# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:40:22 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: 1-[(3~{R})-3-azanylpiperidin-1-yl]-4,4,4-tris(fluoranyl)butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCCN(C1)C(=O)CCC(F)(F)F
#
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
 S8G  S8G  1-[(3~{R})-3-azanylpiperidin-1-yl]-4,4,4-tris(fluoranyl)butan-1-one  ligand  30  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S8G
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
 S8G  N1   N  NT    0  -0.457  40.1146   1.1335  75.3471
 S8G  C4   C  CH2   0  -0.308  41.0779   0.3828  76.1334
 S8G  C5   C  C     0   0.588  40.4195   2.3607  74.8752
 S8G  C6   C  CH2   0  -0.639  39.2968   3.1398  74.2096
 S8G  C7   C  CH2   0  -0.634  39.7806   4.4945  73.7130
 S8G  C8   C  CT    0   1.001  38.6753   5.3075  73.0994
 S8G  N    N  NH2   0  -0.791  41.6642  -0.3963  78.3541
 S8G  C    C  CH1   0  -0.089  40.6691   0.3557  77.6069
 S8G  O    O  O     0  -0.502  41.5436   2.8381  74.9607
 S8G  C1   C  CH2   0  -0.451  39.2384  -0.1702  77.7438
 S8G  C2   C  CH2   0  -0.432  38.2642   0.5770  76.8383
 S8G  C3   C  CH2   0  -0.331  38.7728   0.5760  75.4029
 S8G  F    F  F     0  -0.316  38.1125   4.7025  72.0400
 S8G  F1   F  F     0  -0.312  39.1173   6.4997  72.6698
 S8G  F2   F  F     0  -0.316  37.6785   5.5592  73.9648
 S8G  H1   H  HCH2  0   0.234  41.1192  -0.6417  75.7445
 S8G  H2   H  HCH2  0   0.264  42.0681   0.8157  76.0207
 S8G  H3   H  HCH2  0   0.283  38.4821   3.2671  74.9269
 S8G  H4   H  HCH2  0   0.289  38.8891   2.5537  73.3824
 S8G  H5   H  HCH2  0   0.283  40.5646   4.3738  72.9640
 S8G  H6   H  HCH2  0   0.282  40.2062   5.0766  74.5316
 S8G  H7   H  HNH2  0   0.348  41.4567  -0.3369  79.3437
 S8G  H8   H  HNH2  0   0.337  41.5867  -1.3803  78.1201
 S8G  H10  H  HCH1  0   0.227  40.6985   1.3891  77.9697
 S8G  H11  H  HCH2  0   0.238  38.9194  -0.1082  78.7875
 S8G  H12  H  HCH2  0   0.212  39.2333  -1.2339  77.4741
 S8G  H13  H  HCH2  0   0.225  38.1455   1.6112  77.1770
 S8G  H14  H  HCH2  0   0.241  37.2757   0.1147  76.8735
 S8G  H15  H  HCH2  0   0.276  38.0988   1.1176  74.7453
 S8G  H16  H  HCH2  0   0.248  38.8181  -0.4513  75.0279

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
 S8G  F   C8   single  1.343  0.020  1.343
 S8G  F1  C8   single  1.342  0.020  1.342
 S8G  C8  C7   single  1.503  0.020  1.503
 S8G  C8  F2   single  1.344  0.020  1.344
 S8G  C7  C6   single  1.522  0.020  1.522
 S8G  C6  C5   single  1.520  0.020  1.520
 S8G  O   C5   double  1.224  0.020  1.224
 S8G  C5  N1   single  1.350  0.020  1.350
 S8G  N1  C3   single  1.454  0.020  1.454
 S8G  N1  C4   single  1.452  0.020  1.452
 S8G  C3  C2   single  1.523  0.020  1.523
 S8G  C4  C    single  1.529  0.020  1.529
 S8G  C2  C1   single  1.526  0.020  1.526
 S8G  C1  C    single  1.530  0.020  1.530
 S8G  C   N    single  1.454  0.020  1.454
 S8G  C4  H1   single  0.970  0.020  1.090
 S8G  C4  H2   single  0.970  0.020  1.090
 S8G  C6  H3   single  0.970  0.020  1.090
 S8G  C6  H4   single  0.970  0.020  1.090
 S8G  C7  H5   single  0.970  0.020  1.090
 S8G  C7  H6   single  0.970  0.020  1.090
 S8G  N   H7   single  0.890  0.020  1.040
 S8G  N   H8   single  0.890  0.020  1.040
 S8G  C   H10  single  0.970  0.020  1.090
 S8G  C1  H11  single  0.970  0.020  1.090
 S8G  C1  H12  single  0.970  0.020  1.090
 S8G  C2  H13  single  0.970  0.020  1.090
 S8G  C2  H14  single  0.970  0.020  1.090
 S8G  C3  H15  single  0.970  0.020  1.090
 S8G  C3  H16  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
 S8G  C3   N1  C5   124.78  3.000
 S8G  C3   N1  C4   113.15  3.000
 S8G  C5   N1  C4   120.63  3.000
 S8G  H2   C4  H1   107.52  3.000
 S8G  H2   C4  C    110.52  3.000
 S8G  H1   C4  C    109.59  3.000
 S8G  H2   C4  N1   110.02  3.000
 S8G  H1   C4  N1   108.42  3.000
 S8G  C    C4  N1   110.70  3.000
 S8G  O    C5  C6   120.59  3.000
 S8G  O    C5  N1   122.52  3.000
 S8G  C6   C5  N1   116.89  3.000
 S8G  H4   C6  H3   106.33  3.000
 S8G  H4   C6  C7   110.44  3.000
 S8G  H3   C6  C7   110.33  3.000
 S8G  H4   C6  C5   109.40  3.000
 S8G  H3   C6  C5   108.84  3.000
 S8G  C7   C6  C5   111.37  3.000
 S8G  H6   C7  H5   107.08  3.000
 S8G  H6   C7  C8   107.73  3.000
 S8G  H5   C7  C8   107.93  3.000
 S8G  H6   C7  C6   110.75  3.000
 S8G  H5   C7  C6   110.73  3.000
 S8G  C8   C7  C6   112.40  3.000
 S8G  F2   C8  F1   106.50  3.000
 S8G  F2   C8  F    106.34  3.000
 S8G  F1   C8  F    106.60  3.000
 S8G  F2   C8  C7   112.57  3.000
 S8G  F1   C8  C7   111.66  3.000
 S8G  F    C8  C7   112.73  3.000
 S8G  H8   N   H7   105.46  3.000
 S8G  H8   N   C    109.32  3.000
 S8G  H7   N   C    109.37  3.000
 S8G  H10  C   C1   108.64  3.000
 S8G  H10  C   N    107.42  3.000
 S8G  C1   C   N    114.59  3.000
 S8G  H10  C   C4   107.17  3.000
 S8G  N    C   C4   108.75  3.000
 S8G  C1   C   C4   110.00  3.000
 S8G  H12  C1  H11  106.75  3.000
 S8G  H12  C1  C2   109.02  3.000
 S8G  H11  C1  C2   110.64  3.000
 S8G  H12  C1  C    108.39  3.000
 S8G  H11  C1  C    109.80  3.000
 S8G  C2   C1  C    112.06  3.000
 S8G  H14  C2  H13  106.97  3.000
 S8G  H14  C2  C3   109.42  3.000
 S8G  H13  C2  C3   109.18  3.000
 S8G  H14  C2  C1   110.59  3.000
 S8G  H13  C2  C1   110.38  3.000
 S8G  C3   C2  C1   110.24  3.000
 S8G  H16  C3  H15  106.63  3.000
 S8G  H16  C3  C2   109.72  3.000
 S8G  H15  C3  C2   111.29  3.000
 S8G  H16  C3  N1   107.97  3.000
 S8G  H15  C3  N1   110.99  3.000
 S8G  C2   C3  N1   110.13  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
 S8G  CONST_01  C6  C5  N1  C4   180.00   0.0  0
 S8G  CONST_02  O   C5  N1  C4     0.00   0.0  0
 S8G  CONST_03  C3  N1  C5  C6     0.00   0.0  0
 S8G  CONST_04  C3  N1  C5  O    180.00   0.0  0
 S8G  Var_01    C1  C2  C3  N1   -55.60  30.0  1
 S8G  Var_02    C2  C3  N1  C4    60.61  30.0  1
 S8G  Var_03    C3  N1  C4  C    -60.06  30.0  1
 S8G  Var_04    C3  C2  C1  C     52.76  30.0  1
 S8G  Var_05    C7  C6  C5  N1  -179.41  30.0  1
 S8G  Var_06    C8  C7  C6  C5  -177.72  30.0  1
 S8G  Var_07    F   C8  C7  C6   -60.19  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
 S8G  chir_01  C  C4  C1  N  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
 S8G  plan-1  N1  0.020
 S8G  plan-1  C4  0.020
 S8G  plan-1  C5  0.020
 S8G  plan-1  C6  0.020
 S8G  plan-1  O   0.020
 S8G  plan-1  C3  0.020

