# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 07:36:32 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2R)-morpholin-4-yl(phenyl)ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#C[C@H](N1CCOCC1)c2ccccc2
#
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
 3B1  3B1  (2R)-morpholin-4-yl(phenyl)ethanenitrile  ligand  29  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3B1
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
 3B1  C10  C  CR16  0  -0.242   2.8597   0.8463  -1.3844
 3B1  C01  C  CR16  0  -0.261   1.6554   0.2171  -1.1109
 3B1  N01  N  NS    0  -0.250   0.1710  -3.2398  -0.5851
 3B1  C02  C  CR16  0  -0.257   3.7641   1.0994  -0.3587
 3B1  C03  C  CH2   0  -0.186  -3.5114  -0.0166  -0.3981
 3B1  C04  C  CR6   0   0.083   1.3483  -0.1613   0.1929
 3B1  C05  C  CH2   0  -0.324  -2.3685  -0.8237   0.1875
 3B1  N    N  NT    0  -0.428  -1.1081  -0.1227  -0.0292
 3B1  C06  C  CR16  0  -0.241   3.4592   0.7217   0.9408
 3B1  C07  C  CH2   0  -0.188  -2.3601   1.9611  -0.0381
 3B1  C08  C  CSP   0   0.114   0.0896  -2.1918  -0.1185
 3B1  C09  C  CH1   0  -0.188   0.0330  -0.8551   0.4911
 3B1  O    O  O2    0  -0.482  -3.5757   1.2758   0.1581
 3B1  C11  C  CR16  0  -0.297   2.2509   0.0919   1.2157
 3B1  C    C  CH2   0  -0.311  -1.1873   1.2089   0.5592
 3B1  H1   H  HCR6  0   0.262   3.0945   1.1399  -2.3990
 3B1  H2   H  HCR6  0   0.260   0.9481   0.0281  -1.9094
 3B1  H3   H  HCR6  0   0.262   4.7027   1.5929  -0.5751
 3B1  H5   H  HCH2  0   0.243  -4.4585  -0.5144  -0.1867
 3B1  H6   H  HCH2  0   0.216  -2.5501  -1.0075   1.2589
 3B1  H7   H  HCH2  0   0.259  -2.3482  -1.7943  -0.3127
 3B1  H9   H  HCR6  0   0.262   4.1571   0.9199   1.7435
 3B1  H10  H  HCH2  0   0.206  -2.1775   2.1223  -1.1098
 3B1  H11  H  HCH2  0   0.243  -2.4527   2.9381   0.4379
 3B1  H12  H  HCH1  0   0.302  -0.0411  -1.0207   1.5798
 3B1  H13  H  HCR6  0   0.263   2.0080  -0.1952   2.2316
 3B1  H14  H  HCH2  0   0.215  -1.2957   1.1579   1.6553
 3B1  H15  H  HCH2  0   0.261  -0.2756   1.7683   0.3463
 3B1  H4   H  HCH2  0   0.206  -3.3910   0.0373  -1.4891

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
 3B1  C02  C06  aromatic  1.387  0.020  1.387
 3B1  C02  C10  aromatic  1.391  0.020  1.391
 3B1  C06  C11  aromatic  1.390  0.020  1.390
 3B1  C10  C01  aromatic  1.386  0.020  1.386
 3B1  C11  C04  aromatic  1.387  0.020  1.387
 3B1  C01  C04  aromatic  1.392  0.020  1.392
 3B1  C04  C09  single    1.517  0.020  1.517
 3B1  C09  C08  single    1.470  0.020  1.470
 3B1  C09  N    single    1.452  0.020  1.452
 3B1  C08  N01  triple    1.150  0.020  1.150
 3B1  N    C    single    1.458  0.020  1.458
 3B1  N    C05  single    1.458  0.020  1.458
 3B1  C07  C    single    1.516  0.020  1.516
 3B1  C07  O    single    1.409  0.020  1.409
 3B1  C05  C03  single    1.517  0.020  1.517
 3B1  C03  O    single    1.408  0.020  1.408
 3B1  C10  H1   single    0.930  0.020  1.080
 3B1  C01  H2   single    0.930  0.020  1.080
 3B1  C02  H3   single    0.930  0.020  1.080
 3B1  C03  H4   single    0.970  0.020  1.090
 3B1  C03  H5   single    0.970  0.020  1.090
 3B1  C05  H6   single    0.970  0.020  1.090
 3B1  C05  H7   single    0.970  0.020  1.090
 3B1  C06  H9   single    0.930  0.020  1.080
 3B1  C07  H10  single    0.970  0.020  1.090
 3B1  C07  H11  single    0.970  0.020  1.090
 3B1  C09  H12  single    0.970  0.020  1.090
 3B1  C11  H13  single    0.930  0.020  1.080
 3B1  C    H14  single    0.970  0.020  1.090
 3B1  C    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
 3B1  H1   C10  C02  120.06  3.000
 3B1  H1   C10  C01  119.79  3.000
 3B1  C02  C10  C01  120.15  3.000
 3B1  H2   C01  C04  119.93  3.000
 3B1  H2   C01  C10  120.07  3.000
 3B1  C04  C01  C10  120.00  3.000
 3B1  H3   C02  C06  120.14  3.000
 3B1  H3   C02  C10  119.97  3.000
 3B1  C06  C02  C10  119.89  3.000
 3B1  H5   C03  H4   108.06  3.000
 3B1  H5   C03  O    107.62  3.000
 3B1  H4   C03  O    110.61  3.000
 3B1  H5   C03  C05  109.67  3.000
 3B1  H4   C03  C05  109.07  3.000
 3B1  O    C03  C05  111.73  3.000
 3B1  C11  C04  C09  120.18  3.000
 3B1  C09  C04  C01  119.99  3.000
 3B1  C11  C04  C01  119.83  3.000
 3B1  H7   C05  H6   107.47  3.000
 3B1  H7   C05  N    110.07  3.000
 3B1  H6   C05  N    111.53  3.000
 3B1  H7   C05  C03  108.06  3.000
 3B1  H6   C05  C03  109.87  3.000
 3B1  N    C05  C03  109.76  3.000
 3B1  C    N    C09  111.02  3.000
 3B1  C    N    C05  109.40  3.000
 3B1  C09  N    C05  112.54  3.000
 3B1  H9   C06  C11  119.80  3.000
 3B1  H9   C06  C02  120.22  3.000
 3B1  C11  C06  C02  119.99  3.000
 3B1  H11  C07  H10  107.96  3.000
 3B1  H11  C07  C    109.76  3.000
 3B1  H10  C07  C    109.17  3.000
 3B1  H11  C07  O    107.56  3.000
 3B1  H10  C07  O    110.52  3.000
 3B1  C    C07  O    111.79  3.000
 3B1  C09  C08  N01  180.00  3.000
 3B1  H12  C09  C08  105.97  3.000
 3B1  H12  C09  N    112.10  3.000
 3B1  C08  C09  N    109.89  3.000
 3B1  H12  C09  C04  108.72  3.000
 3B1  N    C09  C04  112.35  3.000
 3B1  C08  C09  C04  107.52  3.000
 3B1  C07  O    C03  110.60  3.000
 3B1  H13  C11  C06  120.03  3.000
 3B1  H13  C11  C04  119.81  3.000
 3B1  C06  C11  C04  120.15  3.000
 3B1  H15  C    H14  107.46  3.000
 3B1  H15  C    C07  108.38  3.000
 3B1  H14  C    C07  109.79  3.000
 3B1  H15  C    N    110.14  3.000
 3B1  H14  C    N    111.36  3.000
 3B1  C07  C    N    109.64  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
 3B1  CONST_01  C11  C06  C02  C10    0.00   0.0  0
 3B1  CONST_02  C11  C04  C01  C10    0.00   0.0  0
 3B1  CONST_03  C06  C02  C10  C01    0.00   0.0  0
 3B1  CONST_04  C06  C11  C04  C01    0.00   0.0  0
 3B1  CONST_05  C04  C11  C06  C02    0.00   0.0  0
 3B1  CONST_06  C04  C01  C10  C02    0.00   0.0  0
 3B1  CONST_07  C09  C04  C01  C10  180.00   0.0  0
 3B1  CONST_08  C09  C04  C11  C06  180.00   0.0  0
 3B1  CONST_09  H9   C06  C02  C10  180.00   0.0  0
 3B1  CONST_10  H3   C02  C10  C01  180.00   0.0  0
 3B1  CONST_11  H13  C11  C04  C01  180.00   0.0  0
 3B1  CONST_12  H2   C01  C10  C02  180.00   0.0  0
 3B1  CONST_13  H1   C10  C01  C04  180.00   0.0  0
 3B1  Var_01    C    N    C05  C03   57.01  30.0  1
 3B1  Var_02    C    C07  O    C03  -57.61  30.0  1
 3B1  Var_03    C07  C    N    C05  -57.05  30.0  1
 3B1  Var_04    O    C07  C    N     57.81  30.0  1
 3B1  Var_05    O    C03  C05  N    -57.63  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 3B1  chir_01  C09  C04  C08  N  positiv

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
 3B1  plan-1  C10  0.020
 3B1  plan-1  C01  0.020
 3B1  plan-1  C02  0.020
 3B1  plan-1  C04  0.020
 3B1  plan-1  C06  0.020
 3B1  plan-1  C09  0.020
 3B1  plan-1  C11  0.020
 3B1  plan-1  H1   0.020
 3B1  plan-1  H2   0.020
 3B1  plan-1  H3   0.020
 3B1  plan-1  H9   0.020
 3B1  plan-1  H13  0.020

