# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 08:56:32 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (1R)-2-[(cyanomethyl)amino]-1-({[2-(difluoromethoxy)benzyl]sulfonyl}methyl)-2-oxoethyl morpholine-4-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)Oc1ccccc1C[S](=O)(=O)C[C@H](OC(=O)N2CCOCC2)C(=O)NCC#N
#
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
 MO9  MO9  '(1R)-2-[(cyanomethyl)amino]-1-({[2-(difluoromethoxy)benzyl]sulfonyl}methyl)-2-oxoethyl morpholine-4-carboxylate'  ligand  52  31  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MO9
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
 MO9  C1    C  CR6   0   0.347   4.2788  -0.5239  -0.2989
 MO9  C2    C  CR6   0   0.030   3.3955  -0.4201  -1.3730
 MO9  C3    C  CR16  0  -0.276   3.5326  -1.3061  -2.4374
 MO9  C4    C  CR16  0  -0.252   4.5243  -2.2729  -2.4385
 MO9  C5    C  CR16  0  -0.254   5.3997  -2.3537  -1.3655
 MO9  C6    C  CR16  0  -0.318   5.2877  -1.4774  -0.2961
 MO9  C7    C  CH2   0  -0.698   2.3139   0.6117  -1.3991
 MO9  C9    C  CH2   0  -0.656  -0.3856   1.2384  -0.9472
 MO9  C10   C  CH1   0  -0.050  -1.5224   1.2017   0.0587
 MO9  C12   C  C     0   0.542  -2.5778   2.2170  -0.3829
 MO9  S8    S  S     0   1.228   0.8363  -0.0446  -0.5945
 MO9  O11   O  O2    0  -0.488  -2.0464  -0.1036   0.0241
 MO9  O13   O  OS    0  -0.658   0.4670  -1.2780  -1.2831
 MO9  O14   O  OS    0  -0.661   1.0475  -0.0897   0.8504
 MO9  N15   N  NH1   0  -0.635  -2.4636   3.4268   0.1846
 MO9  O16   O  O     0  -0.456  -3.4008   1.9525  -1.2362
 MO9  C17   C  CH2   0  -0.374  -3.3445   4.5016  -0.1818
 MO9  C18   C  CSP   0   0.128  -3.0921   4.9780  -1.5446
 MO9  C19   C  C     0   0.787  -3.0502  -0.3649   0.8817
 MO9  N20   N  NT    0  -0.506  -3.4279  -1.6503   0.8404
 MO9  O21   O  O     0  -0.514  -3.5328   0.4988   1.5871
 MO9  C22   C  CH2   0  -0.321  -4.5107  -2.1279   1.6830
 MO9  C23   C  CH2   0  -0.184  -5.4562  -2.9775   0.8515
 MO9  O24   O  O2    0  -0.483  -4.7776  -4.0264   0.1984
 MO9  C25   C  CH2   0  -0.184  -3.7736  -3.5280  -0.6575
 MO9  C26   C  CH2   0  -0.331  -2.7486  -2.7055   0.1027
 MO9  O27   O  O2    0  -0.501   4.1249   0.4071   0.6994
 MO9  C28   C  CH1   0   0.667   4.1699   0.0564   2.0094
 MO9  F29   F  F     0  -0.340   5.4555  -0.0380   2.4389
 MO9  F30   F  F     0  -0.327   3.6185  -1.1527   2.2219
 MO9  N31   N  NS    0  -0.262  -2.8950   5.3653  -2.6086
 MO9  H3    H  HCR6  0   0.266   2.8541  -1.2285  -3.2773
 MO9  H4    H  HCR6  0   0.265   4.6189  -2.9523  -3.2744
 MO9  H5    H  HCR6  0   0.271   6.1856  -3.0969  -1.3574
 MO9  H6    H  HCR6  0   0.283   5.9979  -1.5406   0.5159
 MO9  H71   H  HCH2  0   0.332   2.5757   1.5390  -0.8913
 MO9  H72   H  HCH2  0   0.335   2.0200   0.8466  -2.4233
 MO9  H91   H  HCH2  0   0.333   0.1266   2.2006  -0.8914
 MO9  H92   H  HCH2  0   0.330  -0.7323   1.0834  -1.9699
 MO9  H10   H  HCH1  0   0.301  -1.1427   1.4456   1.0550
 MO9  HN15  H  HNH1  0   0.428  -1.7847   3.5963   0.9094
 MO9  H171  H  HCH2  0   0.322  -4.3927   4.2074  -0.1092
 MO9  H172  H  HCH2  0   0.339  -3.1895   5.3308   0.5057
 MO9  H221  H  HCH2  0   0.249  -4.1001  -2.7162   2.5105
 MO9  H222  H  HCH2  0   0.272  -5.0534  -1.2872   2.1078
 MO9  H231  H  HCH2  0   0.247  -6.2112  -3.4269   1.4975
 MO9  H232  H  HCH2  0   0.210  -5.9703  -2.3371   0.1212
 MO9  H251  H  HCH2  0   0.247  -3.2840  -4.3843  -1.1229
 MO9  H252  H  HCH2  0   0.211  -4.2149  -2.9129  -1.4540
 MO9  H261  H  HCH2  0   0.281  -2.0215  -2.2938  -0.5909
 MO9  H262  H  HCH2  0   0.248  -2.2079  -3.3425   0.8107
 MO9  H28   H  HCH1  0   0.231   3.6574   0.8175   2.5933

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
 MO9  C1   C2    aromatic  1.394  0.020  1.394
 MO9  C1   C6    aromatic  1.388  0.020  1.388
 MO9  C1   O27   single    1.374  0.020  1.374
 MO9  C2   C3    aromatic  1.392  0.020  1.392
 MO9  C2   C7    single    1.495  0.020  1.495
 MO9  C3   C4    aromatic  1.385  0.020  1.385
 MO9  C3   H3    single    0.930  0.020  1.080
 MO9  C4   C5    aromatic  1.387  0.020  1.387
 MO9  C4   H4    single    0.930  0.020  1.080
 MO9  C5   C6    aromatic  1.387  0.020  1.387
 MO9  C5   H5    single    0.930  0.020  1.080
 MO9  C6   H6    single    0.930  0.020  1.080
 MO9  C7   S8    single    1.806  0.020  1.806
 MO9  C7   H71   single    0.970  0.020  1.090
 MO9  C7   H72   single    0.970  0.020  1.090
 MO9  C9   C10   single    1.518  0.020  1.518
 MO9  C9   S8    single    1.806  0.020  1.806
 MO9  C9   H91   single    0.970  0.020  1.090
 MO9  C9   H92   single    0.970  0.020  1.090
 MO9  C10  C12   single    1.530  0.020  1.530
 MO9  C10  O11   single    1.407  0.020  1.407
 MO9  C10  H10   single    0.970  0.020  1.090
 MO9  C12  N15   single    1.341  0.020  1.341
 MO9  C12  O16   double    1.215  0.020  1.215
 MO9  S8   O13   double    1.460  0.020  1.460
 MO9  S8   O14   double    1.461  0.020  1.461
 MO9  O11  C19   single    1.346  0.020  1.346
 MO9  N15  C17   single    1.437  0.020  1.437
 MO9  N15  HN15  single    0.860  0.020  1.020
 MO9  C17  C18   single    1.466  0.020  1.466
 MO9  C17  H171  single    0.970  0.020  1.090
 MO9  C17  H172  single    0.970  0.020  1.090
 MO9  C18  N31   triple    1.149  0.020  1.149
 MO9  C19  N20   single    1.340  0.020  1.340
 MO9  C19  O21   double    1.215  0.020  1.215
 MO9  N20  C22   single    1.453  0.020  1.453
 MO9  N20  C26   single    1.456  0.020  1.456
 MO9  C22  C23   single    1.519  0.020  1.519
 MO9  C22  H221  single    0.970  0.020  1.090
 MO9  C22  H222  single    0.970  0.020  1.090
 MO9  C23  O24   single    1.410  0.020  1.410
 MO9  C23  H231  single    0.970  0.020  1.090
 MO9  C23  H232  single    0.970  0.020  1.090
 MO9  O24  C25   single    1.410  0.020  1.410
 MO9  C25  C26   single    1.518  0.020  1.518
 MO9  C25  H251  single    0.970  0.020  1.090
 MO9  C25  H252  single    0.970  0.020  1.090
 MO9  C26  H261  single    0.970  0.020  1.090
 MO9  C26  H262  single    0.970  0.020  1.090
 MO9  O27  C28   single    1.357  0.020  1.357
 MO9  C28  F29   single    1.359  0.020  1.359
 MO9  C28  F30   single    1.346  0.020  1.346
 MO9  C28  H28   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
 MO9  O27   C1   C6    123.06  3.000
 MO9  O27   C1   C2    116.00  3.000
 MO9  C6    C1   C2    120.87  3.000
 MO9  C7    C2   C3    119.82  3.000
 MO9  C7    C2   C1    121.54  3.000
 MO9  C3    C2   C1    118.64  3.000
 MO9  H3    C3   C4    119.88  3.000
 MO9  H3    C3   C2    119.08  3.000
 MO9  C4    C3   C2    121.03  3.000
 MO9  H4    C4   C5    120.41  3.000
 MO9  H4    C4   C3    120.12  3.000
 MO9  C5    C4   C3    119.47  3.000
 MO9  H5    C5   C6    119.15  3.000
 MO9  H5    C5   C4    120.28  3.000
 MO9  C6    C5   C4    120.57  3.000
 MO9  H6    C6   C5    119.29  3.000
 MO9  H6    C6   C1    121.29  3.000
 MO9  C5    C6   C1    119.41  3.000
 MO9  H72   C7   H71   108.61  3.000
 MO9  H72   C7   S8    106.02  3.000
 MO9  H71   C7   S8    107.36  3.000
 MO9  H72   C7   C2    111.09  3.000
 MO9  H71   C7   C2    113.93  3.000
 MO9  S8    C7   C2    109.47  3.000
 MO9  H92   C9   H91   108.81  3.000
 MO9  H92   C9   S8    107.28  3.000
 MO9  H91   C9   S8    107.38  3.000
 MO9  H92   C9   C10   112.32  3.000
 MO9  H91   C9   C10   109.80  3.000
 MO9  S8    C9   C10   111.09  3.000
 MO9  H10   C10  O11   111.01  3.000
 MO9  H10   C10  C12   110.76  3.000
 MO9  O11   C10  C12   110.59  3.000
 MO9  H10   C10  C9    109.77  3.000
 MO9  O11   C10  C9    106.56  3.000
 MO9  C12   C10  C9    108.01  3.000
 MO9  O16   C12  N15   123.46  3.000
 MO9  O16   C12  C10   121.72  3.000
 MO9  N15   C12  C10   114.70  3.000
 MO9  O14   S8   O13   118.48  3.000
 MO9  O14   S8   C9    108.23  3.000
 MO9  O13   S8   C9    109.68  3.000
 MO9  O14   S8   C7    109.48  3.000
 MO9  O13   S8   C7    107.69  3.000
 MO9  C9    S8   C7    102.03  3.000
 MO9  C19   O11  C10   116.24  3.000
 MO9  HN15  N15  C17   118.08  3.000
 MO9  HN15  N15  C12   120.90  3.000
 MO9  C17   N15  C12   120.97  3.000
 MO9  H172  C17  H171  107.47  3.000
 MO9  H172  C17  C18   108.38  3.000
 MO9  H171  C17  C18   108.36  3.000
 MO9  H172  C17  N15   108.75  3.000
 MO9  H171  C17  N15   111.73  3.000
 MO9  C18   C17  N15   112.00  3.000
 MO9  N31   C18  C17   180.00  3.000
 MO9  O21   C19  N20   125.98  3.000
 MO9  O21   C19  O11   121.88  3.000
 MO9  N20   C19  O11   112.13  3.000
 MO9  C26   N20  C22   113.79  3.000
 MO9  C26   N20  C19   125.39  3.000
 MO9  C22   N20  C19   120.50  3.000
 MO9  H222  C22  H221  107.90  3.000
 MO9  H222  C22  C23   109.61  3.000
 MO9  H221  C22  C23   110.28  3.000
 MO9  H222  C22  N20   110.15  3.000
 MO9  H221  C22  N20   109.60  3.000
 MO9  C23   C22  N20   109.29  3.000
 MO9  H232  C23  H231  108.06  3.000
 MO9  H232  C23  O24   110.54  3.000
 MO9  H231  C23  O24   107.52  3.000
 MO9  H232  C23  C22   109.21  3.000
 MO9  H231  C23  C22   109.71  3.000
 MO9  O24   C23  C22   111.72  3.000
 MO9  C25   O24  C23   111.16  3.000
 MO9  H252  C25  H251  108.09  3.000
 MO9  H252  C25  C26   109.32  3.000
 MO9  H251  C25  C26   109.63  3.000
 MO9  H252  C25  O24   110.60  3.000
 MO9  H251  C25  O24   107.52  3.000
 MO9  C26   C25  O24   111.60  3.000
 MO9  H262  C26  H261  107.64  3.000
 MO9  H262  C26  C25   109.99  3.000
 MO9  H261  C26  C25   109.73  3.000
 MO9  H262  C26  N20   108.93  3.000
 MO9  H261  C26  N20   111.18  3.000
 MO9  C25   C26  N20   109.35  3.000
 MO9  C28   O27  C1    121.52  3.000
 MO9  H28   C28  F30   110.54  3.000
 MO9  H28   C28  F29   108.95  3.000
 MO9  F30   C28  F29   105.98  3.000
 MO9  H28   C28  O27   108.77  3.000
 MO9  F30   C28  O27   111.78  3.000
 MO9  F29   C28  O27   110.77  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
 MO9  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 MO9  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 MO9  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 MO9  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 MO9  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 MO9  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 MO9  CONST_07  O27   C1   C2   C3    180.00   0.0  0
 MO9  CONST_08  C7    C2   C3   C4    180.00   0.0  0
 MO9  CONST_09  O27   C1   C6   C5    180.00   0.0  0
 MO9  CONST_10  C7    C2   C1   C6    180.00   0.0  0
 MO9  CONST_11  H3    C3   C2   C1    180.00   0.0  0
 MO9  CONST_12  H5    C5   C6   C1    180.00   0.0  0
 MO9  CONST_13  H6    C6   C1   C2    180.00   0.0  0
 MO9  CONST_14  H4    C4   C3   C2    180.00   0.0  0
 MO9  CONST_15  C17   N15  C12  C10   180.00   0.0  0
 MO9  CONST_16  C17   N15  C12  O16     0.00   0.0  0
 MO9  CONST_17  HN15  N15  C12  C10     0.00   0.0  0
 MO9  Var_01    O24   C23  C22  N20    54.82  30.0  1
 MO9  Var_02    O24   C25  C26  N20   -54.80  30.0  1
 MO9  Var_03    C25   C26  N20  C22    52.58  30.0  1
 MO9  Var_04    C26   N20  C22  C23   -52.51  30.0  1
 MO9  Var_05    C26   C25  O24  C23    59.28  30.0  1
 MO9  Var_06    S8    C7   C2   C1    -88.13  30.0  2
 MO9  Var_07    C22   N20  C19  O11  -179.27  30.0  2
 MO9  Var_08    F29   C28  O27  C1     82.16  30.0  3
 MO9  Var_09    C9    S8   C7   C2   -172.13  30.0  3
 MO9  Var_10    N20   C19  O11  C10  -175.99  30.0  3
 MO9  Var_11    C10   C9   S8   C7   -157.25  30.0  1
 MO9  Var_12    C18   C17  N15  C12   -69.51  30.0  3

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
 MO9  chir_01  C10  C9  C12  O11  negativ

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
 MO9  plan-1  C1    0.020
 MO9  plan-1  C2    0.020
 MO9  plan-1  C3    0.020
 MO9  plan-1  C4    0.020
 MO9  plan-1  C5    0.020
 MO9  plan-1  C6    0.020
 MO9  plan-1  C7    0.020
 MO9  plan-1  O27   0.020
 MO9  plan-1  H3    0.020
 MO9  plan-1  H4    0.020
 MO9  plan-1  H5    0.020
 MO9  plan-1  H6    0.020
 MO9  plan-2  C10   0.020
 MO9  plan-2  C12   0.020
 MO9  plan-2  N15   0.020
 MO9  plan-2  O16   0.020
 MO9  plan-2  C17   0.020
 MO9  plan-2  HN15  0.020
 MO9  plan-3  O11   0.020
 MO9  plan-3  C19   0.020
 MO9  plan-3  N20   0.020
 MO9  plan-3  O21   0.020

