# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 23:19:51 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (~{E})-2-cyano-~{N}-(2-hydroxyphenyl)-3-(3-methoxy-4-oxidanyl-phenyl)prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)\C=C(/C#N)C(=O)Nc2ccccc2O
#
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
 JYZ  JYZ  (~{E})-2-cyano-~{N}-(2-hydroxyphenyl)-3-(3-methoxy-4-oxidanyl-phenyl)prop-2-enamide  ligand  37  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JYZ
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
 JYZ  C01  C  CH3   0  -0.436   5.4060   2.8142  -0.4392
 JYZ  C03  C  CR6   0   0.323   4.6980   0.5711  -0.1138
 JYZ  C04  C  CR16  0  -0.437   3.3556   0.8798  -0.1460
 JYZ  C05  C  CR6   0   0.166   2.3713  -0.1190  -0.0033
 JYZ  C06  C  C1    0  -0.223   1.0037   0.3308  -0.0508
 JYZ  C07  C  C     0  -0.153  -0.1753  -0.3135   0.1265
 JYZ  C08  C  CSP   0  -0.015  -0.2777  -1.6920   0.4442
 JYZ  C10  C  C     0   0.605  -1.4412   0.4764  -0.0108
 JYZ  C13  C  CR6   0   0.289  -3.8942   0.2574   0.1160
 JYZ  C14  C  CR16  0  -0.296  -4.2697   1.5775   0.3419
 JYZ  C15  C  CR16  0  -0.276  -5.6017   1.9572   0.2360
 JYZ  C16  C  CR16  0  -0.256  -6.5709   1.0194  -0.0810
 JYZ  C17  C  CR16  0  -0.372  -6.2109  -0.3040  -0.2952
 JYZ  C18  C  CR6   0   0.286  -4.8815  -0.6886  -0.2032
 JYZ  C20  C  CR16  0  -0.316   2.7870  -1.4434   0.1618
 JYZ  C21  C  CR16  0  -0.322   4.1317  -1.7591   0.1891
 JYZ  C22  C  CR6   0   0.303   5.0970  -0.7692   0.0564
 JYZ  N09  N  NS    0  -0.242  -0.4243  -2.8070   0.7070
 JYZ  N12  N  NH1   0  -0.772  -2.5781  -0.2172   0.2238
 JYZ  O02  O  O2    0  -0.485   5.7128   1.4477  -0.2320
 JYZ  O11  O  O     0  -0.460  -1.4130   1.6563  -0.3113
 JYZ  O19  O  OH1   0  -0.633  -4.4648  -1.9561  -0.4019
 JYZ  O23  O  OH1   0  -0.607   6.3864  -1.1122   0.0894
 JYZ  H1   H  HCH3  0   0.236   4.8466   2.9636  -1.3659
 JYZ  H2   H  HCH3  0   0.236   4.8336   3.2278   0.3943
 JYZ  H3   H  HCH3  0   0.268   6.3559   3.3368  -0.5104
 JYZ  H4   H  HCR6  0   0.298   3.0356   1.9053  -0.2799
 JYZ  H5   H  H     0   0.288   0.8905   1.3889  -0.2638
 JYZ  H6   H  HCR6  0   0.274  -3.5284   2.3146   0.6076
 JYZ  H7   H  HCR6  0   0.257  -5.8739   2.9890   0.4127
 JYZ  H8   H  HCR6  0   0.261  -7.6106   1.3080  -0.1603
 JYZ  H9   H  HCR6  0   0.276  -6.9663  -1.0422  -0.5390
 JYZ  H10  H  HCR6  0   0.269   2.0782  -2.2504   0.2591
 JYZ  H11  H  HCR6  0   0.281   4.4471  -2.7871   0.3127
 JYZ  H12  H  HNH1  0   0.420  -2.5007  -1.2070   0.4046
 JYZ  H13  H  HOH1  0   0.484  -5.2147  -2.5451  -0.5439
 JYZ  H14  H  HOH1  0   0.482   6.9508  -0.3357  -0.0219

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
 JYZ  C01  O02  single    1.416  0.020  1.416
 JYZ  O02  C03  single    1.346  0.020  1.346
 JYZ  N09  C08  triple    1.155  0.020  1.155
 JYZ  O19  C18  single    1.349  0.020  1.349
 JYZ  C08  C07  single    1.418  0.020  1.418
 JYZ  C03  C04  aromatic  1.378  0.020  1.378
 JYZ  C03  C22  aromatic  1.409  0.020  1.409
 JYZ  C04  C05  aromatic  1.410  0.020  1.410
 JYZ  O23  C22  single    1.335  0.020  1.335
 JYZ  C18  C17  aromatic  1.387  0.020  1.387
 JYZ  C18  C13  aromatic  1.404  0.020  1.404
 JYZ  C22  C21  aromatic  1.389  0.020  1.389
 JYZ  N12  C13  single    1.403  0.020  1.403
 JYZ  N12  C10  single    1.352  0.020  1.352
 JYZ  C17  C16  aromatic  1.388  0.020  1.388
 JYZ  C07  C10  single    1.498  0.020  1.498
 JYZ  C07  C06  double    1.355  0.020  1.355
 JYZ  C05  C06  single    1.440  0.020  1.440
 JYZ  C05  C20  aromatic  1.398  0.020  1.398
 JYZ  C13  C14  aromatic  1.391  0.020  1.391
 JYZ  C10  O11  double    1.218  0.020  1.218
 JYZ  C21  C20  aromatic  1.382  0.020  1.382
 JYZ  C16  C15  aromatic  1.385  0.020  1.385
 JYZ  C14  C15  aromatic  1.389  0.020  1.389
 JYZ  C01  H1   single    0.970  0.020  1.090
 JYZ  C01  H2   single    0.970  0.020  1.090
 JYZ  C01  H3   single    0.970  0.020  1.090
 JYZ  C04  H4   single    0.930  0.020  1.080
 JYZ  C06  H5   single    0.930  0.020  1.080
 JYZ  C14  H6   single    0.930  0.020  1.080
 JYZ  C15  H7   single    0.930  0.020  1.080
 JYZ  C16  H8   single    0.930  0.020  1.080
 JYZ  C17  H9   single    0.930  0.020  1.080
 JYZ  C20  H10  single    0.930  0.020  1.080
 JYZ  C21  H11  single    0.930  0.020  1.080
 JYZ  N12  H12  single    0.860  0.020  1.020
 JYZ  O19  H13  single    0.850  0.020  0.980
 JYZ  O23  H14  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
 JYZ  H3   C01  H2   109.02  3.000
 JYZ  H3   C01  H1   109.04  3.000
 JYZ  H2   C01  H1   109.09  3.000
 JYZ  H3   C01  O02  106.53  3.000
 JYZ  H2   C01  O02  111.55  3.000
 JYZ  H1   C01  O02  111.53  3.000
 JYZ  O02  C03  C22  114.62  3.000
 JYZ  C22  C03  C04  119.47  3.000
 JYZ  O02  C03  C04  125.91  3.000
 JYZ  H4   C04  C05  118.51  3.000
 JYZ  H4   C04  C03  120.21  3.000
 JYZ  C05  C04  C03  121.28  3.000
 JYZ  C20  C05  C06  125.60  3.000
 JYZ  C20  C05  C04  118.40  3.000
 JYZ  C06  C05  C04  116.00  3.000
 JYZ  H5   C06  C07  113.49  3.000
 JYZ  H5   C06  C05  114.20  3.000
 JYZ  C07  C06  C05  132.31  3.000
 JYZ  C10  C07  C08  118.15  3.000
 JYZ  C10  C07  C06  118.19  3.000
 JYZ  C08  C07  C06  123.66  3.000
 JYZ  N09  C08  C07  180.00  3.000
 JYZ  O11  C10  N12  124.00  3.000
 JYZ  O11  C10  C07  120.91  3.000
 JYZ  N12  C10  C07  115.09  3.000
 JYZ  N12  C13  C18  116.69  3.000
 JYZ  N12  C13  C14  124.18  3.000
 JYZ  C18  C13  C14  119.11  3.000
 JYZ  H6   C14  C15  119.40  3.000
 JYZ  H6   C14  C13  120.20  3.000
 JYZ  C15  C14  C13  120.39  3.000
 JYZ  H7   C15  C16  120.46  3.000
 JYZ  H7   C15  C14  119.32  3.000
 JYZ  C16  C15  C14  120.21  3.000
 JYZ  H8   C16  C17  119.48  3.000
 JYZ  H8   C16  C15  120.56  3.000
 JYZ  C17  C16  C15  119.95  3.000
 JYZ  H9   C17  C18  119.61  3.000
 JYZ  H9   C17  C16  120.22  3.000
 JYZ  C18  C17  C16  120.18  3.000
 JYZ  O19  C18  C17  123.15  3.000
 JYZ  C17  C18  C13  120.15  3.000
 JYZ  O19  C18  C13  116.70  3.000
 JYZ  H10  C20  C21  117.84  3.000
 JYZ  H10  C20  C05  121.61  3.000
 JYZ  C21  C20  C05  120.55  3.000
 JYZ  H11  C21  C22  119.03  3.000
 JYZ  H11  C21  C20  120.19  3.000
 JYZ  C22  C21  C20  120.78  3.000
 JYZ  O23  C22  C21  119.07  3.000
 JYZ  C21  C22  C03  119.52  3.000
 JYZ  O23  C22  C03  121.40  3.000
 JYZ  H12  N12  C13  114.67  3.000
 JYZ  H12  N12  C10  118.01  3.000
 JYZ  C13  N12  C10  127.00  3.000
 JYZ  C03  O02  C01  118.56  3.000
 JYZ  H13  O19  C18  110.82  3.000
 JYZ  H14  O23  C22  110.79  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
 JYZ  CONST_01  C20  C05  C04  C03     0.00   0.0  0
 JYZ  CONST_02  C20  C21  C22  C03     0.00   0.0  0
 JYZ  CONST_03  C21  C22  C03  C04     0.00   0.0  0
 JYZ  CONST_04  C21  C20  C05  C04     0.00   0.0  0
 JYZ  CONST_05  C22  C03  C04  C05     0.00   0.0  0
 JYZ  CONST_06  C22  C21  C20  C05     0.00   0.0  0
 JYZ  CONST_07  C16  C17  C18  C13     0.00   0.0  0
 JYZ  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 JYZ  CONST_09  C17  C18  C13  C14     0.00   0.0  0
 JYZ  CONST_10  C17  C16  C15  C14     0.00   0.0  0
 JYZ  CONST_11  C18  C17  C16  C15     0.00   0.0  0
 JYZ  CONST_12  C18  C13  C14  C15     0.00   0.0  0
 JYZ  CONST_13  C06  C05  C04  C03   180.00   0.0  0
 JYZ  CONST_14  O23  C22  C03  C04   180.00   0.0  0
 JYZ  CONST_15  O02  C03  C04  C05   180.00   0.0  0
 JYZ  CONST_16  C21  C20  C05  C06   180.00   0.0  0
 JYZ  CONST_17  O19  C18  C13  C14   180.00   0.0  0
 JYZ  CONST_18  N12  C13  C14  C15   180.00   0.0  0
 JYZ  CONST_19  O19  C18  C17  C16   180.00   0.0  0
 JYZ  CONST_20  N12  C13  C18  C17   180.00   0.0  0
 JYZ  CONST_21  O23  C22  C21  C20   180.00   0.0  0
 JYZ  CONST_22  O02  C03  C22  C21   180.00   0.0  0
 JYZ  CONST_23  H11  C21  C22  C03   180.00   0.0  0
 JYZ  CONST_24  H10  C20  C05  C04   180.00   0.0  0
 JYZ  CONST_25  H9   C17  C18  C13   180.00   0.0  0
 JYZ  CONST_26  H7   C15  C14  C13   180.00   0.0  0
 JYZ  CONST_27  H8   C16  C15  C14   180.00   0.0  0
 JYZ  CONST_28  H6   C14  C15  C16   180.00   0.0  0
 JYZ  CONST_29  H4   C04  C05  C20   180.00   0.0  0
 JYZ  CONST_33  C13  N12  C10  C07   180.00   0.0  0
 JYZ  CONST_34  O11  C10  N12  C13     0.00   0.0  0
 JYZ  Var_01    C04  C03  O02  C01    -1.53  30.0  2
 JYZ  Var_02    C07  C06  C05  C04  -175.45  30.0  2
 JYZ  Var_03    C08  C07  C06  C05     1.08   0.0  2
 JYZ  Var_04    H1   C01  O02  C03   -60.86  30.0  3
 JYZ  Var_05    N12  C10  C07  C06  -177.82  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
 JYZ  plan-1  C03  0.020
 JYZ  plan-1  C04  0.020
 JYZ  plan-1  C05  0.020
 JYZ  plan-1  C06  0.020
 JYZ  plan-1  C20  0.020
 JYZ  plan-1  C21  0.020
 JYZ  plan-1  C22  0.020
 JYZ  plan-1  O02  0.020
 JYZ  plan-1  O23  0.020
 JYZ  plan-1  H4   0.020
 JYZ  plan-1  H10  0.020
 JYZ  plan-1  H11  0.020
 JYZ  plan-2  C13  0.020
 JYZ  plan-2  C14  0.020
 JYZ  plan-2  C15  0.020
 JYZ  plan-2  C16  0.020
 JYZ  plan-2  C17  0.020
 JYZ  plan-2  C18  0.020
 JYZ  plan-2  N12  0.020
 JYZ  plan-2  O19  0.020
 JYZ  plan-2  H6   0.020
 JYZ  plan-2  H7   0.020
 JYZ  plan-2  H8   0.020
 JYZ  plan-2  H9   0.020
 JYZ  plan-3  C07  0.020
 JYZ  plan-3  C10  0.020
 JYZ  plan-3  C13  0.020
 JYZ  plan-3  N12  0.020
 JYZ  plan-3  O11  0.020
 JYZ  plan-3  H12  0.020
 JYZ  plan-4  C05  0.020
 JYZ  plan-4  C06  0.020
 JYZ  plan-4  C07  0.020
 JYZ  plan-4  C08  0.020
 JYZ  plan-4  C10  0.020
 JYZ  plan-4  H5   0.020

