# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:21:17 2021
#   Inital geometry file: a 74 line input string
#   Ligand name: N-benzylpyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1ccccc1)c2cnccn2
#
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
 W7S  W7S  N-benzylpyrazine-2-carboxamide  ligand  27  16  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_W7S
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
 W7S  C10   C  CR16  0  -0.306  -45.1127  -30.9737  -0.2307
 W7S  C15   C  CR16  0  -0.107  -48.2732  -29.3072   6.2801
 W7S  C02   C  C     0   0.548  -47.2141  -29.2607   2.8002
 W7S  C04   C  CH2   0  -0.355  -44.9842  -29.7324   1.9526
 W7S  C05   C  CR6   0   0.111  -45.1912  -30.9989   1.1570
 W7S  C06   C  CR16  0  -0.290  -45.4253  -32.2148   1.7945
 W7S  C07   C  CR16  0  -0.242  -45.5775  -33.3806   1.0575
 W7S  C08   C  CR16  0  -0.270  -45.4934  -33.3474  -0.3295
 W7S  C09   C  CR16  0  -0.242  -45.2588  -32.1398  -0.9719
 W7S  C11   C  CR6   0   0.069  -48.0643  -29.1594   4.0318
 W7S  C12   C  CR16  0  -0.058  -49.4077  -28.8191   3.9272
 W7S  C14   C  CR16  0  -0.087  -49.6170  -28.9653   6.1731
 W7S  N03   N  NH1   0  -0.641  -45.9326  -29.5623   3.0269
 W7S  N13   N  N     0  -0.352  -50.1813  -28.7223   5.0000
 W7S  N16   N  N     0  -0.380  -47.5044  -29.4018   5.2099
 W7S  O01   O  O     0  -0.469  -47.6890  -29.0688   1.6910
 W7S  H101  H  HCR6  0   0.249  -44.9369  -30.0334  -0.7403
 W7S  H041  H  HCH2  0   0.279  -43.9922  -29.7385   2.4057
 W7S  H042  H  HCH2  0   0.260  -45.0204  -28.8687   1.2858
 W7S  H061  H  HCR6  0   0.247  -45.4916  -32.2562   2.8754
 W7S  H071  H  HCR6  0   0.254  -45.7622  -34.3178   1.5670
 W7S  H081  H  HCR6  0   0.255  -45.6139  -34.2564  -0.9047
 W7S  H091  H  HCR6  0   0.255  -45.1985  -32.1017  -2.0519
 W7S  H121  H  HCR6  0   0.284  -49.8613  -28.6206   2.9648
 W7S  H141  H  HCR6  0   0.288  -50.2384  -28.8887   7.0567
 W7S  H031  H  HNH1  0   0.412  -45.6401  -29.7161   3.9792
 W7S  H151  H  HCR6  0   0.286  -47.8234  -29.5048   7.2449

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
 W7S  C09  C08   aromatic  1.388  0.020  1.388
 W7S  C09  C10   aromatic  1.389  0.020  1.389
 W7S  C08  C07   aromatic  1.390  0.020  1.390
 W7S  C10  C05   aromatic  1.390  0.020  1.390
 W7S  C07  C06   aromatic  1.388  0.020  1.388
 W7S  C05  C06   aromatic  1.393  0.020  1.393
 W7S  C05  C04   single    1.510  0.020  1.510
 W7S  C04  N03   single    1.443  0.020  1.443
 W7S  O01  C02   double    1.222  0.020  1.222
 W7S  N03  C02   single    1.336  0.020  1.336
 W7S  C02  C11   single    1.500  0.020  1.500
 W7S  C11  C12   aromatic  1.390  0.020  1.390
 W7S  C11  N16   aromatic  1.327  0.020  1.327
 W7S  C12  N13   aromatic  1.326  0.020  1.326
 W7S  N16  C15   aromatic  1.321  0.020  1.321
 W7S  N13  C14   aromatic  1.324  0.020  1.324
 W7S  C15  C14   aromatic  1.391  0.020  1.391
 W7S  C10  H101  single    0.930  0.020  1.080
 W7S  C15  H151  single    0.930  0.020  1.080
 W7S  C04  H041  single    0.970  0.020  1.090
 W7S  C04  H042  single    0.970  0.020  1.090
 W7S  C06  H061  single    0.930  0.020  1.080
 W7S  C07  H071  single    0.930  0.020  1.080
 W7S  C08  H081  single    0.930  0.020  1.080
 W7S  C09  H091  single    0.930  0.020  1.080
 W7S  C12  H121  single    0.930  0.020  1.080
 W7S  C14  H141  single    0.930  0.020  1.080
 W7S  N03  H031  single    0.860  0.020  1.020

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
 W7S  H101  C10  C09   119.63  3.000
 W7S  H101  C10  C05   119.62  3.000
 W7S  C09   C10  C05   120.75  3.000
 W7S  H151  C15  N16   117.84  3.000
 W7S  H151  C15  C14   120.99  3.000
 W7S  N16   C15  C14   121.17  3.000
 W7S  O01   C02  N03   124.22  3.000
 W7S  N03   C02  C11   114.82  3.000
 W7S  O01   C02  C11   120.96  3.000
 W7S  H042  C04  H041  106.76  3.000
 W7S  H042  C04  N03   109.86  3.000
 W7S  H041  C04  N03   106.81  3.000
 W7S  H042  C04  C05   109.71  3.000
 W7S  H041  C04  C05   109.81  3.000
 W7S  N03   C04  C05   113.64  3.000
 W7S  C06   C05  C04   120.94  3.000
 W7S  C04   C05  C10   120.20  3.000
 W7S  C06   C05  C10   118.83  3.000
 W7S  H061  C06  C07   119.40  3.000
 W7S  H061  C06  C05   120.01  3.000
 W7S  C07   C06  C05   120.59  3.000
 W7S  H071  C07  C08   120.04  3.000
 W7S  H071  C07  C06   119.74  3.000
 W7S  C08   C07  C06   120.22  3.000
 W7S  H081  C08  C09   120.24  3.000
 W7S  H081  C08  C07   120.23  3.000
 W7S  C09   C08  C07   119.53  3.000
 W7S  H091  C09  C08   120.13  3.000
 W7S  H091  C09  C10   119.79  3.000
 W7S  C08   C09  C10   120.08  3.000
 W7S  N16   C11  C12   121.30  3.000
 W7S  N16   C11  C02   118.52  3.000
 W7S  C12   C11  C02   120.18  3.000
 W7S  H121  C12  N13   117.48  3.000
 W7S  H121  C12  C11   121.13  3.000
 W7S  N13   C12  C11   121.39  3.000
 W7S  H141  C14  N13   117.73  3.000
 W7S  H141  C14  C15   120.60  3.000
 W7S  N13   C14  C15   121.67  3.000
 W7S  H031  N03  C04   119.64  3.000
 W7S  H031  N03  C02   118.24  3.000
 W7S  C04   N03  C02   122.06  3.000
 W7S  C14   N13  C12   117.04  3.000
 W7S  C11   N16  C15   117.43  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
 W7S  CONST_01  C07   C08  C09  C10    0.00   0.0  0
 W7S  CONST_02  C07   C06  C05  C10    0.00   0.0  0
 W7S  CONST_03  C12   C11  N16  C15    0.00   0.0  0
 W7S  CONST_04  C12   N13  C14  C15    0.00   0.0  0
 W7S  CONST_05  C08   C09  C10  C05    0.00   0.0  0
 W7S  CONST_06  C08   C07  C06  C05    0.00   0.0  0
 W7S  CONST_07  C09   C08  C07  C06    0.00   0.0  0
 W7S  CONST_08  C09   C10  C05  C06    0.00   0.0  0
 W7S  CONST_09  C14   N13  C12  C11    0.00   0.0  0
 W7S  CONST_10  C14   C15  N16  C11    0.00   0.0  0
 W7S  CONST_11  N16   C11  C12  N13    0.00   0.0  0
 W7S  CONST_12  N16   C15  C14  N13    0.00   0.0  0
 W7S  CONST_13  C02   C11  N16  C15  180.00   0.0  0
 W7S  CONST_14  N13   C12  C11  C02  180.00   0.0  0
 W7S  CONST_15  C09   C10  C05  C04  180.00   0.0  0
 W7S  CONST_16  C07   C06  C05  C04  180.00   0.0  0
 W7S  CONST_17  H081  C08  C09  C10  180.00   0.0  0
 W7S  CONST_18  H061  C06  C05  C10  180.00   0.0  0
 W7S  CONST_19  H091  C09  C10  C05  180.00   0.0  0
 W7S  CONST_20  H071  C07  C06  C05  180.00   0.0  0
 W7S  CONST_21  H101  C10  C05  C06  180.00   0.0  0
 W7S  CONST_22  H151  C15  N16  C11  180.00   0.0  0
 W7S  CONST_23  H141  C14  N13  C12  180.00   0.0  0
 W7S  CONST_24  H121  C12  N13  C14  180.00   0.0  0
 W7S  CONST_25  C11   C02  N03  C04  180.00   0.0  0
 W7S  CONST_26  H031  N03  C02  C11    0.00   0.0  0
 W7S  CONST_27  O01   C02  N03  C04    0.00   0.0  0
 W7S  Var_01    N03   C04  C05  C10  136.72  30.0  2
 W7S  Var_02    O01   C02  C11  C12   -1.20  30.0  2
 W7S  Var_03    C05   C04  N03  C02  -71.66  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
 W7S  plan-1  C10   0.020
 W7S  plan-1  C04   0.020
 W7S  plan-1  C05   0.020
 W7S  plan-1  C06   0.020
 W7S  plan-1  C07   0.020
 W7S  plan-1  C08   0.020
 W7S  plan-1  C09   0.020
 W7S  plan-1  H101  0.020
 W7S  plan-1  H061  0.020
 W7S  plan-1  H071  0.020
 W7S  plan-1  H081  0.020
 W7S  plan-1  H091  0.020
 W7S  plan-2  C15   0.020
 W7S  plan-2  C02   0.020
 W7S  plan-2  C11   0.020
 W7S  plan-2  C12   0.020
 W7S  plan-2  C14   0.020
 W7S  plan-2  N13   0.020
 W7S  plan-2  N16   0.020
 W7S  plan-2  H121  0.020
 W7S  plan-2  H141  0.020
 W7S  plan-2  H151  0.020
 W7S  plan-3  C02   0.020
 W7S  plan-3  C04   0.020
 W7S  plan-3  C11   0.020
 W7S  plan-3  N03   0.020
 W7S  plan-3  O01   0.020
 W7S  plan-3  H031  0.020

