# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 09:56:36 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 2-(5-chloranylpyridin-2-yl)sulfanylethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCSc1ccc(Cl)cn1
#
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
 YPN  YPN  2-(5-chloranylpyridin-2-yl)sulfanylethanol  ligand  19  11  .  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_YPN
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
 YPN  C1    C   CR16  0  -0.075   2.1933  -1.2068   0.0417
 YPN  C2    C   CR16  0  -0.279   0.8711  -1.5941   0.0621
 YPN  C3    C   CR6   0   0.100  -0.1134  -0.6024   0.0626
 YPN  N4    N   N     0  -0.409   0.1726   0.6867   0.0466
 YPN  C5    C   CR16  0  -0.012   1.4452   1.0610   0.0265
 YPN  C6    C   CR6   0  -0.120   2.4861   0.1512   0.0224
 YPN  CL7   CL  CL    0  -0.109   4.1197   0.7016  -0.0050
 YPN  S8    S   S2    0   0.049  -1.7918  -1.1194   0.0847
 YPN  C9    C   CH2   0  -0.561  -2.6780   0.4605   0.0759
 YPN  C10   C   CH2   0  -0.128  -4.1634   0.1572  -0.0017
 YPN  O11   O   OH1   0  -0.650  -4.8416   1.3905   0.0238
 YPN  H1    H   HCR6  0   0.274   2.9821  -1.9457   0.0414
 YPN  H2    H   HCR6  0   0.265   0.6075  -2.6428   0.0788
 YPN  H5    H   HCR6  0   0.266   1.6428   2.1263   0.0120
 YPN  H91C  H   HCH2  0   0.274  -2.4420   1.0141   0.9846
 YPN  H92C  H   HCH2  0   0.276  -2.3602   1.0491  -0.7837
 YPN  H101  H   HCH2  0   0.202  -4.3754  -0.4009  -0.9216
 YPN  H102  H   HCH2  0   0.201  -4.4586  -0.4832   0.8391
 YPN  H11   H   HOH1  0   0.435  -5.7731   1.2150  -0.1261

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
 YPN  C1   C2    aromatic  1.378  0.020  1.378
 YPN  C1   C6    aromatic  1.389  0.020  1.389
 YPN  C2   C3    aromatic  1.397  0.020  1.397
 YPN  C3   N4    aromatic  1.320  0.020  1.320
 YPN  C3   S8    single    1.756  0.020  1.756
 YPN  N4   C5    aromatic  1.327  0.020  1.327
 YPN  C5   C6    aromatic  1.382  0.020  1.382
 YPN  C6   CL7   single    1.724  0.020  1.724
 YPN  S8   C9    single    1.812  0.020  1.812
 YPN  C9   C10   single    1.518  0.020  1.518
 YPN  C10  O11   single    1.408  0.020  1.408
 YPN  C1   H1    single    0.930  0.020  1.080
 YPN  C2   H2    single    0.930  0.020  1.080
 YPN  C5   H5    single    0.930  0.020  1.080
 YPN  C9   H91C  single    0.970  0.020  1.090
 YPN  C9   H92C  single    0.970  0.020  1.090
 YPN  C10  H101  single    0.970  0.020  1.090
 YPN  C10  H102  single    0.970  0.020  1.090
 YPN  O11  H11   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
 YPN  H1    C1   C6    120.96  3.000
 YPN  H1    C1   C2    120.54  3.000
 YPN  C6    C1   C2    118.50  3.000
 YPN  H2    C2   C3    121.10  3.000
 YPN  H2    C2   C1    120.44  3.000
 YPN  C3    C2   C1    118.46  3.000
 YPN  S8    C3   N4    119.64  3.000
 YPN  S8    C3   C2    117.67  3.000
 YPN  N4    C3   C2    122.70  3.000
 YPN  C5    N4   C3    118.91  3.000
 YPN  H5    C5   C6    120.65  3.000
 YPN  H5    C5   N4    116.90  3.000
 YPN  C6    C5   N4    122.45  3.000
 YPN  CL7   C6   C5    120.23  3.000
 YPN  CL7   C6   C1    120.79  3.000
 YPN  C5    C6   C1    118.98  3.000
 YPN  C9    S8   C3    102.16  3.000
 YPN  H92C  C9   H91C  108.68  3.000
 YPN  H92C  C9   C10   110.68  3.000
 YPN  H91C  C9   C10   110.86  3.000
 YPN  H92C  C9   S8    109.41  3.000
 YPN  H91C  C9   S8    109.45  3.000
 YPN  C10   C9   S8    107.74  3.000
 YPN  H102  C10  H101  107.08  3.000
 YPN  H102  C10  O11   111.58  3.000
 YPN  H101  C10  O11   111.59  3.000
 YPN  H102  C10  C9    109.92  3.000
 YPN  H101  C10  C9    109.50  3.000
 YPN  O11   C10  C9    107.18  3.000
 YPN  H11   O11  C10   107.74  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
 YPN  CONST_01  N4   C3   C2  C1    0.00   0.0  0
 YPN  CONST_02  N4   C5   C6  C1    0.00   0.0  0
 YPN  CONST_03  C5   C6   C1  C2    0.00   0.0  0
 YPN  CONST_04  C5   N4   C3  C2    0.00   0.0  0
 YPN  CONST_05  C6   C1   C2  C3    0.00   0.0  0
 YPN  CONST_06  C6   C5   N4  C3    0.00   0.0  0
 YPN  CONST_07  S8   C3   C2  C1  180.00   0.0  0
 YPN  CONST_08  CL7  C6   C1  C2  180.00   0.0  0
 YPN  CONST_09  CL7  C6   C5  N4  180.00   0.0  0
 YPN  CONST_10  S8   C3   N4  C5  180.00   0.0  0
 YPN  CONST_11  H5   C5   C6  C1  180.00   0.0  0
 YPN  CONST_12  H1   C1   C2  C3  180.00   0.0  0
 YPN  CONST_13  H2   C2   C3  N4  180.00   0.0  0
 YPN  Var_01    C10  C9   S8  C3  176.21  30.0  3
 YPN  Var_02    O11  C10  C9  S8  178.65  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
 YPN  plan-1  C1   0.020
 YPN  plan-1  C2   0.020
 YPN  plan-1  C3   0.020
 YPN  plan-1  N4   0.020
 YPN  plan-1  C5   0.020
 YPN  plan-1  C6   0.020
 YPN  plan-1  CL7  0.020
 YPN  plan-1  S8   0.020
 YPN  plan-1  H1   0.020
 YPN  plan-1  H2   0.020
 YPN  plan-1  H5   0.020

