# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 18:21:56 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 2-[(E)-2-nitroethenyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccccc1\C=C\[N+]([O-])=O
#
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
 P7Y  P7Y  2-[(E)-2-nitroethenyl]phenol  ligand  19  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P7Y
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
 P7Y  C1    C  C1     0  -0.098  -1.6174   0.5336  -0.1332
 P7Y  N1    N  N      1   0.402  -2.9693   0.0711  -0.0390
 P7Y  O1    O  O      0  -0.405  -3.1956  -1.0856   0.2451
 P7Y  C2    C  C1     0  -0.277  -0.5902  -0.3006   0.0515
 P7Y  O2    O  O     -1  -0.402  -3.8358   0.8917  -0.2594
 P7Y  C1'   C  CR6    0   0.020   0.8081   0.0829   0.0118
 P7Y  C2'   C  CR6    0   0.329   1.8163  -0.8930  -0.1059
 P7Y  O2'   O  OH1    0  -0.608   1.5832  -2.2070  -0.2403
 P7Y  C3'   C  CR16   0  -0.330   3.1586  -0.5112  -0.0907
 P7Y  C4'   C  CR16   0  -0.237   3.5063   0.8188   0.0279
 P7Y  C5'   C  CR16   0  -0.258   2.5217   1.8011   0.1335
 P7Y  C6'   C  CR16   0  -0.301   1.1966   1.4279   0.1261
 P7Y  H1    H  H      0   0.310  -1.5444   1.5825  -0.3738
 P7Y  H2    H  H      0   0.291  -0.8356  -1.3352   0.2649
 P7Y  HO2'  H  HOH1   0   0.484   0.6570  -2.4134  -0.4008
 P7Y  H3'   H  HCR6   0   0.276   3.9208  -1.2743  -0.1805
 P7Y  H4'   H  HCR6   0   0.271   4.5526   1.0943   0.0380
 P7Y  H5'   H  HCR6   0   0.265   2.7925   2.8428   0.2332
 P7Y  H6'   H  HCR6   0   0.268   0.4374   2.1909   0.2363

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
 P7Y  C1   N1    single    1.432  0.020  1.432
 P7Y  N1   O1    double    1.212  0.020  1.212
 P7Y  N1   O2    single    1.214  0.020  1.214
 P7Y  C2   C1    double    1.336  0.020  1.336
 P7Y  C1'  C2    single    1.450  0.020  1.450
 P7Y  C2'  C1'   aromatic  1.408  0.020  1.408
 P7Y  C2'  O2'   single    1.341  0.020  1.341
 P7Y  C3'  C2'   aromatic  1.396  0.020  1.396
 P7Y  C4'  C3'   aromatic  1.380  0.020  1.380
 P7Y  C4'  C5'   aromatic  1.395  0.020  1.395
 P7Y  C5'  C6'   aromatic  1.377  0.020  1.377
 P7Y  C6'  C1'   aromatic  1.405  0.020  1.405
 P7Y  C1   H1    single    0.930  0.020  1.080
 P7Y  C2   H2    single    0.930  0.020  1.080
 P7Y  O2'  HO2'  single    0.850  0.020  0.980
 P7Y  C3'  H3'   single    0.930  0.020  1.080
 P7Y  C4'  H4'   single    0.930  0.020  1.080
 P7Y  C5'  H5'   single    0.930  0.020  1.080
 P7Y  C6'  H6'   single    0.930  0.020  1.080

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
 P7Y  H1    C1   C2   125.87  3.000
 P7Y  H1    C1   N1   113.12  3.000
 P7Y  C2    C1   N1   121.00  3.000
 P7Y  O2    N1   O1   123.67  3.000
 P7Y  O2    N1   C1   116.34  3.000
 P7Y  O1    N1   C1   119.98  3.000
 P7Y  H2    C2   C1'  118.41  3.000
 P7Y  H2    C2   C1   116.67  3.000
 P7Y  C1'   C2   C1   124.91  3.000
 P7Y  C6'   C1'  C2'  118.19  3.000
 P7Y  C6'   C1'  C2   121.17  3.000
 P7Y  C2'   C1'  C2   120.62  3.000
 P7Y  C3'   C2'  O2'  115.87  3.000
 P7Y  C3'   C2'  C1'  119.88  3.000
 P7Y  O2'   C2'  C1'  124.26  3.000
 P7Y  HO2'  O2'  C2'  113.21  3.000
 P7Y  H3'   C3'  C4'  120.62  3.000
 P7Y  H3'   C3'  C2'  118.92  3.000
 P7Y  C4'   C3'  C2'  120.46  3.000
 P7Y  H4'   C4'  C5'  120.17  3.000
 P7Y  H4'   C4'  C3'  119.33  3.000
 P7Y  C5'   C4'  C3'  120.50  3.000
 P7Y  H5'   C5'  C6'  120.19  3.000
 P7Y  H5'   C5'  C4'  120.59  3.000
 P7Y  C6'   C5'  C4'  119.22  3.000
 P7Y  H6'   C6'  C5'  118.93  3.000
 P7Y  H6'   C6'  C1'  119.31  3.000
 P7Y  C5'   C6'  C1'  121.75  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
 P7Y  CONST_01  C4'  C3'  C2'  C1'     0.00   0.0  0
 P7Y  CONST_02  C4'  C5'  C6'  C1'     0.00   0.0  0
 P7Y  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 P7Y  CONST_04  C5'  C4'  C3'  C2'     0.00   0.0  0
 P7Y  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 P7Y  CONST_06  C6'  C5'  C4'  C3'     0.00   0.0  0
 P7Y  CONST_07  C3'  C2'  C1'  C2    180.00   0.0  0
 P7Y  CONST_08  C5'  C6'  C1'  C2    180.00   0.0  0
 P7Y  CONST_09  C6'  C1'  C2'  O2'   180.00   0.0  0
 P7Y  CONST_10  C4'  C3'  C2'  O2'   180.00   0.0  0
 P7Y  CONST_11  H3'  C3'  C2'  C1'   180.00   0.0  0
 P7Y  CONST_12  H5'  C5'  C6'  C1'   180.00   0.0  0
 P7Y  CONST_13  H6'  C6'  C1'  C2'   180.00   0.0  0
 P7Y  CONST_14  H4'  C4'  C3'  C2'   180.00   0.0  0
 P7Y  Var_01    C2'  C1'  C2   C1   -164.53  30.0  2
 P7Y  Var_02    C1'  C2   C1   N1   -178.25   0.0  2
 P7Y  Var_03    C2   C1   N1   O1      1.87  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
 P7Y  plan-1  C2   0.020
 P7Y  plan-1  C1'  0.020
 P7Y  plan-1  C2'  0.020
 P7Y  plan-1  O2'  0.020
 P7Y  plan-1  C3'  0.020
 P7Y  plan-1  C4'  0.020
 P7Y  plan-1  C5'  0.020
 P7Y  plan-1  C6'  0.020
 P7Y  plan-1  H3'  0.020
 P7Y  plan-1  H4'  0.020
 P7Y  plan-1  H5'  0.020
 P7Y  plan-1  H6'  0.020
 P7Y  plan-2  C1   0.020
 P7Y  plan-2  N1   0.020
 P7Y  plan-2  O1   0.020
 P7Y  plan-2  O2   0.020
 P7Y  plan-3  C1   0.020
 P7Y  plan-3  N1   0.020
 P7Y  plan-3  C2   0.020
 P7Y  plan-3  C1'  0.020
 P7Y  plan-3  H1   0.020
 P7Y  plan-3  H2   0.020

