# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:03:33 2021
#   Inital geometry file: a 102 line input string
#   Ligand name: 2-[(1~{S},5~{R})-3-[2-[(2~{S})-2-methylazetidin-1-yl]-6-(trifluoromethyl)pyrimidin-4-yl]-3-azabicyclo[3.1.0]hexan-6-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCN1c2nc(cc(n2)C(F)(F)F)N3C[C@@H]4[C@H](C3)C4CC(O)=O
#
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
 S6D  S6D  '2-[(1~{S},5~{R})-3-[2-[(2~{S})-2-methylazetidin-1-yl]-6-(trifluoromethyl)pyrimidin-4-yl]-3-azabicyclo[3.1.0]hexan-6-yl]ethanoic acid'  ligand  44  25  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S6D
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
 S6D  N3   N  N     0  -0.511  -4.2506   0.2363  18.0105
 S6D  C4   C  C     0  -0.251  -2.2221  -1.2615  15.3585
 S6D  N2   N  N     0  -0.518  -3.1256  -1.8623  18.0286
 S6D  C7   C  CR16  0  -0.469  -4.5608  -1.2625  19.8485
 S6D  C6   C  CR6   0   0.029  -3.7092  -2.1107  19.1943
 S6D  C9   C  CH2   0  -0.268  -6.4040   0.6981  20.9203
 S6D  C13  C  CH1   0  -0.208  -5.9757   3.1827  21.3391
 S6D  C8   C  CR6   0   0.592  -4.8109  -0.0311  19.1857
 S6D  C16  C  CT    0   1.048  -3.3574  -3.4615  19.7616
 S6D  C2   C  C     0  -0.023  -3.2344   0.6341  15.3370
 S6D  C3   C  C     0  -0.529  -2.4268  -0.1681  14.2909
 S6D  N1   N  N     0  -0.484  -2.8509  -0.3743  16.3214
 S6D  C5   C  CR6   0   0.575  -3.4309  -0.6779  17.4917
 S6D  N4   N  NR5   0  -0.512  -5.6168   0.8997  19.7126
 S6D  C10  C  CR15  0  -0.295  -6.9652   2.0642  21.2199
 S6D  C11  C  CR15  0  -0.277  -6.6815   2.9483  20.0423
 S6D  C12  C  CH2   0  -0.254  -5.9464   2.1333  19.0096
 S6D  C15  C  C     0   0.562  -5.6430   5.6367  21.6984
 S6D  O1   O  O     0  -0.440  -4.8690   5.6996  20.7770
 S6D  O2   O  OH1   0  -0.598  -5.9800   6.6887  22.4386
 S6D  F1   F  F     0  -0.312  -3.7525  -4.4406  18.9409
 S6D  F2   F  F     0  -0.311  -2.0363  -3.5895  19.9189
 S6D  F3   F  F     0  -0.300  -3.9227  -3.6877  20.9496
 S6D  H1   H  H     0   0.233  -2.7850  -2.1810  15.1793
 S6D  H2   H  H     0   0.238  -1.1895  -1.5251  15.5920
 S6D  H3   H  HCR6  0   0.283  -5.0127  -1.5096  20.7953
 S6D  H4   H  HCH2  0   0.250  -7.2107  -0.0240  20.7560
 S6D  H5   H  HCH2  0   0.254  -5.7794   0.3193  21.7327
 S6D  H6   H  HCH1  0   0.259  -4.9268   2.8991  21.3844
 S6D  H7   H  HCH3  0   0.242  -3.3333   2.4571  16.4822
 S6D  H8   H  HCH3  0   0.221  -1.7226   2.0894  15.8455
 S6D  H9   H  HCH3  0   0.230  -2.9885   2.6860  14.7661
 S6D  H10  H  H     0   0.234  -4.3120   0.6146  15.1427
 S6D  H11  H  H     0   0.248  -1.5054   0.3257  13.9844
 S6D  H12  H  H     0   0.255  -2.9782  -0.4747  13.4052
 S6D  H13  H  HCR5  0   0.269  -7.9028   2.1168  21.7596
 S6D  H14  H  HCR5  0   0.267  -7.4060   3.6740  19.6941
 S6D  H15  H  HCH2  0   0.254  -5.0396   2.6204  18.6483
 S6D  H16  H  HCH2  0   0.241  -6.5843   1.9376  18.1420
 S6D  H17  H  HCH2  0   0.284  -7.4181   4.5624  22.1434
 S6D  H18  H  HCH2  0   0.293  -6.0881   4.2239  23.2159
 S6D  H19  H  HOH1  0   0.478  -5.5141   7.4777  22.1241
 S6D  C14  C  CH2   0  -0.612  -6.3380   4.3843  22.1626
 S6D  C1   C  CH3   0  -0.667  -2.7913   2.0490  15.6295

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
 S6D  C3   C4   single    1.542  0.020  1.542
 S6D  C3   C2   single    1.546  0.020  1.546
 S6D  C4   N1   single    1.452  0.020  1.452
 S6D  C2   C1   single    1.511  0.020  1.511
 S6D  C2   N1   single    1.460  0.020  1.460
 S6D  N1   C5   single    1.341  0.020  1.341
 S6D  C5   N3   aromatic  1.333  0.020  1.333
 S6D  C5   N2   aromatic  1.336  0.020  1.336
 S6D  N3   C8   aromatic  1.329  0.020  1.329
 S6D  N2   C6   aromatic  1.327  0.020  1.327
 S6D  F1   C16  single    1.337  0.020  1.337
 S6D  C12  N4   single    1.458  0.020  1.458
 S6D  C12  C11  single    1.507  0.020  1.507
 S6D  C8   N4   single    1.339  0.020  1.339
 S6D  C8   C7   aromatic  1.421  0.020  1.421
 S6D  C6   C16  single    1.507  0.020  1.507
 S6D  C6   C7   aromatic  1.368  0.020  1.368
 S6D  N4   C9   single    1.456  0.020  1.456
 S6D  C16  F2   single    1.337  0.020  1.337
 S6D  C16  F3   single    1.335  0.020  1.335
 S6D  C11  C10  single    1.500  0.020  1.500
 S6D  C11  C13  single    1.495  0.020  1.495
 S6D  O1   C15  double    1.205  0.020  1.205
 S6D  C9   C10  single    1.507  0.020  1.507
 S6D  C10  C13  single    1.498  0.020  1.498
 S6D  C13  C14  single    1.501  0.020  1.501
 S6D  C15  C14  single    1.506  0.020  1.506
 S6D  C15  O2   single    1.330  0.020  1.330
 S6D  C4   H1   single    0.970  0.020  1.090
 S6D  C4   H2   single    0.970  0.020  1.090
 S6D  C7   H3   single    0.930  0.020  1.080
 S6D  C9   H4   single    0.970  0.020  1.090
 S6D  C9   H5   single    0.970  0.020  1.090
 S6D  C13  H6   single    0.970  0.020  1.090
 S6D  C1   H7   single    0.970  0.020  1.090
 S6D  C1   H8   single    0.970  0.020  1.090
 S6D  C1   H9   single    0.970  0.020  1.090
 S6D  C2   H10  single    0.970  0.020  1.090
 S6D  C3   H11  single    0.970  0.020  1.090
 S6D  C3   H12  single    0.970  0.020  1.090
 S6D  C10  H13  single    0.970  0.020  1.090
 S6D  C11  H14  single    0.970  0.020  1.090
 S6D  C12  H15  single    0.970  0.020  1.090
 S6D  C12  H16  single    0.970  0.020  1.090
 S6D  C14  H17  single    0.970  0.020  1.090
 S6D  C14  H18  single    0.970  0.020  1.090
 S6D  O2   H19  single    0.850  0.020  0.980

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
 S6D  C5   N3   C8   117.73  3.000
 S6D  H2   C4   H1   108.62  3.000
 S6D  H2   C4   N1   114.55  3.000
 S6D  H1   C4   N1   113.56  3.000
 S6D  H2   C4   C3   116.43  3.000
 S6D  H1   C4   C3   114.50  3.000
 S6D  N1   C4   C3    88.19  3.000
 S6D  C5   N2   C6   114.74  3.000
 S6D  H3   C7   C8   122.33  3.000
 S6D  H3   C7   C6   122.60  3.000
 S6D  C8   C7   C6   115.07  3.000
 S6D  C16  C6   C7   121.39  3.000
 S6D  C7   C6   N2   125.29  3.000
 S6D  C16  C6   N2   113.32  3.000
 S6D  H5   C9   H4   107.70  3.000
 S6D  H5   C9   C10  112.29  3.000
 S6D  H4   C9   C10  110.69  3.000
 S6D  H5   C9   N4   110.84  3.000
 S6D  H4   C9   N4   111.42  3.000
 S6D  C10  C9   N4   103.93  3.000
 S6D  H6   C13  C14  114.75  3.000
 S6D  H6   C13  C11  116.78  3.000
 S6D  C14  C13  C11  119.17  3.000
 S6D  H6   C13  C10  116.47  3.000
 S6D  C14  C13  C10  118.81  3.000
 S6D  C11  C13  C10   60.14  3.000
 S6D  N4   C8   C7   121.66  3.000
 S6D  C7   C8   N3   120.84  3.000
 S6D  N4   C8   N3   117.50  3.000
 S6D  F3   C16  F2   107.31  3.000
 S6D  F3   C16  F1   107.28  3.000
 S6D  F2   C16  F1   107.10  3.000
 S6D  F3   C16  C6   112.84  3.000
 S6D  F2   C16  C6   111.16  3.000
 S6D  F1   C16  C6   110.87  3.000
 S6D  H10  C2   N1   111.45  3.000
 S6D  H10  C2   C3   112.63  3.000
 S6D  N1   C2   C3    87.75  3.000
 S6D  H10  C2   C1   109.84  3.000
 S6D  N1   C2   C1   116.04  3.000
 S6D  C3   C2   C1   117.62  3.000
 S6D  H12  C3   H11  109.12  3.000
 S6D  H12  C3   C2   115.63  3.000
 S6D  H11  C3   C2   113.40  3.000
 S6D  H12  C3   C4   115.55  3.000
 S6D  H11  C3   C4   113.83  3.000
 S6D  C2   C3   C4    88.21  3.000
 S6D  C5   N1   C2   129.12  3.000
 S6D  C5   N1   C4   128.87  3.000
 S6D  C2   N1   C4    95.08  3.000
 S6D  N1   C5   N2   116.92  3.000
 S6D  N2   C5   N3   126.32  3.000
 S6D  N1   C5   N3   116.77  3.000
 S6D  C12  N4   C8   122.31  3.000
 S6D  C8   N4   C9   123.75  3.000
 S6D  C12  N4   C9   113.27  3.000
 S6D  H13  C10  C11  121.76  3.000
 S6D  H13  C10  C13  119.72  3.000
 S6D  C11  C10  C13   59.83  3.000
 S6D  H13  C10  C9   117.74  3.000
 S6D  C13  C10  C9   116.53  3.000
 S6D  C11  C10  C9   107.93  3.000
 S6D  H14  C11  C12  117.93  3.000
 S6D  H14  C11  C10  121.40  3.000
 S6D  C12  C11  C10  108.15  3.000
 S6D  H14  C11  C13  119.32  3.000
 S6D  C10  C11  C13   60.04  3.000
 S6D  C12  C11  C13  116.68  3.000
 S6D  H16  C12  H15  107.56  3.000
 S6D  H16  C12  C11  110.83  3.000
 S6D  H15  C12  C11  113.01  3.000
 S6D  H16  C12  N4   111.27  3.000
 S6D  H15  C12  N4   110.46  3.000
 S6D  C11  C12  N4   103.74  3.000
 S6D  O2   C15  O1   123.17  3.000
 S6D  O2   C15  C14  111.68  3.000
 S6D  O1   C15  C14  125.15  3.000
 S6D  H19  O2   C15  109.98  3.000
 S6D  H18  C14  H17  105.43  3.000
 S6D  H18  C14  C15  108.25  3.000
 S6D  H17  C14  C15  108.34  3.000
 S6D  H18  C14  C13  110.83  3.000
 S6D  H17  C14  C13  111.02  3.000
 S6D  C15  C14  C13  112.66  3.000
 S6D  H9   C1   H8   108.18  3.000
 S6D  H9   C1   H7   108.10  3.000
 S6D  H8   C1   H7   108.57  3.000
 S6D  H9   C1   C2   109.91  3.000
 S6D  H8   C1   C2   111.11  3.000
 S6D  H7   C1   C2   110.87  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
 S6D  CONST_01  C6   N2   C5   N3      0.00   0.0  0
 S6D  CONST_02  C6   C7   C8   N3      0.00   0.0  0
 S6D  CONST_03  C8   N3   C5   N2      0.00   0.0  0
 S6D  CONST_04  C8   C7   C6   N2      0.00   0.0  0
 S6D  CONST_05  C5   N3   C8   C7      0.00   0.0  0
 S6D  CONST_06  C5   N2   C6   C7      0.00   0.0  0
 S6D  CONST_07  N1   C5   N2   C6    180.00   0.0  0
 S6D  CONST_08  N4   C8   C7   C6    180.00   0.0  0
 S6D  CONST_09  N1   C5   N3   C8    180.00   0.0  0
 S6D  CONST_10  N4   C8   N3   C5    180.00   0.0  0
 S6D  CONST_11  C16  C6   C7   C8    180.00   0.0  0
 S6D  CONST_12  C5   N2   C6   C16   180.00   0.0  0
 S6D  CONST_13  H3   C7   C8   N3    180.00   0.0  0
 S6D  CONST_14  H19  O2   C15  C14   180.00   0.0  0
 S6D  Var_01    C4   N1   C5   N3   -161.84  30.0  1
 S6D  Var_02    C12  N4   C8   N3      3.57  30.0  2
 S6D  Var_03    C11  C12  N4   C9     17.46  30.0  1
 S6D  Var_04    C12  C11  C10  C9      0.09  30.0  1
 S6D  Var_05    N4   C12  C11  C13    54.90  30.0  1
 S6D  Var_06    N4   C9   C10  C13   -54.67  30.0  1
 S6D  Var_07    C10  C9   N4   C8    171.74  30.0  1
 S6D  Var_08    N1   C4   C3   C2     -6.46  30.0  1
 S6D  Var_09    F1   C16  C6   N2    -61.21  30.0  2
 S6D  Var_10    C15  C14  C13  C10  -152.27  30.0  3
 S6D  Var_11    O1   C15  C14  C13    -0.47  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
 S6D  chir_02  C2   C3   C1   N1   positiv
 S6D  chir_03  C13  C11  C10  C14  both
 S6D  chir_04  C10  C13  C9   C11  both
 S6D  chir_05  C11  C13  C10  C12  both

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
 S6D  plan-1  N3   0.020
 S6D  plan-1  N2   0.020
 S6D  plan-1  C7   0.020
 S6D  plan-1  C6   0.020
 S6D  plan-1  C8   0.020
 S6D  plan-1  C16  0.020
 S6D  plan-1  N1   0.020
 S6D  plan-1  C5   0.020
 S6D  plan-1  N4   0.020
 S6D  plan-1  H3   0.020
 S6D  plan-2  C15  0.020
 S6D  plan-2  O1   0.020
 S6D  plan-2  O2   0.020
 S6D  plan-2  H19  0.020
 S6D  plan-2  C14  0.020

