# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 15:06:16 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (~{E})-3-(1,3-benzodioxol-5-yl)-1-(3-nitrophenyl)prop-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cccc(c1)C(=O)\C=C\c2ccc3OCOc3c2
#
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
 JV1  JV1  (~{E})-3-(1,3-benzodioxol-5-yl)-1-(3-nitrophenyl)prop-2-en-1-one  ligand  33  22  .  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_JV1
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
 JV1  C1   C  C      0   0.366  -1.2003  -0.6913  -0.0015
 JV1  C2   C  CR6    0   0.002  -2.4554   0.1272  -0.0194
 JV1  C3   C  CR16   0  -0.298  -3.6685  -0.5543   0.0475
 JV1  C4   C  CR6    0   0.286  -4.8506   0.1602   0.0250
 JV1  C5   C  CR16   0  -0.266  -4.8725   1.5457  -0.0663
 JV1  C6   C  CR16   0  -0.227  -3.6660   2.2175  -0.1333
 JV1  C7   C  CR16   0  -0.283  -2.4675   1.5180  -0.1101
 JV1  N8   N  N      1   0.330  -6.1140  -0.5639   0.0968
 JV1  O9   O  O      0  -0.374  -6.0748  -1.7636   0.2287
 JV1  O10  O  O     -1  -0.372  -7.1357   0.0753   0.0195
 JV1  C11  C  C1     0  -0.414   0.0925  -0.0014   0.0386
 JV1  C12  C  C1     0  -0.217   1.2407  -0.7005   0.0165
 JV1  C13  C  CR6    0   0.139   2.5933  -0.1733   0.0491
 JV1  C14  C  CR16   0  -0.326   2.8711   1.1936   0.1340
 JV1  C15  C  CR16   0  -0.317   4.1752   1.6812   0.1636
 JV1  C16  C  CR56   0   0.306   5.1897   0.7527   0.1046
 JV1  C17  C  CR56   0   0.317   4.9315  -0.6073   0.0187
 JV1  C18  C  CR16   0  -0.392   3.6557  -1.1008  -0.0093
 JV1  O19  O  O      0  -0.411  -1.2864  -1.9074  -0.0174
 JV1  O20  O  O      0  -0.484   6.1025  -1.2824  -0.0466
 JV1  O21  O  O      0  -0.475   6.5200   0.9605   0.1029
 JV1  C22  C  CH2    0   0.069   7.1328  -0.3250   0.1576
 JV1  H1   H  HCR6   0   0.299  -3.6733  -1.6326   0.1141
 JV1  H2   H  HCR6   0   0.307  -5.8018   2.0957  -0.0843
 JV1  H3   H  HCR6   0   0.288  -3.6580   3.2958  -0.2044
 JV1  H4   H  HCR6   0   0.282  -1.5498   2.0848  -0.1709
 JV1  H5   H  H      0   0.275   0.1108   1.0777   0.0891
 JV1  H6   H  H      0   0.269   1.1698  -1.7828  -0.0347
 JV1  H7   H  HCR6   0   0.267   2.0616   1.9087   0.1795
 JV1  H8   H  HCR6   0   0.283   4.3760   2.7416   0.2279
 JV1  H9   H  HCR6   0   0.279   3.4635  -2.1637  -0.0785
 JV1  H10  H  HCH2   0   0.241   7.5910  -0.4721   1.1400
 JV1  H12  H  HCH2   0   0.250   7.8796  -0.4097  -0.6315

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
 JV1  O21  C22  single    1.425  0.020  1.425
 JV1  O21  C16  single    1.346  0.020  1.346
 JV1  C22  O20  single    1.421  0.020  1.421
 JV1  C15  C16  aromatic  1.377  0.020  1.377
 JV1  C15  C14  aromatic  1.393  0.020  1.393
 JV1  C16  C17  aromatic  1.387  0.020  1.387
 JV1  O20  C17  single    1.353  0.020  1.353
 JV1  C14  C13  aromatic  1.397  0.020  1.397
 JV1  C17  C18  aromatic  1.368  0.020  1.368
 JV1  C13  C18  aromatic  1.411  0.020  1.411
 JV1  C13  C12  single    1.452  0.020  1.452
 JV1  C11  C12  double    1.344  0.020  1.344
 JV1  C11  C1   single    1.466  0.020  1.466
 JV1  O19  C1   double    1.219  0.020  1.219
 JV1  C1   C2   single    1.498  0.020  1.498
 JV1  O10  N8   single    1.208  0.020  1.208
 JV1  C3   C2   aromatic  1.393  0.020  1.393
 JV1  C3   C4   aromatic  1.381  0.020  1.381
 JV1  C2   C7   aromatic  1.394  0.020  1.394
 JV1  N8   C4   single    1.458  0.020  1.458
 JV1  N8   O9   double    1.208  0.020  1.208
 JV1  C4   C5   aromatic  1.389  0.020  1.389
 JV1  C7   C6   aromatic  1.388  0.020  1.388
 JV1  C5   C6   aromatic  1.383  0.020  1.383
 JV1  C3   H1   single    0.930  0.020  1.080
 JV1  C5   H2   single    0.930  0.020  1.080
 JV1  C6   H3   single    0.930  0.020  1.080
 JV1  C7   H4   single    0.930  0.020  1.080
 JV1  C11  H5   single    0.930  0.020  1.080
 JV1  C12  H6   single    0.930  0.020  1.080
 JV1  C14  H7   single    0.930  0.020  1.080
 JV1  C15  H8   single    0.930  0.020  1.080
 JV1  C18  H9   single    0.930  0.020  1.080
 JV1  C22  H10  single    0.970  0.020  1.090
 JV1  C22  H12  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
 JV1  O19  C1   C11  122.15  3.000
 JV1  O19  C1   C2   119.05  3.000
 JV1  C11  C1   C2   118.81  3.000
 JV1  C7   C2   C3   118.93  3.000
 JV1  C7   C2   C1   123.58  3.000
 JV1  C3   C2   C1   117.49  3.000
 JV1  H1   C3   C4   120.89  3.000
 JV1  H1   C3   C2   119.68  3.000
 JV1  C4   C3   C2   119.43  3.000
 JV1  N8   C4   C5   119.02  3.000
 JV1  C5   C4   C3   122.05  3.000
 JV1  N8   C4   C3   118.93  3.000
 JV1  H2   C5   C6   120.17  3.000
 JV1  H2   C5   C4   121.52  3.000
 JV1  C6   C5   C4   118.31  3.000
 JV1  H3   C6   C7   119.85  3.000
 JV1  H3   C6   C5   119.63  3.000
 JV1  C7   C6   C5   120.52  3.000
 JV1  H4   C7   C6   117.92  3.000
 JV1  H4   C7   C2   121.31  3.000
 JV1  C6   C7   C2   120.77  3.000
 JV1  O10  N8   O9   124.08  3.000
 JV1  O9   N8   C4   118.08  3.000
 JV1  O10  N8   C4   117.84  3.000
 JV1  H5   C11  C12  120.37  3.000
 JV1  H5   C11  C1   119.10  3.000
 JV1  C12  C11  C1   120.53  3.000
 JV1  H6   C12  C13  115.07  3.000
 JV1  H6   C12  C11  117.60  3.000
 JV1  C13  C12  C11  127.33  3.000
 JV1  C18  C13  C14  119.72  3.000
 JV1  C18  C13  C12  117.49  3.000
 JV1  C14  C13  C12  122.79  3.000
 JV1  H7   C14  C15  117.95  3.000
 JV1  H7   C14  C13  120.05  3.000
 JV1  C15  C14  C13  122.00  3.000
 JV1  H8   C15  C16  121.82  3.000
 JV1  H8   C15  C14  121.24  3.000
 JV1  C16  C15  C14  116.94  3.000
 JV1  O21  C16  C17  109.59  3.000
 JV1  C17  C16  C15  121.79  3.000
 JV1  O21  C16  C15  128.62  3.000
 JV1  O20  C17  C18  128.75  3.000
 JV1  C18  C17  C16  121.91  3.000
 JV1  O20  C17  C16  109.33  3.000
 JV1  H9   C18  C17  121.40  3.000
 JV1  H9   C18  C13  120.95  3.000
 JV1  C17  C18  C13  117.64  3.000
 JV1  C22  O20  C17  106.52  3.000
 JV1  C22  O21  C16  106.59  3.000
 JV1  H12  C22  H10  110.66  3.000
 JV1  H12  C22  O21  109.69  3.000
 JV1  H10  C22  O21  109.62  3.000
 JV1  H12  C22  O20  109.90  3.000
 JV1  H10  C22  O20  110.01  3.000
 JV1  O21  C22  O20  106.89  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
 JV1  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 JV1  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 JV1  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 JV1  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 JV1  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 JV1  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 JV1  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 JV1  CONST_08  C16  C17  C18  C13     0.00   0.0  0
 JV1  CONST_09  C17  C16  C15  C14     0.00   0.0  0
 JV1  CONST_10  C17  C18  C13  C14     0.00   0.0  0
 JV1  CONST_11  C18  C17  C16  C15     0.00   0.0  0
 JV1  CONST_12  C18  C13  C14  C15     0.00   0.0  0
 JV1  CONST_13  C4   C3   C2   C1    180.00   0.0  0
 JV1  CONST_14  C6   C7   C2   C1    180.00   0.0  0
 JV1  CONST_15  N8   C4   C3   C2    180.00   0.0  0
 JV1  CONST_16  N8   C4   C5   C6    180.00   0.0  0
 JV1  CONST_17  C15  C14  C13  C12   180.00   0.0  0
 JV1  CONST_18  C17  C18  C13  C12   180.00   0.0  0
 JV1  CONST_19  H3   C6   C7   C2    180.00   0.0  0
 JV1  CONST_20  H4   C7   C2   C3    180.00   0.0  0
 JV1  CONST_21  H2   C5   C4   C3    180.00   0.0  0
 JV1  CONST_22  H1   C3   C4   C5    180.00   0.0  0
 JV1  CONST_23  H8   C15  C14  C13   180.00   0.0  0
 JV1  CONST_24  H9   C18  C13  C14   180.00   0.0  0
 JV1  CONST_25  H7   C14  C15  C16   180.00   0.0  0
 JV1  CONST_26  O10  N8   C4   C3    180.00   0.0  0
 JV1  CONST_27  O9   N8   C4   C3      0.00   0.0  0
 JV1  CONST_28  O10  N8   C4   C5      0.00   0.0  0
 JV1  CONST_29  O9   N8   C4   C5    180.00   0.0  0
 JV1  Var_01    O20  C22  O21  C16    10.05  30.0  1
 JV1  Var_02    O21  C22  O20  C17   -10.25  30.0  1
 JV1  Var_03    C11  C1   C2   C3   -175.13  30.0  2
 JV1  Var_04    C14  C13  C12  C11     1.15  30.0  2
 JV1  Var_05    C13  C12  C11  C1    179.96   0.0  2
 JV1  Var_06    C12  C11  C1   C2   -178.06  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
 JV1  plan-1  C1   0.020
 JV1  plan-1  C2   0.020
 JV1  plan-1  C3   0.020
 JV1  plan-1  C4   0.020
 JV1  plan-1  C5   0.020
 JV1  plan-1  C6   0.020
 JV1  plan-1  C7   0.020
 JV1  plan-1  N8   0.020
 JV1  plan-1  H1   0.020
 JV1  plan-1  H2   0.020
 JV1  plan-1  H3   0.020
 JV1  plan-1  H4   0.020
 JV1  plan-2  C12  0.020
 JV1  plan-2  C13  0.020
 JV1  plan-2  C14  0.020
 JV1  plan-2  C15  0.020
 JV1  plan-2  C16  0.020
 JV1  plan-2  C17  0.020
 JV1  plan-2  C18  0.020
 JV1  plan-2  O20  0.020
 JV1  plan-2  O21  0.020
 JV1  plan-2  H7   0.020
 JV1  plan-2  H8   0.020
 JV1  plan-2  H9   0.020
 JV1  plan-3  C4   0.020
 JV1  plan-3  N8   0.020
 JV1  plan-3  O9   0.020
 JV1  plan-3  O10  0.020
 JV1  plan-4  C1   0.020
 JV1  plan-4  C2   0.020
 JV1  plan-4  C11  0.020
 JV1  plan-4  O19  0.020
 JV1  plan-5  C1   0.020
 JV1  plan-5  C11  0.020
 JV1  plan-5  C12  0.020
 JV1  plan-5  C13  0.020
 JV1  plan-5  H5   0.020
 JV1  plan-5  H6   0.020

