# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:46:56 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: N-(4-methylpyridin-3-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cnccc1C
#
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
 SZY  SZY  N-(4-methylpyridin-3-yl)acetamide  ligand  21  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SZY
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
 SZY  C10   C  CR6   0   0.158  -1.1977  -0.9654   0.0439
 SZY  C01   C  CH3   0  -0.784   3.5149  -0.5403  -0.1150
 SZY  C02   C  C     0   0.506   2.2005   0.1308   0.1862
 SZY  C05   C  CR6   0   0.211  -0.2080  -0.0217  -0.2437
 SZY  C06   C  CR16  0  -0.085  -0.5687   1.3161  -0.3779
 SZY  C08   C  CR16  0  -0.071  -2.7531   0.8631   0.0468
 SZY  C09   C  CR16  0  -0.369  -2.4967  -0.4909   0.1807
 SZY  C11   C  CH3   0  -0.739  -0.8726  -2.4175   0.1990
 SZY  N04   N  NH1   0  -0.736   1.1220  -0.4366  -0.4155
 SZY  N07   N  N     0  -0.408  -1.8093   1.7556  -0.2277
 SZY  O03   O  O     0  -0.474   2.1168   1.1055   0.9115
 SZY  H012  H  HCH3  0   0.253   3.4223  -1.4269  -0.7391
 SZY  H011  H  HCH3  0   0.273   4.1728   0.1683  -0.6183
 SZY  H013  H  HCH3  0   0.272   3.9974  -0.8237   0.8200
 SZY  H061  H  HCR6  0   0.270   0.1812   2.0575  -0.6255
 SZY  H081  H  HCR6  0   0.264  -3.7634   1.2397   0.1611
 SZY  H091  H  HCR6  0   0.267  -3.3064  -1.1739   0.4027
 SZY  H111  H  HCH3  0   0.259  -0.5477  -2.8597  -0.7455
 SZY  H113  H  HCH3  0   0.259  -0.0677  -2.5696   0.9193
 SZY  H112  H  HCH3  0   0.263  -1.7426  -2.9768   0.5372
 SZY  H041  H  HNH1  0   0.413   1.2741  -1.2844  -0.9392

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
 SZY  C02  C01   single    1.506  0.020  1.506
 SZY  O03  C02   double    1.218  0.020  1.218
 SZY  N04  C02   single    1.359  0.020  1.359
 SZY  C05  N04   single    1.404  0.020  1.404
 SZY  C06  C05   aromatic  1.392  0.020  1.392
 SZY  N07  C06   aromatic  1.325  0.020  1.325
 SZY  C08  N07   aromatic  1.328  0.020  1.328
 SZY  C09  C08   aromatic  1.385  0.020  1.385
 SZY  C10  C09   aromatic  1.390  0.020  1.390
 SZY  C11  C10   single    1.496  0.020  1.496
 SZY  C05  C10   aromatic  1.397  0.020  1.397
 SZY  C01  H012  single    0.970  0.020  1.090
 SZY  C01  H011  single    0.970  0.020  1.090
 SZY  C01  H013  single    0.970  0.020  1.090
 SZY  C06  H061  single    0.930  0.020  1.080
 SZY  C08  H081  single    0.930  0.020  1.080
 SZY  C09  H091  single    0.930  0.020  1.080
 SZY  C11  H111  single    0.970  0.020  1.090
 SZY  C11  H113  single    0.970  0.020  1.090
 SZY  C11  H112  single    0.970  0.020  1.090
 SZY  N04  H041  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
 SZY  C11   C10  C09   121.62  3.000
 SZY  C11   C10  C05   121.53  3.000
 SZY  C09   C10  C05   116.85  3.000
 SZY  H013  C01  H011  107.33  3.000
 SZY  H013  C01  H012  108.54  3.000
 SZY  H011  C01  H012  108.43  3.000
 SZY  H013  C01  C02   109.31  3.000
 SZY  H011  C01  C02   109.23  3.000
 SZY  H012  C01  C02   113.80  3.000
 SZY  O03   C02  N04   122.91  3.000
 SZY  N04   C02  C01   114.70  3.000
 SZY  O03   C02  C01   122.39  3.000
 SZY  N04   C05  C06   121.18  3.000
 SZY  C06   C05  C10   119.04  3.000
 SZY  N04   C05  C10   119.78  3.000
 SZY  H061  C06  N07   116.56  3.000
 SZY  H061  C06  C05   120.03  3.000
 SZY  N07   C06  C05   123.40  3.000
 SZY  H081  C08  N07   116.79  3.000
 SZY  H081  C08  C09   120.13  3.000
 SZY  N07   C08  C09   123.08  3.000
 SZY  H091  C09  C08   119.90  3.000
 SZY  H091  C09  C10   120.27  3.000
 SZY  C08   C09  C10   119.83  3.000
 SZY  H112  C11  H113  108.25  3.000
 SZY  H112  C11  H111  107.37  3.000
 SZY  H113  C11  H111  107.16  3.000
 SZY  H112  C11  C10   110.94  3.000
 SZY  H113  C11  C10   111.35  3.000
 SZY  H111  C11  C10   111.58  3.000
 SZY  H041  N04  C05   117.07  3.000
 SZY  H041  N04  C02   117.48  3.000
 SZY  C05   N04  C02   125.05  3.000
 SZY  C08   N07  C06   117.78  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
 SZY  CONST_01  N07   C08  C09  C10    0.00   0.0  0
 SZY  CONST_02  N07   C06  C05  C10    0.00   0.0  0
 SZY  CONST_03  C08   N07  C06  C05    0.00   0.0  0
 SZY  CONST_04  C08   C09  C10  C05    0.00   0.0  0
 SZY  CONST_05  C09   C10  C05  C06    0.00   0.0  0
 SZY  CONST_06  C09   C08  N07  C06    0.00   0.0  0
 SZY  CONST_07  C11   C10  C05  C06  180.00   0.0  0
 SZY  CONST_08  C11   C10  C09  C08  180.00   0.0  0
 SZY  CONST_09  N04   C05  C10  C09  180.00   0.0  0
 SZY  CONST_10  N07   C06  C05  N04  180.00   0.0  0
 SZY  CONST_11  H081  C08  C09  C10  180.00   0.0  0
 SZY  CONST_12  H061  C06  C05  C10  180.00   0.0  0
 SZY  CONST_13  H091  C09  C10  C05  180.00   0.0  0
 SZY  CONST_17  C05   N04  C02  C01  180.00   0.0  0
 SZY  CONST_18  O03   C02  N04  C05    0.00   0.0  0
 SZY  Var_01    H111  C11  C10  C05  -67.16  30.0  2
 SZY  Var_02    H012  C01  C02  N04   -2.90  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
 SZY  plan-1  C10   0.020
 SZY  plan-1  C05   0.020
 SZY  plan-1  C06   0.020
 SZY  plan-1  C08   0.020
 SZY  plan-1  C09   0.020
 SZY  plan-1  C11   0.020
 SZY  plan-1  N04   0.020
 SZY  plan-1  N07   0.020
 SZY  plan-1  H061  0.020
 SZY  plan-1  H081  0.020
 SZY  plan-1  H091  0.020
 SZY  plan-2  C01   0.020
 SZY  plan-2  C02   0.020
 SZY  plan-2  C05   0.020
 SZY  plan-2  N04   0.020
 SZY  plan-2  O03   0.020
 SZY  plan-2  H041  0.020

