# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 19:13:51 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: N-(pyridin-3-ylmethyl)thioformamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S=CNCc1cccnc1
#
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
 35J  35J  N-(pyridin-3-ylmethyl)thioformamide  ligand  18  10  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_35J
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
 35J  CAJ  C  C1    0  -0.101  -2.4991  -0.5471  -0.7935
 35J  SAB  S  S1    0  -0.362  -3.4172  -1.0380   0.4918
 35J  NAI  N  NH1   0  -0.497  -1.3296   0.0590  -0.7563
 35J  CAG  C  CH2   0  -0.346  -0.6042   0.4211   0.4437
 35J  CAK  C  CR6   0  -0.007   0.8692   0.1973   0.2676
 35J  CAE  C  CR16  0  -0.165   1.3850  -1.0660  -0.0038
 35J  CAC  C  CR16  0  -0.317   2.7531  -1.2172  -0.1466
 35J  CAD  C  CR16  0  -0.065   3.5614  -0.0962  -0.0114
 35J  NAH  N  N     0  -0.399   3.0849   1.1148   0.2460
 35J  CAF  C  CR16  0  -0.096   1.7705   1.2486   0.3776
 35J  H1   H  H     0   0.294  -2.8421  -0.7135  -1.8119
 35J  H3   H  HCH2  0   0.279  -0.8041   1.4652   0.6971
 35J  H4   H  HCH2  0   0.279  -0.9932  -0.1871   1.2615
 35J  H5   H  HCR6  0   0.275   0.7254  -1.9203  -0.0987
 35J  H6   H  HCR6  0   0.275   3.1909  -2.1832  -0.3570
 35J  H7   H  HCR6  0   0.267   4.6371  -0.1835  -0.1165
 35J  H8   H  HCR6  0   0.263   1.4056   2.2502   0.5844
 35J  H2   H  HNH1  0   0.424  -0.9180   0.3242  -1.6395

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
 35J  CAJ  SAB  double    1.654  0.020  1.654
 35J  CAJ  NAI  single    1.318  0.020  1.318
 35J  NAI  CAG  single    1.448  0.020  1.448
 35J  CAG  CAK  single    1.501  0.020  1.501
 35J  CAE  CAK  aromatic  1.391  0.020  1.391
 35J  CAE  CAC  aromatic  1.384  0.020  1.384
 35J  CAK  CAF  aromatic  1.389  0.020  1.389
 35J  CAC  CAD  aromatic  1.389  0.020  1.389
 35J  CAF  NAH  aromatic  1.328  0.020  1.328
 35J  CAD  NAH  aromatic  1.326  0.020  1.326
 35J  CAJ  H1   single    0.930  0.020  1.080
 35J  CAG  H3   single    0.970  0.020  1.090
 35J  CAG  H4   single    0.970  0.020  1.090
 35J  CAE  H5   single    0.930  0.020  1.080
 35J  CAC  H6   single    0.930  0.020  1.080
 35J  CAD  H7   single    0.930  0.020  1.080
 35J  CAF  H8   single    0.930  0.020  1.080
 35J  NAI  H2   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
 35J  H1   CAJ  NAI  112.13  3.000
 35J  H1   CAJ  SAB  120.48  3.000
 35J  NAI  CAJ  SAB  127.39  3.000
 35J  H2   NAI  CAG  117.06  3.000
 35J  H2   NAI  CAJ  117.25  3.000
 35J  CAG  NAI  CAJ  125.65  3.000
 35J  H4   CAG  H3   107.07  3.000
 35J  H4   CAG  CAK  110.80  3.000
 35J  H3   CAG  CAK  110.45  3.000
 35J  H4   CAG  NAI  107.65  3.000
 35J  H3   CAG  NAI  109.84  3.000
 35J  CAK  CAG  NAI  110.93  3.000
 35J  CAF  CAK  CAE  117.52  3.000
 35J  CAF  CAK  CAG  120.99  3.000
 35J  CAE  CAK  CAG  121.49  3.000
 35J  H5   CAE  CAC  120.45  3.000
 35J  H5   CAE  CAK  120.48  3.000
 35J  CAC  CAE  CAK  119.07  3.000
 35J  H6   CAC  CAD  120.30  3.000
 35J  H6   CAC  CAE  121.20  3.000
 35J  CAD  CAC  CAE  118.50  3.000
 35J  H7   CAD  NAH  116.66  3.000
 35J  H7   CAD  CAC  120.20  3.000
 35J  NAH  CAD  CAC  123.15  3.000
 35J  CAF  NAH  CAD  117.83  3.000
 35J  H8   CAF  NAH  116.39  3.000
 35J  H8   CAF  CAK  119.68  3.000
 35J  NAH  CAF  CAK  123.93  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
 35J  CONST_01  CAD  CAC  CAE  CAK    0.00   0.0  0
 35J  CONST_02  CAD  NAH  CAF  CAK    0.00   0.0  0
 35J  CONST_03  NAH  CAF  CAK  CAE    0.00   0.0  0
 35J  CONST_04  NAH  CAD  CAC  CAE    0.00   0.0  0
 35J  CONST_05  CAF  CAK  CAE  CAC    0.00   0.0  0
 35J  CONST_06  CAF  NAH  CAD  CAC    0.00   0.0  0
 35J  CONST_07  CAC  CAE  CAK  CAG  180.00   0.0  0
 35J  CONST_08  NAH  CAF  CAK  CAG  180.00   0.0  0
 35J  CONST_09  H6   CAC  CAE  CAK  180.00   0.0  0
 35J  CONST_10  H8   CAF  CAK  CAE  180.00   0.0  0
 35J  CONST_11  H7   CAD  CAC  CAE  180.00   0.0  0
 35J  CONST_12  H5   CAE  CAC  CAD  180.00   0.0  0
 35J  Var_01    CAE  CAK  CAG  NAI  -60.72  30.0  2
 35J  Var_02    CAK  CAG  NAI  CAJ  141.17  30.0  3
 35J  Var_03    CAG  NAI  CAJ  SAB    0.02  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
 35J  plan-1  CAG  0.020
 35J  plan-1  CAK  0.020
 35J  plan-1  CAE  0.020
 35J  plan-1  CAC  0.020
 35J  plan-1  CAD  0.020
 35J  plan-1  NAH  0.020
 35J  plan-1  CAF  0.020
 35J  plan-1  H5   0.020
 35J  plan-1  H6   0.020
 35J  plan-1  H7   0.020
 35J  plan-1  H8   0.020
 35J  plan-2  CAJ  0.020
 35J  plan-2  SAB  0.020
 35J  plan-2  NAI  0.020
 35J  plan-2  H1   0.020

