# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 11:29:42 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: 6-morpholin-4-ylpyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(nc1)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
 LR8  LR8  6-morpholin-4-ylpyridine-3-carboxamide  ligand  28  15  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LR8
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
 LR8  C1   C  CR6   0  -0.171  14.3654   2.9837  19.7050
 LR8  C2   C  CR16  0  -0.145  14.1366   1.6188  19.5016
 LR8  C3   C  CR16  0  -0.404  12.9105   1.1676  19.0845
 LR8  C4   C  CR6   0   0.564  11.8711   2.1049  18.8830
 LR8  C5   C  CH2   0  -0.318   9.6651   2.7311  18.0277
 LR8  C6   C  CH2   0  -0.191   8.2549   2.3225  18.4030
 LR8  N    N  NH2   0  -0.822  15.9579   4.7566  20.0821
 LR8  C    C  C     0   0.486  15.6999   3.4400  20.1658
 LR8  O    O  O     0  -0.491  16.5186   2.6419  20.6086
 LR8  C7   C  CH2   0  -0.182   8.8338   0.0830  18.4698
 LR8  C8   C  CH2   0  -0.320  10.2805   0.3858  18.1158
 LR8  C9   C  CR16  0  -0.064  13.2811   3.8200  19.4752
 LR8  N1   N  NT    0  -0.509  10.6168   1.7416  18.5063
 LR8  N2   N  N     0  -0.477  12.0900   3.4091  19.0800
 LR8  O1   O  O2    0  -0.481   7.9429   1.0305  17.9324
 LR8  H1   H  HCR6  0   0.269  14.9355   0.9065  19.6593
 LR8  H2   H  HCR6  0   0.274  12.7694   0.1116  18.9139
 LR8  H3   H  HCH2  0   0.234   9.7488   2.8328  16.9377
 LR8  H4   H  HCH2  0   0.273   9.8898   3.6992  18.4655
 LR8  H5   H  HCH2  0   0.244   7.5419   3.0173  17.9575
 LR8  H6   H  HCH2  0   0.208   8.1407   2.3715  19.4952
 LR8  H7   H  HNH2  0   0.403  16.8580   5.1029  20.3710
 LR8  H8   H  HNH2  0   0.408  15.3589   5.4031  19.6001
 LR8  H9   H  HCH2  0   0.209   8.7355   0.0398  19.5636
 LR8  H10  H  HCH2  0   0.247   8.5618  -0.8937  18.0680
 LR8  H11  H  HCH2  0   0.266  10.8973  -0.3374  18.6439
 LR8  H12  H  HCH2  0   0.240  10.4485   0.2446  17.0408
 LR8  H13  H  HCR6  0   0.251  13.3582   4.8918  19.6303

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
 LR8  O1  C6   single    1.410  0.020  1.410
 LR8  O1  C7   single    1.407  0.020  1.407
 LR8  C5  C6   single    1.515  0.020  1.515
 LR8  C5  N1   single    1.454  0.020  1.454
 LR8  C8  C7   single    1.520  0.020  1.520
 LR8  C8  N1   single    1.450  0.020  1.450
 LR8  N1  C4   single    1.359  0.020  1.359
 LR8  C4  C3   aromatic  1.414  0.020  1.414
 LR8  C4  N2   aromatic  1.337  0.020  1.337
 LR8  C3  C2   aromatic  1.371  0.020  1.371
 LR8  N2  C9   aromatic  1.320  0.020  1.320
 LR8  C2  C1   aromatic  1.399  0.020  1.399
 LR8  C9  C1   aromatic  1.388  0.020  1.388
 LR8  C1  C    single    1.484  0.020  1.484
 LR8  C   N    single    1.344  0.020  1.344
 LR8  C   O    double    1.226  0.020  1.226
 LR8  C2  H1   single    0.930  0.020  1.080
 LR8  C3  H2   single    0.930  0.020  1.080
 LR8  C5  H3   single    0.970  0.020  1.090
 LR8  C5  H4   single    0.970  0.020  1.090
 LR8  C6  H5   single    0.970  0.020  1.090
 LR8  C6  H6   single    0.970  0.020  1.090
 LR8  N   H7   single    0.860  0.020  1.020
 LR8  N   H8   single    0.860  0.020  1.020
 LR8  C7  H9   single    0.970  0.020  1.090
 LR8  C7  H10  single    0.970  0.020  1.090
 LR8  C8  H11  single    0.970  0.020  1.090
 LR8  C8  H12  single    0.970  0.020  1.090
 LR8  C9  H13  single    0.930  0.020  1.080

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
 LR8  C9   C1  C    124.65  3.000
 LR8  C    C1  C2   119.49  3.000
 LR8  C9   C1  C2   115.84  3.000
 LR8  H1   C2  C3   119.21  3.000
 LR8  H1   C2  C1   120.03  3.000
 LR8  C3   C2  C1   120.76  3.000
 LR8  H2   C3  C4   122.02  3.000
 LR8  H2   C3  C2   119.14  3.000
 LR8  C4   C3  C2   118.85  3.000
 LR8  N2   C4  N1   116.92  3.000
 LR8  N2   C4  C3   120.35  3.000
 LR8  N1   C4  C3   122.73  3.000
 LR8  H4   C5  H3   107.57  3.000
 LR8  H4   C5  N1   109.79  3.000
 LR8  H3   C5  N1   109.87  3.000
 LR8  H4   C5  C6   109.45  3.000
 LR8  H3   C5  C6   109.99  3.000
 LR8  N1   C5  C6   110.13  3.000
 LR8  H6   C6  H5   108.03  3.000
 LR8  H6   C6  O1   110.46  3.000
 LR8  H5   C6  O1   107.61  3.000
 LR8  H6   C6  C5   109.32  3.000
 LR8  H5   C6  C5   109.60  3.000
 LR8  O1   C6  C5   111.73  3.000
 LR8  H8   N   H7   116.71  3.000
 LR8  H8   N   C    123.08  3.000
 LR8  H7   N   C    119.38  3.000
 LR8  O    C   N    122.14  3.000
 LR8  O    C   C1   120.83  3.000
 LR8  N    C   C1   117.03  3.000
 LR8  H10  C7  H9   108.01  3.000
 LR8  H10  C7  O1   107.72  3.000
 LR8  H9   C7  O1   110.48  3.000
 LR8  H10  C7  C8   109.27  3.000
 LR8  H9   C7  C8   108.95  3.000
 LR8  O1   C7  C8   112.30  3.000
 LR8  H12  C8  H11  107.66  3.000
 LR8  H12  C8  N1   110.40  3.000
 LR8  H11  C8  N1   111.06  3.000
 LR8  H12  C8  C7   110.38  3.000
 LR8  H11  C8  C7   107.12  3.000
 LR8  N1   C8  C7   110.14  3.000
 LR8  H13  C9  N2   114.45  3.000
 LR8  H13  C9  C1   121.03  3.000
 LR8  N2   C9  C1   124.51  3.000
 LR8  C8   N1  C5   113.31  3.000
 LR8  C8   N1  C4   122.58  3.000
 LR8  C5   N1  C4   120.89  3.000
 LR8  C9   N2  C4   119.69  3.000
 LR8  C7   O1  C6   110.45  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
 LR8  CONST_01  C4   C3  C2  C1     0.00   0.0  0
 LR8  CONST_02  C4   N2  C9  C1     0.00   0.0  0
 LR8  CONST_03  N2   C4  C3  C2     0.00   0.0  0
 LR8  CONST_04  N2   C9  C1  C2     0.00   0.0  0
 LR8  CONST_05  C9   N2  C4  C3     0.00   0.0  0
 LR8  CONST_06  C9   C1  C2  C3     0.00   0.0  0
 LR8  CONST_07  N1   C4  C3  C2   180.00   0.0  0
 LR8  CONST_08  N1   C4  N2  C9   180.00   0.0  0
 LR8  CONST_09  C    C1  C2  C3   180.00   0.0  0
 LR8  CONST_10  N2   C9  C1  C    180.00   0.0  0
 LR8  CONST_11  H2   C3  C2  C1   180.00   0.0  0
 LR8  CONST_12  H13  C9  C1  C2   180.00   0.0  0
 LR8  CONST_13  H1   C2  C3  C4   180.00   0.0  0
 LR8  CONST_14  H7   N   C   C1   180.00   0.0  0
 LR8  CONST_15  H8   N   C   C1     0.00   0.0  0
 LR8  Var_01    C5   N1  C4  C3  -166.38  30.0  2
 LR8  Var_02    C6   C5  N1  C4  -148.30  30.0  1
 LR8  Var_03    C7   C8  N1  C4   149.52  30.0  1
 LR8  Var_04    C8   C7  O1  C6   -58.87  30.0  1
 LR8  Var_05    O1   C6  C5  N1   -55.32  30.0  1
 LR8  Var_06    O1   C7  C8  N1    54.01  30.0  1
 LR8  Var_07    H5   C6  O1  C7   179.81  30.0  1
 LR8  Var_08    N    C   C1  C2   166.62  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
 LR8  plan-1  C1   0.020
 LR8  plan-1  C2   0.020
 LR8  plan-1  C3   0.020
 LR8  plan-1  C4   0.020
 LR8  plan-1  C    0.020
 LR8  plan-1  C9   0.020
 LR8  plan-1  N1   0.020
 LR8  plan-1  N2   0.020
 LR8  plan-1  H1   0.020
 LR8  plan-1  H2   0.020
 LR8  plan-1  H13  0.020
 LR8  plan-2  C1   0.020
 LR8  plan-2  N    0.020
 LR8  plan-2  C    0.020
 LR8  plan-2  O    0.020
 LR8  plan-2  H7   0.020
 LR8  plan-2  H8   0.020

