# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 09:42:01 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: 1-[(~{E})-[2,5-bis(oxidanyl)phenyl]methylideneamino]-3-ethyl-thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=S)N/N=C/c1cc(O)ccc1O
#
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
 A7L  A7L  "N-(2,5-dihydroxybenzylidene)-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_A7L
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
 A7L  C1   C  CR6   0   0.366  56.5923  34.0650  -10.6162
 A7L  C2   C  CR16  0  -0.428  57.2943  33.4147   -9.6206
 A7L  C3   C  CR6   0  -0.038  57.0723  32.0599   -9.3326
 A7L  C4   C  CR6   0   0.285  56.1282  31.3513  -10.0862
 A7L  C5   C  CR16  0  -0.317  55.4204  32.0184  -11.0861
 A7L  C6   C  C1    0  -0.066  57.8123  31.4175   -8.2511
 A7L  C7   C  C     0   0.424  60.4635  31.9793   -6.0414
 A7L  C9   C  CH3   0  -0.656  63.2065  33.6713   -6.6512
 A7L  N    N  N     0  -0.212  58.7850  32.0113   -7.6823
 A7L  C    C  CR16  0  -0.323  55.6405  33.3536  -11.3505
 A7L  O    O  OH1   0  -0.624  55.8263  30.0439   -9.9143
 A7L  C8   C  CH2   0  -0.287  61.9017  33.9726   -5.9319
 A7L  N1   N  NH1   0  -0.481  59.4205  31.3898   -6.6805
 A7L  N2   N  NH1   0  -0.598  60.7872  33.2011   -6.4416
 A7L  O1   O  OH1   0  -0.636  56.7717  35.3697  -10.9193
 A7L  S    S  S1    0  -0.430  61.2303  31.1316   -4.8091
 A7L  H1   H  HCR6  0   0.278  58.0253  33.9572   -9.0317
 A7L  H2   H  HCR6  0   0.269  54.6894  31.4691  -11.6659
 A7L  H4   H  H     0   0.246  57.5084  30.4246   -7.9149
 A7L  H9   H  HCH3  0   0.232  64.0082  34.2909   -6.2488
 A7L  H10  H  HCH3  0   0.228  63.4899  32.6268   -6.5233
 A7L  H11  H  HCH3  0   0.228  63.1246  33.8785   -7.7182
 A7L  H    H  HCR6  0   0.269  55.0783  33.8495  -12.1319
 A7L  H3   H  HOH1  0   0.475  56.4974  29.5702   -9.4144
 A7L  H7   H  HCH2  0   0.244  61.9988  33.7783   -4.8648
 A7L  H8   H  HCH2  0   0.253  61.6382  35.0233   -6.0491
 A7L  H5   H  HNH1  0   0.411  59.1535  30.4581   -6.3809
 A7L  H6   H  HNH1  0   0.415  60.2665  33.5836   -7.2190
 A7L  H12  H  HOH1  0   0.471  57.4538  35.7537  -10.3574

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
 A7L  C   C5   aromatic  1.379  0.020  1.379
 A7L  C   C1   aromatic  1.397  0.020  1.397
 A7L  C5  C4   aromatic  1.395  0.020  1.395
 A7L  O1  C1   single    1.351  0.020  1.351
 A7L  C1  C2   aromatic  1.381  0.020  1.381
 A7L  C4  O    single    1.353  0.020  1.353
 A7L  C4  C3   aromatic  1.400  0.020  1.400
 A7L  C2  C3   aromatic  1.403  0.020  1.403
 A7L  C3  C6   single    1.459  0.020  1.459
 A7L  C6  N    double    1.274  0.020  1.274
 A7L  N   N1   single    1.339  0.020  1.339
 A7L  C9  C8   single    1.520  0.020  1.520
 A7L  N2  C8   single    1.448  0.020  1.448
 A7L  N2  C7   single    1.326  0.020  1.326
 A7L  N1  C7   single    1.358  0.020  1.358
 A7L  C7  S    double    1.681  0.020  1.681
 A7L  C2  H1   single    0.930  0.020  1.080
 A7L  C5  H2   single    0.930  0.020  1.080
 A7L  C6  H4   single    0.930  0.020  1.080
 A7L  C9  H9   single    0.970  0.020  1.090
 A7L  C9  H10  single    0.970  0.020  1.090
 A7L  C9  H11  single    0.970  0.020  1.090
 A7L  C   H    single    0.930  0.020  1.080
 A7L  O   H3   single    0.850  0.020  0.980
 A7L  C8  H7   single    0.970  0.020  1.090
 A7L  C8  H8   single    0.970  0.020  1.090
 A7L  N1  H5   single    0.860  0.020  1.020
 A7L  N2  H6   single    0.860  0.020  1.020
 A7L  O1  H12  single    0.850  0.020  0.980

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
 A7L  O1   C1  C    117.66  3.000
 A7L  O1   C1  C2   123.29  3.000
 A7L  C    C1  C2   119.05  3.000
 A7L  H1   C2  C3   118.58  3.000
 A7L  H1   C2  C1   119.92  3.000
 A7L  C3   C2  C1   121.49  3.000
 A7L  C6   C3  C4   121.19  3.000
 A7L  C6   C3  C2   119.80  3.000
 A7L  C4   C3  C2   119.01  3.000
 A7L  O    C4  C5   116.11  3.000
 A7L  O    C4  C3   124.83  3.000
 A7L  C5   C4  C3   119.06  3.000
 A7L  H2   C5  C    119.77  3.000
 A7L  H2   C5  C4   118.93  3.000
 A7L  C    C5  C4   121.30  3.000
 A7L  H4   C6  N    119.94  3.000
 A7L  H4   C6  C3   119.18  3.000
 A7L  N    C6  C3   120.87  3.000
 A7L  S    C7  N2   125.08  3.000
 A7L  S    C7  N1   118.46  3.000
 A7L  N2   C7  N1   116.46  3.000
 A7L  H11  C9  H10  108.46  3.000
 A7L  H11  C9  H9   107.97  3.000
 A7L  H10  C9  H9   108.07  3.000
 A7L  H11  C9  C8   111.16  3.000
 A7L  H10  C9  C8   110.95  3.000
 A7L  H9   C9  C8   110.11  3.000
 A7L  N1   N   C6   118.70  3.000
 A7L  H    C   C5   119.93  3.000
 A7L  H    C   C1   119.99  3.000
 A7L  C5   C   C1   120.08  3.000
 A7L  H3   O   C4   112.73  3.000
 A7L  H8   C8  H7   107.40  3.000
 A7L  H8   C8  N2   106.84  3.000
 A7L  H7   C8  N2   108.57  3.000
 A7L  H8   C8  C9   110.36  3.000
 A7L  H7   C8  C9   110.60  3.000
 A7L  N2   C8  C9   112.86  3.000
 A7L  H5   N1  N    121.48  3.000
 A7L  H5   N1  C7   117.50  3.000
 A7L  N    N1  C7   121.00  3.000
 A7L  H6   N2  C8   117.74  3.000
 A7L  H6   N2  C7   117.07  3.000
 A7L  C8   N2  C7   124.94  3.000
 A7L  H12  O1  C1   110.36  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
 A7L  CONST_01  C4   C5  C   C1     0.00   0.0  0
 A7L  CONST_02  C4   C3  C2  C1     0.00   0.0  0
 A7L  CONST_03  C5   C   C1  C2     0.00   0.0  0
 A7L  CONST_04  C5   C4  C3  C2     0.00   0.0  0
 A7L  CONST_05  C    C5  C4  C3     0.00   0.0  0
 A7L  CONST_06  C    C1  C2  C3     0.00   0.0  0
 A7L  CONST_07  C6   C3  C2  C1   180.00   0.0  0
 A7L  CONST_08  O    C4  C3  C2   180.00   0.0  0
 A7L  CONST_09  O1   C1  C2  C3   180.00   0.0  0
 A7L  CONST_10  O1   C1  C   C5   180.00   0.0  0
 A7L  CONST_11  C6   C3  C4  C5   180.00   0.0  0
 A7L  CONST_12  O    C4  C5  C    180.00   0.0  0
 A7L  CONST_13  H2   C5  C   C1   180.00   0.0  0
 A7L  CONST_14  H    C   C1  C2   180.00   0.0  0
 A7L  CONST_15  H2   C5  C4  C3   180.00   0.0  0
 A7L  CONST_16  H    C   C5  C4   180.00   0.0  0
 A7L  CONST_17  H1   C2  C3  C4   180.00   0.0  0
 A7L  CONST_18  H1   C2  C1  C    180.00   0.0  0
 A7L  CONST_19  N2   C7  N1  N      0.00   0.0  0
 A7L  CONST_20  S    C7  N1  N    180.00   0.0  0
 A7L  CONST_21  N1   C7  N2  C8   180.00   0.0  0
 A7L  CONST_22  S    C7  N2  C8     0.00   0.0  0
 A7L  CONST_23  H6   N2  C7  N1     0.00   0.0  0
 A7L  CONST_24  H5   N1  C7  N2   180.00   0.0  0
 A7L  CONST_25  H6   N2  C7  S    180.00   0.0  0
 A7L  CONST_26  H5   N1  C7  S      0.00   0.0  0
 A7L  Var_01    N    C6  C3  C2    -9.63  30.0  2
 A7L  Var_02    N    C6  C3  C4   171.03  30.0  2
 A7L  Var_03    H4   C6  C3  C2   168.96  30.0  2
 A7L  Var_04    H4   C6  C3  C4   -10.37  30.0  2
 A7L  Var_05    N1   N   C6  C3   178.98   0.0  2
 A7L  Var_06    C7   N1  N   C6   179.99  30.0  3
 A7L  Var_07    C9   C8  N2  C7    86.01  30.0  3
 A7L  Var_08    H4   C6  N   N1     0.39   0.0  2
 A7L  Var_09    H5   N1  N   C6     1.05  30.0  3
 A7L  Var_10    H7   C8  N2  C7   -36.98  30.0  3
 A7L  Var_11    H8   C8  N2  C7  -152.53  30.0  3
 A7L  Var_12    H6   N2  C8  C9   -88.06  30.0  2
 A7L  Var_13    H9   C9  C8  N2   178.71  30.0  3
 A7L  Var_14    H10  C9  C8  N2   -61.69  30.0  3
 A7L  Var_15    H11  C9  C8  N2    59.09  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
 A7L  plan-1  C1  0.020
 A7L  plan-1  C2  0.020
 A7L  plan-1  C3  0.020
 A7L  plan-1  C4  0.020
 A7L  plan-1  C5  0.020
 A7L  plan-1  C6  0.020
 A7L  plan-1  C   0.020
 A7L  plan-1  O   0.020
 A7L  plan-1  O1  0.020
 A7L  plan-1  H1  0.020
 A7L  plan-1  H2  0.020
 A7L  plan-1  H   0.020
 A7L  plan-2  C7  0.020
 A7L  plan-2  N   0.020
 A7L  plan-2  C8  0.020
 A7L  plan-2  N1  0.020
 A7L  plan-2  N2  0.020
 A7L  plan-2  S   0.020
 A7L  plan-2  H5  0.020
 A7L  plan-2  H6  0.020
 A7L  plan-3  C3  0.020
 A7L  plan-3  C6  0.020
 A7L  plan-3  N   0.020
 A7L  plan-3  N1  0.020
 A7L  plan-3  H4  0.020

