# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 09:27:49 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: ~{N}-(2-phenoxyethyl)methanethioamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S=CNCCOc1ccccc1
#
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
 HYR  HYR  "N-(2-phenoxyethyl)methanethioamide"
  ligand  23  12  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HYR
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
 HYR  C10  C  CR16  0  -0.280  -10.0015  17.8842  72.6221
 HYR  C11  C  CR16  0  -0.240  -11.3272  17.9625  72.2084
 HYR  C12  C  CR16  0  -0.346  -11.7733  17.2222  71.1278
 HYR  C2   C  C1    0  -0.100  -10.8518  17.7019  66.6660
 HYR  C4   C  CH2   0  -0.327   -9.8182  15.6556  67.5730
 HYR  C5   C  CH2   0  -0.221  -10.6243  14.8722  68.5995
 HYR  C7   C  CR6   0   0.399  -10.8959  16.3828  70.4393
 HYR  C8   C  CR16  0  -0.372   -9.5671  16.2988  70.8479
 HYR  C9   C  CR16  0  -0.241   -9.1337  17.0506  71.9352
 HYR  N3   N  NH1   0  -0.490  -10.6653  16.3973  66.6684
 HYR  O6   O  O2    0  -0.475  -11.4360  15.6930  69.4113
 HYR  S13  S  S1    0  -0.364  -10.1480  18.8337  67.6465
 HYR  H1   H  HCR6  0   0.250   -9.6530  18.4655  73.4652
 HYR  H2   H  HCR6  0   0.254  -12.0223  18.6077  72.7306
 HYR  H3   H  HCR6  0   0.259  -12.8058  17.2883  70.8074
 HYR  H4   H  H     0   0.288  -11.5556  18.0106  65.8955
 HYR  H5   H  HCH2  0   0.278   -9.2271  14.9441  66.9937
 HYR  H6   H  HCH2  0   0.267   -9.1281  16.3542  68.0431
 HYR  H7   H  HCH2  0   0.267  -11.3126  14.1981  68.0879
 HYR  H8   H  HCH2  0   0.244   -9.9472  14.2491  69.1913
 HYR  H9   H  HCR6  0   0.273   -8.8534  15.6637  70.3407
 HYR  H10  H  HCR6  0   0.256   -8.0974  16.9777  72.2398
 HYR  H12  H  HNH1  0   0.422  -11.1832  15.8604  65.9872

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
 HYR  S13  C2   double    1.655  0.020  1.655
 HYR  C2   N3   single    1.318  0.020  1.318
 HYR  N3   C4   single    1.444  0.020  1.444
 HYR  C4   C5   single    1.522  0.020  1.522
 HYR  C5   O6   single    1.411  0.020  1.411
 HYR  O6   C7   single    1.351  0.020  1.351
 HYR  C7   C12  aromatic  1.396  0.020  1.396
 HYR  C7   C8   aromatic  1.393  0.020  1.393
 HYR  C12  C11  aromatic  1.384  0.020  1.384
 HYR  C8   C9   aromatic  1.391  0.020  1.391
 HYR  C11  C10  aromatic  1.391  0.020  1.391
 HYR  C9   C10  aromatic  1.386  0.020  1.386
 HYR  C10  H1   single    0.930  0.020  1.080
 HYR  C11  H2   single    0.930  0.020  1.080
 HYR  C12  H3   single    0.930  0.020  1.080
 HYR  C2   H4   single    0.930  0.020  1.080
 HYR  C4   H5   single    0.970  0.020  1.090
 HYR  C4   H6   single    0.970  0.020  1.090
 HYR  C5   H7   single    0.970  0.020  1.090
 HYR  C5   H8   single    0.970  0.020  1.090
 HYR  C8   H9   single    0.930  0.020  1.080
 HYR  C9   H10  single    0.930  0.020  1.080
 HYR  N3   H12  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
 HYR  H1   C10  C9   120.53  3.000
 HYR  H1   C10  C11  120.57  3.000
 HYR  C9   C10  C11  118.91  3.000
 HYR  H2   C11  C12  119.24  3.000
 HYR  H2   C11  C10  120.13  3.000
 HYR  C12  C11  C10  120.62  3.000
 HYR  H3   C12  C7   119.34  3.000
 HYR  H3   C12  C11  120.38  3.000
 HYR  C7   C12  C11  120.28  3.000
 HYR  H4   C2   S13  120.04  3.000
 HYR  H4   C2   N3   111.94  3.000
 HYR  S13  C2   N3   128.01  3.000
 HYR  H6   C4   H5   107.71  3.000
 HYR  H6   C4   N3   108.22  3.000
 HYR  H5   C4   N3   108.66  3.000
 HYR  H6   C4   C5   112.01  3.000
 HYR  H5   C4   C5   108.02  3.000
 HYR  N3   C4   C5   112.09  3.000
 HYR  H8   C5   H7   106.99  3.000
 HYR  H8   C5   O6   112.09  3.000
 HYR  H7   C5   O6   105.45  3.000
 HYR  H8   C5   C4   109.27  3.000
 HYR  H7   C5   C4   109.63  3.000
 HYR  O6   C5   C4   113.16  3.000
 HYR  O6   C7   C8   125.03  3.000
 HYR  C8   C7   C12  119.42  3.000
 HYR  O6   C7   C12  115.54  3.000
 HYR  H9   C8   C9   118.57  3.000
 HYR  H9   C8   C7   121.83  3.000
 HYR  C9   C8   C7   119.60  3.000
 HYR  H10  C9   C8   118.80  3.000
 HYR  H10  C9   C10  120.04  3.000
 HYR  C8   C9   C10  121.16  3.000
 HYR  H12  N3   C4   116.75  3.000
 HYR  H12  N3   C2   116.89  3.000
 HYR  C4   N3   C2   126.34  3.000
 HYR  C7   O6   C5   120.32  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
 HYR  CONST_01  C7   C12  C11  C10     0.00   0.0  0
 HYR  CONST_02  C7   C8   C9   C10     0.00   0.0  0
 HYR  CONST_03  C8   C7   C12  C11     0.00   0.0  0
 HYR  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 HYR  CONST_05  C9   C8   C7   C12     0.00   0.0  0
 HYR  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 HYR  CONST_07  O6   C7   C12  C11   180.00   0.0  0
 HYR  CONST_08  O6   C7   C8   C9    180.00   0.0  0
 HYR  CONST_09  H3   C12  C11  C10   180.00   0.0  0
 HYR  CONST_10  H9   C8   C9   C10   180.00   0.0  0
 HYR  CONST_11  H10  C9   C10  C11   180.00   0.0  0
 HYR  CONST_12  H9   C8   C7   C12   180.00   0.0  0
 HYR  CONST_13  H1   C10  C11  C12   180.00   0.0  0
 HYR  CONST_14  H2   C11  C12  C7    180.00   0.0  0
 HYR  CONST_15  H10  C9   C8   C7    180.00   0.0  0
 HYR  CONST_16  H3   C12  C7   C8    180.00   0.0  0
 HYR  CONST_17  H1   C10  C9   C8    180.00   0.0  0
 HYR  CONST_18  H2   C11  C10  C9    180.00   0.0  0
 HYR  Var_01    C5   O6   C7   C12   176.44  30.0  2
 HYR  Var_02    C8   C7   O6   C5     -4.27  30.0  2
 HYR  Var_03    C7   O6   C5   C4    -78.38  30.0  3
 HYR  Var_04    H7   C5   O6   C7    161.80  30.0  1
 HYR  Var_05    H8   C5   O6   C7     45.74  30.0  1
 HYR  Var_06    C5   C4   N3   C2    106.57  30.0  3
 HYR  Var_07    S13  C2   N3   C4      2.00  30.0  2
 HYR  Var_08    O6   C5   C4   N3    -60.18  30.0  3
 HYR  Var_09    H5   C4   N3   C2   -134.13  30.0  3
 HYR  Var_10    H6   C4   N3   C2    -17.43  30.0  3
 HYR  Var_11    H4   C2   N3   C4   -178.78  30.0  2
 HYR  Var_12    H12  N3   C4   C5    -71.73  30.0  1
 HYR  Var_13    H7   C5   C4   N3     57.21  30.0  3
 HYR  Var_14    H8   C5   C4   N3    174.16  30.0  3
 HYR  Var_15    H5   C4   C5   O6   -179.86  30.0  2
 HYR  Var_16    H6   C4   C5   O6     61.68  30.0  2
 HYR  Var_17    H12  N3   C2   S13  -179.70  30.0  2

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
 HYR  plan-1  C10  0.020
 HYR  plan-1  C11  0.020
 HYR  plan-1  C12  0.020
 HYR  plan-1  C7   0.020
 HYR  plan-1  C8   0.020
 HYR  plan-1  C9   0.020
 HYR  plan-1  O6   0.020
 HYR  plan-1  H1   0.020
 HYR  plan-1  H2   0.020
 HYR  plan-1  H3   0.020
 HYR  plan-1  H9   0.020
 HYR  plan-1  H10  0.020
 HYR  plan-2  C2   0.020
 HYR  plan-2  N3   0.020
 HYR  plan-2  S13  0.020
 HYR  plan-2  H4   0.020

