H5    0.020
 613  plan-2  N2    0.020
 613  plan-2  N3    0.020
 613  plan-2  N4    0.020
 613  plan-2  C8    0.020
 613  plan-2  C9    0.020
 613  plan-2  C11   0.020
 613  plan-2  HN3   0.020
 613  plan-2  HN4   0.020
 613  plan-2  HN4A  0.020

