# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 06:50:40 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: 1-[(~{E})-1-(3-methoxy-4-oxidanyl-phenyl)ethylideneamino]thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)\C(C)=N\NC(N)=S
#
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
 A3X  A3X  "N-(3-metoxy-4-hydroxy-acetophenone)thiosemicarbazone"
  ligand  29  16  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A3X
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
 A3X  C1   C  CR6   0   0.280  55.0351  34.8535  -10.1693
 A3X  N2   N  NH2   0  -0.771  59.8137  34.1144   -5.2517
 A3X  C3   C  CR16  0  -0.331  55.9042  32.6583   -9.6942
 A3X  C5   C  CR16  0  -0.428  56.7245  34.5506   -8.4686
 A3X  C7   C  C     0   0.380  60.0054  32.8097   -5.3897
 A3X  C9   C  CH3   0  -0.432  56.5703  37.3411   -8.0183
 A3X  N    N  N     0  -0.265  58.3782  32.8595   -7.0624
 A3X  C    C  CR6   0   0.333  55.8872  35.3834   -9.1801
 A3X  O    O  OH1   0  -0.621  54.2102  35.6430  -10.8776
 A3X  C2   C  CR16  0  -0.325  55.0552  33.4933  -10.4119
 A3X  C4   C  CR6   0   0.040  56.7505  33.1689   -8.7168
 A3X  C8   C  CH3   0  -0.776  57.6772  30.8296   -8.2984
 A3X  N1   N  NH1   0  -0.465  59.2542  32.1713   -6.3133
 A3X  O1   O  O2    0  -0.488  55.7941  36.7205   -9.0229
 A3X  S    S  S1    0  -0.443  61.1181  31.9359   -4.4801
 A3X  H4   H  HNH2  0   0.415  60.3570  34.6254   -4.5788
 A3X  H5   H  HNH2  0   0.425  59.1417  34.6091   -5.8175
 A3X  H1   H  HCR6  0   0.256  55.8856  31.6015   -9.9205
 A3X  H2   H  HCR6  0   0.294  57.3787  34.9578   -7.7106
 A3X  H10  H  HCH3  0   0.263  56.3348  38.4015   -8.0557
 A3X  H11  H  HCH3  0   0.231  56.3251  36.9578   -7.0245
 A3X  H12  H  HCH3  0   0.231  57.6409  37.2097   -8.1944
 A3X  H9   H  HOH1  0   0.472  54.3010  36.5614  -10.5938
 A3X  H    H  HCR6  0   0.266  54.4015  33.0815  -11.1705
 A3X  H6   H  HCH3  0   0.267  58.3987  30.2412   -7.7377
 A3X  H7   H  HCH3  0   0.273  56.6954  30.3908   -8.1157
 A3X  H8   H  HCH3  0   0.273  57.9029  30.6879   -9.3555
 A3X  H3   H  HNH1  0   0.409  59.4041  31.1758   -6.4125
 A3X  C6   C  C     0   0.238  57.6645  32.2905   -7.9574

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
 A3X  O   C1   single    1.344  0.020  1.344
 A3X  C2  C1   aromatic  1.382  0.020  1.382
 A3X  C2  C3   aromatic  1.390  0.020  1.390
 A3X  C1  C    aromatic  1.409  0.020  1.409
 A3X  C3  C4   aromatic  1.390  0.020  1.390
 A3X  C   O1   single    1.350  0.020  1.350
 A3X  C   C5   aromatic  1.379  0.020  1.379
 A3X  O1  C9   single    1.413  0.020  1.413
 A3X  C4  C5   aromatic  1.404  0.020  1.404
 A3X  C4  C6   single    1.478  0.020  1.478
 A3X  C6  C8   single    1.500  0.020  1.500
 A3X  C6  N    double    1.278  0.020  1.278
 A3X  N   N1   single    1.342  0.020  1.342
 A3X  N2  C7   single    1.326  0.020  1.326
 A3X  N1  C7   single    1.351  0.020  1.351
 A3X  C7  S    double    1.682  0.020  1.682
 A3X  N2  H4   single    0.860  0.020  1.020
 A3X  N2  H5   single    0.860  0.020  1.020
 A3X  C3  H1   single    0.930  0.020  1.080
 A3X  C5  H2   single    0.930  0.020  1.080
 A3X  C9  H10  single    0.970  0.020  1.090
 A3X  C9  H11  single    0.970  0.020  1.090
 A3X  C9  H12  single    0.970  0.020  1.090
 A3X  O   H9   single    0.850  0.020  0.980
 A3X  C2  H    single    0.930  0.020  1.080
 A3X  C8  H6   single    0.970  0.020  1.090
 A3X  C8  H7   single    0.970  0.020  1.090
 A3X  C8  H8   single    0.970  0.020  1.090
 A3X  N1  H3   single    0.860  0.020  1.020

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
 A3X  C2   C1  O    119.65  3.000
 A3X  C2   C1  C    118.99  3.000
 A3X  O    C1  C    121.36  3.000
 A3X  H5   N2  H4   119.13  3.000
 A3X  H5   N2  C7   121.38  3.000
 A3X  H4   N2  C7   119.48  3.000
 A3X  H1   C3  C4   121.12  3.000
 A3X  H1   C3  C2   117.94  3.000
 A3X  C4   C3  C2   120.94  3.000
 A3X  H2   C5  C4   118.91  3.000
 A3X  H2   C5  C    120.13  3.000
 A3X  C4   C5  C    120.96  3.000
 A3X  S    C7  N1   119.48  3.000
 A3X  S    C7  N2   123.40  3.000
 A3X  N1   C7  N2   117.12  3.000
 A3X  H12  C9  H11  108.91  3.000
 A3X  H12  C9  H10  108.90  3.000
 A3X  H11  C9  H10  108.95  3.000
 A3X  H12  C9  O1   111.76  3.000
 A3X  H11  C9  O1   111.67  3.000
 A3X  H10  C9  O1   106.56  3.000
 A3X  N1   N   C6   121.79  3.000
 A3X  O1   C   C5   125.47  3.000
 A3X  C5   C   C1   120.16  3.000
 A3X  O1   C   C1   114.37  3.000
 A3X  H9   O   C1   110.25  3.000
 A3X  H    C2  C3   120.12  3.000
 A3X  H    C2  C1   119.25  3.000
 A3X  C3   C2  C1   120.62  3.000
 A3X  C6   C4  C5   120.37  3.000
 A3X  C6   C4  C3   121.30  3.000
 A3X  C5   C4  C3   118.33  3.000
 A3X  H8   C8  H7   107.25  3.000
 A3X  H8   C8  H6   107.01  3.000
 A3X  H7   C8  H6   107.06  3.000
 A3X  H8   C8  C6   110.41  3.000
 A3X  H7   C8  C6   110.25  3.000
 A3X  H6   C8  C6   114.55  3.000
 A3X  H3   N1  N    123.13  3.000
 A3X  H3   N1  C7   116.73  3.000
 A3X  N    N1  C7   120.14  3.000
 A3X  C    O1  C9   118.69  3.000
 A3X  C8   C6  C4   117.86  3.000
 A3X  C8   C6  N    126.01  3.000
 A3X  C4   C6  N    116.14  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
 A3X  CONST_01  C4   C3  C2  C1     0.00   0.0  0
 A3X  CONST_02  C4   C5  C   C1     0.00   0.0  0
 A3X  CONST_03  C    C1  C2  C3     0.00   0.0  0
 A3X  CONST_04  C    C5  C4  C3     0.00   0.0  0
 A3X  CONST_05  C2   C1  C   C5     0.00   0.0  0
 A3X  CONST_06  C2   C3  C4  C5     0.00   0.0  0
 A3X  CONST_07  O    C1  C2  C3   180.00   0.0  0
 A3X  CONST_08  O    C1  C   C5   180.00   0.0  0
 A3X  CONST_09  C2   C3  C4  C6   180.00   0.0  0
 A3X  CONST_10  C    C5  C4  C6   180.00   0.0  0
 A3X  CONST_11  O1   C   C1  C2   180.00   0.0  0
 A3X  CONST_12  O1   C   C5  C4   180.00   0.0  0
 A3X  CONST_13  H1   C3  C2  C1   180.00   0.0  0
 A3X  CONST_14  H2   C5  C   C1   180.00   0.0  0
 A3X  CONST_15  H2   C5  C4  C3   180.00   0.0  0
 A3X  CONST_16  H1   C3  C4  C5   180.00   0.0  0
 A3X  CONST_17  H    C2  C1  C    180.00   0.0  0
 A3X  CONST_18  H    C2  C3  C4   180.00   0.0  0
 A3X  CONST_19  N    N1  C7  N2     0.00   0.0  0
 A3X  CONST_20  S    C7  N1  N    180.00   0.0  0
 A3X  CONST_21  H3   N1  C7  N2   180.00   0.0  0
 A3X  CONST_22  H4   N2  C7  N1   180.00   0.0  0
 A3X  CONST_23  H5   N2  C7  N1     0.00   0.0  0
 A3X  CONST_24  H4   N2  C7  S      0.00   0.0  0
 A3X  CONST_25  H5   N2  C7  S    180.00   0.0  0
 A3X  CONST_26  H3   N1  C7  S      0.00   0.0  0
 A3X  Var_01    C9   O1  C   C1   177.55  30.0  2
 A3X  Var_02    C8   C6  C4  C3     1.53  30.0  2
 A3X  Var_03    N    C6  C4  C3  -178.55  30.0  2
 A3X  Var_04    C9   O1  C   C5    -2.56  30.0  2
 A3X  Var_05    C8   C6  C4  C5  -178.10  30.0  2
 A3X  Var_06    N    C6  C4  C5     1.82  30.0  2
 A3X  Var_07    N1   N   C6  C4  -179.47   0.0  2
 A3X  Var_08    H10  C9  O1  C   -179.22  30.0  3
 A3X  Var_09    H11  C9  O1  C    -60.35  30.0  3
 A3X  Var_10    H12  C9  O1  C     61.92  30.0  3
 A3X  Var_11    H6   C8  C6  C4   177.48  30.0  3
 A3X  Var_12    H7   C8  C6  C4   -61.70  30.0  3
 A3X  Var_13    H8   C8  C6  C4    56.62  30.0  3
 A3X  Var_14    N1   N   C6  C8     0.44   0.0  2
 A3X  Var_15    C7   N1  N   C6   179.05  30.0  3
 A3X  Var_16    H3   N1  N   C6     0.29  30.0  3
 A3X  Var_17    H6   C8  C6  N     -2.42  30.0  3
 A3X  Var_18    H7   C8  C6  N    118.39  30.0  3
 A3X  Var_19    H8   C8  C6  N   -123.29  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
 A3X  plan-1  C1  0.020
 A3X  plan-1  C3  0.020
 A3X  plan-1  C5  0.020
 A3X  plan-1  C   0.020
 A3X  plan-1  O   0.020
 A3X  plan-1  C2  0.020
 A3X  plan-1  C4  0.020
 A3X  plan-1  O1  0.020
 A3X  plan-1  H1  0.020
 A3X  plan-1  H2  0.020
 A3X  plan-1  H   0.020
 A3X  plan-1  C6  0.020
 A3X  plan-2  N2  0.020
 A3X  plan-2  C7  0.020
 A3X  plan-2  N   0.020
 A3X  plan-2  N1  0.020
 A3X  plan-2  S   0.020
 A3X  plan-2  H4  0.020
 A3X  plan-2  H5  0.020
 A3X  plan-2  H3  0.020
 A3X  plan-3  N   0.020
 A3X  plan-3  C4  0.020
 A3X  plan-3  C8  0.020
 A3X  plan-3  N1  0.020
 A3X  plan-3  C6  0.020

