# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 09:41:04 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-[2-amino-5-(4-fluorophenyl)pyrimidin-4-yl]-N,N-dimethylazetidine-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)[S](=O)(=O)N1CC(C1)c2nc(N)ncc2c3ccc(F)cc3
#
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
 L7R  L7R  "3-[2-amino-5-(4-fluorophenyl)pyrimidin-4-yl]-N,N-dimethylazetidine-1-sulfonamide"
  ligand  42  24  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L7R
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
 L7R  F    F  F     0  -0.313  -83.1683   -0.7158  34.4539
 L7R  C2   C  CR6   0   0.517  -82.7568   -1.9165  34.8896
 L7R  C1   C  CR16  0  -0.395  -82.9542   -3.0236  34.0872
 L7R  C3   C  CR16  0  -0.395  -82.1522   -2.0090  36.1278
 L7R  C4   C  CR16  0  -0.286  -81.7285   -3.2541  36.5683
 L7R  C5   C  CR6   0   0.018  -81.9071   -4.3970  35.7885
 L7R  C    C  CR16  0  -0.284  -82.5309   -4.2608  34.5478
 L7R  C6   C  CR6   0  -0.068  -81.4869   -5.7162  36.2936
 L7R  C9   C  CR6   0   0.348  -80.6472   -6.6046  35.6123
 L7R  N2   N  N     0  -0.471  -80.3441   -7.7913  36.1146
 L7R  C8   C  CR6   0   0.542  -80.8472   -8.1240  37.3036
 L7R  N1   N  NH2   0  -0.821  -80.5226   -9.3304  37.8020
 L7R  N    N  N     0  -0.448  -81.6256   -7.3363  38.0555
 L7R  C7   C  CR16  0  -0.032  -81.9270   -6.1630  37.5382
 L7R  C10  C  C     0  -0.440  -80.0400   -6.2733  34.2813
 L7R  C12  C  C     0  -0.241  -78.6736   -6.9331  34.0054
 L7R  N3   N  N     0  -0.569  -79.3692   -7.9259  33.1812
 L7R  C11  C  C     0  -0.255  -80.5990   -7.1276  33.1121
 L7R  S    S  S     0   1.515  -78.7046   -8.6835  31.8930
 L7R  O    O  OS    0  -0.656  -77.8611   -7.8168  31.0837
 L7R  O1   O  OS    0  -0.661  -79.8109   -9.3574  31.2283
 L7R  N4   N  N     0  -0.565  -77.6966   -9.7073  32.7076
 L7R  C14  C  CH3   0  -0.525  -78.3593  -10.7461  33.4875
 L7R  C13  C  CH3   0  -0.519  -76.4999  -10.1583  32.0072
 L7R  H1   H  HCR6  0   0.280  -83.4390   -2.9272  33.1245
 L7R  H2   H  HCR6  0   0.280  -82.0068   -1.1263  36.7367
 L7R  H3   H  HCR6  0   0.265  -81.2415   -3.3317  37.5324
 L7R  H4   H  HCR6  0   0.271  -82.7102   -5.1348  33.9340
 L7R  H5   H  HNH2  0   0.397  -80.0818  -10.0072  37.2039
 L7R  H6   H  HNH2  0   0.397  -81.0109   -9.6733  38.6107
 L7R  H7   H  HCR6  0   0.267  -82.5703   -5.5249  38.1375
 L7R  H8   H  H     0   0.291  -80.0619   -5.2030  34.0939
 L7R  H9   H  H     0   0.259  -78.1438   -7.3564  34.8563
 L7R  H10  H  H     0   0.259  -78.0078   -6.2790  33.4380
 L7R  H11  H  H     0   0.262  -80.7114   -6.5472  32.1937
 L7R  H12  H  H     0   0.263  -81.5084   -7.6956  33.3029
 L7R  H13  H  HCH3  0   0.260  -79.1785  -10.3242  34.0653
 L7R  H14  H  HCH3  0   0.238  -78.7384  -11.5626  32.8676
 L7R  H15  H  HCH3  0   0.258  -77.6334  -11.1533  34.1893
 L7R  H16  H  HCH3  0   0.257  -75.8492  -10.6246  32.7448
 L7R  H17  H  HCH3  0   0.234  -76.7123  -10.8939  31.2263
 L7R  H18  H  HCH3  0   0.264  -75.9641   -9.3191  31.5749

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
 L7R  O1   S    double    1.456  0.020  1.456
 L7R  C13  N4   single    1.458  0.020  1.458
 L7R  O    S    double    1.455  0.020  1.455
 L7R  S    N4   single    1.652  0.020  1.652
 L7R  S    N3   single    1.636  0.020  1.636
 L7R  N4   C14  single    1.458  0.020  1.458
 L7R  C11  N3   single    1.468  0.020  1.468
 L7R  C11  C10  single    1.552  0.020  1.552
 L7R  N3   C12  single    1.466  0.020  1.466
 L7R  C12  C10  single    1.542  0.020  1.542
 L7R  C1   C    aromatic  1.386  0.020  1.386
 L7R  C1   C2   aromatic  1.381  0.020  1.381
 L7R  C10  C9   single    1.500  0.020  1.500
 L7R  F    C2   single    1.342  0.020  1.342
 L7R  C    C5   aromatic  1.395  0.020  1.395
 L7R  C2   C3   aromatic  1.381  0.020  1.381
 L7R  C9   N2   aromatic  1.324  0.020  1.324
 L7R  C9   C6   aromatic  1.399  0.020  1.399
 L7R  C5   C6   single    1.474  0.020  1.474
 L7R  C5   C4   aromatic  1.395  0.020  1.395
 L7R  N2   C8   aromatic  1.333  0.020  1.333
 L7R  C3   C4   aromatic  1.387  0.020  1.387
 L7R  C6   C7   aromatic  1.394  0.020  1.394
 L7R  C8   N1   single    1.345  0.020  1.345
 L7R  C8   N    aromatic  1.339  0.020  1.339
 L7R  C7   N    aromatic  1.317  0.020  1.317
 L7R  C1   H1   single    0.930  0.020  1.080
 L7R  C3   H2   single    0.930  0.020  1.080
 L7R  C4   H3   single    0.930  0.020  1.080
 L7R  C    H4   single    0.930  0.020  1.080
 L7R  N1   H5   single    0.890  0.020  1.040
 L7R  N1   H6   single    0.890  0.020  1.040
 L7R  C7   H7   single    0.930  0.020  1.080
 L7R  C10  H8   single    0.970  0.020  1.090
 L7R  C12  H9   single    0.970  0.020  1.090
 L7R  C12  H10  single    0.970  0.020  1.090
 L7R  C11  H11  single    0.970  0.020  1.090
 L7R  C11  H12  single    0.970  0.020  1.090
 L7R  C14  H13  single    0.970  0.020  1.090
 L7R  C14  H14  single    0.970  0.020  1.090
 L7R  C14  H15  single    0.970  0.020  1.090
 L7R  C13  H16  single    0.970  0.020  1.090
 L7R  C13  H17  single    0.970  0.020  1.090
 L7R  C13  H18  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
 L7R  C3   C2   C1   121.98  3.000
 L7R  C3   C2   F    119.03  3.000
 L7R  C1   C2   F    118.99  3.000
 L7R  H1   C1   C    120.79  3.000
 L7R  H1   C1   C2   120.61  3.000
 L7R  C    C1   C2   118.59  3.000
 L7R  H2   C3   C4   120.83  3.000
 L7R  H2   C3   C2   120.57  3.000
 L7R  C4   C3   C2   118.59  3.000
 L7R  H3   C4   C5   119.77  3.000
 L7R  H3   C4   C3   118.98  3.000
 L7R  C5   C4   C3   121.25  3.000
 L7R  C6   C5   C    121.31  3.000
 L7R  C6   C5   C4   120.35  3.000
 L7R  C    C5   C4   118.31  3.000
 L7R  H4   C    C5   119.94  3.000
 L7R  H4   C    C1   118.77  3.000
 L7R  C5   C    C1   121.27  3.000
 L7R  C7   C6   C9   114.87  3.000
 L7R  C7   C6   C5   120.20  3.000
 L7R  C9   C6   C5   124.93  3.000
 L7R  C10  C9   N2   116.23  3.000
 L7R  N2   C9   C6   121.46  3.000
 L7R  C10  C9   C6   122.32  3.000
 L7R  C8   N2   C9   118.40  3.000
 L7R  N    C8   N1   117.39  3.000
 L7R  N    C8   N2   125.00  3.000
 L7R  N1   C8   N2   117.59  3.000
 L7R  H6   N1   H5   117.53  3.000
 L7R  H6   N1   C8   119.13  3.000
 L7R  H5   N1   C8   119.30  3.000
 L7R  C7   N    C8   115.89  3.000
 L7R  H7   C7   N    116.24  3.000
 L7R  H7   C7   C6   119.42  3.000
 L7R  N    C7   C6   124.34  3.000
 L7R  H8   C10  C11  113.88  3.000
 L7R  H8   C10  C12  114.10  3.000
 L7R  C11  C10  C12   87.07  3.000
 L7R  H8   C10  C9   111.24  3.000
 L7R  C12  C10  C9   115.02  3.000
 L7R  C11  C10  C9   113.64  3.000
 L7R  H10  C12  H9   110.02  3.000
 L7R  H10  C12  N3   113.75  3.000
 L7R  H9   C12  N3   114.03  3.000
 L7R  H10  C12  C10  112.14  3.000
 L7R  H9   C12  C10  117.26  3.000
 L7R  N3   C12  C10   88.27  3.000
 L7R  S    N3   C11  123.73  3.000
 L7R  C11  N3   C12   93.20  3.000
 L7R  S    N3   C12  124.31  3.000
 L7R  H12  C11  H11  109.79  3.000
 L7R  H12  C11  N3   114.06  3.000
 L7R  H11  C11  N3   114.51  3.000
 L7R  H12  C11  C10  117.11  3.000
 L7R  H11  C11  C10  112.21  3.000
 L7R  N3   C11  C10   87.83  3.000
 L7R  N4   S    O1   113.70  3.000
 L7R  N4   S    O    106.84  3.000
 L7R  O1   S    O    117.53  3.000
 L7R  N4   S    N3    98.43  3.000
 L7R  O    S    N3   113.44  3.000
 L7R  O1   S    N3   105.37  3.000
 L7R  C13  N4   C14  114.18  3.000
 L7R  C14  N4   S    115.34  3.000
 L7R  C13  N4   S    117.11  3.000
 L7R  H15  C14  H14  108.51  3.000
 L7R  H15  C14  H13  107.75  3.000
 L7R  H14  C14  H13  109.26  3.000
 L7R  H15  C14  N4   107.95  3.000
 L7R  H14  C14  N4   112.73  3.000
 L7R  H13  C14  N4   110.49  3.000
 L7R  H18  C13  H17  109.36  3.000
 L7R  H18  C13  H16  107.82  3.000
 L7R  H17  C13  H16  108.17  3.000
 L7R  H18  C13  N4   110.93  3.000
 L7R  H17  C13  N4   113.06  3.000
 L7R  H16  C13  N4   107.31  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
 L7R  CONST_01  C5   C    C1   C2      0.00   0.0  0
 L7R  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 L7R  CONST_03  C6   C5   C    C1    180.00   0.0  0
 L7R  CONST_04  C4   C5   C    C1      0.00   0.0  0
 L7R  CONST_05  C4   C3   C2   C1      0.00   0.0  0
 L7R  CONST_06  C    C1   C2   C3      0.00   0.0  0
 L7R  CONST_07  C    C5   C4   C3      0.00   0.0  0
 L7R  CONST_08  C6   C5   C4   C3    180.00   0.0  0
 L7R  CONST_11  N2   C9   C6   C5    180.00   0.0  0
 L7R  CONST_12  N    C7   C6   C5    180.00   0.0  0
 L7R  CONST_15  C8   N2   C9   C6      0.00   0.0  0
 L7R  CONST_16  C8   N    C7   C6      0.00   0.0  0
 L7R  CONST_17  N    C8   N2   C9      0.00   0.0  0
 L7R  CONST_18  N    C7   C6   C9      0.00   0.0  0
 L7R  CONST_19  C7   C6   C9   N2      0.00   0.0  0
 L7R  CONST_20  C7   N    C8   N2      0.00   0.0  0
 L7R  CONST_21  C10  C9   C6   C5      0.00   0.0  0
 L7R  CONST_22  C10  C9   N2   C8    180.00   0.0  0
 L7R  CONST_23  C10  C9   C6   C7    180.00   0.0  0
 L7R  CONST_24  C    C1   C2   F     180.00   0.0  0
 L7R  CONST_25  C4   C3   C2   F     180.00   0.0  0
 L7R  CONST_26  N1   C8   N2   C9    180.00   0.0  0
 L7R  CONST_27  C7   N    C8   N1    180.00   0.0  0
 L7R  CONST_28  H4   C    C1   C2    180.00   0.0  0
 L7R  CONST_29  H3   C4   C3   C2    180.00   0.0  0
 L7R  CONST_30  H2   C3   C2   C1    180.00   0.0  0
 L7R  CONST_31  H1   C1   C2   C3    180.00   0.0  0
 L7R  CONST_32  H4   C    C5   C4    180.00   0.0  0
 L7R  CONST_33  H1   C1   C    C5    180.00   0.0  0
 L7R  CONST_34  H7   C7   C6   C5      0.00   0.0  0
 L7R  CONST_35  H2   C3   C4   C5    180.00   0.0  0
 L7R  CONST_36  H3   C4   C5   C     180.00   0.0  0
 L7R  CONST_37  H4   C    C5   C6      0.00   0.0  0
 L7R  CONST_38  H3   C4   C5   C6      0.00   0.0  0
 L7R  CONST_39  H7   C7   C6   C9    180.00   0.0  0
 L7R  CONST_40  H7   C7   N    C8    180.00   0.0  0
 L7R  CONST_41  H5   N1   C8   N2      0.00   0.0  0
 L7R  CONST_42  H6   N1   C8   N2    180.00   0.0  0
 L7R  CONST_43  H5   N1   C8   N     180.00   0.0  0
 L7R  CONST_44  H6   N1   C8   N       0.00   0.0  0
 L7R  Var_01    C12  N3   C11  C10   -14.71  30.0  1
 L7R  Var_02    S    N3   C11  C10  -150.44  30.0  1
 L7R  Var_03    S    N3   C12  C10   150.15  30.0  1
 L7R  Var_04    H11  C11  N3   C12    98.77  30.0  1
 L7R  Var_05    H12  C11  N3   C12  -133.56  30.0  1
 L7R  Var_06    H9   C12  N3   C11   134.02  30.0  1
 L7R  Var_07    H10  C12  N3   C11   -98.69  30.0  1
 L7R  Var_08    O1   S    N3   C12  -168.80  30.0  3
 L7R  Var_09    O    S    N3   C12   -38.88  30.0  3
 L7R  Var_10    N4   S    N3   C12    73.67  30.0  3
 L7R  Var_11    O1   S    N3   C11   -46.34  30.0  3
 L7R  Var_12    O    S    N3   C11    83.58  30.0  3
 L7R  Var_13    N4   S    N3   C11  -163.87  30.0  3
 L7R  Var_14    H11  C11  N3   S     -36.96  30.0  1
 L7R  Var_15    H12  C11  N3   S      90.71  30.0  1
 L7R  Var_16    H9   C12  N3   S     -90.63  30.0  1
 L7R  Var_17    H10  C12  N3   S      36.66  30.0  1
 L7R  Var_18    C13  N4   S    N3   -153.54  30.0  3
 L7R  Var_19    C14  N4   S    N3     67.73  30.0  3
 L7R  Var_20    C13  N4   S    O     -35.83  30.0  3
 L7R  Var_21    C14  N4   S    O    -174.56  30.0  3
 L7R  Var_22    C13  N4   S    O1     95.49  30.0  3
 L7R  Var_23    C14  N4   S    O1    -43.23  30.0  3
 L7R  Var_24    H16  C13  N4   S     167.29  30.0  3
 L7R  Var_25    H17  C13  N4   S     -73.53  30.0  3
 L7R  Var_26    H18  C13  N4   S      49.75  30.0  3
 L7R  Var_27    H13  C14  N4   S     -46.01  30.0  3
 L7R  Var_28    H14  C14  N4   S      76.56  30.0  3
 L7R  Var_29    H15  C14  N4   S    -163.60  30.0  3
 L7R  Var_30    H16  C13  N4   C14   -53.52  30.0  3
 L7R  Var_31    H17  C13  N4   C14    65.66  30.0  3
 L7R  Var_32    H18  C13  N4   C14  -171.06  30.0  3
 L7R  Var_33    H13  C14  N4   C13   174.05  30.0  3
 L7R  Var_34    H14  C14  N4   C13   -63.37  30.0  3
 L7R  Var_35    H15  C14  N4   C13    56.46  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
 L7R  chir_01  C10  C11  C12  C9  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
 L7R  plan-1  F    0.020
 L7R  plan-1  C2   0.020
 L7R  plan-1  C1   0.020
 L7R  plan-1  C3   0.020
 L7R  plan-1  C4   0.020
 L7R  plan-1  C5   0.020
 L7R  plan-1  C    0.020
 L7R  plan-1  C6   0.020
 L7R  plan-1  H1   0.020
 L7R  plan-1  H2   0.020
 L7R  plan-1  H3   0.020
 L7R  plan-1  H4   0.020
 L7R  plan-2  C5   0.020
 L7R  plan-2  C6   0.020
 L7R  plan-2  C9   0.020
 L7R  plan-2  N2   0.020
 L7R  plan-2  C8   0.020
 L7R  plan-2  N1   0.020
 L7R  plan-2  N    0.020
 L7R  plan-2  C7   0.020
 L7R  plan-2  C10  0.020
 L7R  plan-2  H7   0.020
 L7R  plan-3  C8   0.020
 L7R  plan-3  N1   0.020
 L7R  plan-3  H5   0.020
 L7R  plan-3  H6   0.020

