# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 07:46:52 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 1-[(~{E})-(3,5-dimethoxy-4-oxidanyl-phenyl)methylideneamino]thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(\C=N\NC(N)=S)cc(OC)c1O
#
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
 A5I  A5I  "N-(3,5-dimetoxy-4-hydroxybenzyliden)thiosemicarbazone"
  ligand  30  17  .  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_A5I
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
 A5I  N1   N  NH1   0  -0.463  59.3101  31.6524   -6.8417
 A5I  C7   C  C     0   0.384  60.1159  31.9336   -5.7960
 A5I  C8   C  CH3   0  -0.437  54.7138  32.0941  -12.4159
 A5I  N2   N  NH2   0  -0.768  60.0865  33.1756   -5.3314
 A5I  C9   C  CH3   0  -0.432  56.4847  37.2659   -7.8000
 A5I  C1   C  CR6   0   0.188  55.2678  35.0360  -10.3777
 A5I  C5   C  CR16  0  -0.456  56.8321  34.5708   -8.5883
 A5I  C6   C  C1    0  -0.062  57.8062  32.2864   -8.3838
 A5I  C4   C  CR6   0   0.084  56.9388  33.2548   -9.0393
 A5I  C3   C  CR16  0  -0.468  56.2125  32.8321  -10.1508
 A5I  C2   C  CR6   0   0.339  55.3775  33.7169  -10.8235
 A5I  N    N  N     0  -0.223  58.5307  32.6031   -7.3861
 A5I  C    C  CR6   0   0.340  56.0002  35.4517   -9.2573
 A5I  O    O  O2    0  -0.465  54.6384  33.4092  -11.9055
 A5I  O2   O  O2    0  -0.489  55.8091  36.7457   -8.9277
 A5I  S    S  S1    0  -0.439  61.0932  30.7269   -5.1514
 A5I  H3   H  HNH1  0   0.412  59.3222  30.7074   -7.2097
 A5I  H8   H  HCH3  0   0.260  54.0521  32.0597  -13.2779
 A5I  H6   H  HCH3  0   0.228  55.7261  31.8383  -12.7401
 A5I  H7   H  HCH3  0   0.228  54.3798  31.3512  -11.6865
 A5I  H4   H  HNH2  0   0.416  60.6727  33.4268   -4.5551
 A5I  H5   H  HNH2  0   0.418  59.4920  33.8784   -5.7426
 A5I  H12  H  HCH3  0   0.263  56.1916  38.3092   -7.7181
 A5I  H10  H  HCH3  0   0.232  56.2000  36.7444   -6.8827
 A5I  H11  H  HCH3  0   0.232  57.5697  37.2108   -7.9170
 A5I  H9   H  HOH1  0   0.472  54.4756  36.7464  -10.6383
 A5I  H1   H  HCR6  0   0.284  57.3997  34.8875   -7.7242
 A5I  H2   H  H     0   0.253  57.8092  31.2745   -8.7951
 A5I  H    H  HCR6  0   0.283  56.3115  31.8066  -10.4821
 A5I  O1   O  OH1   0  -0.613  54.4538  35.8719  -11.0470

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
 A5I  C8  O    single    1.413  0.020  1.413
 A5I  O   C2   single    1.346  0.020  1.346
 A5I  O1  C1   single    1.345  0.020  1.345
 A5I  C2  C1   aromatic  1.397  0.020  1.397
 A5I  C2  C3   aromatic  1.390  0.020  1.390
 A5I  C1  C    aromatic  1.402  0.020  1.402
 A5I  C3  C4   aromatic  1.393  0.020  1.393
 A5I  C   O2   single    1.349  0.020  1.349
 A5I  C   C5   aromatic  1.384  0.020  1.384
 A5I  C4  C5   aromatic  1.395  0.020  1.395
 A5I  C4  C6   single    1.456  0.020  1.456
 A5I  O2  C9   single    1.414  0.020  1.414
 A5I  C6  N    double    1.273  0.020  1.273
 A5I  N   N1   single    1.344  0.020  1.344
 A5I  N1  C7   single    1.350  0.020  1.350
 A5I  N2  C7   single    1.326  0.020  1.326
 A5I  C7  S    double    1.681  0.020  1.681
 A5I  N1  H3   single    0.860  0.020  1.020
 A5I  C8  H8   single    0.970  0.020  1.090
 A5I  C8  H6   single    0.970  0.020  1.090
 A5I  C8  H7   single    0.970  0.020  1.090
 A5I  N2  H4   single    0.860  0.020  1.020
 A5I  N2  H5   single    0.860  0.020  1.020
 A5I  C9  H12  single    0.970  0.020  1.090
 A5I  C9  H10  single    0.970  0.020  1.090
 A5I  C9  H11  single    0.970  0.020  1.090
 A5I  O1  H9   single    0.850  0.020  0.980
 A5I  C5  H1   single    0.930  0.020  1.080
 A5I  C6  H2   single    0.930  0.020  1.080
 A5I  C3  H    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
 A5I  H3   N1  N    121.26  3.000
 A5I  H3   N1  C7   117.91  3.000
 A5I  N    N1  C7   120.83  3.000
 A5I  S    C7  N2   123.41  3.000
 A5I  S    C7  N1   119.64  3.000
 A5I  N2   C7  N1   116.95  3.000
 A5I  H7   C8  H6   108.77  3.000
 A5I  H7   C8  H8   108.75  3.000
 A5I  H6   C8  H8   108.72  3.000
 A5I  H7   C8  O    112.03  3.000
 A5I  H6   C8  O    111.99  3.000
 A5I  H8   C8  O    106.46  3.000
 A5I  H5   N2  H4   119.01  3.000
 A5I  H5   N2  C7   121.53  3.000
 A5I  H4   N2  C7   119.46  3.000
 A5I  H11  C9  H10  108.94  3.000
 A5I  H11  C9  H12  108.92  3.000
 A5I  H10  C9  H12  108.94  3.000
 A5I  H11  C9  O2   111.75  3.000
 A5I  H10  C9  O2   111.68  3.000
 A5I  H12  C9  O2   106.52  3.000
 A5I  C    C1  C2   119.62  3.000
 A5I  C    C1  O1   121.98  3.000
 A5I  C2   C1  O1   118.40  3.000
 A5I  H1   C5  C    121.02  3.000
 A5I  H1   C5  C4   119.63  3.000
 A5I  C    C5  C4   119.34  3.000
 A5I  H2   C6  N    121.60  3.000
 A5I  H2   C6  C4   116.63  3.000
 A5I  N    C6  C4   121.76  3.000
 A5I  C3   C4  C6   117.90  3.000
 A5I  C6   C4  C5   121.83  3.000
 A5I  C3   C4  C5   120.27  3.000
 A5I  H    C3  C2   120.66  3.000
 A5I  H    C3  C4   118.95  3.000
 A5I  C2   C3  C4   120.40  3.000
 A5I  O    C2  C3   124.98  3.000
 A5I  C3   C2  C1   119.59  3.000
 A5I  O    C2  C1   115.43  3.000
 A5I  C6   N   N1   118.12  3.000
 A5I  O2   C   C5   125.28  3.000
 A5I  C5   C   C1   120.78  3.000
 A5I  O2   C   C1   113.94  3.000
 A5I  C2   O   C8   118.29  3.000
 A5I  C    O2  C9   118.69  3.000
 A5I  H9   O1  C1   109.79  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
 A5I  CONST_01  C4   C3  C2  C1     0.00   0.0  0
 A5I  CONST_02  C4   C5  C   C1     0.00   0.0  0
 A5I  CONST_03  C2   C1  C   C5     0.00   0.0  0
 A5I  CONST_04  C2   C3  C4  C5     0.00   0.0  0
 A5I  CONST_05  C    C1  C2  C3     0.00   0.0  0
 A5I  CONST_06  C    C5  C4  C3     0.00   0.0  0
 A5I  CONST_07  C3   C2  C1  O1   180.00   0.0  0
 A5I  CONST_08  C5   C   C1  O1   180.00   0.0  0
 A5I  CONST_09  C2   C3  C4  C6   180.00   0.0  0
 A5I  CONST_10  C    C5  C4  C6   180.00   0.0  0
 A5I  CONST_11  O    C2  C3  C4   180.00   0.0  0
 A5I  CONST_12  O2   C   C5  C4   180.00   0.0  0
 A5I  CONST_13  O2   C   C1  C2   180.00   0.0  0
 A5I  CONST_14  O    C2  C1  C    180.00   0.0  0
 A5I  CONST_15  H    C3  C2  C1   180.00   0.0  0
 A5I  CONST_16  H1   C5  C   C1   180.00   0.0  0
 A5I  CONST_17  H    C3  C4  C5   180.00   0.0  0
 A5I  CONST_18  H1   C5  C4  C3   180.00   0.0  0
 A5I  CONST_19  N    N1  C7  N2     0.00   0.0  0
 A5I  CONST_20  S    C7  N1  N    180.00   0.0  0
 A5I  CONST_21  H4   N2  C7  N1   180.00   0.0  0
 A5I  CONST_22  H5   N2  C7  N1     0.00   0.0  0
 A5I  CONST_23  H3   N1  C7  N2   180.00   0.0  0
 A5I  CONST_24  H3   N1  C7  S      0.00   0.0  0
 A5I  CONST_25  H4   N2  C7  S      0.00   0.0  0
 A5I  CONST_26  H5   N2  C7  S    180.00   0.0  0
 A5I  Var_01    C1   C2  O   C8   179.39  30.0  2
 A5I  Var_02    C3   C2  O   C8    -0.56  30.0  2
 A5I  Var_03    C1   C   O2  C9   179.08  30.0  2
 A5I  Var_04    C5   C   O2  C9    -1.03  30.0  2
 A5I  Var_05    N    C6  C4  C5    -1.58  30.0  2
 A5I  Var_06    N    C6  C4  C3   178.00  30.0  2
 A5I  Var_07    H2   C6  C4  C5   178.78  30.0  2
 A5I  Var_08    H2   C6  C4  C3    -1.63  30.0  2
 A5I  Var_09    C4   C6  N   N1  -179.63   0.0  2
 A5I  Var_10    H8   C8  O   C2  -179.85  30.0  3
 A5I  Var_11    H6   C8  O   C2   -61.15  30.0  3
 A5I  Var_12    H7   C8  O   C2    61.38  30.0  3
 A5I  Var_13    H12  C9  O2  C    180.00  30.0  3
 A5I  Var_14    H10  C9  O2  C    -61.16  30.0  3
 A5I  Var_15    H11  C9  O2  C     61.16  30.0  3
 A5I  Var_16    C6   N   N1  C7   178.93  30.0  2
 A5I  Var_17    H2   C6  N   N1    -0.02   0.0  2
 A5I  Var_18    H3   N1  N   C6    -0.18  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
 A5I  plan-1  C1  0.020
 A5I  plan-1  C5  0.020
 A5I  plan-1  C6  0.020
 A5I  plan-1  C4  0.020
 A5I  plan-1  C3  0.020
 A5I  plan-1  C2  0.020
 A5I  plan-1  C   0.020
 A5I  plan-1  O   0.020
 A5I  plan-1  O2  0.020
 A5I  plan-1  H1  0.020
 A5I  plan-1  H   0.020
 A5I  plan-1  O1  0.020
 A5I  plan-2  N1  0.020
 A5I  plan-2  C7  0.020
 A5I  plan-2  N2  0.020
 A5I  plan-2  N   0.020
 A5I  plan-2  S   0.020
 A5I  plan-2  H3  0.020
 A5I  plan-2  H4  0.020
 A5I  plan-2  H5  0.020
 A5I  plan-3  N1  0.020
 A5I  plan-3  C6  0.020
 A5I  plan-3  C4  0.020
 A5I  plan-3  N   0.020
 A5I  plan-3  H2  0.020

