# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:55:23 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (~{E})-3-[3,4-bis(oxidanyl)phenyl]-2-cyano-prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)/C(=C/c1ccc(O)c(O)c1)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
 JGB  JGB  (~{E})-3-[3,4-bis(oxidanyl)phenyl]-2-cyano-prop-2-enamide  ligand  23  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JGB
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
 JGB  C02  C  C     0   0.509  -3.4887  -0.4388  -0.1905
 JGB  C04  C  C     0  -0.163  -2.0994   0.1089  -0.0316
 JGB  C05  C  C1    0  -0.144  -1.0581  -0.7528  -0.0905
 JGB  C06  C  CR6   0  -0.014   0.3677  -0.5665   0.0178
 JGB  C07  C  CR16  0  -0.295   1.0137   0.6692   0.1908
 JGB  C08  C  CR6   0   0.264   2.3861   0.7451   0.2835
 JGB  C10  C  CR6   0   0.276   3.1556  -0.4323   0.2061
 JGB  C12  C  CR16  0  -0.280   2.5294  -1.6570   0.0331
 JGB  C13  C  CR16  0  -0.285   1.1511  -1.7227  -0.0618
 JGB  C14  C  CSP   0   0.017  -1.9594   1.5038   0.1847
 JGB  N01  N  NH2   0  -0.886  -4.4823   0.4571  -0.1583
 JGB  N15  N  NS    0  -0.210  -1.9096   2.6405   0.3818
 JGB  O03  O  O     0  -0.361  -3.6746  -1.6374  -0.3350
 JGB  O09  O  OH1   0  -0.659   2.9656   1.9485   0.4464
 JGB  O11  O  OH1   0  -0.648   4.4818  -0.2712   0.3056
 JGB  H1   H  H     0   0.311  -1.3545  -1.7843  -0.2503
 JGB  H2   H  HCR6  0   0.316   0.4588   1.5942   0.2518
 JGB  H3   H  HCR6  0   0.283   3.1221  -2.5618  -0.0288
 JGB  H4   H  HCR6  0   0.254   0.6776  -2.6859  -0.2018
 JGB  H5   H  HNH2  0   0.384  -4.3403   1.4492  -0.0772
 JGB  H6   H  HNH2  0   0.401  -5.4339   0.1438  -0.2619
 JGB  H7   H  HOH1  0   0.456   3.9265   1.8679   0.4692
 JGB  H8   H  HOH1  0   0.477   4.9481  -1.1110   0.2170

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
 JGB  O11  C10  single    1.340  0.020  1.340
 JGB  C12  C10  aromatic  1.386  0.020  1.386
 JGB  C12  C13  aromatic  1.383  0.020  1.383
 JGB  C10  C08  aromatic  1.409  0.020  1.409
 JGB  C13  C06  aromatic  1.399  0.020  1.399
 JGB  C08  O09  single    1.346  0.020  1.346
 JGB  C08  C07  aromatic  1.378  0.020  1.378
 JGB  C06  C07  aromatic  1.405  0.020  1.405
 JGB  C06  C05  single    1.442  0.020  1.442
 JGB  C05  C04  double    1.353  0.020  1.353
 JGB  C04  C14  single    1.418  0.020  1.418
 JGB  C04  C02  single    1.502  0.020  1.502
 JGB  O03  C02  double    1.222  0.020  1.222
 JGB  C14  N15  triple    1.155  0.020  1.155
 JGB  C02  N01  single    1.338  0.020  1.338
 JGB  C05  H1   single    0.930  0.020  1.080
 JGB  C07  H2   single    0.930  0.020  1.080
 JGB  C12  H3   single    0.930  0.020  1.080
 JGB  C13  H4   single    0.930  0.020  1.080
 JGB  N01  H5   single    0.860  0.020  1.020
 JGB  N01  H6   single    0.860  0.020  1.020
 JGB  O09  H7   single    0.850  0.020  0.980
 JGB  O11  H8   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
 JGB  O03  C02  N01  123.14  3.000
 JGB  N01  C02  C04  116.12  3.000
 JGB  O03  C02  C04  120.74  3.000
 JGB  C14  C04  C05  123.85  3.000
 JGB  C14  C04  C02  117.78  3.000
 JGB  C05  C04  C02  118.37  3.000
 JGB  H1   C05  C06  113.82  3.000
 JGB  H1   C05  C04  113.69  3.000
 JGB  C06  C05  C04  132.49  3.000
 JGB  C13  C06  C07  118.45  3.000
 JGB  C07  C06  C05  125.27  3.000
 JGB  C13  C06  C05  116.28  3.000
 JGB  H2   C07  C08  117.43  3.000
 JGB  H2   C07  C06  121.59  3.000
 JGB  C08  C07  C06  120.99  3.000
 JGB  O09  C08  C10  121.26  3.000
 JGB  O09  C08  C07  119.11  3.000
 JGB  C10  C08  C07  119.63  3.000
 JGB  O11  C10  C12  124.24  3.000
 JGB  C12  C10  C08  119.90  3.000
 JGB  O11  C10  C08  115.86  3.000
 JGB  H3   C12  C13  120.10  3.000
 JGB  H3   C12  C10  119.85  3.000
 JGB  C13  C12  C10  120.04  3.000
 JGB  H4   C13  C12  119.15  3.000
 JGB  H4   C13  C06  119.86  3.000
 JGB  C12  C13  C06  120.99  3.000
 JGB  N15  C14  C04  180.00  3.000
 JGB  H6   N01  H5   116.66  3.000
 JGB  H6   N01  C02  119.39  3.000
 JGB  H5   N01  C02  123.89  3.000
 JGB  H7   O09  C08  110.93  3.000
 JGB  H8   O11  C10  111.53  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
 JGB  CONST_01  C10  C12  C13  C06    0.00   0.0  0
 JGB  CONST_02  C10  C08  C07  C06    0.00   0.0  0
 JGB  CONST_03  C12  C10  C08  C07    0.00   0.0  0
 JGB  CONST_04  C12  C13  C06  C07    0.00   0.0  0
 JGB  CONST_05  C13  C12  C10  C08    0.00   0.0  0
 JGB  CONST_06  C13  C06  C07  C08    0.00   0.0  0
 JGB  CONST_07  C12  C13  C06  C05  180.00   0.0  0
 JGB  CONST_08  C08  C07  C06  C05  180.00   0.0  0
 JGB  CONST_09  O09  C08  C07  C06  180.00   0.0  0
 JGB  CONST_10  O11  C10  C08  C07  180.00   0.0  0
 JGB  CONST_11  O09  C08  C10  C12  180.00   0.0  0
 JGB  CONST_12  O11  C10  C12  C13  180.00   0.0  0
 JGB  CONST_13  H3   C12  C13  C06  180.00   0.0  0
 JGB  CONST_14  H4   C13  C06  C07  180.00   0.0  0
 JGB  CONST_15  H2   C07  C08  C10  180.00   0.0  0
 JGB  CONST_16  H5   N01  C02  C04    0.00   0.0  0
 JGB  CONST_17  H6   N01  C02  C04  180.00   0.0  0
 JGB  Var_01    C13  C06  C05  C04  178.42  30.0  2
 JGB  Var_02    C06  C05  C04  C02  179.88   0.0  2
 JGB  Var_03    O03  C02  C04  C05    1.85  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
 JGB  plan-1  C05  0.020
 JGB  plan-1  C06  0.020
 JGB  plan-1  C07  0.020
 JGB  plan-1  C08  0.020
 JGB  plan-1  C10  0.020
 JGB  plan-1  C12  0.020
 JGB  plan-1  C13  0.020
 JGB  plan-1  O09  0.020
 JGB  plan-1  O11  0.020
 JGB  plan-1  H2   0.020
 JGB  plan-1  H3   0.020
 JGB  plan-1  H4   0.020
 JGB  plan-2  C02  0.020
 JGB  plan-2  C04  0.020
 JGB  plan-2  N01  0.020
 JGB  plan-2  O03  0.020
 JGB  plan-2  H5   0.020
 JGB  plan-2  H6   0.020
 JGB  plan-3  C02  0.020
 JGB  plan-3  C04  0.020
 JGB  plan-3  C05  0.020
 JGB  plan-3  C06  0.020
 JGB  plan-3  C14  0.020
 JGB  plan-3  H1   0.020

