# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 00:42:31 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-[(~{Z})-1-cyano-2-[5-[2-(dimethylamino)ethyl-methyl-amino]pyrazin-2-yl]ethenyl]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCN(C)c1cnc(cn1)\C=C(/C#N)c2ccc(cc2)C#N
#
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
 J8L  J8L  "4-[(~{Z})-1-cyano-2-[5-[2-(dimethylamino)ethyl-methyl-amino]pyrazin-2-yl]ethenyl]benzenecarbonitrile"
  ligand  45  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 PERFECT
;

data_comp_J8L
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
 J8L  C10  C  CSP   0   0.017  -0.1653  21.2049  14.6128
 J8L  C13  C  CR16  0  -0.218  -0.8880  17.0606  14.2721
 J8L  C15  C  CR16  0  -0.220   1.0625  16.6346  15.6289
 J8L  C17  C  CSP   0   0.053  -0.3989  14.7807  14.9987
 J8L  C20  C  CH2   0  -0.345   5.6906  26.1081  14.8037
 J8L  C21  C  CH2   0  -0.313   6.0237  26.9158  16.0659
 J8L  C24  C  CH3   0  -0.514   4.4684  26.1945  17.8211
 J8L  C01  C  CR16  0  -0.164   2.3643  24.3447  14.6532
 J8L  C02  C  CR6   0   0.517   3.7730  24.5857  14.7235
 J8L  C04  C  CR16  0  -0.065   4.0780  22.3424  14.9559
 J8L  C05  C  CR6   0   0.176   2.7078  22.1017  14.8613
 J8L  C07  C  C1    0  -0.285   2.2082  20.7563  14.9175
 J8L  C08  C  C     0   0.013   0.9315  20.3160  14.8187
 J8L  C09  C  CR6   0   0.152   0.5772  18.8850  14.8875
 J8L  C12  C  CR16  0  -0.292  -0.5647  18.4033  14.2411
 J8L  C14  C  CR6   0  -0.009  -0.0713  16.1681  14.9637
 J8L  C16  C  CR16  0  -0.312   1.3748  17.9788  15.5935
 J8L  C23  C  CH3   0  -0.523   6.5928  25.0910  17.5651
 J8L  C25  C  CH3   0  -0.562   3.4021  26.9536  14.3895
 J8L  N03  N  N     0  -0.437   4.6004  23.5487  14.8928
 J8L  N06  N  N     0  -0.374   1.8716  23.1429  14.7190
 J8L  N11  N  NS    0  -0.252  -1.1226  21.8267  14.4457
 J8L  N18  N  NS    0  -0.247  -0.6621  13.6591  15.0265
 J8L  N22  N  NT    0  -0.392   5.8316  26.2980  17.3554
 J8L  H1   H  HCR6  0   0.284  -1.7706  16.7061  13.7571
 J8L  H2   H  HCR6  0   0.285   1.6898  15.9496  16.1829
 J8L  H3   H  HCH2  0   0.274   6.2425  25.1723  14.7920
 J8L  H4   H  HCH2  0   0.252   6.0280  26.6877  13.9393
 J8L  H5   H  HCH2  0   0.240   7.0813  27.1847  15.9727
 J8L  H6   H  HCH2  0   0.237   5.4710  27.8595  16.0539
 J8L  H7   H  HCH3  0   0.229   4.4635  26.0285  18.9012
 J8L  H8   H  HCH3  0   0.229   3.9375  27.1281  17.6311
 J8L  H9   H  HCH3  0   0.195   3.8838  25.3799  17.3719
 J8L  H10  H  HCR6  0   0.282   1.6580  25.1589  14.5512
 J8L  H11  H  HCR6  0   0.277   4.7709  21.5173  15.0899
 J8L  H12  H  H     0   0.285   2.9777  20.0011  15.0337
 J8L  H13  H  HCR6  0   0.273  -1.2078  19.0765  13.6898
 J8L  H14  H  HCR6  0   0.273   2.2404  18.3213  16.1438
 J8L  H15  H  HCH3  0   0.229   6.5807  24.8270  18.6246
 J8L  H16  H  HCH3  0   0.199   6.2200  24.2212  17.0055
 J8L  H17  H  HCH3  0   0.228   7.6339  25.2507  17.2773
 J8L  H18  H  HCH3  0   0.275   4.0104  27.8340  14.2018
 J8L  H19  H  HCH3  0   0.261   2.7763  26.7926  13.5107
 J8L  H20  H  HCH3  0   0.253   2.7539  27.1675  15.2421
 J8L  N19  N  NT    0  -0.465   4.2761  25.8237  14.6307

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
 J8L  N11  C10  triple    1.154  0.020  1.154
 J8L  C10  C08  single    1.427  0.020  1.427
 J8L  C12  C13  aromatic  1.381  0.020  1.381
 J8L  C12  C09  aromatic  1.398  0.020  1.398
 J8L  C13  C14  aromatic  1.394  0.020  1.394
 J8L  C08  C09  single    1.476  0.020  1.476
 J8L  C08  C07  double    1.354  0.020  1.354
 J8L  C09  C16  aromatic  1.398  0.020  1.398
 J8L  N06  C01  aromatic  1.301  0.020  1.301
 J8L  N06  C05  aromatic  1.343  0.020  1.343
 J8L  C01  C02  aromatic  1.431  0.020  1.431
 J8L  C14  C17  single    1.426  0.020  1.426
 J8L  C14  C15  aromatic  1.395  0.020  1.395
 J8L  C17  N18  triple    1.152  0.020  1.152
 J8L  C05  C07  single    1.436  0.020  1.436
 J8L  C05  C04  aromatic  1.394  0.020  1.394
 J8L  C02  N19  single    1.340  0.020  1.340
 J8L  C02  N03  aromatic  1.337  0.020  1.337
 J8L  C25  N19  single    1.449  0.020  1.449
 J8L  C20  N19  single    1.453  0.020  1.453
 J8L  C20  C21  single    1.535  0.020  1.535
 J8L  C16  C15  aromatic  1.380  0.020  1.380
 J8L  C04  N03  aromatic  1.316  0.020  1.316
 J8L  C21  N22  single    1.443  0.020  1.443
 J8L  N22  C23  single    1.442  0.020  1.442
 J8L  N22  C24  single    1.444  0.020  1.444
 J8L  C13  H1   single    0.930  0.020  1.080
 J8L  C15  H2   single    0.930  0.020  1.080
 J8L  C20  H3   single    0.970  0.020  1.090
 J8L  C20  H4   single    0.970  0.020  1.090
 J8L  C21  H5   single    0.970  0.020  1.090
 J8L  C21  H6   single    0.970  0.020  1.090
 J8L  C24  H7   single    0.970  0.020  1.090
 J8L  C24  H8   single    0.970  0.020  1.090
 J8L  C24  H9   single    0.970  0.020  1.090
 J8L  C01  H10  single    0.930  0.020  1.080
 J8L  C04  H11  single    0.930  0.020  1.080
 J8L  C07  H12  single    0.930  0.020  1.080
 J8L  C12  H13  single    0.930  0.020  1.080
 J8L  C16  H14  single    0.930  0.020  1.080
 J8L  C23  H15  single    0.970  0.020  1.090
 J8L  C23  H16  single    0.970  0.020  1.090
 J8L  C23  H17  single    0.970  0.020  1.090
 J8L  C25  H18  single    0.970  0.020  1.090
 J8L  C25  H19  single    0.970  0.020  1.090
 J8L  C25  H20  single    0.970  0.020  1.090

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
 J8L  N11  C10  C08  180.00  3.000
 J8L  H1   C13  C14  120.30  3.000
 J8L  H1   C13  C12  119.93  3.000
 J8L  C14  C13  C12  119.77  3.000
 J8L  H2   C15  C16  119.91  3.000
 J8L  H2   C15  C14  120.26  3.000
 J8L  C16  C15  C14  119.82  3.000
 J8L  N18  C17  C14  180.00  3.000
 J8L  H4   C20  H3   106.92  3.000
 J8L  H4   C20  N19  108.04  3.000
 J8L  H3   C20  N19  108.94  3.000
 J8L  H4   C20  C21  107.70  3.000
 J8L  H3   C20  C21  110.60  3.000
 J8L  N19  C20  C21  114.34  3.000
 J8L  H6   C21  H5   105.97  3.000
 J8L  H6   C21  N22  108.18  3.000
 J8L  H5   C21  N22  108.05  3.000
 J8L  H6   C21  C20  109.59  3.000
 J8L  H5   C21  C20  105.59  3.000
 J8L  N22  C21  C20  118.73  3.000
 J8L  H9   C24  H8   107.72  3.000
 J8L  H9   C24  H7   106.81  3.000
 J8L  H8   C24  H7   107.46  3.000
 J8L  H9   C24  N22  115.06  3.000
 J8L  H8   C24  N22  110.00  3.000
 J8L  H7   C24  N22  109.50  3.000
 J8L  H10  C01  N06  116.91  3.000
 J8L  H10  C01  C02  121.35  3.000
 J8L  N06  C01  C02  121.74  3.000
 J8L  N19  C02  N03  119.54  3.000
 J8L  N03  C02  C01  118.99  3.000
 J8L  N19  C02  C01  121.46  3.000
 J8L  H11  C04  N03  116.69  3.000
 J8L  H11  C04  C05  120.28  3.000
 J8L  N03  C04  C05  123.03  3.000
 J8L  N06  C05  C07  120.92  3.000
 J8L  C07  C05  C04  120.06  3.000
 J8L  N06  C05  C04  119.02  3.000
 J8L  H12  C07  C08  116.77  3.000
 J8L  H12  C07  C05  114.19  3.000
 J8L  C08  C07  C05  129.03  3.000
 J8L  C09  C08  C07  122.56  3.000
 J8L  C07  C08  C10  122.19  3.000
 J8L  C09  C08  C10  115.23  3.000
 J8L  C16  C09  C12  118.43  3.000
 J8L  C16  C09  C08  120.99  3.000
 J8L  C12  C09  C08  120.58  3.000
 J8L  H13  C12  C09  120.45  3.000
 J8L  H13  C12  C13  118.49  3.000
 J8L  C09  C12  C13  121.05  3.000
 J8L  C17  C14  C15  120.03  3.000
 J8L  C15  C14  C13  119.92  3.000
 J8L  C17  C14  C13  120.05  3.000
 J8L  H14  C16  C09  120.54  3.000
 J8L  H14  C16  C15  118.45  3.000
 J8L  C09  C16  C15  120.99  3.000
 J8L  H17  C23  H16  107.75  3.000
 J8L  H17  C23  H15  107.56  3.000
 J8L  H16  C23  H15  107.39  3.000
 J8L  H17  C23  N22  110.03  3.000
 J8L  H16  C23  N22  114.15  3.000
 J8L  H15  C23  N22  109.73  3.000
 J8L  H20  C25  H19  108.50  3.000
 J8L  H20  C25  H18  107.97  3.000
 J8L  H19  C25  H18  107.56  3.000
 J8L  H20  C25  N19  112.38  3.000
 J8L  H19  C25  N19  111.42  3.000
 J8L  H18  C25  N19  108.84  3.000
 J8L  C04  N03  C02  118.11  3.000
 J8L  C05  N06  C01  119.07  3.000
 J8L  C23  N22  C24  113.03  3.000
 J8L  C24  N22  C21  116.40  3.000
 J8L  C23  N22  C21  114.71  3.000
 J8L  C25  N19  C02  120.38  3.000
 J8L  C25  N19  C20  117.03  3.000
 J8L  C02  N19  C20  122.56  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
 J8L  CONST_01  C16  C09  C12  C13     0.00   0.0  0
 J8L  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 J8L  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 J8L  CONST_04  C12  C09  C16  C15     0.00   0.0  0
 J8L  CONST_05  C04  C05  N06  C01     0.00   0.0  0
 J8L  CONST_06  C04  N03  C02  C01     0.00   0.0  0
 J8L  CONST_07  C05  N06  C01  C02     0.00   0.0  0
 J8L  CONST_08  C05  C04  N03  C02     0.00   0.0  0
 J8L  CONST_09  C14  C13  C12  C09     0.00   0.0  0
 J8L  CONST_10  C14  C15  C16  C09     0.00   0.0  0
 J8L  CONST_11  N06  C01  C02  N03     0.00   0.0  0
 J8L  CONST_12  N06  C05  C04  N03     0.00   0.0  0
 J8L  CONST_13  C08  C09  C12  C13   180.00   0.0  0
 J8L  CONST_14  C08  C09  C16  C15   180.00   0.0  0
 J8L  CONST_15  C12  C13  C14  C17   180.00   0.0  0
 J8L  CONST_16  C16  C15  C14  C17   180.00   0.0  0
 J8L  CONST_17  C07  C05  N06  C01   180.00   0.0  0
 J8L  CONST_18  N19  C02  N03  C04   180.00   0.0  0
 J8L  CONST_19  N03  C04  C05  C07   180.00   0.0  0
 J8L  CONST_20  N19  C02  C01  N06   180.00   0.0  0
 J8L  CONST_21  H2   C15  C14  C13   180.00   0.0  0
 J8L  CONST_22  H1   C13  C14  C15   180.00   0.0  0
 J8L  CONST_23  H11  C04  N03  C02   180.00   0.0  0
 J8L  CONST_24  H10  C01  N06  C05   180.00   0.0  0
 J8L  CONST_25  H1   C13  C12  C09   180.00   0.0  0
 J8L  CONST_26  H2   C15  C16  C09   180.00   0.0  0
 J8L  CONST_27  H14  C16  C09  C12   180.00   0.0  0
 J8L  CONST_28  H13  C12  C13  C14   180.00   0.0  0
 J8L  CONST_29  H14  C16  C15  C14   180.00   0.0  0
 J8L  CONST_30  H13  C12  C09  C16   180.00   0.0  0
 J8L  CONST_31  H10  C01  C02  N03   180.00   0.0  0
 J8L  CONST_32  H11  C04  C05  N06   180.00   0.0  0
 J8L  CONST_33  C01  C02  N19  C20   180.00   0.0  0
 J8L  CONST_34  N03  C02  N19  C20     0.00   0.0  0
 J8L  CONST_35  C25  N19  C02  C01     0.00   0.0  0
 J8L  CONST_36  N03  C02  N19  C25   180.00   0.0  0
 J8L  Var_01    C09  C08  C07  C05   179.56   0.0  2
 J8L  Var_02    C12  C09  C08  C10    26.51  30.0  2
 J8L  Var_03    C16  C09  C08  C10  -153.76  30.0  2
 J8L  Var_04    C08  C07  C05  C04  -178.58  30.0  2
 J8L  Var_05    C12  C09  C08  C07  -152.27  30.0  2
 J8L  Var_06    C16  C09  C08  C07    27.47  30.0  2
 J8L  Var_07    N06  C05  C07  C08     1.48  30.0  2
 J8L  Var_08    H12  C07  C05  C04    -0.07  30.0  2
 J8L  Var_09    H12  C07  C05  N06   179.99  30.0  2
 J8L  Var_10    C05  C07  C08  C10     0.87   0.0  2
 J8L  Var_11    C02  N19  C20  C21  -112.11  30.0  3
 J8L  Var_12    N11  C10  C08  C09     0.22  30.0  2
 J8L  Var_13    H12  C07  C08  C09     1.08   0.0  2
 J8L  Var_14    H18  C25  N19  C02  -171.67  30.0  3
 J8L  Var_15    H19  C25  N19  C02   -53.23  30.0  3
 J8L  Var_16    H20  C25  N19  C02    68.79  30.0  3
 J8L  Var_17    H3   C20  N19  C02    12.19  30.0  2
 J8L  Var_18    H4   C20  N19  C02   128.01  30.0  2
 J8L  Var_19    C23  N22  C21  C20    59.26  30.0  3
 J8L  Var_20    C24  N22  C21  C20   -75.92  30.0  3
 J8L  Var_21    C25  N19  C20  C21    66.02  30.0  3
 J8L  Var_22    N11  C10  C08  C07   179.01  30.0  2
 J8L  Var_23    N22  C21  C20  N19    67.55  30.0  3
 J8L  Var_24    H12  C07  C08  C10  -177.61   0.0  2
 J8L  Var_25    H18  C25  N19  C20    10.16  30.0  3
 J8L  Var_26    H19  C25  N19  C20   128.60  30.0  3
 J8L  Var_27    H20  C25  N19  C20  -109.38  30.0  3
 J8L  Var_28    H15  C23  N22  C21   166.40  30.0  3
 J8L  Var_29    H16  C23  N22  C21   -73.03  30.0  3
 J8L  Var_30    H17  C23  N22  C21    48.24  30.0  3
 J8L  Var_31    H7   C24  N22  C21  -161.49  30.0  3
 J8L  Var_32    H8   C24  N22  C21   -43.61  30.0  3
 J8L  Var_33    H9   C24  N22  C21    78.24  30.0  3
 J8L  Var_34    H5   C21  N22  C24   164.02  30.0  2
 J8L  Var_35    H6   C21  N22  C24    49.71  30.0  2
 J8L  Var_36    H15  C23  N22  C24   -56.93  30.0  3
 J8L  Var_37    H16  C23  N22  C24    63.65  30.0  3
 J8L  Var_38    H17  C23  N22  C24  -175.08  30.0  3
 J8L  Var_39    H5   C21  N22  C23   -60.81  30.0  2
 J8L  Var_40    H6   C21  N22  C23  -175.11  30.0  2
 J8L  Var_41    H7   C24  N22  C23    62.61  30.0  3
 J8L  Var_42    H8   C24  N22  C23  -179.51  30.0  3
 J8L  Var_43    H9   C24  N22  C23   -57.67  30.0  3
 J8L  Var_44    H3   C20  N19  C25  -169.68  30.0  2
 J8L  Var_45    H4   C20  N19  C25   -53.87  30.0  2
 J8L  Var_46    H5   C21  C20  N19  -171.13  30.0  3
 J8L  Var_47    H6   C21  C20  N19   -57.39  30.0  3
 J8L  Var_48    H3   C20  C21  N22   -55.86  30.0  1
 J8L  Var_49    H4   C20  C21  N22  -172.37  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
 J8L  plan-1  C13  0.020
 J8L  plan-1  C15  0.020
 J8L  plan-1  C17  0.020
 J8L  plan-1  C08  0.020
 J8L  plan-1  C09  0.020
 J8L  plan-1  C12  0.020
 J8L  plan-1  C14  0.020
 J8L  plan-1  C16  0.020
 J8L  plan-1  N18  0.020
 J8L  plan-1  H1   0.020
 J8L  plan-1  H2   0.020
 J8L  plan-1  H13  0.020
 J8L  plan-1  H14  0.020
 J8L  plan-2  C01  0.020
 J8L  plan-2  C02  0.020
 J8L  plan-2  C04  0.020
 J8L  plan-2  C05  0.020
 J8L  plan-2  C07  0.020
 J8L  plan-2  N03  0.020
 J8L  plan-2  N06  0.020
 J8L  plan-2  H10  0.020
 J8L  plan-2  H11  0.020
 J8L  plan-2  N19  0.020
 J8L  plan-3  C20  0.020
 J8L  plan-3  C02  0.020
 J8L  plan-3  C25  0.020
 J8L  plan-3  N19  0.020
 J8L  plan-4  C10  0.020
 J8L  plan-4  C05  0.020
 J8L  plan-4  C07  0.020
 J8L  plan-4  C08  0.020
 J8L  plan-4  C09  0.020
 J8L  plan-4  H12  0.020

