# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 11:55:00 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 1-pyridin-4-ylthiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=S)Nc1ccncc1
#
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
 YS6  YS6  '1-pyridin-4-ylthiourea   '  ligand  17  10  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YS6
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
 YS6  S     S  S1    0  -0.395   2.2261  -1.3997   0.0180
 YS6  C5    C  C     0   0.377   2.0344   0.2575  -0.1444
 YS6  N2    N  NH2   0  -0.772   3.0940   1.0621  -0.2109
 YS6  N1    N  NH1   0  -0.725   0.8439   0.9111  -0.1938
 YS6  C4    C  CR6   0   0.466  -0.4600   0.4311  -0.1559
 YS6  C     C  CR16  0  -0.409  -1.4452   1.3043   0.3092
 YS6  C3    C  CR16  0  -0.347  -0.8718  -0.8247  -0.5966
 YS6  C2    C  CR16  0  -0.073  -2.2210  -1.1341  -0.5255
 YS6  N     N  N     0  -0.415  -3.1629  -0.3152  -0.0733
 YS6  C1    C  CR16  0  -0.063  -2.7621   0.8867   0.3281
 YS6  H21N  H  HNH2  0   0.421   4.0156   0.6653  -0.1518
 YS6  H22N  H  HNH2  0   0.416   3.0232   2.0654  -0.2819
 YS6  H1    H  HNH1  0   0.419   0.9014   1.9191  -0.1428
 YS6  H     H  HCR6  0   0.285  -1.1891   2.2959   0.6602
 YS6  H3    H  HCR6  0   0.283  -0.1751  -1.5467  -0.9894
 YS6  HA    H  HCR6  0   0.267  -3.5291   1.5612   0.6920
 YS6  H2    H  HCR6  0   0.265  -2.5511  -2.1090  -0.8668

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
 YS6  S   C5    double    1.676  0.020  1.676
 YS6  C5  N2    single    1.332  0.020  1.332
 YS6  C5  N1    single    1.359  0.020  1.359
 YS6  N1  C4    single    1.390  0.020  1.390
 YS6  C4  C     aromatic  1.396  0.020  1.396
 YS6  C4  C3    aromatic  1.393  0.020  1.393
 YS6  C   C1    aromatic  1.382  0.020  1.382
 YS6  C3  C2    aromatic  1.386  0.020  1.386
 YS6  C2  N     aromatic  1.328  0.020  1.328
 YS6  N   C1    aromatic  1.329  0.020  1.329
 YS6  N2  H21N  single    0.860  0.020  1.020
 YS6  N2  H22N  single    0.860  0.020  1.020
 YS6  N1  H1    single    0.860  0.020  1.020
 YS6  C   H     single    0.930  0.020  1.080
 YS6  C3  H3    single    0.930  0.020  1.080
 YS6  C1  HA    single    0.930  0.020  1.080
 YS6  C2  H2    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
 YS6  N1    C5  N2    113.86  3.000
 YS6  N1    C5  S     125.39  3.000
 YS6  N2    C5  S     120.73  3.000
 YS6  H22N  N2  H21N  117.47  3.000
 YS6  H22N  N2  C5    123.28  3.000
 YS6  H21N  N2  C5    119.21  3.000
 YS6  H1    N1  C4    113.34  3.000
 YS6  H1    N1  C5    115.34  3.000
 YS6  C4    N1  C5    130.90  3.000
 YS6  C3    C4  C     117.42  3.000
 YS6  C3    C4  N1    125.44  3.000
 YS6  C     C4  N1    117.07  3.000
 YS6  H     C   C1    119.86  3.000
 YS6  H     C   C4    120.92  3.000
 YS6  C1    C   C4    119.22  3.000
 YS6  H3    C3  C2    119.91  3.000
 YS6  H3    C3  C4    121.89  3.000
 YS6  C2    C3  C4    118.21  3.000
 YS6  H2    C2  N     116.48  3.000
 YS6  H2    C2  C3    118.74  3.000
 YS6  N     C2  C3    124.78  3.000
 YS6  C1    N   C2    116.53  3.000
 YS6  HA    C1  N     116.78  3.000
 YS6  HA    C1  C     119.40  3.000
 YS6  N     C1  C     123.83  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
 YS6  CONST_01  N     C1  C   C4    0.00  0.0  0
 YS6  CONST_02  N     C2  C3  C4    0.00  0.0  0
 YS6  CONST_03  C2    C3  C4  C     0.00  0.0  0
 YS6  CONST_04  C2    N   C1  C     0.00  0.0  0
 YS6  CONST_05  C1    C   C4  C3    0.00  0.0  0
 YS6  CONST_06  C1    N   C2  C3    0.00  0.0  0
 YS6  CONST_07  C1    C   C4  N1  180.00  0.0  0
 YS6  CONST_08  C2    C3  C4  N1  180.00  0.0  0
 YS6  CONST_09  HA    C1  C   C4  180.00  0.0  0
 YS6  CONST_10  H2    C2  C3  C4  180.00  0.0  0
 YS6  CONST_11  H3    C3  C4  C   180.00  0.0  0
 YS6  CONST_12  H     C   C4  C3  180.00  0.0  0
 YS6  CONST_16  C4    N1  C5  S     0.00  0.0  0
 YS6  CONST_17  C4    N1  C5  N2  180.00  0.0  0
 YS6  CONST_18  H21N  N2  C5  S     0.00  0.0  0
 YS6  CONST_19  H22N  N2  C5  S   180.00  0.0  0

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
 YS6  plan-1  N1    0.020
 YS6  plan-1  C4    0.020
 YS6  plan-1  C     0.020
 YS6  plan-1  C3    0.020
 YS6  plan-1  C2    0.020
 YS6  plan-1  N     0.020
 YS6  plan-1  C1    0.020
 YS6  plan-1  H     0.020
 YS6  plan-1  H3    0.020
 YS6  plan-1  HA    0.020
 YS6  plan-1  H2    0.020
 YS6  plan-2  S     0.020
 YS6  plan-2  C5    0.020
 YS6  plan-2  N2    0.020
 YS6  plan-2  N1    0.020
 YS6  plan-2  C4    0.020
 YS6  plan-2  H21N  0.020
 YS6  plan-2  H22N  0.020
 YS6  plan-2  H1    0.020

