# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:06:55 2021
#   Inital geometry file: a 101 line input string
#   Ligand name: 6-[(3~{R},4~{S})-3,4-bis(oxidanyl)pyrrolidin-1-yl]-2-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@H](O)CN1c2nc(cc(c2C#N)C(F)(F)F)N3C[C@H](O)[C@H](O)C3
#
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
 RZA  RZA  6-[(3~{R},4~{S})-3,4-bis(oxidanyl)pyrrolidin-1-yl]-2-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile  ligand  42  25  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RZA
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
 RZA  N3   N  NT    0  -0.507  -6.0518   0.2880  20.3413
 RZA  C4   C  C     0  -0.298  -2.8043  -1.9585  15.9611
 RZA  N2   N  N     0  -0.516  -4.6531  -0.4962  18.7341
 RZA  C7   C  CR6   0  -0.030  -4.1884  -2.8014  20.1739
 RZA  C6   C  CR6   0  -0.151  -3.5264  -2.6056  18.9449
 RZA  C9   C  CR6   0   0.598  -5.2459  -0.6847  19.9069
 RZA  C13  C  CH2   0  -0.304  -6.7283   0.2963  21.6248
 RZA  C8   C  CR16  0  -0.530  -5.0511  -1.8691  20.6698
 RZA  C2   C  C     0  -0.061  -3.6964  -0.0187  16.1696
 RZA  C3   C  C     0  -0.008  -2.9974  -0.7701  15.0104
 RZA  N1   N  N     0  -0.500  -3.2753  -1.1087  17.0526
 RZA  C5   C  CR6   0   0.534  -3.8251  -1.4094  18.2411
 RZA  C10  C  CH2   0  -0.282  -6.3304   1.4862  19.5569
 RZA  C11  C  CH1   0  -0.032  -7.4971   2.1215  20.2879
 RZA  C12  C  CH1   0   0.004  -7.1983   1.7504  21.7386
 RZA  O1   O  OH1   0  -0.666  -8.3300   1.9411  22.5368
 RZA  O2   O  OH1   0  -0.668  -8.6850   1.5146  19.8383
 RZA  F1   F  F     0  -0.292  -4.6607  -4.1458  22.0571
 RZA  F2   F  F     0  -0.311  -4.1803  -5.1486  20.2188
 RZA  F3   F  F     0  -0.312  -2.6395  -4.1300  21.3264
 RZA  C15  C  CSP   0  -0.010  -2.5605  -3.5205  18.4750
 RZA  N4   N  NS    0  -0.270  -1.7561  -4.2621  18.1023
 RZA  O3   O  OH1   0  -0.659  -3.7517  -1.0820  13.8816
 RZA  H1   H  H     0   0.252  -3.4770  -2.7931  15.7436
 RZA  H2   H  H     0   0.261  -1.7868  -2.3312  16.0645
 RZA  H3   H  HCH2  0   0.249  -7.5799  -0.3914  21.6400
 RZA  H4   H  HCH2  0   0.260  -6.0526   0.0235  22.4376
 RZA  H5   H  HCR6  0   0.293  -5.5701  -2.0187  21.6034
 RZA  H6   H  HCH3  0   0.247  -3.6714   1.7338  17.4240
 RZA  H7   H  HCH3  0   0.224  -2.1097   1.3512  16.6844
 RZA  H8   H  HCH3  0   0.233  -3.4057   2.0524  15.7086
 RZA  H9   H  H     0   0.245  -4.7843  -0.0086  16.0407
 RZA  H10  H  H     0   0.230  -2.0438  -0.2976  14.7486
 RZA  H11  H  HCH2  0   0.266  -6.5697   1.2399  18.5221
 RZA  H12  H  HCH2  0   0.253  -5.4673   2.1572  19.5457
 RZA  H13  H  HCH1  0   0.245  -7.5162   3.2078  20.1405
 RZA  H14  H  HCH1  0   0.234  -6.3543   2.3649  22.0791
 RZA  H15  H  HOH1  0   0.463  -8.1023   1.7725  23.4560
 RZA  H16  H  HOH1  0   0.452  -9.3937   1.7454  20.4487
 RZA  H17  H  HOH1  0   0.457  -3.7924  -0.3056  13.3148
 RZA  C14  C  CT    0   1.078  -3.9224  -4.0603  20.9521
 RZA  C1   C  CH3   0  -0.671  -3.1888   1.3589  16.5230

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
 RZA  O3   C3   single    1.393  0.020  1.393
 RZA  C3   C4   single    1.534  0.020  1.534
 RZA  C3   C2   single    1.548  0.020  1.548
 RZA  C4   N1   single    1.461  0.020  1.461
 RZA  C2   C1   single    1.510  0.020  1.510
 RZA  C2   N1   single    1.465  0.020  1.465
 RZA  N1   C5   single    1.344  0.020  1.344
 RZA  N4   C15  triple    1.156  0.020  1.156
 RZA  C5   N2   aromatic  1.328  0.020  1.328
 RZA  C5   C6   aromatic  1.420  0.020  1.420
 RZA  C15  C6   single    1.411  0.020  1.411
 RZA  N2   C9   aromatic  1.327  0.020  1.327
 RZA  C6   C7   aromatic  1.410  0.020  1.410
 RZA  C10  C11  single    1.516  0.020  1.516
 RZA  C10  N3   single    1.459  0.020  1.459
 RZA  C9   N3   single    1.336  0.020  1.336
 RZA  C9   C8   aromatic  1.422  0.020  1.422
 RZA  O2   C11  single    1.408  0.020  1.408
 RZA  C7   C8   aromatic  1.364  0.020  1.364
 RZA  C7   C14  single    1.504  0.020  1.504
 RZA  C11  C12  single    1.527  0.020  1.527
 RZA  N3   C13  single    1.451  0.020  1.451
 RZA  F2   C14  single    1.337  0.020  1.337
 RZA  C14  F3   single    1.338  0.020  1.338
 RZA  C14  F1   single    1.332  0.020  1.332
 RZA  C13  C12  single    1.532  0.020  1.532
 RZA  C12  O1   single    1.398  0.020  1.398
 RZA  C4   H1   single    0.970  0.020  1.090
 RZA  C4   H2   single    0.970  0.020  1.090
 RZA  C13  H3   single    0.970  0.020  1.090
 RZA  C13  H4   single    0.970  0.020  1.090
 RZA  C8   H5   single    0.930  0.020  1.080
 RZA  C1   H6   single    0.970  0.020  1.090
 RZA  C1   H7   single    0.970  0.020  1.090
 RZA  C1   H8   single    0.970  0.020  1.090
 RZA  C2   H9   single    0.970  0.020  1.090
 RZA  C3   H10  single    0.970  0.020  1.090
 RZA  C10  H11  single    0.970  0.020  1.090
 RZA  C10  H12  single    0.970  0.020  1.090
 RZA  C11  H13  single    0.970  0.020  1.090
 RZA  C12  H14  single    0.970  0.020  1.090
 RZA  O1   H15  single    0.850  0.020  0.980
 RZA  O2   H16  single    0.850  0.020  0.980
 RZA  O3   H17  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
 RZA  C10  N3   C13  112.45  3.000
 RZA  C13  N3   C9   124.97  3.000
 RZA  C10  N3   C9   122.57  3.000
 RZA  H2   C4   H1   109.43  3.000
 RZA  H2   C4   N1   115.42  3.000
 RZA  H1   C4   N1   113.21  3.000
 RZA  H2   C4   C3   116.22  3.000
 RZA  H1   C4   C3   112.98  3.000
 RZA  N1   C4   C3    88.38  3.000
 RZA  C5   N2   C9   120.59  3.000
 RZA  C14  C7   C8   119.74  3.000
 RZA  C14  C7   C6   118.97  3.000
 RZA  C8   C7   C6   121.28  3.000
 RZA  C15  C6   C5   121.68  3.000
 RZA  C15  C6   C7   121.46  3.000
 RZA  C5   C6   C7   116.77  3.000
 RZA  C8   C9   N2   122.07  3.000
 RZA  C8   C9   N3   120.96  3.000
 RZA  N2   C9   N3   116.96  3.000
 RZA  H4   C13  H3   108.31  3.000
 RZA  H4   C13  C12  111.82  3.000
 RZA  H3   C13  C12  110.88  3.000
 RZA  H4   C13  N3   111.64  3.000
 RZA  H3   C13  N3   111.80  3.000
 RZA  C12  C13  N3   102.36  3.000
 RZA  H5   C8   C9   120.93  3.000
 RZA  H5   C8   C7   121.62  3.000
 RZA  C9   C8   C7   117.45  3.000
 RZA  H9   C2   N1   111.30  3.000
 RZA  H9   C2   C3   111.39  3.000
 RZA  N1   C2   C3    87.73  3.000
 RZA  H9   C2   C1   110.67  3.000
 RZA  N1   C2   C1   116.18  3.000
 RZA  C3   C2   C1   117.79  3.000
 RZA  H10  C3   O3   111.97  3.000
 RZA  H10  C3   C2   111.25  3.000
 RZA  O3   C3   C2   118.10  3.000
 RZA  H10  C3   C4   111.87  3.000
 RZA  C2   C3   C4    88.21  3.000
 RZA  O3   C3   C4   113.39  3.000
 RZA  C5   N1   C2   125.60  3.000
 RZA  C5   N1   C4   131.48  3.000
 RZA  C2   N1   C4    94.31  3.000
 RZA  N1   C5   C6   122.75  3.000
 RZA  C6   C5   N2   121.78  3.000
 RZA  N1   C5   N2   115.45  3.000
 RZA  H12  C10  H11  107.59  3.000
 RZA  H12  C10  C11  110.81  3.000
 RZA  H11  C10  C11  112.54  3.000
 RZA  H12  C10  N3   111.03  3.000
 RZA  H11  C10  N3   111.51  3.000
 RZA  C11  C10  N3   103.40  3.000
 RZA  H13  C11  O2   111.69  3.000
 RZA  H13  C11  C12  111.83  3.000
 RZA  O2   C11  C12  111.34  3.000
 RZA  H13  C11  C10  111.33  3.000
 RZA  C12  C11  C10  101.87  3.000
 RZA  O2   C11  C10  108.34  3.000
 RZA  H14  C12  O1   111.65  3.000
 RZA  H14  C12  C11  108.00  3.000
 RZA  O1   C12  C11  110.54  3.000
 RZA  H14  C12  C13  108.56  3.000
 RZA  O1   C12  C13  114.84  3.000
 RZA  C11  C12  C13  102.71  3.000
 RZA  H15  O1   C12  109.28  3.000
 RZA  H16  O2   C11  108.37  3.000
 RZA  N4   C15  C6   180.00  3.000
 RZA  H17  O3   C3   108.64  3.000
 RZA  F3   C14  F2   107.21  3.000
 RZA  F3   C14  F1   107.22  3.000
 RZA  F2   C14  F1   107.21  3.000
 RZA  F1   C14  C7   112.65  3.000
 RZA  F3   C14  C7   110.98  3.000
 RZA  F2   C14  C7   111.31  3.000
 RZA  H8   C1   H7   108.15  3.000
 RZA  H8   C1   H6   108.10  3.000
 RZA  H7   C1   H6   108.57  3.000
 RZA  H8   C1   C2   109.77  3.000
 RZA  H7   C1   C2   111.14  3.000
 RZA  H6   C1   C2   111.02  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
 RZA  CONST_01  C7   C6   C5  N2     0.00   0.0  0
 RZA  CONST_02  C7   C8   C9  N2     0.00   0.0  0
 RZA  CONST_03  C9   N2   C5  C6     0.00   0.0  0
 RZA  CONST_04  C9   C8   C7  C6     0.00   0.0  0
 RZA  CONST_05  C5   N2   C9  C8     0.00   0.0  0
 RZA  CONST_06  C5   C6   C7  C8     0.00   0.0  0
 RZA  CONST_07  C5   N2   C9  N3   180.00   0.0  0
 RZA  CONST_08  C7   C8   C9  N3   180.00   0.0  0
 RZA  CONST_09  N1   C5   C6  C7   180.00   0.0  0
 RZA  CONST_10  N1   C5   N2  C9   180.00   0.0  0
 RZA  CONST_11  C15  C6   C5  N2   180.00   0.0  0
 RZA  CONST_12  C14  C7   C8  C9   180.00   0.0  0
 RZA  CONST_13  C15  C6   C7  C8   180.00   0.0  0
 RZA  CONST_14  C15  C6   C5  N1     0.00   0.0  0
 RZA  CONST_15  C14  C7   C6  C5   180.00   0.0  0
 RZA  CONST_16  H5   C8   C9  N3     0.00   0.0  0
 RZA  Var_01    N2   C5   N1  C4  -151.37  30.0  2
 RZA  Var_02    C10  N3   C9  N2     2.59  30.0  2
 RZA  Var_03    C11  C10  N3  C9   167.82  30.0  1
 RZA  Var_04    C12  C13  N3  C9   166.23  30.0  1
 RZA  Var_05    C3   C4   N1  C2     9.11  30.0  1
 RZA  Var_06    F2   C14  C7  C6   -56.45  30.0  2

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
 RZA  chir_01  C2   C3   C1   N1   positiv
 RZA  chir_02  C3   O3   C4   C2   positiv
 RZA  chir_03  C11  C10  O2   C12  negativ
 RZA  chir_04  C12  O1   C11  C13  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
 RZA  plan-1  N3   0.020
 RZA  plan-1  N2   0.020
 RZA  plan-1  C7   0.020
 RZA  plan-1  C6   0.020
 RZA  plan-1  C9   0.020
 RZA  plan-1  C8   0.020
 RZA  plan-1  N1   0.020
 RZA  plan-1  C5   0.020
 RZA  plan-1  C15  0.020
 RZA  plan-1  N4   0.020
 RZA  plan-1  H5   0.020
 RZA  plan-1  C14  0.020

