# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 12:39:38 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 4,6-dimethyl-2-(morpholin-4-yl)pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c(C#N)c(n1)N2CCOCC2
#
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
 A1Y  A1Y  4,6-dimethyl-2-(morpholin-4-yl)pyridine-3-carbonitrile  ligand  31  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A1Y
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
 A1Y  N3   N  NT    0  -0.515   1.1427   0.1941   0.0614
 A1Y  C4   C  CR6   0   0.274  -1.9990   1.7742   0.4454
 A1Y  N2   N  NS    0  -0.255  -0.2880  -3.1141  -0.5452
 A1Y  C7   C  CSP   0   0.013  -0.6334  -2.0184  -0.4314
 A1Y  C6   C  CR6   0  -0.161  -1.0989  -0.6888  -0.2663
 A1Y  C9   C  CH2   0  -0.182   3.1548  -0.9446  -0.6872
 A1Y  C8   C  CH2   0  -0.339   1.8204  -0.3612  -1.1064
 A1Y  C2   C  CR6   0   0.252  -2.4774  -0.4504  -0.3076
 A1Y  C3   C  CR16  0  -0.428  -2.9201   0.8160   0.0383
 A1Y  N1   N  N     0  -0.481  -0.6884   1.5505   0.4365
 A1Y  C5   C  CR6   0   0.532  -0.2175   0.3696   0.0633
 A1Y  O1   O  O2    0  -0.482   3.9589   0.0214  -0.0502
 A1Y  C10  C  CH2   0  -0.187   3.3054   0.5608   1.0767
 A1Y  C11  C  CH2   0  -0.316   1.9699   1.1913   0.7224
 A1Y  H7   H  HCH2  0   0.208   2.9824  -1.8057  -0.0260
 A1Y  H8   H  HCH2  0   0.244   3.6955  -1.2953  -1.5670
 A1Y  H5   H  HCH2  0   0.268   1.2303  -1.1370  -1.5856
 A1Y  H6   H  HCH2  0   0.246   1.9782   0.4301  -1.8515
 A1Y  H3   H  HCH3  0   0.266  -3.4261  -2.3330   0.0762
 A1Y  H2   H  HCH3  0   0.267  -4.4543  -1.1528  -0.7335
 A1Y  H1   H  HCH3  0   0.263  -3.1831  -1.9893  -1.6285
 A1Y  H4   H  HCR6  0   0.266  -3.9769   1.0464   0.0251
 A1Y  H10  H  HCH2  0   0.207   3.1424  -0.2177   1.8348
 A1Y  H9   H  HCH2  0   0.244   3.9637   1.3171   1.5064
 A1Y  H11  H  HCH2  0   0.229   2.1179   2.0732   0.0863
 A1Y  H12  H  HCH2  0   0.262   1.4874   1.5253   1.6389
 A1Y  H14  H  HCH3  0   0.260  -2.2211   3.2397   1.9787
 A1Y  H13  H  HCH3  0   0.257  -1.9098   3.9121   0.3872
 A1Y  H15  H  HCH3  0   0.249  -3.5118   3.2677   0.7761
 A1Y  C12  C  CH3   0  -0.717  -2.4428   3.1223   0.9164
 A1Y  C1   C  CH3   0  -0.744  -3.4386  -1.5366  -0.6699

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
 A1Y  O1   C9   single    1.409  0.020  1.409
 A1Y  O1   C10  single    1.410  0.020  1.410
 A1Y  C9   C8   single    1.515  0.020  1.515
 A1Y  C10  C11  single    1.519  0.020  1.519
 A1Y  C8   N3   single    1.460  0.020  1.460
 A1Y  C11  N3   single    1.454  0.020  1.454
 A1Y  N3   C5   single    1.371  0.020  1.371
 A1Y  C5   N1   aromatic  1.325  0.020  1.325
 A1Y  C5   C6   aromatic  1.416  0.020  1.416
 A1Y  N1   C4   aromatic  1.330  0.020  1.330
 A1Y  N2   C7   triple    1.154  0.020  1.154
 A1Y  C7   C6   single    1.418  0.020  1.418
 A1Y  C6   C2   aromatic  1.400  0.020  1.400
 A1Y  C4   C12  single    1.495  0.020  1.495
 A1Y  C4   C3   aromatic  1.390  0.020  1.390
 A1Y  C2   C3   aromatic  1.385  0.020  1.385
 A1Y  C2   C1   single    1.495  0.020  1.495
 A1Y  C9   H7   single    0.970  0.020  1.090
 A1Y  C9   H8   single    0.970  0.020  1.090
 A1Y  C8   H5   single    0.970  0.020  1.090
 A1Y  C8   H6   single    0.970  0.020  1.090
 A1Y  C1   H3   single    0.970  0.020  1.090
 A1Y  C1   H2   single    0.970  0.020  1.090
 A1Y  C1   H1   single    0.970  0.020  1.090
 A1Y  C3   H4   single    0.930  0.020  1.080
 A1Y  C10  H10  single    0.970  0.020  1.090
 A1Y  C10  H9   single    0.970  0.020  1.090
 A1Y  C11  H11  single    0.970  0.020  1.090
 A1Y  C11  H12  single    0.970  0.020  1.090
 A1Y  C12  H14  single    0.970  0.020  1.090
 A1Y  C12  H13  single    0.970  0.020  1.090
 A1Y  C12  H15  single    0.970  0.020  1.090

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
 A1Y  C11  N3   C5   118.41  3.000
 A1Y  C5   N3   C8   120.67  3.000
 A1Y  C11  N3   C8   111.12  3.000
 A1Y  C12  C4   N1   116.51  3.000
 A1Y  C12  C4   C3   121.13  3.000
 A1Y  N1   C4   C3   122.36  3.000
 A1Y  C6   C7   N2   180.00  3.000
 A1Y  C5   C6   C2   119.51  3.000
 A1Y  C2   C6   C7   118.65  3.000
 A1Y  C5   C6   C7   121.56  3.000
 A1Y  H8   C9   H7   108.12  3.000
 A1Y  H8   C9   O1   107.59  3.000
 A1Y  H7   C9   O1   110.77  3.000
 A1Y  H8   C9   C8   109.70  3.000
 A1Y  H7   C9   C8   109.27  3.000
 A1Y  O1   C9   C8   111.32  3.000
 A1Y  H6   C8   H5   107.06  3.000
 A1Y  H6   C8   C9   109.79  3.000
 A1Y  H5   C8   C9   108.99  3.000
 A1Y  H6   C8   N3   109.59  3.000
 A1Y  H5   C8   N3   111.86  3.000
 A1Y  C9   C8   N3   109.50  3.000
 A1Y  C3   C2   C1   121.28  3.000
 A1Y  C1   C2   C6   121.11  3.000
 A1Y  C3   C2   C6   117.58  3.000
 A1Y  H4   C3   C2   120.25  3.000
 A1Y  H4   C3   C4   120.27  3.000
 A1Y  C2   C3   C4   119.44  3.000
 A1Y  C5   N1   C4   120.14  3.000
 A1Y  N1   C5   C6   120.70  3.000
 A1Y  C6   C5   N3   121.42  3.000
 A1Y  N1   C5   N3   117.83  3.000
 A1Y  C10  O1   C9   111.04  3.000
 A1Y  H9   C10  H10  107.99  3.000
 A1Y  H9   C10  C11  109.56  3.000
 A1Y  H10  C10  C11  108.94  3.000
 A1Y  H9   C10  O1   107.48  3.000
 A1Y  H10  C10  O1   110.44  3.000
 A1Y  C11  C10  O1   112.33  3.000
 A1Y  H12  C11  H11  107.53  3.000
 A1Y  H12  C11  C10  108.71  3.000
 A1Y  H11  C11  C10  110.50  3.000
 A1Y  H12  C11  N3   109.94  3.000
 A1Y  H11  C11  N3   111.37  3.000
 A1Y  C10  C11  N3   108.75  3.000
 A1Y  H15  C12  H13  108.73  3.000
 A1Y  H15  C12  H14  108.11  3.000
 A1Y  H13  C12  H14  107.17  3.000
 A1Y  H15  C12  C4   111.80  3.000
 A1Y  H13  C12  C4   110.81  3.000
 A1Y  H14  C12  C4   110.07  3.000
 A1Y  H1   C1   H2   108.30  3.000
 A1Y  H1   C1   H3   107.18  3.000
 A1Y  H2   C1   H3   107.95  3.000
 A1Y  H1   C1   C2   111.35  3.000
 A1Y  H2   C1   C2   110.99  3.000
 A1Y  H3   C1   C2   110.93  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
 A1Y  CONST_01  C6   C5   N1   C4    0.00   0.0  0
 A1Y  CONST_02  C6   C2   C3   C4    0.00   0.0  0
 A1Y  CONST_03  N1   C5   C6   C2    0.00   0.0  0
 A1Y  CONST_04  N1   C4   C3   C2    0.00   0.0  0
 A1Y  CONST_05  C5   N1   C4   C3    0.00   0.0  0
 A1Y  CONST_06  C5   C6   C2   C3    0.00   0.0  0
 A1Y  CONST_07  C4   N1   C5   N3  180.00   0.0  0
 A1Y  CONST_08  C2   C6   C5   N3  180.00   0.0  0
 A1Y  CONST_09  C7   C6   C5   N3    0.00   0.0  0
 A1Y  CONST_10  C1   C2   C3   C4  180.00   0.0  0
 A1Y  CONST_11  N1   C5   C6   C7  180.00   0.0  0
 A1Y  CONST_12  C3   C2   C6   C7  180.00   0.0  0
 A1Y  CONST_13  C5   C6   C2   C1  180.00   0.0  0
 A1Y  CONST_14  C12  C4   C3   C2  180.00   0.0  0
 A1Y  CONST_15  C12  C4   N1   C5  180.00   0.0  0
 A1Y  CONST_16  H4   C3   C2   C6  180.00   0.0  0
 A1Y  Var_01    O1   C9   C8   N3  -56.96  30.0  1
 A1Y  Var_02    O1   C10  C11  N3   56.45  30.0  1
 A1Y  Var_03    C8   N3   C5   C6   52.44  30.0  2
 A1Y  Var_04    C11  C10  O1   C9  -57.87  30.0  1
 A1Y  Var_05    C10  C11  N3   C8  -55.89  30.0  1
 A1Y  Var_06    H3   C1   C2   C6   64.81  30.0  2
 A1Y  Var_07    H14  C12  C4   C3  113.17  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
 A1Y  plan-1  N3   0.020
 A1Y  plan-1  C4   0.020
 A1Y  plan-1  N2   0.020
 A1Y  plan-1  C7   0.020
 A1Y  plan-1  C6   0.020
 A1Y  plan-1  C2   0.020
 A1Y  plan-1  C3   0.020
 A1Y  plan-1  N1   0.020
 A1Y  plan-1  C5   0.020
 A1Y  plan-1  H4   0.020
 A1Y  plan-1  C12  0.020
 A1Y  plan-1  C1   0.020

