# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:01:35 2021
#   Inital geometry file: a 57 line input string
#   Ligand name: N-(3-methylpyridin-4-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccncc1C
#
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
 WKY  WKY  N-(3-methylpyridin-4-yl)acetamide  ligand  21  11  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WKY
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
 WKY  C10  C  CR6   0  -0.047  -30.4651  -7.1853  -17.5226
 WKY  C01  C  CH3   0  -0.795  -28.4332  -8.8350  -21.4780
 WKY  C02  C  C     0   0.515  -28.2675  -8.8883  -19.9816
 WKY  C05  C  CR6   0   0.428  -29.3924  -7.9900  -17.9469
 WKY  C06  C  CR16  0  -0.380  -28.5713  -8.5547  -16.9705
 WKY  C07  C  CR16  0  -0.077  -28.8510  -8.2981  -15.6388
 WKY  C09  C  CR16  0  -0.112  -30.6317  -7.0130  -16.1573
 WKY  C11  C  CH3   0  -0.770  -31.4034  -6.5272  -18.4883
 WKY  N04  N  NH1   0  -0.737  -29.2206  -8.1695  -19.3112
 WKY  N08  N  N     0  -0.413  -29.8577  -7.5454  -15.2183
 WKY  O03  O  O     0  -0.451  -27.3793  -9.5071  -19.4315
 WKY  H1   H  HCH3  0   0.271  -27.6340  -9.3870  -21.9642
 WKY  H2   H  HCH3  0   0.275  -29.3906  -9.2670  -21.7734
 WKY  H3   H  HCH3  0   0.273  -28.4182  -7.8035  -21.8323
 WKY  H4   H  HCR6  0   0.289  -27.7306  -9.1781  -17.2221
 WKY  H5   H  HCR6  0   0.261  -28.2143  -8.7319  -14.8751
 WKY  H6   H  HCR6  0   0.255  -31.4560  -6.3971  -15.8093
 WKY  H7   H  HCH3  0   0.257  -31.9275  -7.2538  -19.1132
 WKY  H8   H  HCH3  0   0.269  -32.1613  -5.9567  -17.9545
 WKY  H9   H  HCH3  0   0.257  -30.8860  -5.8332  -19.1550
 WKY  H10  H  HNH1  0   0.434  -29.8973  -7.7065  -19.8987

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
 WKY  C01  C02  single    1.507  0.020  1.507
 WKY  C02  O03  double    1.214  0.020  1.214
 WKY  C02  N04  single    1.369  0.020  1.369
 WKY  N04  C05  single    1.387  0.020  1.387
 WKY  C11  C10  single    1.499  0.020  1.499
 WKY  C05  C10  aromatic  1.406  0.020  1.406
 WKY  C05  C06  aromatic  1.395  0.020  1.395
 WKY  C10  C09  aromatic  1.386  0.020  1.386
 WKY  C06  C07  aromatic  1.385  0.020  1.385
 WKY  C09  N08  aromatic  1.328  0.020  1.328
 WKY  C07  N08  aromatic  1.325  0.020  1.325
 WKY  C01  H1   single    0.970  0.020  1.090
 WKY  C01  H2   single    0.970  0.020  1.090
 WKY  C01  H3   single    0.970  0.020  1.090
 WKY  C06  H4   single    0.930  0.020  1.080
 WKY  C07  H5   single    0.930  0.020  1.080
 WKY  C09  H6   single    0.930  0.020  1.080
 WKY  C11  H7   single    0.970  0.020  1.090
 WKY  C11  H8   single    0.970  0.020  1.090
 WKY  C11  H9   single    0.970  0.020  1.090
 WKY  N04  H10  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
 WKY  C11  C10  C09  120.32  3.000
 WKY  C09  C10  C05  117.38  3.000
 WKY  C11  C10  C05  122.30  3.000
 WKY  H3   C01  H2   107.37  3.000
 WKY  H3   C01  H1   108.97  3.000
 WKY  H2   C01  H1   108.86  3.000
 WKY  H3   C01  C02  110.77  3.000
 WKY  H2   C01  C02  110.57  3.000
 WKY  H1   C01  C02  110.23  3.000
 WKY  O03  C02  N04  123.71  3.000
 WKY  N04  C02  C01  113.03  3.000
 WKY  O03  C02  C01  123.26  3.000
 WKY  N04  C05  C06  124.28  3.000
 WKY  C06  C05  C10  117.99  3.000
 WKY  N04  C05  C10  117.73  3.000
 WKY  H4   C06  C07  119.34  3.000
 WKY  H4   C06  C05  122.04  3.000
 WKY  C07  C06  C05  118.63  3.000
 WKY  H5   C07  N08  116.71  3.000
 WKY  H5   C07  C06  118.97  3.000
 WKY  N08  C07  C06  124.32  3.000
 WKY  H6   C09  N08  116.29  3.000
 WKY  H6   C09  C10  118.51  3.000
 WKY  N08  C09  C10  125.20  3.000
 WKY  H9   C11  H8   107.22  3.000
 WKY  H9   C11  H7   107.50  3.000
 WKY  H8   C11  H7   107.16  3.000
 WKY  H9   C11  C10  112.06  3.000
 WKY  H8   C11  C10  110.49  3.000
 WKY  H7   C11  C10  112.15  3.000
 WKY  H10  N04  C05  115.50  3.000
 WKY  H10  N04  C02  115.01  3.000
 WKY  C05  N04  C02  129.49  3.000
 WKY  C09  N08  C07  116.48  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
 WKY  CONST_01  C07  C06  C05  C10    0.00   0.0  0
 WKY  CONST_02  C07  N08  C09  C10    0.00   0.0  0
 WKY  CONST_03  N08  C09  C10  C05    0.00   0.0  0
 WKY  CONST_04  N08  C07  C06  C05    0.00   0.0  0
 WKY  CONST_05  C09  C10  C05  C06    0.00   0.0  0
 WKY  CONST_06  C09  N08  C07  C06    0.00   0.0  0
 WKY  CONST_07  C11  C10  C05  C06  180.00   0.0  0
 WKY  CONST_08  N04  C05  C06  C07  180.00   0.0  0
 WKY  CONST_09  N04  C05  C10  C09  180.00   0.0  0
 WKY  CONST_10  N08  C09  C10  C11  180.00   0.0  0
 WKY  CONST_11  H4   C06  C05  C10  180.00   0.0  0
 WKY  CONST_12  H6   C09  C10  C05  180.00   0.0  0
 WKY  CONST_13  H5   C07  C06  C05  180.00   0.0  0
 WKY  CONST_14  C02  N04  C05  C10  180.00   0.0  0
 WKY  CONST_15  C06  C05  N04  C02    0.00   0.0  0
 WKY  CONST_16  H10  N04  C05  C10    0.00   0.0  0
 WKY  CONST_17  C05  N04  C02  C01  180.00   0.0  0
 WKY  CONST_18  O03  C02  N04  C05    0.00   0.0  0
 WKY  Var_01    H7   C11  C10  C05   60.24  30.0  2
 WKY  Var_02    H1   C01  C02  N04  177.84  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
 WKY  plan-1  C10  0.020
 WKY  plan-1  C05  0.020
 WKY  plan-1  C06  0.020
 WKY  plan-1  C07  0.020
 WKY  plan-1  C09  0.020
 WKY  plan-1  C11  0.020
 WKY  plan-1  N04  0.020
 WKY  plan-1  N08  0.020
 WKY  plan-1  H4   0.020
 WKY  plan-1  H5   0.020
 WKY  plan-1  H6   0.020
 WKY  plan-2  C01  0.020
 WKY  plan-2  C02  0.020
 WKY  plan-2  C05  0.020
 WKY  plan-2  N04  0.020
 WKY  plan-2  O03  0.020
 WKY  plan-2  H10  0.020

