# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 18:13:55 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-[5-azanyl-6-(phenylmethyl)pyrazin-2-yl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(nc1Cc2ccccc2)c3ccc(O)cc3
#
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
 VKB  VKB  "4-[5-azanyl-6-(phenylmethyl)pyrazin-2-yl]phenol"
  ligand  36  21  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VKB
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
 VKB  C1   C  CR16  0  -0.125  42.2828  -24.0535   9.8861
 VKB  N1   N  N     0  -0.407  43.3625  -24.3966  10.5745
 VKB  C2   C  CR6   0   0.161  40.9961  -24.2878  10.3499
 VKB  C    C  CR6   0   0.403  43.1966  -25.0036  11.7405
 VKB  O    O  OH1   0  -0.626  36.3726  -22.8083   7.4908
 VKB  C11  C  CR6   0   0.091  42.0048  -25.1853  14.7180
 VKB  C12  C  CR16  0  -0.321  42.8726  -25.6552  15.6997
 VKB  C13  C  CR16  0  -0.240  43.1726  -24.8806  16.8145
 VKB  C14  C  CR16  0  -0.266  42.6037  -23.6242  16.9613
 VKB  C15  C  CR16  0  -0.238  41.7320  -23.1482  15.9887
 VKB  C16  C  CR16  0  -0.276  41.4376  -23.9216  14.8757
 VKB  C3   C  CR6   0   0.047  39.7841  -23.8947   9.6111
 VKB  C4   C  CR16  0  -0.314  39.8117  -22.9253   8.6049
 VKB  C5   C  CR16  0  -0.318  38.6708  -22.5727   7.9064
 VKB  C6   C  CR6   0   0.343  37.4529  -23.1811   8.2025
 VKB  C7   C  CR16  0  -0.363  37.4036  -24.1384   9.2135
 VKB  C8   C  CR16  0  -0.278  38.5534  -24.4837   9.9033
 VKB  C9   C  CR6   0   0.171  41.8906  -25.2975  12.2111
 VKB  N2   N  N     0  -0.400  40.8410  -24.9285  11.5152
 VKB  H1   H  HCR6  0   0.259  42.4618  -23.5855   8.9251
 VKB  H2   H  HNH2  0   0.388  45.1757  -24.9767  12.1133
 VKB  H3   H  HNH2  0   0.401  44.2476  -25.4889  13.4250
 VKB  H4   H  HOH1  0   0.473  35.5912  -23.2934   7.7803
 VKB  H5   H  HCH2  0   0.283  40.6272  -26.3339  13.5442
 VKB  H6   H  HCH2  0   0.271  42.2736  -26.9420  13.5236
 VKB  H7   H  HCR6  0   0.259  43.3183  -26.6380  15.5936
 VKB  H8   H  HCR6  0   0.255  43.8529  -25.2613  17.5655
 VKB  H9   H  HCR6  0   0.255  42.8369  -23.0182  17.8272
 VKB  H10  H  HCR6  0   0.255  41.2812  -22.1699  16.0972
 VKB  H11  H  HCR6  0   0.251  40.7572  -23.5391  14.1239
 VKB  H12  H  HCR6  0   0.248  40.7341  -22.4150   8.3588
 VKB  H13  H  HCR6  0   0.262  38.7203  -21.8159   7.1334
 VKB  H14  H  HCR6  0   0.269  36.4646  -24.6204   9.4628
 VKB  H15  H  HCR6  0   0.252  38.4906  -25.2333  10.6808
 VKB  N    N  NH2   0  -0.834  44.3087  -25.3844  12.4256
 VKB  C10  C  CH2   0  -0.591  41.6742  -26.0272  13.5057

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
 VKB  O    C6   single    1.346  0.020  1.346
 VKB  C5   C6   aromatic  1.393  0.020  1.393
 VKB  C5   C4   aromatic  1.383  0.020  1.383
 VKB  C6   C7   aromatic  1.393  0.020  1.393
 VKB  C4   C3   aromatic  1.397  0.020  1.397
 VKB  C7   C8   aromatic  1.385  0.020  1.385
 VKB  C3   C8   aromatic  1.395  0.020  1.395
 VKB  C3   C2   single    1.473  0.020  1.473
 VKB  C1   C2   aromatic  1.388  0.020  1.388
 VKB  C1   N1   aromatic  1.326  0.020  1.326
 VKB  C2   N2   aromatic  1.339  0.020  1.339
 VKB  N1   C    aromatic  1.325  0.020  1.325
 VKB  N2   C9   aromatic  1.312  0.020  1.312
 VKB  C    C9   aromatic  1.419  0.020  1.419
 VKB  C    N    single    1.361  0.020  1.361
 VKB  C9   C10  single    1.502  0.020  1.502
 VKB  C10  C11  single    1.512  0.020  1.512
 VKB  C11  C16  aromatic  1.394  0.020  1.394
 VKB  C11  C12  aromatic  1.392  0.020  1.392
 VKB  C16  C15  aromatic  1.387  0.020  1.387
 VKB  C12  C13  aromatic  1.390  0.020  1.390
 VKB  C15  C14  aromatic  1.390  0.020  1.390
 VKB  C13  C14  aromatic  1.387  0.020  1.387
 VKB  C1   H1   single    0.930  0.020  1.080
 VKB  N    H2   single    0.890  0.020  1.040
 VKB  N    H3   single    0.890  0.020  1.040
 VKB  O    H4   single    0.850  0.020  0.980
 VKB  C10  H5   single    0.970  0.020  1.090
 VKB  C10  H6   single    0.970  0.020  1.090
 VKB  C12  H7   single    0.930  0.020  1.080
 VKB  C13  H8   single    0.930  0.020  1.080
 VKB  C14  H9   single    0.930  0.020  1.080
 VKB  C15  H10  single    0.930  0.020  1.080
 VKB  C16  H11  single    0.930  0.020  1.080
 VKB  C4   H12  single    0.930  0.020  1.080
 VKB  C5   H13  single    0.930  0.020  1.080
 VKB  C7   H14  single    0.930  0.020  1.080
 VKB  C8   H15  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
 VKB  H1   C1   C2   121.49  3.000
 VKB  H1   C1   N1   115.96  3.000
 VKB  C2   C1   N1   122.54  3.000
 VKB  C    N1   C1   118.27  3.000
 VKB  N2   C2   C3   117.97  3.000
 VKB  N2   C2   C1   118.63  3.000
 VKB  C3   C2   C1   123.39  3.000
 VKB  C9   C    N    121.83  3.000
 VKB  N    C    N1   117.97  3.000
 VKB  C9   C    N1   120.13  3.000
 VKB  H4   O    C6   110.62  3.000
 VKB  C16  C11  C12  118.67  3.000
 VKB  C12  C11  C10  120.91  3.000
 VKB  C16  C11  C10  120.42  3.000
 VKB  H7   C12  C13  119.65  3.000
 VKB  H7   C12  C11  119.55  3.000
 VKB  C13  C12  C11  120.80  3.000
 VKB  H8   C13  C14  120.19  3.000
 VKB  H8   C13  C12  119.74  3.000
 VKB  C14  C13  C12  120.07  3.000
 VKB  H9   C14  C15  120.20  3.000
 VKB  H9   C14  C13  120.23  3.000
 VKB  C15  C14  C13  119.56  3.000
 VKB  H10  C15  C16  119.73  3.000
 VKB  H10  C15  C14  120.04  3.000
 VKB  C16  C15  C14  120.24  3.000
 VKB  H11  C16  C15  119.55  3.000
 VKB  H11  C16  C11  119.79  3.000
 VKB  C15  C16  C11  120.66  3.000
 VKB  C8   C3   C4   117.45  3.000
 VKB  C8   C3   C2   120.54  3.000
 VKB  C4   C3   C2   122.01  3.000
 VKB  H12  C4   C5   117.89  3.000
 VKB  H12  C4   C3   120.50  3.000
 VKB  C5   C4   C3   121.61  3.000
 VKB  H13  C5   C6   119.79  3.000
 VKB  H13  C5   C4   120.06  3.000
 VKB  C6   C5   C4   120.15  3.000
 VKB  C7   C6   C5   119.03  3.000
 VKB  C7   C6   O    123.06  3.000
 VKB  C5   C6   O    117.91  3.000
 VKB  H14  C7   C8   119.58  3.000
 VKB  H14  C7   C6   120.19  3.000
 VKB  C8   C7   C6   120.23  3.000
 VKB  H15  C8   C7   118.85  3.000
 VKB  H15  C8   C3   119.62  3.000
 VKB  C7   C8   C3   121.53  3.000
 VKB  N2   C9   C10  118.59  3.000
 VKB  C10  C9   C    121.27  3.000
 VKB  N2   C9   C    120.14  3.000
 VKB  C9   N2   C2   120.23  3.000
 VKB  H3   N    H2   113.69  3.000
 VKB  H3   N    C    118.65  3.000
 VKB  H2   N    C    115.72  3.000
 VKB  H6   C10  H5   106.86  3.000
 VKB  H6   C10  C9   109.97  3.000
 VKB  H5   C10  C9   107.76  3.000
 VKB  H6   C10  C11  109.43  3.000
 VKB  H5   C10  C11  109.74  3.000
 VKB  C9   C10  C11  112.90  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
 VKB  CONST_03  C9   N2   C2   C1      0.00   0.0  0
 VKB  CONST_04  C9   C    N1   C1      0.00   0.0  0
 VKB  CONST_05  C3   C2   C1   N1    180.00   0.0  0
 VKB  CONST_06  N2   C2   C1   N1      0.00   0.0  0
 VKB  CONST_07  N2   C9   C    N1      0.00   0.0  0
 VKB  CONST_08  C5   C4   C3   C2    180.00   0.0  0
 VKB  CONST_09  C7   C8   C3   C2    180.00   0.0  0
 VKB  CONST_10  C    N1   C1   C2      0.00   0.0  0
 VKB  CONST_11  C    C9   N2   C2      0.00   0.0  0
 VKB  CONST_12  C14  C15  C16  C11     0.00   0.0  0
 VKB  CONST_13  C14  C13  C12  C11     0.00   0.0  0
 VKB  CONST_14  C15  C16  C11  C12     0.00   0.0  0
 VKB  CONST_15  C15  C14  C13  C12     0.00   0.0  0
 VKB  CONST_16  C16  C11  C12  C13     0.00   0.0  0
 VKB  CONST_17  C16  C15  C14  C13     0.00   0.0  0
 VKB  CONST_18  C6   C5   C4   C3      0.00   0.0  0
 VKB  CONST_19  C6   C7   C8   C3      0.00   0.0  0
 VKB  CONST_20  C9   N2   C2   C3    180.00   0.0  0
 VKB  CONST_21  C7   C6   C5   C4      0.00   0.0  0
 VKB  CONST_22  C7   C8   C3   C4      0.00   0.0  0
 VKB  CONST_24  C8   C7   C6   C5      0.00   0.0  0
 VKB  CONST_25  C8   C3   C4   C5      0.00   0.0  0
 VKB  CONST_27  N    C    N1   C1    180.00   0.0  0
 VKB  CONST_28  C10  C9   C    N1    180.00   0.0  0
 VKB  CONST_29  C10  C9   N2   C2    180.00   0.0  0
 VKB  CONST_30  N2   C9   C    N     180.00   0.0  0
 VKB  CONST_31  C4   C5   C6   O     180.00   0.0  0
 VKB  CONST_32  C8   C7   C6   O     180.00   0.0  0
 VKB  CONST_33  C15  C16  C11  C10   180.00   0.0  0
 VKB  CONST_34  C13  C12  C11  C10   180.00   0.0  0
 VKB  CONST_35  H12  C4   C3   C2      0.00   0.0  0
 VKB  CONST_36  H15  C8   C3   C2      0.00   0.0  0
 VKB  CONST_37  H1   C1   N1   C     180.00   0.0  0
 VKB  CONST_38  H10  C15  C16  C11   180.00   0.0  0
 VKB  CONST_39  H8   C13  C12  C11   180.00   0.0  0
 VKB  CONST_40  H11  C16  C11  C12   180.00   0.0  0
 VKB  CONST_41  H9   C14  C13  C12   180.00   0.0  0
 VKB  CONST_42  H10  C15  C14  C13   180.00   0.0  0
 VKB  CONST_43  H11  C16  C15  C14   180.00   0.0  0
 VKB  CONST_44  H7   C12  C13  C14   180.00   0.0  0
 VKB  CONST_45  H8   C13  C14  C15   180.00   0.0  0
 VKB  CONST_46  H7   C12  C11  C16   180.00   0.0  0
 VKB  CONST_47  H9   C14  C15  C16   180.00   0.0  0
 VKB  CONST_48  H13  C5   C4   C3    180.00   0.0  0
 VKB  CONST_49  H14  C7   C8   C3    180.00   0.0  0
 VKB  CONST_50  H1   C1   C2   C3      0.00   0.0  0
 VKB  CONST_51  H15  C8   C3   C4    180.00   0.0  0
 VKB  CONST_52  H14  C7   C6   C5    180.00   0.0  0
 VKB  CONST_53  H12  C4   C5   C6    180.00   0.0  0
 VKB  CONST_54  H15  C8   C7   C6    180.00   0.0  0
 VKB  CONST_55  H13  C5   C6   C7    180.00   0.0  0
 VKB  CONST_56  H12  C4   C3   C8    180.00   0.0  0
 VKB  CONST_57  H1   C1   C2   N2    180.00   0.0  0
 VKB  CONST_58  H2   N    C    N1      0.00   0.0  0
 VKB  CONST_60  H2   N    C    C9    180.00   0.0  0
 VKB  Var_01    C11  C10  C9   C      71.28  30.0  2
 VKB  Var_02    N2   C9   C10  C11  -108.54  30.0  2
 VKB  Var_03    C9   C10  C11  C12  -127.61  30.0  3
 VKB  Var_04    C9   C10  C11  C16    52.72  30.0  3
 VKB  Var_05    H5   C10  C9   C    -167.36  30.0  2
 VKB  Var_06    H6   C10  C9   C     -51.24  30.0  2
 VKB  Var_07    H5   C10  C11  C12   112.17  30.0  3
 VKB  Var_08    H6   C10  C11  C12    -4.79  30.0  3
 VKB  Var_09    H5   C10  C11  C16   -67.51  30.0  3
 VKB  Var_10    H6   C10  C11  C16   175.54  30.0  3
 VKB  Var_11    H5   C10  C9   N2     12.82  30.0  2
 VKB  Var_12    H6   C10  C9   N2    128.94  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
 VKB  plan-1  C1   0.020
 VKB  plan-1  N1   0.020
 VKB  plan-1  C2   0.020
 VKB  plan-1  C    0.020
 VKB  plan-1  C3   0.020
 VKB  plan-1  C9   0.020
 VKB  plan-1  N2   0.020
 VKB  plan-1  H1   0.020
 VKB  plan-1  N    0.020
 VKB  plan-1  C10  0.020
 VKB  plan-2  C11  0.020
 VKB  plan-2  C12  0.020
 VKB  plan-2  C13  0.020
 VKB  plan-2  C14  0.020
 VKB  plan-2  C15  0.020
 VKB  plan-2  C16  0.020
 VKB  plan-2  H7   0.020
 VKB  plan-2  H8   0.020
 VKB  plan-2  H9   0.020
 VKB  plan-2  H10  0.020
 VKB  plan-2  H11  0.020
 VKB  plan-2  C10  0.020
 VKB  plan-3  C2   0.020
 VKB  plan-3  O    0.020
 VKB  plan-3  C3   0.020
 VKB  plan-3  C4   0.020
 VKB  plan-3  C5   0.020
 VKB  plan-3  C6   0.020
 VKB  plan-3  C7   0.020
 VKB  plan-3  C8   0.020
 VKB  plan-3  H12  0.020
 VKB  plan-3  H13  0.020
 VKB  plan-3  H14  0.020
 VKB  plan-3  H15  0.020
 VKB  plan-4  C    0.020
 VKB  plan-4  H2   0.020
 VKB  plan-4  H3   0.020
 VKB  plan-4  N    0.020

