# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:55:36 2021
#   Inital geometry file: a 53 line input string
#   Ligand name: 6-methoxypyridine-3-carbothioamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cn1)C(N)=S
#
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
 SN4  SN4  6-methoxypyridine-3-carbothioamide  ligand  19  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SN4
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
 SN4  N1  N  NH2   0  -0.734  52.5366  113.6604  29.5253
 SN4  C4  C  CR6   0  -0.038  51.6561  115.6124  30.5545
 SN4  C5  C  CR16  0  -0.062  50.4943  116.2573  30.9750
 SN4  C6  C  C     0   0.142  51.6145  114.6075  29.4770
 SN4  N   N  N     0  -0.431  50.4617  117.1663  31.9307
 SN4  C   C  CH3   0  -0.443  52.5779  118.9170  34.1588
 SN4  C1  C  CR6   0   0.516  51.5962  117.5116  32.5229
 SN4  C2  C  CR16  0  -0.434  52.8264  116.9412  32.1840
 SN4  C3  C  CR16  0  -0.159  52.8403  115.9796  31.1949
 SN4  S   S  S1    0  -0.362  50.4848  114.6779  28.2523
 SN4  H1  H  HNH2  0   0.417  52.5841  112.9657  28.7971
 SN4  H2  H  HNH2  0   0.425  53.1474  113.5346  30.3170
 SN4  H3  H  HCR6  0   0.272  49.5467  116.0078  30.5115
 SN4  H4  H  HCH3  0   0.269  52.2141  119.6547  34.8686
 SN4  H5  H  HCH3  0   0.239  53.0758  118.1146  34.7068
 SN4  H6  H  HCH3  0   0.240  53.2963  119.3936  33.4887
 SN4  H7  H  HCR6  0   0.296  53.7505  117.2320  32.6619
 SN4  H8  H  HCR6  0   0.282  53.7908  115.5455  30.9109
 SN4  O   O  O2    0  -0.435  51.4388  118.4465  33.4553

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
 SN4  S   C6  double    1.668  0.020  1.668
 SN4  C6  N1  single    1.323  0.020  1.323
 SN4  C6  C4  single    1.474  0.020  1.474
 SN4  C4  C5  aromatic  1.394  0.020  1.394
 SN4  C4  C3  aromatic  1.395  0.020  1.395
 SN4  C5  N   aromatic  1.319  0.020  1.319
 SN4  C3  C2  aromatic  1.380  0.020  1.380
 SN4  N   C1  aromatic  1.325  0.020  1.325
 SN4  C2  C1  aromatic  1.398  0.020  1.398
 SN4  C1  O   single    1.330  0.020  1.330
 SN4  O   C   single    1.419  0.020  1.419
 SN4  N1  H1  single    0.860  0.020  1.020
 SN4  N1  H2  single    0.860  0.020  1.020
 SN4  C5  H3  single    0.930  0.020  1.080
 SN4  C   H4  single    0.970  0.020  1.090
 SN4  C   H5  single    0.970  0.020  1.090
 SN4  C   H6  single    0.970  0.020  1.090
 SN4  C2  H7  single    0.930  0.020  1.080
 SN4  C3  H8  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
 SN4  H2  N1  H1  116.94  3.000
 SN4  H2  N1  C6  122.72  3.000
 SN4  H1  N1  C6  120.01  3.000
 SN4  C3  C4  C6  122.61  3.000
 SN4  C3  C4  C5  116.56  3.000
 SN4  C6  C4  C5  120.83  3.000
 SN4  H3  C5  N   116.53  3.000
 SN4  H3  C5  C4  119.55  3.000
 SN4  N   C5  C4  123.91  3.000
 SN4  S   C6  C4  121.82  3.000
 SN4  C4  C6  N1  116.21  3.000
 SN4  S   C6  N1  121.96  3.000
 SN4  C1  N   C5  118.81  3.000
 SN4  H6  C   H5  109.20  3.000
 SN4  H6  C   H4  108.96  3.000
 SN4  H5  C   H4  108.90  3.000
 SN4  H6  C   O   111.63  3.000
 SN4  H5  C   O   111.79  3.000
 SN4  H4  C   O   106.27  3.000
 SN4  C2  C1  O   124.13  3.000
 SN4  O   C1  N   113.27  3.000
 SN4  C2  C1  N   122.60  3.000
 SN4  H7  C2  C3  119.75  3.000
 SN4  H7  C2  C1  122.40  3.000
 SN4  C3  C2  C1  117.85  3.000
 SN4  H8  C3  C2  118.44  3.000
 SN4  H8  C3  C4  121.27  3.000
 SN4  C2  C3  C4  120.26  3.000
 SN4  C1  O   C   119.06  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
 SN4  CONST_01  C1  N   C5  C4     0.00   0.0  0
 SN4  CONST_02  C1  C2  C3  C4     0.00   0.0  0
 SN4  CONST_03  C2  C3  C4  C5     0.00   0.0  0
 SN4  CONST_04  C2  C1  N   C5     0.00   0.0  0
 SN4  CONST_05  C3  C4  C5  N      0.00   0.0  0
 SN4  CONST_06  C3  C2  C1  N      0.00   0.0  0
 SN4  CONST_07  O   C1  N   C5   180.00   0.0  0
 SN4  CONST_08  N   C5  C4  C6   180.00   0.0  0
 SN4  CONST_09  C2  C3  C4  C6   180.00   0.0  0
 SN4  CONST_10  C3  C2  C1  O    180.00   0.0  0
 SN4  CONST_11  H7  C2  C3  C4   180.00   0.0  0
 SN4  CONST_12  H8  C3  C4  C5   180.00   0.0  0
 SN4  CONST_13  H3  C5  N   C1   180.00   0.0  0
 SN4  Var_01    C5  C4  C6  N1  -151.19  30.0  2
 SN4  Var_02    C2  C1  O   C      0.40  30.0  3
 SN4  Var_03    H1  N1  C6  C4  -177.55  30.0  2
 SN4  Var_04    H4  C   O   C1  -179.23  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
 SN4  plan-1  C4  0.020
 SN4  plan-1  C5  0.020
 SN4  plan-1  C6  0.020
 SN4  plan-1  N   0.020
 SN4  plan-1  C1  0.020
 SN4  plan-1  C2  0.020
 SN4  plan-1  C3  0.020
 SN4  plan-1  H3  0.020
 SN4  plan-1  H7  0.020
 SN4  plan-1  H8  0.020
 SN4  plan-1  O   0.020
 SN4  plan-2  N1  0.020
 SN4  plan-2  C4  0.020
 SN4  plan-2  C6  0.020
 SN4  plan-2  S   0.020

