# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 16:32:16 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 4,6-dimethyl-2-{[3-(morpholin-4-yl)propyl]amino}pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c(C#N)c(NCCCN2CCOCC2)n1
#
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
 46Y  46Y  4,6-dimethyl-2-{[3-(morpholin-4-yl)propyl]amino}pyridine-3-carbonitrile  ligand  42  20  .  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_46Y
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
 46Y  C4   C  CR6   0   0.550  -2.3152  -0.0917  -0.1034
 46Y  C5   C  CR6   0  -0.181  -3.3637   0.8576  -0.2431
 46Y  C6   C  CSP   0  -0.003  -3.0598   2.2107  -0.5257
 46Y  N2   N  NH1   0  -0.683  -1.0279   0.2706  -0.2272
 46Y  C14  C  CH3   0  -0.719  -4.0480  -3.2095   0.6149
 46Y  C1   C  CR6   0   0.257  -4.6892   0.4457  -0.0902
 46Y  C    C  CH3   0  -0.745  -5.8154   1.4189  -0.2279
 46Y  N    N  N     0  -0.496  -2.5758  -1.3677   0.1677
 46Y  C3   C  CR6   0   0.275  -3.8364  -1.7588   0.3186
 46Y  C2   C  CR16  0  -0.446  -4.9177  -0.8907   0.1987
 46Y  H4   H  HNH1  0   0.403  -0.8176   1.2041  -0.5412
 46Y  H6   H  HCH3  0   0.256  -3.4385  -3.5208   1.4636
 46Y  H7   H  HCH3  0   0.248  -5.0902  -3.4297   0.8350
 46Y  H8   H  HCH3  0   0.259  -3.7436  -3.8176  -0.2388
 46Y  H9   H  HCH3  0   0.263  -5.7981   1.9056  -1.2042
 46Y  H10  H  HCH3  0   0.266  -6.7775   0.9249  -0.1126
 46Y  H11  H  HCH3  0   0.264  -5.7451   2.2054   0.5250
 46Y  H12  H  HCR6  0   0.261  -5.9272  -1.2550   0.3317
 46Y  N1   N  NS    0  -0.257  -2.7897   3.3101  -0.7559
 46Y  C7   C  CH2   0  -0.235   0.0758  -0.6646  -0.1753
 46Y  C8   C  CH2   0  -0.502   1.3939   0.0935  -0.1482
 46Y  C9   C  CH2   0  -0.252   2.5747  -0.8669  -0.1217
 46Y  N3   N  NT    0  -0.428   3.8560  -0.2006  -0.2495
 46Y  C11  C  CH2   0  -0.302   4.9215  -1.1505  -0.5132
 46Y  C12  C  CH2   0  -0.188   6.2374  -0.4228  -0.7085
 46Y  O1   O  O2    0  -0.485   6.5626   0.3674   0.4137
 46Y  C15  C  CH2   0  -0.184   5.5336   1.2906   0.6914
 46Y  C16  C  CH2   0  -0.310   4.1989   0.6031   0.9108
 46Y  H1   H  HCH2  0   0.237  -0.0166  -1.2860   0.7176
 46Y  H2   H  HCH2  0   0.228   0.0477  -1.3426  -1.0355
 46Y  H3   H  HCH2  0   0.235   1.4762   0.7322  -1.0329
 46Y  H5   H  HCH2  0   0.243   1.4034   0.7503   0.7252
 46Y  H13  H  HCH2  0   0.194   2.5272  -1.4856   0.7916
 46Y  H14  H  HCH2  0   0.232   2.4785  -1.5578  -0.9647
 46Y  H15  H  HCH2  0   0.196   5.0276  -1.8859   0.3036
 46Y  H16  H  HCH2  0   0.241   4.6904  -1.7111  -1.4224
 46Y  H17  H  HCH2  0   0.235   7.0461  -1.1420  -0.8471
 46Y  H18  H  HCH2  0   0.199   6.1799   0.1988  -1.6138
 46Y  H19  H  HCH2  0   0.235   5.8220   1.8418   1.5877
 46Y  H20  H  HCH2  0   0.199   5.4329   2.0121  -0.1318
 46Y  H21  H  HCH2  0   0.244   3.4450   1.3763   1.0689
 46Y  H22  H  HCH2  0   0.196   4.2367  -0.0071   1.8307

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
 46Y  N2   C4   single    1.343  0.020  1.343
 46Y  N    C4   aromatic  1.330  0.020  1.330
 46Y  N    C3   aromatic  1.328  0.020  1.328
 46Y  C4   C5   aromatic  1.421  0.020  1.421
 46Y  C14  C3   single    1.496  0.020  1.496
 46Y  C3   C2   aromatic  1.392  0.020  1.392
 46Y  C5   C6   single    1.415  0.020  1.415
 46Y  C5   C1   aromatic  1.396  0.020  1.396
 46Y  C2   C1   aromatic  1.386  0.020  1.386
 46Y  C1   C    single    1.495  0.020  1.495
 46Y  N2   H4   single    0.860  0.020  1.020
 46Y  C14  H6   single    0.970  0.020  1.090
 46Y  C14  H7   single    0.970  0.020  1.090
 46Y  C14  H8   single    0.970  0.020  1.090
 46Y  C    H9   single    0.970  0.020  1.090
 46Y  C    H10  single    0.970  0.020  1.090
 46Y  C    H11  single    0.970  0.020  1.090
 46Y  C2   H12  single    0.930  0.020  1.080
 46Y  C6   N1   triple    1.155  0.020  1.155
 46Y  N2   C7   single    1.447  0.020  1.447
 46Y  C7   C8   single    1.521  0.020  1.521
 46Y  C8   C9   single    1.522  0.020  1.522
 46Y  C9   N3   single    1.450  0.020  1.450
 46Y  N3   C11  single    1.452  0.020  1.452
 46Y  C11  C12  single    1.516  0.020  1.516
 46Y  C12  O1   single    1.410  0.020  1.410
 46Y  O1   C15  single    1.410  0.020  1.410
 46Y  C15  C16  single    1.517  0.020  1.517
 46Y  C16  N3   single    1.452  0.020  1.452
 46Y  C7   H1   single    0.970  0.020  1.090
 46Y  C7   H2   single    0.970  0.020  1.090
 46Y  C8   H3   single    0.970  0.020  1.090
 46Y  C8   H5   single    0.970  0.020  1.090
 46Y  C9   H13  single    0.970  0.020  1.090
 46Y  C9   H14  single    0.970  0.020  1.090
 46Y  C11  H15  single    0.970  0.020  1.090
 46Y  C11  H16  single    0.970  0.020  1.090
 46Y  C12  H17  single    0.970  0.020  1.090
 46Y  C12  H18  single    0.970  0.020  1.090
 46Y  C15  H19  single    0.970  0.020  1.090
 46Y  C15  H20  single    0.970  0.020  1.090
 46Y  C16  H21  single    0.970  0.020  1.090
 46Y  C16  H22  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
 46Y  N    C4   N2   117.73  3.000
 46Y  N    C4   C5   121.07  3.000
 46Y  N2   C4   C5   121.19  3.000
 46Y  C1   C5   C6   120.50  3.000
 46Y  C1   C5   C4   119.51  3.000
 46Y  C6   C5   C4   119.99  3.000
 46Y  N1   C6   C5   180.00  3.000
 46Y  C7   N2   H4   116.79  3.000
 46Y  C7   N2   C4   123.59  3.000
 46Y  H4   N2   C4   118.61  3.000
 46Y  H8   C14  H7   108.22  3.000
 46Y  H8   C14  H6   107.09  3.000
 46Y  H7   C14  H6   108.68  3.000
 46Y  H8   C14  C3   110.24  3.000
 46Y  H7   C14  C3   111.84  3.000
 46Y  H6   C14  C3   110.62  3.000
 46Y  C2   C1   C    121.51  3.000
 46Y  C    C1   C5   120.87  3.000
 46Y  C2   C1   C5   117.62  3.000
 46Y  H11  C    H10  108.14  3.000
 46Y  H11  C    H9   107.16  3.000
 46Y  H10  C    H9   108.15  3.000
 46Y  H11  C    C1   110.93  3.000
 46Y  H10  C    C1   111.16  3.000
 46Y  H9   C    C1   111.16  3.000
 46Y  C3   N    C4   119.44  3.000
 46Y  C2   C3   N    122.94  3.000
 46Y  C2   C3   C14  120.81  3.000
 46Y  N    C3   C14  116.25  3.000
 46Y  H12  C2   C3   120.30  3.000
 46Y  H12  C2   C1   120.29  3.000
 46Y  C3   C2   C1   119.42  3.000
 46Y  H2   C7   H1   106.72  3.000
 46Y  H2   C7   C8   110.16  3.000
 46Y  H1   C7   C8   110.03  3.000
 46Y  H2   C7   N2   110.62  3.000
 46Y  H1   C7   N2   109.42  3.000
 46Y  C8   C7   N2   109.84  3.000
 46Y  H5   C8   H3   107.14  3.000
 46Y  H5   C8   C9   111.01  3.000
 46Y  H3   C8   C9   108.90  3.000
 46Y  H5   C8   C7   108.75  3.000
 46Y  H3   C8   C7   109.98  3.000
 46Y  C9   C8   C7   110.99  3.000
 46Y  H14  C9   H13  106.24  3.000
 46Y  H14  C9   N3   107.46  3.000
 46Y  H13  C9   N3   111.62  3.000
 46Y  H14  C9   C8   108.47  3.000
 46Y  H13  C9   C8   109.54  3.000
 46Y  N3   C9   C8   113.21  3.000
 46Y  C16  N3   C11  109.51  3.000
 46Y  C16  N3   C9   113.11  3.000
 46Y  C11  N3   C9   111.34  3.000
 46Y  H16  C11  H15  107.10  3.000
 46Y  H16  C11  C12  108.82  3.000
 46Y  H15  C11  C12  109.37  3.000
 46Y  H16  C11  N3   109.36  3.000
 46Y  H15  C11  N3   111.83  3.000
 46Y  C12  C11  N3   110.26  3.000
 46Y  H18  C12  H17  107.86  3.000
 46Y  H18  C12  O1   110.51  3.000
 46Y  H17  C12  O1   107.43  3.000
 46Y  H18  C12  C11  109.39  3.000
 46Y  H17  C12  C11  110.07  3.000
 46Y  O1   C12  C11  111.50  3.000
 46Y  C15  O1   C12  110.80  3.000
 46Y  H20  C15  H19  107.93  3.000
 46Y  H20  C15  C16  108.97  3.000
 46Y  H19  C15  C16  110.04  3.000
 46Y  H20  C15  O1   110.43  3.000
 46Y  H19  C15  O1   107.43  3.000
 46Y  C16  C15  O1   111.95  3.000
 46Y  H22  C16  H21  107.12  3.000
 46Y  H22  C16  C15  109.91  3.000
 46Y  H21  C16  C15  107.91  3.000
 46Y  H22  C16  N3   111.57  3.000
 46Y  H21  C16  N3   110.16  3.000
 46Y  C15  C16  N3   110.05  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
 46Y  CONST_01  C2   C3   N    C4      0.00   0.0  0
 46Y  CONST_02  C2   C1   C5   C4      0.00   0.0  0
 46Y  CONST_03  C3   N    C4   C5      0.00   0.0  0
 46Y  CONST_04  C3   C2   C1   C5      0.00   0.0  0
 46Y  CONST_05  N    C4   C5   C1      0.00   0.0  0
 46Y  CONST_06  N    C3   C2   C1      0.00   0.0  0
 46Y  CONST_07  C14  C3   N    C4    180.00   0.0  0
 46Y  CONST_08  C    C1   C5   C4    180.00   0.0  0
 46Y  CONST_09  N    C4   C5   C6    180.00   0.0  0
 46Y  CONST_10  C2   C1   C5   C6    180.00   0.0  0
 46Y  CONST_11  C3   N    C4   N2    180.00   0.0  0
 46Y  CONST_12  C1   C5   C4   N2    180.00   0.0  0
 46Y  CONST_13  C1   C2   C3   C14   180.00   0.0  0
 46Y  CONST_14  C3   C2   C1   C     180.00   0.0  0
 46Y  CONST_15  H12  C2   C1   C5    180.00   0.0  0
 46Y  CONST_16  C7   N2   C4   C5    180.00   0.0  0
 46Y  CONST_17  C7   N2   C4   N       0.00   0.0  0
 46Y  CONST_18  H4   N2   C4   C5      0.00   0.0  0
 46Y  Var_01    O1   C12  C11  N3     57.51  30.0  1
 46Y  Var_02    O1   C15  C16  N3    -56.93  30.0  1
 46Y  Var_03    C15  C16  N3   C11    56.40  30.0  1
 46Y  Var_04    C16  N3   C11  C12   -56.88  30.0  1
 46Y  Var_05    C16  C15  O1   C12    56.83  30.0  1
 46Y  Var_06    C11  N3   C9   C8   -167.46  30.0  3
 46Y  Var_07    H9   C    C1   C5     57.53  30.0  2
 46Y  Var_08    H6   C14  C3   N      52.28  30.0  2
 46Y  Var_09    C8   C7   N2   C4   -171.92  30.0  3
 46Y  Var_10    N3   C9   C8   C7    173.36  30.0  3
 46Y  Var_11    C9   C8   C7   N2   -178.86  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
 46Y  plan-1  C4   0.020
 46Y  plan-1  C5   0.020
 46Y  plan-1  C6   0.020
 46Y  plan-1  N2   0.020
 46Y  plan-1  C14  0.020
 46Y  plan-1  C1   0.020
 46Y  plan-1  C    0.020
 46Y  plan-1  N    0.020
 46Y  plan-1  C3   0.020
 46Y  plan-1  C2   0.020
 46Y  plan-1  H12  0.020
 46Y  plan-1  N1   0.020
 46Y  plan-2  C4   0.020
 46Y  plan-2  N2   0.020
 46Y  plan-2  H4   0.020
 46Y  plan-2  C7   0.020

