# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 07:08:48 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]pyrazin-2-yl]ethenyl]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCO)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
 J8O  J8O  "4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]pyrazin-2-yl]ethenyl]benzenecarbonitrile"
  ligand  38  23  .  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
;

data_comp_J8O
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
 J8O  C13  C  C     0   0.001  31.9956  16.2290   3.2881
 J8O  C15  C  CSP   0  -0.011  32.8481  15.3821   4.0523
 J8O  C17  C  CR16  0  -0.290  33.3659  18.2033   3.9548
 J8O  C20  C  CR16  0  -0.222  31.2038  19.9021   3.5653
 J8O  C21  C  CR16  0  -0.305  31.0611  18.5439   3.3600
 J8O  C01  C  CR16  0  -0.149  29.9128  13.0688   0.3397
 J8O  C02  C  CR6   0   0.513  30.3067  11.8861   1.0382
 J8O  C04  C  CR16  0  -0.092  31.1357  13.2200   2.6973
 J8O  C05  C  CR6   0   0.204  30.8476  14.3750   1.9742
 J8O  C08  C  CH2   0  -0.373  29.4311  10.3594  -0.6688
 J8O  C09  C  CH2   0  -0.148  27.9701  10.0294  -0.4242
 J8O  C11  C  CH3   0  -0.531  30.5254   9.5130   1.3853
 J8O  C12  C  C1    0  -0.276  31.1425  15.7327   2.3602
 J8O  C14  C  CR6   0   0.150  32.1413  17.6753   3.5373
 J8O  C18  C  CR16  0  -0.218  33.5186  19.5596   4.1667
 J8O  C19  C  CR6   0  -0.007  32.4360  20.4154   3.9687
 J8O  N03  N  N     0  -0.437  30.8711  12.0107   2.2436
 J8O  N06  N  N     0  -0.379  30.1886  14.2516   0.8020
 J8O  N16  N  NS    0  -0.240  33.5556  14.7272   4.6861
 J8O  N23  N  NS    0  -0.246  32.7165  22.9459   4.3760
 J8O  O10  O  OH1   0  -0.659  27.3541  11.1314   0.1941
 J8O  H1   H  HCR6  0   0.275  34.2201  17.5557   4.1045
 J8O  H2   H  HCR6  0   0.285  30.3574  20.5613   3.4272
 J8O  H3   H  HCR6  0   0.276  30.0886  18.1602   3.0824
 J8O  H4   H  HCR6  0   0.272  29.3605  13.0288  -0.5891
 J8O  H5   H  HCR6  0   0.271  31.5677  13.2620   3.6889
 J8O  H6   H  HCH2  0   0.275  29.9027   9.5037  -1.1548
 J8O  H7   H  HCH2  0   0.268  29.5255  11.1898  -1.3668
 J8O  H8   H  HCH2  0   0.209  27.5138   9.7842  -1.3920
 J8O  H9   H  HCH2  0   0.207  27.9051   9.1264   0.1959
 J8O  H10  H  HCH3  0   0.254  31.5645   9.5815   1.7031
 J8O  H11  H  HCH3  0   0.245  29.9013   9.4383   2.2772
 J8O  H12  H  HCH3  0   0.253  30.4043   8.6035   0.8028
 J8O  H13  H  H     0   0.288  30.6097  16.4620   1.7592
 J8O  H14  H  HCR6  0   0.285  34.4754  19.9536   4.4814
 J8O  H15  H  HOH1  0   0.457  26.4746  10.8693   0.4803
 J8O  N07  N  NT    0  -0.461  30.1551  10.6444   0.5544
 J8O  C22  C  CSP   0   0.054  32.5876  21.8159   4.1916

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
 J8O  C08  C09  single    1.518  0.020  1.518
 J8O  C08  N07  single    1.450  0.020  1.450
 J8O  C09  O10  single    1.406  0.020  1.406
 J8O  C01  N06  aromatic  1.299  0.020  1.299
 J8O  C01  C02  aromatic  1.429  0.020  1.429
 J8O  N07  C02  single    1.341  0.020  1.341
 J8O  N07  C11  single    1.452  0.020  1.452
 J8O  N06  C05  aromatic  1.350  0.020  1.350
 J8O  C02  N03  aromatic  1.337  0.020  1.337
 J8O  C05  C12  single    1.442  0.020  1.442
 J8O  C05  C04  aromatic  1.393  0.020  1.393
 J8O  N03  C04  aromatic  1.318  0.020  1.318
 J8O  C12  C13  double    1.355  0.020  1.355
 J8O  C21  C20  aromatic  1.381  0.020  1.381
 J8O  C21  C14  aromatic  1.397  0.020  1.397
 J8O  C20  C19  aromatic  1.394  0.020  1.394
 J8O  C13  C14  single    1.475  0.020  1.475
 J8O  C13  C15  single    1.424  0.020  1.424
 J8O  C14  C17  aromatic  1.397  0.020  1.397
 J8O  C19  C22  single    1.426  0.020  1.426
 J8O  C19  C18  aromatic  1.394  0.020  1.394
 J8O  C15  N16  triple    1.154  0.020  1.154
 J8O  C22  N23  triple    1.152  0.020  1.152
 J8O  C17  C18  aromatic  1.381  0.020  1.381
 J8O  C17  H1   single    0.930  0.020  1.080
 J8O  C20  H2   single    0.930  0.020  1.080
 J8O  C21  H3   single    0.930  0.020  1.080
 J8O  C01  H4   single    0.930  0.020  1.080
 J8O  C04  H5   single    0.930  0.020  1.080
 J8O  C08  H6   single    0.970  0.020  1.090
 J8O  C08  H7   single    0.970  0.020  1.090
 J8O  C09  H8   single    0.970  0.020  1.090
 J8O  C09  H9   single    0.970  0.020  1.090
 J8O  C11  H10  single    0.970  0.020  1.090
 J8O  C11  H11  single    0.970  0.020  1.090
 J8O  C11  H12  single    0.970  0.020  1.090
 J8O  C12  H13  single    0.930  0.020  1.080
 J8O  C18  H14  single    0.930  0.020  1.080
 J8O  O10  H15  single    0.850  0.020  0.980

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
 J8O  C14  C13  C12  122.49  3.000
 J8O  C14  C13  C15  115.68  3.000
 J8O  C12  C13  C15  121.79  3.000
 J8O  N16  C15  C13  180.00  3.000
 J8O  H1   C17  C18  118.63  3.000
 J8O  H1   C17  C14  120.46  3.000
 J8O  C18  C17  C14  120.91  3.000
 J8O  H2   C20  C19  120.27  3.000
 J8O  H2   C20  C21  119.97  3.000
 J8O  C19  C20  C21  119.75  3.000
 J8O  H3   C21  C14  120.47  3.000
 J8O  H3   C21  C20  118.68  3.000
 J8O  C14  C21  C20  120.84  3.000
 J8O  H4   C01  N06  116.59  3.000
 J8O  H4   C01  C02  122.01  3.000
 J8O  N06  C01  C02  121.40  3.000
 J8O  N07  C02  N03  117.34  3.000
 J8O  N03  C02  C01  118.68  3.000
 J8O  N07  C02  C01  123.97  3.000
 J8O  H5   C04  N03  115.53  3.000
 J8O  H5   C04  C05  121.73  3.000
 J8O  N03  C04  C05  122.71  3.000
 J8O  N06  C05  C12  114.72  3.000
 J8O  C12  C05  C04  126.84  3.000
 J8O  N06  C05  C04  118.41  3.000
 J8O  H7   C08  H6   105.96  3.000
 J8O  H7   C08  N07  110.35  3.000
 J8O  H6   C08  N07  108.31  3.000
 J8O  H7   C08  C09  110.65  3.000
 J8O  H6   C08  C09  108.50  3.000
 J8O  N07  C08  C09  112.80  3.000
 J8O  H9   C09  H8   106.84  3.000
 J8O  H9   C09  O10  111.75  3.000
 J8O  H8   C09  O10  112.38  3.000
 J8O  H9   C09  C08  109.09  3.000
 J8O  H8   C09  C08  107.86  3.000
 J8O  O10  C09  C08  108.80  3.000
 J8O  H12  C11  H11  108.48  3.000
 J8O  H12  C11  H10  108.39  3.000
 J8O  H11  C11  H10  108.16  3.000
 J8O  H12  C11  N07  108.49  3.000
 J8O  H11  C11  N07  112.04  3.000
 J8O  H10  C11  N07  111.19  3.000
 J8O  H13  C12  C05  112.60  3.000
 J8O  H13  C12  C13  116.27  3.000
 J8O  C05  C12  C13  131.07  3.000
 J8O  C21  C14  C17  118.71  3.000
 J8O  C17  C14  C13  120.50  3.000
 J8O  C21  C14  C13  120.79  3.000
 J8O  H14  C18  C19  120.31  3.000
 J8O  H14  C18  C17  120.01  3.000
 J8O  C19  C18  C17  119.68  3.000
 J8O  C18  C19  C22  119.87  3.000
 J8O  C18  C19  C20  120.09  3.000
 J8O  C22  C19  C20  120.04  3.000
 J8O  C04  N03  C02  118.72  3.000
 J8O  C05  N06  C01  119.70  3.000
 J8O  H15  O10  C09  108.55  3.000
 J8O  C11  N07  C08  117.20  3.000
 J8O  C11  N07  C02  119.09  3.000
 J8O  C08  N07  C02  122.87  3.000
 J8O  N23  C22  C19  180.00  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
 J8O  CONST_01  C20  C21  C14  C17     0.00   0.0  0
 J8O  CONST_02  C20  C19  C18  C17     0.00   0.0  0
 J8O  CONST_03  C18  C19  C20  C21     0.00   0.0  0
 J8O  CONST_04  C18  C17  C14  C21     0.00   0.0  0
 J8O  CONST_05  C04  C05  N06  C01     0.00   0.0  0
 J8O  CONST_06  C04  N03  C02  C01     0.00   0.0  0
 J8O  CONST_07  C05  N06  C01  C02     0.00   0.0  0
 J8O  CONST_08  C05  C04  N03  C02     0.00   0.0  0
 J8O  CONST_09  C19  C20  C21  C14     0.00   0.0  0
 J8O  CONST_10  C19  C18  C17  C14     0.00   0.0  0
 J8O  CONST_11  N06  C01  C02  N03     0.00   0.0  0
 J8O  CONST_12  N06  C05  C04  N03     0.00   0.0  0
 J8O  CONST_13  C20  C21  C14  C13   180.00   0.0  0
 J8O  CONST_14  C18  C17  C14  C13   180.00   0.0  0
 J8O  CONST_15  C22  C19  C18  C17   180.00   0.0  0
 J8O  CONST_16  C22  C19  C20  C21   180.00   0.0  0
 J8O  CONST_17  C12  C05  N06  C01   180.00   0.0  0
 J8O  CONST_18  N07  C02  N03  C04   180.00   0.0  0
 J8O  CONST_19  N03  C04  C05  C12   180.00   0.0  0
 J8O  CONST_20  N07  C02  C01  N06   180.00   0.0  0
 J8O  CONST_21  H3   C21  C14  C17   180.00   0.0  0
 J8O  CONST_22  H14  C18  C19  C20   180.00   0.0  0
 J8O  CONST_23  H1   C17  C14  C21   180.00   0.0  0
 J8O  CONST_24  H5   C04  N03  C02   180.00   0.0  0
 J8O  CONST_25  H4   C01  N06  C05   180.00   0.0  0
 J8O  CONST_26  H2   C20  C21  C14   180.00   0.0  0
 J8O  CONST_27  H14  C18  C17  C14   180.00   0.0  0
 J8O  CONST_28  H2   C20  C19  C18   180.00   0.0  0
 J8O  CONST_29  H3   C21  C20  C19   180.00   0.0  0
 J8O  CONST_30  H1   C17  C18  C19   180.00   0.0  0
 J8O  CONST_31  H4   C01  C02  N03   180.00   0.0  0
 J8O  CONST_32  H5   C04  C05  N06   180.00   0.0  0
 J8O  CONST_33  C08  N07  C02  C01     0.00   0.0  0
 J8O  CONST_34  C11  N07  C02  C01   180.00   0.0  0
 J8O  CONST_35  N03  C02  N07  C08   180.00   0.0  0
 J8O  CONST_36  N03  C02  N07  C11     0.00   0.0  0
 J8O  Var_01    C14  C13  C12  C05  -179.50   0.0  2
 J8O  Var_02    N06  C05  C12  C13  -164.74  30.0  3
 J8O  Var_03    C04  C05  C12  C13    17.30  30.0  3
 J8O  Var_04    C21  C14  C13  C15  -151.23  30.0  2
 J8O  Var_05    C17  C14  C13  C15    28.83  30.0  2
 J8O  Var_06    C12  C13  C14  C17  -148.90  30.0  2
 J8O  Var_07    C12  C13  C14  C21    31.04  30.0  2
 J8O  Var_08    H13  C12  C05  C04  -165.79  30.0  2
 J8O  Var_09    H13  C12  C05  N06    12.16  30.0  2
 J8O  Var_10    C05  C12  C13  C15     2.91   0.0  2
 J8O  Var_11    C09  C08  N07  C02   -93.08  30.0  2
 J8O  Var_12    N16  C15  C13  C14    -4.16  30.0  3
 J8O  Var_13    H13  C12  C13  C14     3.69   0.0  2
 J8O  Var_14    H6   C08  N07  C02   146.81  30.0  2
 J8O  Var_15    H7   C08  N07  C02    31.24  30.0  2
 J8O  Var_16    H10  C11  N07  C02   -56.71  30.0  3
 J8O  Var_17    H11  C11  N07  C02    64.46  30.0  3
 J8O  Var_18    H12  C11  N07  C02  -175.81  30.0  3
 J8O  Var_19    C11  N07  C08  C09    76.36  30.0  3
 J8O  Var_20    N16  C15  C13  C12   173.59  30.0  3
 J8O  Var_21    O10  C09  C08  N07    60.39  30.0  3
 J8O  Var_22    H13  C12  C13  C15  -173.91   0.0  2
 J8O  Var_23    H10  C11  N07  C08   133.43  30.0  3
 J8O  Var_24    H11  C11  N07  C08  -105.40  30.0  3
 J8O  Var_25    H12  C11  N07  C08    14.33  30.0  3
 J8O  Var_26    H6   C08  N07  C11   -43.75  30.0  2
 J8O  Var_27    H7   C08  N07  C11  -159.31  30.0  2
 J8O  Var_28    H8   C09  C08  N07  -177.46  30.0  3
 J8O  Var_29    H9   C09  C08  N07   -61.76  30.0  3
 J8O  Var_30    H6   C08  C09  O10  -179.62  30.0  2
 J8O  Var_31    H7   C08  C09  O10   -63.77  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
 J8O  plan-1  C13  0.020
 J8O  plan-1  C17  0.020
 J8O  plan-1  C20  0.020
 J8O  plan-1  C21  0.020
 J8O  plan-1  C14  0.020
 J8O  plan-1  C18  0.020
 J8O  plan-1  C19  0.020
 J8O  plan-1  N23  0.020
 J8O  plan-1  H1   0.020
 J8O  plan-1  H2   0.020
 J8O  plan-1  H3   0.020
 J8O  plan-1  H14  0.020
 J8O  plan-1  C22  0.020
 J8O  plan-2  C01  0.020
 J8O  plan-2  C02  0.020
 J8O  plan-2  C04  0.020
 J8O  plan-2  C05  0.020
 J8O  plan-2  C12  0.020
 J8O  plan-2  N03  0.020
 J8O  plan-2  N06  0.020
 J8O  plan-2  H4   0.020
 J8O  plan-2  H5   0.020
 J8O  plan-2  N07  0.020
 J8O  plan-3  C02  0.020
 J8O  plan-3  C08  0.020
 J8O  plan-3  C11  0.020
 J8O  plan-3  N07  0.020
 J8O  plan-4  C13  0.020
 J8O  plan-4  C15  0.020
 J8O  plan-4  C05  0.020
 J8O  plan-4  C12  0.020
 J8O  plan-4  C14  0.020
 J8O  plan-4  H13  0.020

