# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 14:15:29 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: (3S)-3-methyl-1-(6-methylpyridin-2-yl)piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CN(CCN1)c2cccc(C)n2
#
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
 8AB  8AB  "(3S)-3-methyl-1-(6-methylpyridin-2-yl)piperazine"
  ligand  31  14  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8AB
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
 8AB  C10  C  CR16  0  -0.141   0.0363  -14.9387  -10.3264
 8AB  C13  C  CH3   0  -0.722   2.1981  -14.7078   -7.2522
 8AB  C02  C  CH1   0  -0.094  -3.4226  -16.5891   -5.5948
 8AB  C03  C  CH2   0  -0.252  -2.1690  -16.7281   -6.4436
 8AB  N04  N  NT    0  -0.513  -2.2988  -16.0297   -7.7123
 8AB  C05  C  CH2   0  -0.291  -3.5002  -16.3573   -8.4533
 8AB  C06  C  CH2   0  -0.295  -4.7238  -16.2395   -7.5615
 8AB  N07  N  NH1   0  -0.597  -4.5596  -17.0486   -6.3729
 8AB  C08  C  CR6   0   0.527  -1.1663  -15.6166   -8.3715
 8AB  C09  C  CR16  0  -0.423  -1.1343  -15.4058   -9.7628
 8AB  C11  C  CR16  0  -0.376   1.1503  -14.6987   -9.5351
 8AB  C12  C  CR6   0   0.245   1.0404  -14.9552   -8.1736
 8AB  N14  N  N     0  -0.494  -0.0820  -15.4024   -7.6228
 8AB  H1   H  HCR6  0   0.259   0.0808  -14.7736  -11.3957
 8AB  H2   H  HCH3  0   0.243   2.0750  -15.2482   -6.3155
 8AB  H3   H  HCH3  0   0.243   3.1420  -15.0059   -7.7080
 8AB  H4   H  HCH3  0   0.249   2.2786  -13.6448   -7.0143
 8AB  H8   H  HCH1  0   0.196  -3.5242  -15.5231   -5.3259
 8AB  H9   H  HCH2  0   0.206  -1.9766  -17.7975   -6.6170
 8AB  H10  H  HCH2  0   0.255  -1.3185  -16.3231   -5.9025
 8AB  H11  H  HCH2  0   0.249  -3.6288  -15.6587   -9.2780
 8AB  H12  H  HCH2  0   0.218  -3.4431  -17.3687   -8.8791
 8AB  H13  H  HCH2  0   0.196  -4.8850  -15.1744   -7.3315
 8AB  H14  H  HCH2  0   0.239  -5.5942  -16.5865   -8.1211
 8AB  H15  H  HNH1  0   0.350  -5.3996  -16.9984   -5.8096
 8AB  H17  H  HCR6  0   0.263  -1.9808  -15.6174  -10.3979
 8AB  H18  H  HCR6  0   0.247   2.0775  -14.3370   -9.9586
 8AB  C01  C  CH3   0  -0.670  -3.2900  -17.4012   -4.3193
 8AB  H5   H  HCH3  0   0.234  -4.1852  -17.3074   -3.7021
 8AB  H6   H  HCH3  0   0.222  -3.1446  -18.4594   -4.5432
 8AB  H7   H  HCH3  0   0.229  -2.4424  -17.0570   -3.7262

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
 8AB  C10  C09  aromatic  1.381  0.020  1.381
 8AB  C10  C11  aromatic  1.387  0.020  1.387
 8AB  C09  C08  aromatic  1.407  0.020  1.407
 8AB  C11  C12  aromatic  1.390  0.020  1.390
 8AB  C05  N04  single    1.449  0.020  1.449
 8AB  C05  C06  single    1.519  0.020  1.519
 8AB  C08  N04  single    1.374  0.020  1.374
 8AB  C08  N14  aromatic  1.335  0.020  1.335
 8AB  C12  N14  aromatic  1.328  0.020  1.328
 8AB  C12  C13  single    1.500  0.020  1.500
 8AB  N04  C03  single    1.454  0.020  1.454
 8AB  C06  N07  single    1.447  0.020  1.447
 8AB  C03  C02  single    1.520  0.020  1.520
 8AB  N07  C02  single    1.452  0.020  1.452
 8AB  C02  C01  single    1.518  0.020  1.518
 8AB  C10  H1   single    0.930  0.020  1.080
 8AB  C13  H2   single    0.970  0.020  1.090
 8AB  C13  H3   single    0.970  0.020  1.090
 8AB  C13  H4   single    0.970  0.020  1.090
 8AB  C01  H5   single    0.970  0.020  1.090
 8AB  C01  H6   single    0.970  0.020  1.090
 8AB  C01  H7   single    0.970  0.020  1.090
 8AB  C02  H8   single    0.970  0.020  1.090
 8AB  C03  H9   single    0.970  0.020  1.090
 8AB  C03  H10  single    0.970  0.020  1.090
 8AB  C05  H11  single    0.970  0.020  1.090
 8AB  C05  H12  single    0.970  0.020  1.090
 8AB  C06  H13  single    0.970  0.020  1.090
 8AB  C06  H14  single    0.970  0.020  1.090
 8AB  N07  H15  single    0.890  0.020  1.040
 8AB  C09  H17  single    0.930  0.020  1.080
 8AB  C11  H18  single    0.930  0.020  1.080

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
 8AB  H1   C10  C11  120.26  3.000
 8AB  H1   C10  C09  119.31  3.000
 8AB  C11  C10  C09  120.43  3.000
 8AB  H4   C13  H3   107.07  3.000
 8AB  H4   C13  H2   107.70  3.000
 8AB  H3   C13  H2   108.79  3.000
 8AB  H4   C13  C12  110.56  3.000
 8AB  H3   C13  C12  111.49  3.000
 8AB  H2   C13  C12  111.06  3.000
 8AB  H8   C02  N07  111.34  3.000
 8AB  H8   C02  C03  107.47  3.000
 8AB  N07  C02  C03  108.51  3.000
 8AB  H8   C02  C01  108.66  3.000
 8AB  N07  C02  C01  110.44  3.000
 8AB  C03  C02  C01  110.38  3.000
 8AB  H10  C03  H9   107.69  3.000
 8AB  H10  C03  N04  108.99  3.000
 8AB  H9   C03  N04  110.18  3.000
 8AB  H10  C03  C02  109.47  3.000
 8AB  H9   C03  C02  108.73  3.000
 8AB  N04  C03  C02  111.69  3.000
 8AB  C08  N04  C05  120.40  3.000
 8AB  C08  N04  C03  119.31  3.000
 8AB  C05  N04  C03  114.31  3.000
 8AB  H12  C05  H11  107.66  3.000
 8AB  H12  C05  C06  109.93  3.000
 8AB  H11  C05  C06  107.46  3.000
 8AB  H12  C05  N04  111.29  3.000
 8AB  H11  C05  N04  109.89  3.000
 8AB  C06  C05  N04  110.49  3.000
 8AB  H14  C06  H13  107.33  3.000
 8AB  H14  C06  N07  109.50  3.000
 8AB  H13  C06  N07  112.68  3.000
 8AB  H14  C06  C05  108.47  3.000
 8AB  H13  C06  C05  108.40  3.000
 8AB  N07  C06  C05  110.34  3.000
 8AB  H15  N07  C06  109.58  3.000
 8AB  H15  N07  C02  109.61  3.000
 8AB  C06  N07  C02  110.61  3.000
 8AB  N14  C08  C09  120.79  3.000
 8AB  N14  C08  N04  116.66  3.000
 8AB  C09  C08  N04  122.55  3.000
 8AB  H17  C09  C08  122.32  3.000
 8AB  H17  C09  C10  119.41  3.000
 8AB  C08  C09  C10  118.26  3.000
 8AB  H18  C11  C12  120.87  3.000
 8AB  H18  C11  C10  121.52  3.000
 8AB  C12  C11  C10  117.60  3.000
 8AB  N14  C12  C11  122.37  3.000
 8AB  N14  C12  C13  116.94  3.000
 8AB  C11  C12  C13  120.68  3.000
 8AB  C12  N14  C08  120.53  3.000
 8AB  H7   C01  H6   108.31  3.000
 8AB  H7   C01  H5   107.63  3.000
 8AB  H6   C01  H5   107.98  3.000
 8AB  H7   C01  C02  110.86  3.000
 8AB  H6   C01  C02  110.98  3.000
 8AB  H5   C01  C02  110.96  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
 8AB  CONST_01  N14  C08  C09  C10     0.00   0.0  0
 8AB  CONST_02  N14  C12  C11  C10     0.00   0.0  0
 8AB  CONST_03  C11  C10  C09  C08     0.00   0.0  0
 8AB  CONST_04  C11  C12  N14  C08     0.00   0.0  0
 8AB  CONST_05  C12  C11  C10  C09     0.00   0.0  0
 8AB  CONST_06  C12  N14  C08  C09     0.00   0.0  0
 8AB  CONST_07  N04  C08  C09  C10   180.00   0.0  0
 8AB  CONST_08  C12  N14  C08  N04   180.00   0.0  0
 8AB  CONST_09  C13  C12  C11  C10   180.00   0.0  0
 8AB  CONST_10  C08  N14  C12  C13   180.00   0.0  0
 8AB  CONST_11  H17  C09  C08  N04     0.00   0.0  0
 8AB  CONST_12  H1   C10  C09  C08   180.00   0.0  0
 8AB  CONST_13  H18  C11  C10  C09   180.00   0.0  0
 8AB  CONST_14  H17  C09  C10  C11   180.00   0.0  0
 8AB  CONST_15  H1   C10  C11  C12   180.00   0.0  0
 8AB  CONST_16  H17  C09  C08  N14   180.00   0.0  0
 8AB  CONST_17  H18  C11  C12  N14   180.00   0.0  0
 8AB  Var_01    C05  N04  C03  C02   -51.29  30.0  1
 8AB  Var_02    C08  N04  C03  C02   155.81  30.0  1
 8AB  Var_03    C05  C06  N07  C02    61.86  30.0  1
 8AB  Var_04    C06  C05  N04  C03    50.12  30.0  1
 8AB  Var_05    C09  C08  N04  C03   155.53  30.0  2
 8AB  Var_06    N14  C08  N04  C03   -25.33  30.0  2
 8AB  Var_07    N07  C06  C05  N04   -54.56  30.0  1
 8AB  Var_08    C09  C08  N04  C05     4.30  30.0  2
 8AB  Var_09    N14  C08  N04  C05  -176.56  30.0  2
 8AB  Var_10    C08  N04  C05  C06  -157.30  30.0  1
 8AB  Var_11    H13  C06  N07  C02   -59.45  30.0  1
 8AB  Var_12    H14  C06  N07  C02  -178.82  30.0  1
 8AB  Var_13    H11  C05  N04  C03   168.54  30.0  1
 8AB  Var_14    H12  C05  N04  C03   -72.30  30.0  1
 8AB  Var_15    H13  C06  C05  N04    69.27  30.0  1
 8AB  Var_16    H14  C06  C05  N04  -174.49  30.0  1
 8AB  Var_17    H9   C03  N04  C05    69.66  30.0  1
 8AB  Var_18    H10  C03  N04  C05  -172.38  30.0  1
 8AB  Var_19    H15  N07  C06  C05  -177.18  30.0  1
 8AB  Var_20    H11  C05  C06  N07  -174.45  30.0  1
 8AB  Var_21    H12  C05  C06  N07    68.66  30.0  1
 8AB  Var_22    H11  C05  N04  C08   -38.89  30.0  1
 8AB  Var_23    H12  C05  N04  C08    80.28  30.0  1
 8AB  Var_24    H9   C03  N04  C08   -83.24  30.0  1
 8AB  Var_25    H10  C03  N04  C08    34.73  30.0  1
 8AB  Var_26    H2   C13  C12  C11  -161.32  30.0  2
 8AB  Var_27    H3   C13  C12  C11   -39.81  30.0  2
 8AB  Var_28    H4   C13  C12  C11    79.18  30.0  2
 8AB  Var_29    H2   C13  C12  N14    19.81  30.0  2
 8AB  Var_30    H3   C13  C12  N14   141.32  30.0  2
 8AB  Var_31    H4   C13  C12  N14   -99.70  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
 8AB  chir_01  C02  C03  N07  C01  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
 8AB  plan-1  C10  0.020
 8AB  plan-1  C13  0.020
 8AB  plan-1  N04  0.020
 8AB  plan-1  C08  0.020
 8AB  plan-1  C09  0.020
 8AB  plan-1  C11  0.020
 8AB  plan-1  C12  0.020
 8AB  plan-1  N14  0.020
 8AB  plan-1  H1   0.020
 8AB  plan-1  H17  0.020
 8AB  plan-1  H18  0.020

