# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 07:18:04 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: 1-[4-(piperazin-1-yl)pyridin-3-yl]-N-[(quinoxalin-6-yl)methyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCN1)c2ccncc2CNCc3ccc4nccnc4c3
#
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
 KWL  KWL  "1-[4-(piperazin-1-yl)pyridin-3-yl]-N-[(quinoxalin-6-yl)methyl]methanamine"
  ligand  47  25  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KWL
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
 KWL  C11  C  CR16  0  -0.409  -15.8707   5.1440  -16.2368
 KWL  C13  C  CH2   0  -0.366  -13.1753   3.6691  -14.3467
 KWL  C14  C  CH2   0  -0.297  -11.9635   2.7712  -14.6300
 KWL  N    N  N     0  -0.375  -19.7737  -4.8634  -14.5103
 KWL  C    C  CR66  0   0.213  -18.8840  -3.8453  -14.4923
 KWL  C1   C  CR16  0  -0.121  -21.0360  -4.5430  -14.5709
 KWL  C10  C  CR16  0  -0.082  -17.2505   5.2164  -16.2579
 KWL  C12  C  CR6   0   0.416  -15.2397   4.0442  -15.6414
 KWL  C15  C  CH2   0  -0.353  -11.5848   4.3853  -16.3512
 KWL  C16  C  CH2   0  -0.310  -13.0690   4.7896  -16.4663
 KWL  C17  C  CR16  0  -0.282  -16.6034  -3.0872  -14.4102
 KWL  C18  C  CR16  0  -0.288  -17.5001  -4.1173  -14.4268
 KWL  C2   C  CR16  0  -0.117  -21.4693  -3.1968  -14.6174
 KWL  C3   C  CR66  0   0.259  -19.3155  -2.4987  -14.5402
 KWL  C4   C  CR16  0  -0.375  -18.3659  -1.4554  -14.5181
 KWL  C5   C  CR6   0   0.063  -17.0260  -1.7345  -14.4521
 KWL  C6   C  CH2   0  -0.286  -15.9832  -0.6501  -14.3961
 KWL  C8   C  CR6   0  -0.058  -16.0791   3.0200  -15.1488
 KWL  C9   C  CR16  0  -0.117  -17.4500   3.2233  -15.2180
 KWL  N1   N  N     0  -0.380  -20.6336  -2.1970  -14.6039
 KWL  N2   N  NH1   0  -0.613  -16.4821   0.6239  -14.8569
 KWL  N3   N  N     0  -0.419  -18.0478   4.2899  -15.7434
 KWL  N4   N  NT    0  -0.506  -13.8660   3.9414  -15.5970
 KWL  N5   N  NH1   0  -0.575  -11.3963   3.0061  -15.9518
 KWL  H10  H  HCR6  0   0.271  -15.3002   5.9577  -16.6614
 KWL  H12  H  HCH2  0   0.247  -12.8572   4.6182  -13.8938
 KWL  H11  H  HCH2  0   0.269  -13.8366   3.2058  -13.6189
 KWL  H13  H  HCH2  0   0.235  -12.2502   1.7205  -14.5615
 KWL  H14  H  HCH2  0   0.222  -11.2070   2.9472  -13.8593
 KWL  H9   H  HCR6  0   0.253  -17.7312   6.0811  -16.7039
 KWL  H16  H  HCH2  0   0.253  -11.0917   4.5660  -17.3071
 KWL  H17  H  HCH2  0   0.236  -11.0794   5.0223  -15.6208
 KWL  H18  H  HCH2  0   0.221  -13.1722   5.8564  -16.2220
 KWL  H19  H  HCH2  0   0.245  -13.4180   4.6562  -17.4929
 KWL  H20  H  HCR6  0   0.260  -15.5422  -3.3023  -14.3673
 KWL  H21  H  HCR6  0   0.266  -17.1705  -5.1480  -14.3958
 KWL  H1   H  HCR6  0   0.274  -22.5291  -2.9727  -14.6669
 KWL  H2   H  HCR6  0   0.262  -18.7214  -0.4339  -14.5539
 KWL  H3   H  HCH2  0   0.223  -15.0885  -0.9868  -14.9423
 KWL  H4   H  HCH2  0   0.254  -15.6629  -0.5367  -13.3544
 KWL  H8   H  HCR6  0   0.255  -18.1076   2.4484  -14.8401
 KWL  H22  H  HNH1  0   0.351  -16.7101   0.5551  -15.8424
 KWL  H15  H  HNH1  0   0.346  -11.8538   2.4022  -16.6226
 KWL  C7   C  CH2   0  -0.309  -15.5354   1.7020  -14.6580
 KWL  H    H  HCR6  0   0.274  -21.7643  -5.3461  -14.5850
 KWL  H7   H  HCH2  0   0.246  -15.3137   1.7482  -13.5859
 KWL  H6   H  HCH2  0   0.225  -14.5720   1.5107  -15.1556

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
 KWL  C16  C15  single    1.543  0.020  1.543
 KWL  C16  N4   single    1.453  0.020  1.453
 KWL  C15  N5   single    1.448  0.020  1.448
 KWL  C10  N3   aromatic  1.326  0.020  1.326
 KWL  C10  C11  aromatic  1.382  0.020  1.382
 KWL  N3   C9   aromatic  1.331  0.020  1.331
 KWL  C11  C12  aromatic  1.401  0.020  1.401
 KWL  N2   C6   single    1.444  0.020  1.444
 KWL  N2   C7   single    1.449  0.020  1.449
 KWL  C9   C8   aromatic  1.388  0.020  1.388
 KWL  C12  C8   aromatic  1.413  0.020  1.413
 KWL  C12  N4   single    1.378  0.020  1.378
 KWL  N5   C14  single    1.457  0.020  1.457
 KWL  C8   C7   single    1.508  0.020  1.508
 KWL  N4   C13  single    1.454  0.020  1.454
 KWL  C6   C5   single    1.505  0.020  1.505
 KWL  C4   C5   aromatic  1.370  0.020  1.370
 KWL  C4   C3   aromatic  1.411  0.020  1.411
 KWL  C5   C17  aromatic  1.418  0.020  1.418
 KWL  N1   C3   aromatic  1.354  0.020  1.354
 KWL  N1   C2   aromatic  1.303  0.020  1.303
 KWL  C3   C    aromatic  1.415  0.020  1.415
 KWL  C17  C18  aromatic  1.366  0.020  1.366
 KWL  C2   C1   aromatic  1.415  0.020  1.415
 KWL  C    C18  aromatic  1.412  0.020  1.412
 KWL  C    N    aromatic  1.352  0.020  1.352
 KWL  C14  C13  single    1.535  0.020  1.535
 KWL  C1   N    aromatic  1.304  0.020  1.304
 KWL  C11  H10  single    0.930  0.020  1.080
 KWL  C13  H12  single    0.970  0.020  1.090
 KWL  C13  H11  single    0.970  0.020  1.090
 KWL  C14  H13  single    0.970  0.020  1.090
 KWL  C14  H14  single    0.970  0.020  1.090
 KWL  C1   H    single    0.930  0.020  1.080
 KWL  C10  H9   single    0.930  0.020  1.080
 KWL  C15  H16  single    0.970  0.020  1.090
 KWL  C15  H17  single    0.970  0.020  1.090
 KWL  C16  H18  single    0.970  0.020  1.090
 KWL  C16  H19  single    0.970  0.020  1.090
 KWL  C17  H20  single    0.930  0.020  1.080
 KWL  C18  H21  single    0.930  0.020  1.080
 KWL  C2   H1   single    0.930  0.020  1.080
 KWL  C4   H2   single    0.930  0.020  1.080
 KWL  C6   H3   single    0.970  0.020  1.090
 KWL  C6   H4   single    0.970  0.020  1.090
 KWL  C7   H7   single    0.970  0.020  1.090
 KWL  C7   H6   single    0.970  0.020  1.090
 KWL  C9   H8   single    0.930  0.020  1.080
 KWL  N2   H22  single    0.890  0.020  1.040
 KWL  N5   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
 KWL  H10  C11  C12  121.36  3.000
 KWL  H10  C11  C10  118.79  3.000
 KWL  C12  C11  C10  119.83  3.000
 KWL  H11  C13  H12  105.57  3.000
 KWL  H11  C13  N4   111.50  3.000
 KWL  H12  C13  N4   109.28  3.000
 KWL  H11  C13  C14  110.76  3.000
 KWL  H12  C13  C14  110.67  3.000
 KWL  N4   C13  C14  109.02  3.000
 KWL  H14  C14  H13  106.99  3.000
 KWL  H14  C14  N5   110.11  3.000
 KWL  H13  C14  N5   108.32  3.000
 KWL  H14  C14  C13  108.78  3.000
 KWL  H13  C14  C13  110.14  3.000
 KWL  N5   C14  C13  112.36  3.000
 KWL  C1   N    C    116.92  3.000
 KWL  C3   C    C18  118.93  3.000
 KWL  C18  C    N    120.04  3.000
 KWL  C3   C    N    121.03  3.000
 KWL  H    C1   C2   119.90  3.000
 KWL  H    C1   N    117.97  3.000
 KWL  C2   C1   N    122.13  3.000
 KWL  H9   C10  N3   116.74  3.000
 KWL  H9   C10  C11  119.36  3.000
 KWL  N3   C10  C11  123.90  3.000
 KWL  N4   C12  C8   121.79  3.000
 KWL  N4   C12  C11  121.41  3.000
 KWL  C8   C12  C11  116.73  3.000
 KWL  H17  C15  H16  106.26  3.000
 KWL  H17  C15  N5   108.09  3.000
 KWL  H16  C15  N5   109.91  3.000
 KWL  H17  C15  C16  110.00  3.000
 KWL  H16  C15  C16  109.04  3.000
 KWL  N5   C15  C16  113.29  3.000
 KWL  H19  C16  H18  107.30  3.000
 KWL  H19  C16  N4   108.40  3.000
 KWL  H18  C16  N4   112.46  3.000
 KWL  H19  C16  C15  110.21  3.000
 KWL  H18  C16  C15  109.16  3.000
 KWL  N4   C16  C15  109.28  3.000
 KWL  H20  C17  C5   118.84  3.000
 KWL  H20  C17  C18  119.59  3.000
 KWL  C5   C17  C18  121.57  3.000
 KWL  H21  C18  C17  121.19  3.000
 KWL  H21  C18  C    118.89  3.000
 KWL  C17  C18  C    119.92  3.000
 KWL  H1   C2   N1   117.95  3.000
 KWL  H1   C2   C1   119.83  3.000
 KWL  N1   C2   C1   122.22  3.000
 KWL  N1   C3   C4   119.42  3.000
 KWL  N1   C3   C    120.71  3.000
 KWL  C4   C3   C    119.87  3.000
 KWL  H2   C4   C5   121.00  3.000
 KWL  H2   C4   C3   118.45  3.000
 KWL  C5   C4   C3   120.55  3.000
 KWL  C6   C5   C4   122.17  3.000
 KWL  C4   C5   C17  119.15  3.000
 KWL  C6   C5   C17  118.67  3.000
 KWL  H4   C6   H3   105.41  3.000
 KWL  H4   C6   N2   108.25  3.000
 KWL  H3   C6   N2   113.10  3.000
 KWL  H4   C6   C5   108.20  3.000
 KWL  H3   C6   C5   108.91  3.000
 KWL  N2   C6   C5   112.61  3.000
 KWL  C9   C8   C7   120.04  3.000
 KWL  C7   C8   C12  122.20  3.000
 KWL  C9   C8   C12  117.60  3.000
 KWL  H8   C9   N3   115.97  3.000
 KWL  H8   C9   C8   118.49  3.000
 KWL  N3   C9   C8   125.51  3.000
 KWL  C3   N1   C2   117.00  3.000
 KWL  H22  N2   C7   109.32  3.000
 KWL  H22  N2   C6   109.15  3.000
 KWL  C7   N2   C6   112.77  3.000
 KWL  C9   N3   C10  116.30  3.000
 KWL  C16  N4   C12  118.95  3.000
 KWL  C12  N4   C13  121.01  3.000
 KWL  C16  N4   C13  111.30  3.000
 KWL  H15  N5   C15  109.07  3.000
 KWL  H15  N5   C14  109.21  3.000
 KWL  C15  N5   C14  110.67  3.000
 KWL  H6   C7   H7   105.81  3.000
 KWL  H6   C7   N2   112.36  3.000
 KWL  H7   C7   N2   107.33  3.000
 KWL  H6   C7   C8   108.68  3.000
 KWL  H7   C7   C8   110.77  3.000
 KWL  N2   C7   C8   111.73  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
 KWL  CONST_01  C9   N3   C10  C11     0.00   0.0  0
 KWL  CONST_02  C9   C8   C12  C11     0.00   0.0  0
 KWL  CONST_03  C4   C3   C    N     180.00   0.0  0
 KWL  CONST_04  N1   C3   C    N       0.00   0.0  0
 KWL  CONST_05  C17  C18  C    N     180.00   0.0  0
 KWL  CONST_06  N1   C2   C1   N       0.00   0.0  0
 KWL  CONST_07  C5   C4   C3   C       0.00   0.0  0
 KWL  CONST_08  C2   N1   C3   C       0.00   0.0  0
 KWL  CONST_09  C5   C17  C18  C       0.00   0.0  0
 KWL  CONST_10  C2   C1   N    C       0.00   0.0  0
 KWL  CONST_11  C3   N1   C2   C1      0.00   0.0  0
 KWL  CONST_12  C3   C    N    C1      0.00   0.0  0
 KWL  CONST_13  C18  C    N    C1    180.00   0.0  0
 KWL  CONST_14  C8   C9   N3   C10     0.00   0.0  0
 KWL  CONST_15  C8   C12  C11  C10     0.00   0.0  0
 KWL  CONST_16  N3   C10  C11  C12     0.00   0.0  0
 KWL  CONST_17  N3   C9   C8   C12     0.00   0.0  0
 KWL  CONST_18  C3   C4   C5   C17     0.00   0.0  0
 KWL  CONST_19  C3   C    C18  C17     0.00   0.0  0
 KWL  CONST_20  C4   C5   C17  C18     0.00   0.0  0
 KWL  CONST_21  C4   C3   C    C18     0.00   0.0  0
 KWL  CONST_22  N1   C3   C    C18   180.00   0.0  0
 KWL  CONST_23  C4   C3   N1   C2    180.00   0.0  0
 KWL  CONST_24  N1   C3   C4   C5    180.00   0.0  0
 KWL  CONST_25  N4   C12  C11  C10   180.00   0.0  0
 KWL  CONST_26  N4   C12  C8   C9    180.00   0.0  0
 KWL  CONST_27  C7   C8   C12  C11   180.00   0.0  0
 KWL  CONST_28  C6   C5   C17  C18   180.00   0.0  0
 KWL  CONST_29  C6   C5   C4   C3    180.00   0.0  0
 KWL  CONST_30  N3   C9   C8   C7    180.00   0.0  0
 KWL  CONST_31  N4   C12  C8   C7      0.00   0.0  0
 KWL  CONST_32  H21  C18  C    N       0.00   0.0  0
 KWL  CONST_33  H1   C2   C1   N     180.00   0.0  0
 KWL  CONST_34  H2   C4   C3   C     180.00   0.0  0
 KWL  CONST_35  H20  C17  C18  C     180.00   0.0  0
 KWL  CONST_36  H    C1   N    C     180.00   0.0  0
 KWL  CONST_37  H8   C9   N3   C10   180.00   0.0  0
 KWL  CONST_38  H9   C10  C11  C12   180.00   0.0  0
 KWL  CONST_39  H8   C9   C8   C12   180.00   0.0  0
 KWL  CONST_40  H2   C4   C5   C17   180.00   0.0  0
 KWL  CONST_41  H1   C2   N1   C3    180.00   0.0  0
 KWL  CONST_42  H21  C18  C    C3    180.00   0.0  0
 KWL  CONST_43  H20  C17  C5   C4    180.00   0.0  0
 KWL  CONST_44  H21  C18  C17  C5    180.00   0.0  0
 KWL  CONST_45  H10  C11  C12  C8    180.00   0.0  0
 KWL  CONST_46  H9   C10  N3   C9    180.00   0.0  0
 KWL  CONST_47  H2   C4   C3   N1      0.00   0.0  0
 KWL  CONST_48  H    C1   C2   N1    180.00   0.0  0
 KWL  CONST_49  H10  C11  C10  N3    180.00   0.0  0
 KWL  CONST_50  H10  C11  C12  N4      0.00   0.0  0
 KWL  Var_01    C16  N4   C12  C11   -16.00  30.0  2
 KWL  Var_02    C13  N4   C12  C11   128.76  30.0  2
 KWL  Var_03    C15  C16  N4   C13    38.30  30.0  1
 KWL  Var_04    C8   C12  N4   C13   -54.34  30.0  1
 KWL  Var_05    C15  N5   C14  C13    30.78  30.0  1
 KWL  Var_06    C16  C15  N5   C14   -61.95  30.0  1
 KWL  Var_07    C16  N4   C13  C14   -68.67  30.0  1
 KWL  Var_08    C12  N4   C13  C14   144.15  30.0  1
 KWL  Var_09    C15  C16  N4   C12  -173.77  30.0  1
 KWL  Var_10    C8   C12  N4   C16   160.91  30.0  1
 KWL  Var_11    N5   C15  C16  N4     25.84  30.0  1
 KWL  Var_12    N5   C14  C13  N4     31.04  30.0  1
 KWL  Var_13    H18  C16  N4   C13   -83.09  30.0  1
 KWL  Var_14    H19  C16  N4   C13   158.44  30.0  1
 KWL  Var_15    H15  N5   C14  C13   -89.30  30.0  1
 KWL  Var_16    H16  C15  N5   C14   175.79  30.0  1
 KWL  Var_17    H17  C15  N5   C14    60.22  30.0  1
 KWL  Var_18    H18  C16  N4   C12    64.84  30.0  1
 KWL  Var_19    H19  C16  N4   C12   -53.62  30.0  1
 KWL  Var_20    H12  C13  N4   C12   -94.77  30.0  1
 KWL  Var_21    H11  C13  N4   C12    21.55  30.0  1
 KWL  Var_22    H13  C14  N5   C15   152.68  30.0  1
 KWL  Var_23    H14  C14  N5   C15   -90.64  30.0  1
 KWL  Var_24    H15  N5   C15  C16    58.21  30.0  1
 KWL  Var_25    H12  C13  N4   C16    52.41  30.0  1
 KWL  Var_26    H11  C13  N4   C16   168.73  30.0  1
 KWL  Var_27    H16  C15  C16  N4    148.59  30.0  1
 KWL  Var_28    H17  C15  C16  N4    -95.25  30.0  1
 KWL  Var_29    H13  C14  C13  N4    -89.82  30.0  1
 KWL  Var_30    H14  C14  C13  N4    153.21  30.0  1
 KWL  Var_31    H18  C16  C15  N5    149.22  30.0  1
 KWL  Var_32    H19  C16  C15  N5    -93.18  30.0  1
 KWL  Var_33    H12  C13  C14  N5    -89.19  30.0  1
 KWL  Var_34    H11  C13  C14  N5    154.09  30.0  1
 KWL  Var_35    N2   C7   C8   C12  -150.28  30.0  2
 KWL  Var_36    N2   C6   C5   C17   161.91  30.0  1
 KWL  Var_37    N2   C6   C5   C4    -19.26  30.0  1
 KWL  Var_38    N2   C7   C8   C9     25.00  30.0  2
 KWL  Var_39    H7   C7   C8   C12    90.11  30.0  2
 KWL  Var_40    H6   C7   C8   C12   -25.73  30.0  2
 KWL  Var_41    H3   C6   C5   C17    35.61  30.0  1
 KWL  Var_42    H4   C6   C5   C17   -78.49  30.0  1
 KWL  Var_43    H3   C6   C5   C4   -145.56  30.0  1
 KWL  Var_44    H4   C6   C5   C4    100.34  30.0  1
 KWL  Var_45    H7   C7   C8   C9    -94.61  30.0  2
 KWL  Var_46    H6   C7   C8   C9    149.55  30.0  2
 KWL  Var_47    C7   N2   C6   C5    173.16  30.0  1
 KWL  Var_48    C8   C7   N2   C6    179.92  30.0  3
 KWL  Var_49    H22  N2   C6   C5    -65.12  30.0  1
 KWL  Var_50    H22  N2   C7   C8     58.30  30.0  1
 KWL  Var_51    H7   C7   N2   C6    -58.47  30.0  3
 KWL  Var_52    H6   C7   N2   C6     57.45  30.0  3
 KWL  Var_53    H3   C6   N2   C7    -62.83  30.0  3
 KWL  Var_54    H4   C6   N2   C7     53.59  30.0  3

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
 KWL  plan-1  C11  0.020
 KWL  plan-1  C10  0.020
 KWL  plan-1  C12  0.020
 KWL  plan-1  C8   0.020
 KWL  plan-1  C9   0.020
 KWL  plan-1  N3   0.020
 KWL  plan-1  N4   0.020
 KWL  plan-1  H10  0.020
 KWL  plan-1  H9   0.020
 KWL  plan-1  H8   0.020
 KWL  plan-1  C7   0.020
 KWL  plan-2  N    0.020
 KWL  plan-2  C    0.020
 KWL  plan-2  C1   0.020
 KWL  plan-2  C17  0.020
 KWL  plan-2  C18  0.020
 KWL  plan-2  C2   0.020
 KWL  plan-2  C3   0.020
 KWL  plan-2  C4   0.020
 KWL  plan-2  C5   0.020
 KWL  plan-2  C6   0.020
 KWL  plan-2  N1   0.020
 KWL  plan-2  H20  0.020
 KWL  plan-2  H21  0.020
 KWL  plan-2  H1   0.020
 KWL  plan-2  H2   0.020
 KWL  plan-2  H    0.020

