# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:40:03 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (6S)-6-hydroperoxy-6-hydroxy-4-nitrocyclohexa-2,4-dien-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OO[C@@]1(O)C=C(C=CC1=O)[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
 XX3  XX3  (6S)-6-hydroperoxy-6-hydroxy-4-nitrocyclohexa-2,4-dien-1-one  ligand  18  13  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XX3
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
 XX3  O8    O  OH1    0  -0.624   0.1319  -2.4634  -3.4952
 XX3  C2    C  CT     0   0.358   0.5185  -1.1602  -3.3058
 XX3  O12   O  O2     0  -0.286   0.0569  -0.4237  -4.4175
 XX3  O13   O  OH1    0  -0.448   0.4084   0.9216  -4.1789
 XX3  C1    C  C      0   0.393  -0.2333  -0.6952  -2.0351
 XX3  O7    O  O      0  -0.372  -1.4385  -0.6288  -2.0728
 XX3  C6    C  C1     0  -0.353   0.5497  -0.3829  -0.8458
 XX3  C5    C  C1     0  -0.228   1.8887  -0.3889  -0.8719
 XX3  C3    C  C1     0  -0.273   2.0176  -1.0557  -3.2250
 XX3  C4    C  C      0   0.288   2.6155  -0.7268  -2.0841
 XX3  N9    N  N      1   0.337   4.0773  -0.6985  -2.0317
 XX3  O10   O  O     -1  -0.360   4.5866  -0.4804  -0.9599
 XX3  O11   O  O      0  -0.366   4.6879  -0.8958  -3.0521
 XX3  HO8   H  HOH1   0   0.483   0.6748  -2.8910  -4.1719
 XX3  HO13  H  HOH1   0   0.486  -0.4549   1.3363  -4.0341
 XX3  H6    H  H      0   0.300   0.0166  -0.1099   0.0548
 XX3  H5    H  H      0   0.320   2.4422  -0.1286   0.0184
 XX3  H31   H  H      0   0.344   2.5759  -1.2986  -4.1219

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
 XX3  O8   C2    single  1.372  0.020  1.372
 XX3  O8   HO8   single  0.850  0.020  0.980
 XX3  C2   O12   single  1.411  0.020  1.411
 XX3  C2   C3    single  1.505  0.020  1.505
 XX3  C2   C1    single  1.548  0.020  1.548
 XX3  O12  O13   single  1.411  0.020  1.411
 XX3  O13  HO13  single  0.850  0.020  0.980
 XX3  C1   C6    single  1.458  0.020  1.458
 XX3  C1   O7    double  1.208  0.020  1.208
 XX3  C6   C5    double  1.339  0.020  1.339
 XX3  C6   H6    single  0.930  0.020  1.080
 XX3  C5   C4    single  1.453  0.020  1.453
 XX3  C5   H5    single  0.930  0.020  1.080
 XX3  C3   C4    double  1.329  0.020  1.329
 XX3  C3   H31   single  0.930  0.020  1.080
 XX3  C4   N9    single  1.463  0.020  1.463
 XX3  N9   O10   single  1.207  0.020  1.207
 XX3  N9   O11   double  1.205  0.020  1.205

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
 XX3  HO8   O8   C2   111.00  3.000
 XX3  C3    C2   C1   114.76  3.000
 XX3  C1    C2   O12  109.33  3.000
 XX3  C3    C2   O12  109.38  3.000
 XX3  C1    C2   O8   105.18  3.000
 XX3  C3    C2   O8   110.73  3.000
 XX3  O12   C2   O8   107.14  3.000
 XX3  O13   O12  C2   106.44  3.000
 XX3  HO13  O13  O12  102.21  3.000
 XX3  C6    C1   O7   123.35  3.000
 XX3  O7    C1   C2   118.39  3.000
 XX3  C6    C1   C2   118.25  3.000
 XX3  H6    C6   C5   120.68  3.000
 XX3  H6    C6   C1   117.95  3.000
 XX3  C5    C6   C1   121.34  3.000
 XX3  H5    C5   C4   119.16  3.000
 XX3  H5    C5   C6   119.68  3.000
 XX3  C4    C5   C6   121.16  3.000
 XX3  H31   C3   C4   122.26  3.000
 XX3  H31   C3   C2   116.94  3.000
 XX3  C4    C3   C2   120.75  3.000
 XX3  N9    C4   C3   119.00  3.000
 XX3  N9    C4   C5   117.73  3.000
 XX3  C3    C4   C5   123.26  3.000
 XX3  O11   N9   O10  124.59  3.000
 XX3  O11   N9   C4   118.21  3.000
 XX3  O10   N9   C4   117.20  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
 XX3  Var_01  C5   C4  C3  C2  -2.94  30.0  1
 XX3  Var_02  C5   C6  C1  C2   5.39  30.0  1
 XX3  Var_03  C4   C5  C6  C1  -0.92  30.0  1
 XX3  Var_04  C3   C4  C5  C6  -0.48  30.0  1
 XX3  Var_05  O10  N9  C4  C5   4.69  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 XX3  chir_01  C2  O12  C3  C1  negativ

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
 XX3  plan-1  C2   0.020
 XX3  plan-1  C1   0.020
 XX3  plan-1  O7   0.020
 XX3  plan-1  C6   0.020
 XX3  plan-2  C4   0.020
 XX3  plan-2  N9   0.020
 XX3  plan-2  O10  0.020
 XX3  plan-2  O11  0.020

