# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 22:36:09 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 1-(3-chloranyl-5-iodanyl-pyridin-2-yl)piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(I)cnc1N2CCNCC2
#
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
 1KE  1KE  "1-(3-chloranyl-5-iodanyl-pyridin-2-yl)piperazine"
  ligand  25  14  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1KE
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
 1KE  CL1  CL  CL    0  -0.090  32.9357  17.4591  -37.4863
 1KE  C9   C   CR6   0  -0.155  32.6361  17.4477  -39.1875
 1KE  C10  C   CR16  0  -0.075  32.6401  18.6495  -39.8632
 1KE  C11  C   CR6   0  -0.316  32.5351  18.6303  -41.2480
 1KE  I1   I   I     0   0.084  32.5395  20.4109  -42.3480
 1KE  C12  C   CR16  0  -0.035  32.4550  17.4074  -41.8881
 1KE  N13  N   N     0  -0.435  32.4156  16.2642  -41.2221
 1KE  C8   C   CR6   0   0.546  32.4799  16.2389  -39.8965
 1KE  N3   N   NT    0  -0.493  32.4592  15.0197  -39.2567
 1KE  C2   C   CH2   0  -0.315  31.3821  14.7479  -38.3039
 1KE  C1   C   CH2   0  -0.315  31.7967  13.6130  -37.3798
 1KE  C4   C   CH2   0  -0.298  32.7725  13.8408  -40.0510
 1KE  C5   C   CH2   0  -0.321  33.1713  12.7061  -39.1140
 1KE  N1   N   NH1   0  -0.577  32.1830  12.4063  -38.0913
 1KE  H1   H   HCR6  0   0.308  32.7586  19.5758  -39.3170
 1KE  H2   H   HCR6  0   0.281  32.4122  17.3395  -42.9692
 1KE  H3   H   HCH2  0   0.251  31.1417  15.6350  -37.7225
 1KE  H4   H   HCH2  0   0.226  30.4706  14.4643  -38.8501
 1KE  H5   H   HCH2  0   0.224  32.6430  13.9468  -36.7715
 1KE  H6   H   HCH2  0   0.240  30.9776  13.3824  -36.6965
 1KE  H7   H   HCH2  0   0.214  31.9170  13.5338  -40.6689
 1KE  H8   H   HCH2  0   0.248  33.5968  14.0653  -40.7274
 1KE  H9   H   HCH2  0   0.240  33.3621  11.8063  -39.7017
 1KE  H10  H   HCH2  0   0.223  34.1102  12.9728  -38.6193
 1KE  H11  H   HNH1  0   0.341  31.3607  12.0126  -38.5358

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
 1KE  I1   C11  single    2.093  0.020  2.093
 1KE  C12  N13  aromatic  1.324  0.020  1.324
 1KE  C12  C11  aromatic  1.383  0.020  1.383
 1KE  N13  C8   aromatic  1.327  0.020  1.327
 1KE  C11  C10  aromatic  1.389  0.020  1.389
 1KE  C4   N3   single    1.456  0.020  1.456
 1KE  C4   C5   single    1.525  0.020  1.525
 1KE  C8   N3   single    1.377  0.020  1.377
 1KE  C8   C9   aromatic  1.410  0.020  1.410
 1KE  C10  C9   aromatic  1.379  0.020  1.379
 1KE  N3   C2   single    1.464  0.020  1.464
 1KE  C9   CL1  single    1.727  0.020  1.727
 1KE  C5   N1   single    1.453  0.020  1.453
 1KE  C2   C1   single    1.521  0.020  1.521
 1KE  N1   C1   single    1.453  0.020  1.453
 1KE  C10  H1   single    0.930  0.020  1.080
 1KE  C12  H2   single    0.930  0.020  1.080
 1KE  C2   H3   single    0.970  0.020  1.090
 1KE  C2   H4   single    0.970  0.020  1.090
 1KE  C1   H5   single    0.970  0.020  1.090
 1KE  C1   H6   single    0.970  0.020  1.090
 1KE  C4   H7   single    0.970  0.020  1.090
 1KE  C4   H8   single    0.970  0.020  1.090
 1KE  C5   H9   single    0.970  0.020  1.090
 1KE  C5   H10  single    0.970  0.020  1.090
 1KE  N1   H11  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
 1KE  C8   C9   C10  120.07  3.000
 1KE  C10  C9   CL1  118.45  3.000
 1KE  C8   C9   CL1  121.33  3.000
 1KE  H1   C10  C11  121.57  3.000
 1KE  H1   C10  C9   119.95  3.000
 1KE  C11  C10  C9   118.45  3.000
 1KE  C12  C11  I1   120.62  3.000
 1KE  C12  C11  C10  118.57  3.000
 1KE  I1   C11  C10  120.80  3.000
 1KE  H2   C12  N13  116.52  3.000
 1KE  H2   C12  C11  121.29  3.000
 1KE  N13  C12  C11  122.19  3.000
 1KE  C8   N13  C12  121.16  3.000
 1KE  N3   C8   N13  118.69  3.000
 1KE  N3   C8   C9   121.81  3.000
 1KE  N13  C8   C9   119.42  3.000
 1KE  C4   N3   C2   111.30  3.000
 1KE  C2   N3   C8   118.55  3.000
 1KE  C4   N3   C8   117.41  3.000
 1KE  H4   C2   H3   107.01  3.000
 1KE  H4   C2   C1   109.59  3.000
 1KE  H3   C2   C1   110.13  3.000
 1KE  H4   C2   N3   109.54  3.000
 1KE  H3   C2   N3   111.05  3.000
 1KE  C1   C2   N3   109.48  3.000
 1KE  H6   C1   H5   107.27  3.000
 1KE  H6   C1   N1   109.30  3.000
 1KE  H5   C1   N1   108.66  3.000
 1KE  H6   C1   C2   109.48  3.000
 1KE  H5   C1   C2   108.72  3.000
 1KE  N1   C1   C2   113.24  3.000
 1KE  H8   C4   H7   107.30  3.000
 1KE  H8   C4   C5   109.69  3.000
 1KE  H7   C4   C5   109.96  3.000
 1KE  H8   C4   N3   109.55  3.000
 1KE  H7   C4   N3   111.43  3.000
 1KE  C5   C4   N3   108.89  3.000
 1KE  H10  C5   H9   107.12  3.000
 1KE  H10  C5   N1   108.39  3.000
 1KE  H9   C5   N1   109.13  3.000
 1KE  H10  C5   C4   108.72  3.000
 1KE  H9   C5   C4   109.17  3.000
 1KE  N1   C5   C4   114.08  3.000
 1KE  H11  N1   C5   108.84  3.000
 1KE  H11  N1   C1   108.75  3.000
 1KE  C5   N1   C1   110.73  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
 1KE  CONST_01  C12  N13  C8   C9      0.00   0.0  0
 1KE  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 1KE  CONST_03  N13  C12  C11  C10     0.00   0.0  0
 1KE  CONST_04  N13  C8   C9   C10     0.00   0.0  0
 1KE  CONST_05  C8   N13  C12  C11     0.00   0.0  0
 1KE  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 1KE  CONST_07  N3   C8   C9   C10   180.00   0.0  0
 1KE  CONST_08  N3   C8   N13  C12   180.00   0.0  0
 1KE  CONST_09  N13  C8   C9   CL1   180.00   0.0  0
 1KE  CONST_10  N3   C8   C9   CL1     0.00   0.0  0
 1KE  CONST_11  C11  C10  C9   CL1   180.00   0.0  0
 1KE  CONST_12  I1   C11  C10  C9    180.00   0.0  0
 1KE  CONST_13  N13  C12  C11  I1    180.00   0.0  0
 1KE  CONST_14  H2   C12  C11  C10   180.00   0.0  0
 1KE  CONST_15  H1   C10  C11  C12   180.00   0.0  0
 1KE  CONST_16  H2   C12  N13  C8    180.00   0.0  0
 1KE  CONST_17  H1   C10  C9   C8    180.00   0.0  0
 1KE  Var_01    C4   N3   C8   C9   -158.56  30.0  2
 1KE  Var_02    C2   N3   C8   C9     63.02  30.0  2
 1KE  Var_03    C4   N3   C8   N13    18.13  30.0  2
 1KE  Var_04    C2   N3   C8   N13  -120.29  30.0  2
 1KE  Var_05    C5   C4   N3   C8    160.45  30.0  1
 1KE  Var_06    C1   C2   N3   C8   -160.24  30.0  1
 1KE  Var_07    N1   C5   C4   N3     55.01  30.0  1
 1KE  Var_08    N1   C1   C2   N3    -55.41  30.0  1
 1KE  Var_09    C5   C4   N3   C2    -58.28  30.0  1
 1KE  Var_10    C5   N1   C1   C2     51.44  30.0  1
 1KE  Var_11    C4   N3   C2   C1     58.99  30.0  1
 1KE  Var_12    C4   C5   N1   C1    -51.54  30.0  1
 1KE  Var_13    H7   C4   N3   C8    -78.10  30.0  1
 1KE  Var_14    H8   C4   N3   C8     40.49  30.0  1
 1KE  Var_15    H3   C2   N3   C8    -38.41  30.0  1
 1KE  Var_16    H4   C2   N3   C8     79.57  30.0  1
 1KE  Var_17    H9   C5   C4   N3    177.38  30.0  1
 1KE  Var_18    H10  C5   C4   N3    -66.08  30.0  1
 1KE  Var_19    H5   C1   C2   N3     65.46  30.0  1
 1KE  Var_20    H6   C1   C2   N3   -177.65  30.0  1
 1KE  Var_21    H7   C4   N3   C2     63.17  30.0  1
 1KE  Var_22    H8   C4   N3   C2   -178.25  30.0  1
 1KE  Var_23    H11  N1   C1   C2    -68.11  30.0  1
 1KE  Var_24    H9   C5   N1   C1   -173.93  30.0  1
 1KE  Var_25    H10  C5   N1   C1     69.73  30.0  1
 1KE  Var_26    H3   C2   N3   C4   -179.19  30.0  1
 1KE  Var_27    H4   C2   N3   C4    -61.21  30.0  1
 1KE  Var_28    H11  N1   C5   C4     67.96  30.0  1
 1KE  Var_29    H5   C1   N1   C5    -69.46  30.0  1
 1KE  Var_30    H6   C1   N1   C5    173.78  30.0  1
 1KE  Var_31    H7   C4   C5   N1    -67.35  30.0  1
 1KE  Var_32    H8   C4   C5   N1    174.88  30.0  1
 1KE  Var_33    H3   C2   C1   N1   -177.79  30.0  1
 1KE  Var_34    H4   C2   C1   N1     64.75  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
 1KE  plan-1  CL1  0.020
 1KE  plan-1  C9   0.020
 1KE  plan-1  C10  0.020
 1KE  plan-1  C11  0.020
 1KE  plan-1  I1   0.020
 1KE  plan-1  C12  0.020
 1KE  plan-1  N13  0.020
 1KE  plan-1  C8   0.020
 1KE  plan-1  N3   0.020
 1KE  plan-1  H1   0.020
 1KE  plan-1  H2   0.020

