# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 14:59:08 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (~{E})-2-cyano-~{N},~{N}-diethyl-3-[3-nitro-4,5-bis(oxidanyl)phenyl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)C(=O)C(=C/c1cc(O)c(O)c(c1)[N+]([O-])=O)/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
 PD9  PD9  (~{E})-2-cyano-~{N},~{N}-diethyl-3-[3-nitro-4,5-bis(oxidanyl)phenyl]prop-2-enamide  ligand  37  22  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PD9
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
 PD9  C4   C  CR6    0   0.222  -3.0996   0.6353  -0.2799
 PD9  C5   C  CR16   0  -0.399  -1.7564   0.9670  -0.1372
 PD9  C6   C  CR6    0   0.264  -3.5760  -0.6413   0.0422
 PD9  C10  C  CR16   0  -0.403  -1.3187  -1.2569   0.6580
 PD9  C11  C  CR6    0   0.162  -0.8493   0.0267   0.3236
 PD9  C12  C  C1     0  -0.223   0.5297   0.4666   0.4292
 PD9  C14  C  CSP    0   0.057   1.7275  -1.5880   1.0047
 PD9  N15  N  NS     0  -0.247   1.8225  -2.7043   1.2822
 PD9  C16  C  C      0   0.559   2.9545   0.5815   0.7849
 PD9  O17  O  O      0  -0.474   2.9661   1.6090   1.4450
 PD9  C19  C  CH2    0  -0.320   5.2926   0.8231   0.2830
 PD9  C20  C  CH2    0  -0.335   3.9897  -0.9001  -0.9171
 PD9  C21  C  CH3    0  -0.662   5.4300   1.9825  -0.6925
 PD9  O21  O  O      0  -0.419  -5.1854   1.3460  -0.8842
 PD9  N20  N  N      1   0.365  -4.0054   1.6430  -0.7683
 PD9  O22  O  O     -1  -0.352  -3.5761   2.7316  -1.0431
 PD9  O7   O  OH1    0  -0.597  -4.8251  -1.0615  -0.0535
 PD9  C8   C  CR6    0   0.347  -2.6450  -1.5885   0.5256
 PD9  O9   O  OH1    0  -0.618  -3.0470  -2.8215   0.8612
 PD9  C13  C  C      0  -0.151   1.6674  -0.2045   0.6934
 PD9  N18  N  NT     0  -0.442   4.0334   0.0993   0.1442
 PD9  C22  C  CH3    0  -0.660   4.7455  -2.1768  -0.5900
 PD9  H1   H  HCR6   0   0.310  -1.4198   1.9610  -0.3948
 PD9  H2   H  HCR6   0   0.288  -0.6557  -2.0201   1.0383
 PD9  H3   H  H      0   0.295   0.6625   1.5249   0.2338
 PD9  H4   H  HCH2   0   0.252   6.0990   0.1065   0.1261
 PD9  H5   H  HCH2   0   0.257   5.3870   1.1752   1.3086
 PD9  H6   H  HCH2   0   0.267   2.9541  -1.1245  -1.1665
 PD9  H7   H  HCH2   0   0.264   4.4095  -0.4463  -1.8191
 PD9  H8   H  HCH3   0   0.235   4.6613   2.7355  -0.5256
 PD9  H9   H  HCH3   0   0.238   6.4022   2.4588  -0.5659
 PD9  H10  H  HCH3   0   0.228   5.3623   1.6456  -1.7276
 PD9  H11  H  HOH1   0   0.496  -5.3865  -0.3337  -0.3850
 PD9  H12  H  HOH1   0   0.485  -4.0013  -2.9230   0.7551
 PD9  H13  H  HCH3   0   0.240   4.6619  -2.8703  -1.4264
 PD9  H14  H  HCH3   0   0.234   5.8073  -1.9921  -0.4265
 PD9  H15  H  HCH3   0   0.236   4.3459  -2.6663   0.2966

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
 PD9  C22  C20  single    1.519  0.020  1.519
 PD9  C21  C19  single    1.521  0.020  1.521
 PD9  C20  N18  single    1.458  0.020  1.458
 PD9  C19  N18  single    1.459  0.020  1.459
 PD9  N18  C16  single    1.344  0.020  1.344
 PD9  C16  O17  double    1.221  0.020  1.221
 PD9  C16  C13  single    1.511  0.020  1.511
 PD9  C13  C14  single    1.419  0.020  1.419
 PD9  C13  C12  double    1.347  0.020  1.347
 PD9  C14  N15  triple    1.154  0.020  1.154
 PD9  C12  C11  single    1.451  0.020  1.451
 PD9  C10  C11  aromatic  1.407  0.020  1.407
 PD9  C10  C8   aromatic  1.373  0.020  1.373
 PD9  C11  C5   aromatic  1.385  0.020  1.385
 PD9  O9   C8   single    1.340  0.020  1.340
 PD9  C8   C6   aromatic  1.413  0.020  1.413
 PD9  C5   C4   aromatic  1.391  0.020  1.391
 PD9  C6   C4   aromatic  1.400  0.020  1.400
 PD9  C6   O7   single    1.321  0.020  1.321
 PD9  C4   N20  single    1.440  0.020  1.440
 PD9  N20  O22  single    1.202  0.020  1.202
 PD9  N20  O21  double    1.222  0.020  1.222
 PD9  C5   H1   single    0.930  0.020  1.080
 PD9  C10  H2   single    0.930  0.020  1.080
 PD9  C12  H3   single    0.930  0.020  1.080
 PD9  C19  H4   single    0.970  0.020  1.090
 PD9  C19  H5   single    0.970  0.020  1.090
 PD9  C20  H6   single    0.970  0.020  1.090
 PD9  C20  H7   single    0.970  0.020  1.090
 PD9  C21  H8   single    0.970  0.020  1.090
 PD9  C21  H9   single    0.970  0.020  1.090
 PD9  C21  H10  single    0.970  0.020  1.090
 PD9  O7   H11  single    0.850  0.020  0.980
 PD9  O9   H12  single    0.850  0.020  0.980
 PD9  C22  H13  single    0.970  0.020  1.090
 PD9  C22  H14  single    0.970  0.020  1.090
 PD9  C22  H15  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
 PD9  N20  C4   C6   120.13  3.000
 PD9  N20  C4   C5   118.37  3.000
 PD9  C6   C4   C5   121.50  3.000
 PD9  H1   C5   C11  119.98  3.000
 PD9  H1   C5   C4   119.71  3.000
 PD9  C11  C5   C4   120.30  3.000
 PD9  C8   C6   O7   115.74  3.000
 PD9  O7   C6   C4   126.51  3.000
 PD9  C8   C6   C4   117.75  3.000
 PD9  H2   C10  C8   117.13  3.000
 PD9  H2   C10  C11  121.57  3.000
 PD9  C8   C10  C11  121.30  3.000
 PD9  C12  C11  C10  125.18  3.000
 PD9  C10  C11  C5   118.67  3.000
 PD9  C12  C11  C5   116.14  3.000
 PD9  H3   C12  C13  114.71  3.000
 PD9  H3   C12  C11  113.52  3.000
 PD9  C13  C12  C11  131.75  3.000
 PD9  C13  C14  N15  180.00  3.000
 PD9  N18  C16  C13  117.92  3.000
 PD9  C13  C16  O17  118.59  3.000
 PD9  N18  C16  O17  123.49  3.000
 PD9  H5   C19  H4   106.51  3.000
 PD9  H5   C19  N18  108.96  3.000
 PD9  H4   C19  N18  107.38  3.000
 PD9  H5   C19  C21  110.48  3.000
 PD9  H4   C19  C21  109.99  3.000
 PD9  N18  C19  C21  113.26  3.000
 PD9  H7   C20  H6   105.18  3.000
 PD9  H7   C20  C22  109.59  3.000
 PD9  H6   C20  C22  110.45  3.000
 PD9  H7   C20  N18  107.72  3.000
 PD9  H6   C20  N18  109.66  3.000
 PD9  C22  C20  N18  113.84  3.000
 PD9  H10  C21  H9   107.49  3.000
 PD9  H10  C21  H8   108.38  3.000
 PD9  H9   C21  H8   108.03  3.000
 PD9  H10  C21  C19  111.57  3.000
 PD9  H9   C21  C19  109.81  3.000
 PD9  H8   C21  C19  111.41  3.000
 PD9  O22  N20  O21  122.90  3.000
 PD9  O21  N20  C4   117.99  3.000
 PD9  O22  N20  C4   119.12  3.000
 PD9  H11  O7   C6   109.32  3.000
 PD9  O9   C8   C10  119.20  3.000
 PD9  O9   C8   C6   120.32  3.000
 PD9  C10  C8   C6   120.48  3.000
 PD9  H12  O9   C8   111.46  3.000
 PD9  C16  C13  C14  117.24  3.000
 PD9  C14  C13  C12  124.36  3.000
 PD9  C16  C13  C12  118.18  3.000
 PD9  C20  N18  C19  115.78  3.000
 PD9  C19  N18  C16  117.99  3.000
 PD9  C20  N18  C16  124.65  3.000
 PD9  H15  C22  H14  108.15  3.000
 PD9  H15  C22  H13  108.10  3.000
 PD9  H14  C22  H13  107.32  3.000
 PD9  H15  C22  C20  111.75  3.000
 PD9  H14  C22  C20  111.99  3.000
 PD9  H13  C22  C20  109.35  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
 PD9  CONST_01  C10  C11  C5   C4      0.00   0.0  0
 PD9  CONST_02  C10  C8   C6   C4      0.00   0.0  0
 PD9  CONST_03  C8   C10  C11  C5      0.00   0.0  0
 PD9  CONST_04  C8   C6   C4   C5      0.00   0.0  0
 PD9  CONST_05  C11  C10  C8   C6      0.00   0.0  0
 PD9  CONST_06  C11  C5   C4   C6      0.00   0.0  0
 PD9  CONST_07  C12  C11  C5   C4    180.00   0.0  0
 PD9  CONST_08  O9   C8   C6   C4    180.00   0.0  0
 PD9  CONST_09  O7   C6   C4   C5    180.00   0.0  0
 PD9  CONST_10  O7   C6   C8   C10   180.00   0.0  0
 PD9  CONST_11  O9   C8   C10  C11   180.00   0.0  0
 PD9  CONST_12  N20  C4   C5   C11   180.00   0.0  0
 PD9  CONST_13  C8   C10  C11  C12   180.00   0.0  0
 PD9  CONST_14  C8   C6   C4   N20   180.00   0.0  0
 PD9  CONST_15  H2   C10  C11  C5    180.00   0.0  0
 PD9  CONST_16  H1   C5   C4   C6    180.00   0.0  0
 PD9  CONST_17  O22  N20  C4   C5      0.00   0.0  0
 PD9  CONST_18  O21  N20  C4   C5    180.00   0.0  0
 PD9  CONST_19  O22  N20  C4   C6    180.00   0.0  0
 PD9  CONST_20  O21  N20  C4   C6      0.00   0.0  0
 PD9  CONST_22  C19  N18  C16  O17     0.00   0.0  0
 PD9  CONST_23  C13  C16  N18  C19   180.00   0.0  0
 PD9  Var_01    C13  C12  C11  C5   -171.84  30.0  3
 PD9  Var_02    C16  C13  C12  C11  -177.60   0.0  2
 PD9  Var_03    N18  C16  C13  C12  -134.10  30.0  1
 PD9  Var_04    C22  C20  N18  C16  -119.31  30.0  3
 PD9  Var_05    C21  C19  N18  C16   -84.29  30.0  2
 PD9  Var_06    H13  C22  C20  N18   179.76  30.0  3
 PD9  Var_07    H8   C21  C19  N18    62.44  30.0  3

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
 PD9  plan-1  C4   0.020
 PD9  plan-1  C5   0.020
 PD9  plan-1  C6   0.020
 PD9  plan-1  C10  0.020
 PD9  plan-1  C11  0.020
 PD9  plan-1  C12  0.020
 PD9  plan-1  N20  0.020
 PD9  plan-1  O7   0.020
 PD9  plan-1  C8   0.020
 PD9  plan-1  O9   0.020
 PD9  plan-1  H1   0.020
 PD9  plan-1  H2   0.020
 PD9  plan-2  C16  0.020
 PD9  plan-2  O17  0.020
 PD9  plan-2  C19  0.020
 PD9  plan-2  C20  0.020
 PD9  plan-2  C13  0.020
 PD9  plan-2  N18  0.020
 PD9  plan-3  C4   0.020
 PD9  plan-3  O21  0.020
 PD9  plan-3  N20  0.020
 PD9  plan-3  O22  0.020
 PD9  plan-4  C11  0.020
 PD9  plan-4  C12  0.020
 PD9  plan-4  C14  0.020
 PD9  plan-4  C16  0.020
 PD9  plan-4  C13  0.020
 PD9  plan-4  H3   0.020

