# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 02:19:17 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: 4-[(~{Z})-1-cyano-2-[6-[2-hydroxyethyl(methyl)amino]pyridin-3-yl]ethenyl]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCO)c1ccc(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
 J8R  J8R  "4-[(~{Z})-1-cyano-2-[6-[2-hydroxyethyl(methyl)amino]pyridin-3-yl]ethenyl]benzenecarbonitrile"
  ligand  39  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 PERFECT
;

data_comp_J8R
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
 J8R  C10  C  CH3   0  -0.557  30.2943   7.3043   0.9571
 J8R  C13  C  C     0  -0.005  31.8805  14.1266   3.2631
 J8R  C15  C  CR16  0  -0.296  33.0656  16.1706   4.0684
 J8R  C17  C  CR6   0  -0.011  32.0264  18.3333   3.9843
 J8R  C20  C  CSP   0  -0.012  32.7273  13.3341   4.0863
 J8R  C22  C  CSP   0   0.052  32.0738  19.7373   4.2280
 J8R  C01  C  CR16  0  -0.382  31.0233   9.8120   2.0183
 J8R  C02  C  CR6   0   0.562  30.1317   9.7231   0.9182
 J8R  C04  C  CR16  0  -0.076  29.9869  12.0052   0.8340
 J8R  C05  C  CR6   0   0.037  30.8556  12.2141   1.9146
 J8R  C06  C  CR16  0  -0.202  31.3725  11.0424   2.5021
 J8R  C08  C  CH2   0  -0.354  28.7096   8.4138  -0.5800
 J8R  C09  C  CH2   0  -0.155  27.4028   7.9357   0.0280
 J8R  C12  C  C1    0  -0.284  31.0929  13.5738   2.3037
 J8R  C14  C  CR6   0   0.161  31.9269  15.5791   3.5126
 J8R  C16  C  CR16  0  -0.218  33.1211  17.5310   4.3022
 J8R  C18  C  CR16  0  -0.220  30.8789  17.7583   3.4374
 J8R  C19  C  CR16  0  -0.317  30.8319  16.3970   3.2136
 J8R  N03  N  N     0  -0.469  29.6359  10.8356   0.3546
 J8R  N07  N  NT    0  -0.466  29.7747   8.5343   0.3981
 J8R  N21  N  NS    0  -0.253  33.4277  12.7238   4.7716
 J8R  N23  N  NS    0  -0.248  32.1101  20.8723   4.4256
 J8R  O11  O  OH1   0  -0.660  26.9750   8.8636   0.9949
 J8R  H1   H  HCH3  0   0.257  31.3846   7.3082   0.9799
 J8R  H2   H  HCH3  0   0.247  29.9275   7.1164   1.9692
 J8R  H3   H  HCH3  0   0.271  29.9847   6.4734   0.3282
 J8R  H4   H  HCR6  0   0.272  33.9311  15.5689   4.3141
 J8R  H5   H  HCR6  0   0.283  31.4190   8.9280   2.4951
 J8R  H6   H  HCR6  0   0.268  29.5511  12.8678   0.3360
 J8R  H7   H  HCR6  0   0.272  32.0414  11.0816   3.3486
 J8R  H8   H  HCH2  0   0.255  29.0158   7.6968  -1.3453
 J8R  H9   H  HCH2  0   0.270  28.5683   9.3730  -1.0702
 J8R  H10  H  HCH2  0   0.206  26.6789   7.8267  -0.7906
 J8R  H11  H  HCH2  0   0.203  27.5389   6.9356   0.4599
 J8R  H12  H  H     0   0.277  30.5373  14.2874   1.7039
 J8R  H13  H  HCR6  0   0.284  34.0141  17.9691   4.7269
 J8R  H14  H  HCR6  0   0.284  30.0200  18.3729   3.2042
 J8R  H15  H  HCR6  0   0.272  29.9164  15.9711   2.8261
 J8R  H16  H  HOH1  0   0.454  26.2157   8.4933   1.4542

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
 J8R  C08  C09  single    1.519  0.020  1.519
 J8R  C08  N07  single    1.451  0.020  1.451
 J8R  C09  O11  single    1.407  0.020  1.407
 J8R  N07  C10  single    1.448  0.020  1.448
 J8R  N07  C02  single    1.346  0.020  1.346
 J8R  N03  C04  aromatic  1.312  0.020  1.312
 J8R  N03  C02  aromatic  1.342  0.020  1.342
 J8R  C04  C05  aromatic  1.402  0.020  1.402
 J8R  C02  C01  aromatic  1.419  0.020  1.419
 J8R  C05  C12  single    1.434  0.020  1.434
 J8R  C05  C06  aromatic  1.409  0.020  1.409
 J8R  C01  C06  aromatic  1.367  0.020  1.367
 J8R  C12  C13  double    1.359  0.020  1.359
 J8R  C19  C18  aromatic  1.380  0.020  1.380
 J8R  C19  C14  aromatic  1.399  0.020  1.399
 J8R  C18  C17  aromatic  1.395  0.020  1.395
 J8R  C13  C14  single    1.475  0.020  1.475
 J8R  C13  C20  single    1.422  0.020  1.422
 J8R  C14  C15  aromatic  1.398  0.020  1.398
 J8R  C17  C22  single    1.426  0.020  1.426
 J8R  C17  C16  aromatic  1.394  0.020  1.394
 J8R  C22  N23  triple    1.153  0.020  1.153
 J8R  C20  N21  triple    1.154  0.020  1.154
 J8R  C15  C16  aromatic  1.381  0.020  1.381
 J8R  C10  H1   single    0.970  0.020  1.090
 J8R  C10  H2   single    0.970  0.020  1.090
 J8R  C10  H3   single    0.970  0.020  1.090
 J8R  C15  H4   single    0.930  0.020  1.080
 J8R  C01  H5   single    0.930  0.020  1.080
 J8R  C04  H6   single    0.930  0.020  1.080
 J8R  C06  H7   single    0.930  0.020  1.080
 J8R  C08  H8   single    0.970  0.020  1.090
 J8R  C08  H9   single    0.970  0.020  1.090
 J8R  C09  H10  single    0.970  0.020  1.090
 J8R  C09  H11  single    0.970  0.020  1.090
 J8R  C12  H12  single    0.930  0.020  1.080
 J8R  C16  H13  single    0.930  0.020  1.080
 J8R  C18  H14  single    0.930  0.020  1.080
 J8R  C19  H15  single    0.930  0.020  1.080
 J8R  O11  H16  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
 J8R  H3   C10  H2   107.99  3.000
 J8R  H3   C10  H1   107.43  3.000
 J8R  H2   C10  H1   108.47  3.000
 J8R  H3   C10  N07  108.90  3.000
 J8R  H2   C10  N07  112.54  3.000
 J8R  H1   C10  N07  111.34  3.000
 J8R  C14  C13  C12  122.58  3.000
 J8R  C14  C13  C20  115.61  3.000
 J8R  C12  C13  C20  121.81  3.000
 J8R  H4   C15  C16  118.48  3.000
 J8R  H4   C15  C14  120.42  3.000
 J8R  C16  C15  C14  121.10  3.000
 J8R  C18  C17  C16  119.87  3.000
 J8R  C16  C17  C22  120.11  3.000
 J8R  C18  C17  C22  120.02  3.000
 J8R  N21  C20  C13  180.00  3.000
 J8R  N23  C22  C17  180.00  3.000
 J8R  H5   C01  C06  119.14  3.000
 J8R  H5   C01  C02  121.43  3.000
 J8R  C06  C01  C02  119.41  3.000
 J8R  N07  C02  N03  118.16  3.000
 J8R  N03  C02  C01  120.39  3.000
 J8R  N07  C02  C01  121.44  3.000
 J8R  H6   C04  N03  115.64  3.000
 J8R  H6   C04  C05  118.89  3.000
 J8R  N03  C04  C05  125.47  3.000
 J8R  C12  C05  C06  127.93  3.000
 J8R  C06  C05  C04  115.13  3.000
 J8R  C12  C05  C04  116.93  3.000
 J8R  H7   C06  C05  121.60  3.000
 J8R  H7   C06  C01  117.92  3.000
 J8R  C05  C06  C01  120.47  3.000
 J8R  H9   C08  H8   107.45  3.000
 J8R  H9   C08  N07  109.04  3.000
 J8R  H8   C08  N07  108.72  3.000
 J8R  H9   C08  C09  110.29  3.000
 J8R  H8   C08  C09  108.37  3.000
 J8R  N07  C08  C09  112.82  3.000
 J8R  H11  C09  H10  106.53  3.000
 J8R  H11  C09  O11  111.60  3.000
 J8R  H10  C09  O11  112.17  3.000
 J8R  H11  C09  C08  109.73  3.000
 J8R  H10  C09  C08  107.46  3.000
 J8R  O11  C09  C08  109.22  3.000
 J8R  H12  C12  C05  112.88  3.000
 J8R  H12  C12  C13  114.80  3.000
 J8R  C05  C12  C13  132.32  3.000
 J8R  C19  C14  C15  118.36  3.000
 J8R  C15  C14  C13  120.63  3.000
 J8R  C19  C14  C13  121.00  3.000
 J8R  H13  C16  C17  120.32  3.000
 J8R  H13  C16  C15  119.90  3.000
 J8R  C17  C16  C15  119.78  3.000
 J8R  H14  C18  C19  119.89  3.000
 J8R  H14  C18  C17  120.23  3.000
 J8R  C19  C18  C17  119.87  3.000
 J8R  H15  C19  C18  118.37  3.000
 J8R  H15  C19  C14  120.59  3.000
 J8R  C18  C19  C14  121.01  3.000
 J8R  C04  N03  C02  119.13  3.000
 J8R  C08  N07  C02  121.91  3.000
 J8R  C02  N07  C10  120.41  3.000
 J8R  C08  N07  C10  116.95  3.000
 J8R  H16  O11  C09  108.33  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
 J8R  CONST_01  C18  C19  C14  C15     0.00   0.0  0
 J8R  CONST_02  C18  C17  C16  C15     0.00   0.0  0
 J8R  CONST_03  C14  C19  C18  C17     0.00   0.0  0
 J8R  CONST_04  C14  C15  C16  C17     0.00   0.0  0
 J8R  CONST_05  C04  N03  C02  C01     0.00   0.0  0
 J8R  CONST_06  C04  C05  C06  C01     0.00   0.0  0
 J8R  CONST_07  C05  C04  N03  C02     0.00   0.0  0
 J8R  CONST_08  C05  C06  C01  C02     0.00   0.0  0
 J8R  CONST_09  N03  C04  C05  C06     0.00   0.0  0
 J8R  CONST_10  N03  C02  C01  C06     0.00   0.0  0
 J8R  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 J8R  CONST_12  C19  C14  C15  C16     0.00   0.0  0
 J8R  CONST_13  C18  C19  C14  C13   180.00   0.0  0
 J8R  CONST_14  C16  C15  C14  C13   180.00   0.0  0
 J8R  CONST_15  C22  C17  C16  C15   180.00   0.0  0
 J8R  CONST_16  C19  C18  C17  C22   180.00   0.0  0
 J8R  CONST_17  C12  C05  C06  C01   180.00   0.0  0
 J8R  CONST_18  N07  C02  N03  C04   180.00   0.0  0
 J8R  CONST_19  N07  C02  C01  C06   180.00   0.0  0
 J8R  CONST_20  N03  C04  C05  C12   180.00   0.0  0
 J8R  CONST_21  H15  C19  C14  C15   180.00   0.0  0
 J8R  CONST_22  H15  C19  C18  C17   180.00   0.0  0
 J8R  CONST_23  H4   C15  C16  C17   180.00   0.0  0
 J8R  CONST_24  H6   C04  N03  C02   180.00   0.0  0
 J8R  CONST_25  H7   C06  C01  C02   180.00   0.0  0
 J8R  CONST_26  H7   C06  C05  C04   180.00   0.0  0
 J8R  CONST_27  H5   C01  C06  C05   180.00   0.0  0
 J8R  CONST_28  H6   C04  C05  C06   180.00   0.0  0
 J8R  CONST_29  H14  C18  C19  C14   180.00   0.0  0
 J8R  CONST_30  H13  C16  C15  C14   180.00   0.0  0
 J8R  CONST_31  H14  C18  C17  C16   180.00   0.0  0
 J8R  CONST_32  H13  C16  C17  C18   180.00   0.0  0
 J8R  CONST_33  H4   C15  C14  C19   180.00   0.0  0
 J8R  CONST_34  H5   C01  C02  N03   180.00   0.0  0
 J8R  CONST_35  N03  C02  N07  C10   180.00   0.0  0
 J8R  CONST_36  C01  C02  N07  C10     0.00   0.0  0
 J8R  CONST_37  C08  N07  C02  C01   180.00   0.0  0
 J8R  CONST_38  N03  C02  N07  C08     0.00   0.0  0
 J8R  Var_01    C14  C13  C12  C05  -177.78   0.0  2
 J8R  Var_02    C04  C05  C12  C13  -178.33  30.0  2
 J8R  Var_03    C06  C05  C12  C13     2.92  30.0  2
 J8R  Var_04    C12  C13  C14  C15  -153.76  30.0  3
 J8R  Var_05    C20  C13  C14  C15    25.64  30.0  3
 J8R  Var_06    C19  C14  C13  C20  -153.68  30.0  2
 J8R  Var_07    C19  C14  C13  C12    26.91  30.0  2
 J8R  Var_08    H12  C12  C05  C04     1.09  30.0  2
 J8R  Var_09    H12  C12  C05  C06  -177.67  30.0  2
 J8R  Var_10    C05  C12  C13  C20     2.85   0.0  2
 J8R  Var_11    C09  C08  N07  C02  -100.81  30.0  2
 J8R  Var_12    N21  C20  C13  C14    -1.60  30.0  3
 J8R  Var_13    H12  C12  C13  C14     2.81   0.0  2
 J8R  Var_14    H8   C08  N07  C02   138.96  30.0  2
 J8R  Var_15    H9   C08  N07  C02    22.09  30.0  2
 J8R  Var_16    H1   C10  N07  C02   -55.01  30.0  3
 J8R  Var_17    H2   C10  N07  C02    67.02  30.0  3
 J8R  Var_18    H3   C10  N07  C02  -173.28  30.0  3
 J8R  Var_19    C09  C08  N07  C10    69.40  30.0  2
 J8R  Var_20    N21  C20  C13  C12   177.81  30.0  3
 J8R  Var_21    O11  C09  C08  N07    60.95  30.0  3
 J8R  Var_22    H12  C12  C13  C20  -176.56   0.0  2
 J8R  Var_23    H8   C08  N07  C10   -50.83  30.0  2
 J8R  Var_24    H9   C08  N07  C10  -167.70  30.0  2
 J8R  Var_25    H1   C10  N07  C08   134.63  30.0  3
 J8R  Var_26    H2   C10  N07  C08  -103.34  30.0  3
 J8R  Var_27    H3   C10  N07  C08    16.36  30.0  3
 J8R  Var_28    H10  C09  C08  N07  -177.14  30.0  3
 J8R  Var_29    H11  C09  C08  N07   -61.69  30.0  3
 J8R  Var_30    H8   C08  C09  O11  -178.61  30.0  1
 J8R  Var_31    H9   C08  C09  O11   -61.25  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
 J8R  plan-1  C13  0.020
 J8R  plan-1  C15  0.020
 J8R  plan-1  C17  0.020
 J8R  plan-1  C22  0.020
 J8R  plan-1  C14  0.020
 J8R  plan-1  C16  0.020
 J8R  plan-1  C18  0.020
 J8R  plan-1  C19  0.020
 J8R  plan-1  N23  0.020
 J8R  plan-1  H4   0.020
 J8R  plan-1  H13  0.020
 J8R  plan-1  H14  0.020
 J8R  plan-1  H15  0.020
 J8R  plan-2  C01  0.020
 J8R  plan-2  C02  0.020
 J8R  plan-2  C04  0.020
 J8R  plan-2  C05  0.020
 J8R  plan-2  C06  0.020
 J8R  plan-2  C12  0.020
 J8R  plan-2  N03  0.020
 J8R  plan-2  N07  0.020
 J8R  plan-2  H5   0.020
 J8R  plan-2  H6   0.020
 J8R  plan-2  H7   0.020
 J8R  plan-3  C10  0.020
 J8R  plan-3  C02  0.020
 J8R  plan-3  C08  0.020
 J8R  plan-3  N07  0.020
 J8R  plan-4  C13  0.020
 J8R  plan-4  C20  0.020
 J8R  plan-4  C05  0.020
 J8R  plan-4  C12  0.020
 J8R  plan-4  C14  0.020
 J8R  plan-4  H12  0.020

