# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 15:48:04 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (4S,6S)-6-{[(3R,4R)-4-{2-[(2,2-difluoro-2-phenylethyl)amino]ethoxy}pyrrolidin-3-yl]methyl}-4-methyl-3,4,5,6-tetrahydropyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1C[C@@H](C[C@@H]2CNC[C@@H]2OCCNCC(F)(F)c3ccccc3)N=C(N)C1
#
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
 3XE  3XE  (4S,6S)-6-{[(3R,4R)-4-{2-[(2,2-difluoro-2-phenylethyl)amino]ethoxy}pyrrolidin-3-yl]methyl}-4-methyl-3,4,5,6-tetrahydropyridin-2-amine  ligand  60  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3XE
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
 3XE  C1    C  CH2   0  -0.158  -0.2870   2.7260  -1.6103
 3XE  O1    O  O2    0  -0.487   0.7304   2.0003  -0.9669
 3XE  C2    C  CH2   0  -0.300  -1.4828   1.8211  -1.7985
 3XE  N2    N  NH1   0  -0.612  -2.0404   1.4123  -0.5224
 3XE  C3    C  CH2   0  -0.360  -3.1805   0.5421  -0.6778
 3XE  C4    C  CT    0   0.770  -3.9276   0.3384   0.6258
 3XE  F5    F  F     0  -0.350  -3.0678  -0.1645   1.5669
 3XE  F6    F  F     0  -0.342  -4.3355   1.5432   1.1193
 3XE  N1'   N  NH1   0  -0.619   2.9635   3.4860   1.1954
 3XE  C11   C  CR6   0  -0.094  -5.1099  -0.5798   0.4778
 3XE  C12   C  CR16  0  -0.291  -4.9480  -1.9552   0.6108
 3XE  C13   C  CR16  0  -0.238  -6.0290  -2.8051   0.4233
 3XE  C14   C  CR16  0  -0.256  -7.2766  -2.2881   0.1017
 3XE  C15   C  CR16  0  -0.238  -7.4385  -0.9163  -0.0352
 3XE  C16   C  CR16  0  -0.291  -6.3597  -0.0633   0.1511
 3XE  N1A   N  N     0  -0.411   4.5536  -0.6700   0.7094
 3XE  C2'   C  CH2   0  -0.301   1.8352   3.7716   0.3206
 3XE  C2A   C  CH1   0  -0.089   4.1243  -0.5575  -0.6682
 3XE  C3'   C  CH1   0   0.049   1.9311   2.7172  -0.8048
 3XE  C3A   C  CH2   0  -0.435   3.8864  -1.8934  -1.3681
 3XE  C4'   C  CH1   0  -0.274   3.0628   1.7674  -0.3518
 3XE  C4A   C  CH1   0  -0.242   5.0107  -2.8750  -1.0791
 3XE  C5'   C  CH2   0  -0.261   3.1647   2.0477   1.1437
 3XE  C5A   C  CH2   0  -0.519   5.0750  -3.0814   0.4273
 3XE  C6A   C  C     0   0.387   4.9504  -1.7816   1.1836
 3XE  N6A   N  NH2   0  -0.818   5.2568  -1.8756   2.5177
 3XE  C7A   C  CH2   0  -0.401   2.8713   0.3146  -0.7674
 3XE  C8A   C  CH3   0  -0.654   4.8322  -4.1943  -1.8144
 3XE  H1    H  HCH2  0   0.199  -0.5841   3.6080  -1.0263
 3XE  H1A   H  HCH2  0   0.206   0.0532   3.0864  -2.5916
 3XE  H2    H  HCH2  0   0.233  -2.2434   2.3780  -2.3521
 3XE  H2A   H  HCH2  0   0.202  -1.1942   0.9693  -2.4342
 3XE  HN2   H  HNH1  0   0.349  -1.3202   0.9370   0.0069
 3XE  H3    H  HCH2  0   0.256  -3.8803   0.9947  -1.3860
 3XE  H3A   H  HCH2  0   0.234  -2.9346  -0.4497  -1.0864
 3XE  HN1'  H  HNH1  0   0.346   2.7925   3.8143   2.1363
 3XE  H12   H  HCR6  0   0.263  -3.9828  -2.3763   0.8599
 3XE  H13   H  HCR6  0   0.263  -5.8941  -3.8734   0.5295
 3XE  H14   H  HCR6  0   0.262  -8.1182  -2.9524  -0.0441
 3XE  H15   H  HCR6  0   0.263  -8.4072  -0.5058  -0.2880
 3XE  H16   H  HCR6  0   0.263  -6.5042   1.0028   0.0359
 3XE  H2'   H  HCH2  0   0.206   0.8648   3.6547   0.8248
 3XE  H2'A  H  HCH2  0   0.221   1.8823   4.7965  -0.0551
 3XE  H2AA  H  HCH1  0   0.202   4.9218  -0.0328  -1.2163
 3XE  H3'   H  HCH1  0   0.211   2.1961   3.1851  -1.7628
 3XE  H3AA  H  HCH2  0   0.209   2.9364  -2.3261  -1.0273
 3XE  H3AB  H  HCH2  0   0.228   3.7857  -1.7254  -2.4440
 3XE  H4'   H  HCH1  0   0.231   3.9831   2.1377  -0.8188
 3XE  H4A   H  HCH1  0   0.224   5.9543  -2.4207  -1.4051
 3XE  H5'   H  HCH2  0   0.230   4.1298   1.7650   1.5597
 3XE  H5'A  H  HCH2  0   0.179   2.3941   1.4723   1.6826
 3XE  H5A   H  HCH2  0   0.254   4.2645  -3.7458   0.7479
 3XE  H5AA  H  HCH2  0   0.255   6.0056  -3.5785   0.7154
 3XE  HN6A  H  HNH2  0   0.379   5.9264  -2.5783   2.7849
 3XE  HN6B  H  HNH2  0   0.370   5.3827  -0.9976   2.9966
 3XE  H7A   H  HCH2  0   0.218   2.5398   0.2843  -1.8102
 3XE  H7AA  H  HCH2  0   0.209   2.0728  -0.1487  -0.1804
 3XE  H8A   H  HCH3  0   0.228   4.8127  -4.0426  -2.8949
 3XE  H8AA  H  HCH3  0   0.226   5.6430  -4.8910  -1.5933
 3XE  H8AB  H  HCH3  0   0.214   3.8938  -4.6752  -1.5288

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
 3XE  O1   C1    single    1.406  0.020  1.406
 3XE  C1   C2    single    1.511  0.020  1.511
 3XE  C1   H1    single    0.970  0.020  1.090
 3XE  C1   H1A   single    0.970  0.020  1.090
 3XE  C3'  O1    single    1.408  0.020  1.408
 3XE  N2   C2    single    1.451  0.020  1.451
 3XE  C2   H2    single    0.970  0.020  1.090
 3XE  C2   H2A   single    0.970  0.020  1.090
 3XE  N2   C3    single    1.443  0.020  1.443
 3XE  N2   HN2   single    0.890  0.020  1.040
 3XE  C3   C4    single    1.516  0.020  1.516
 3XE  C3   H3    single    0.970  0.020  1.090
 3XE  C3   H3A   single    0.970  0.020  1.090
 3XE  F6   C4    single    1.364  0.020  1.364
 3XE  C4   C11   single    1.504  0.020  1.504
 3XE  C4   F5    single    1.370  0.020  1.370
 3XE  N1'  C5'   single    1.453  0.020  1.453
 3XE  N1'  C2'   single    1.456  0.020  1.456
 3XE  N1'  HN1'  single    0.890  0.020  1.040
 3XE  C16  C11   aromatic  1.391  0.020  1.391
 3XE  C11  C12   aromatic  1.391  0.020  1.391
 3XE  C12  C13   aromatic  1.388  0.020  1.388
 3XE  C12  H12   single    0.930  0.020  1.080
 3XE  C14  C13   aromatic  1.388  0.020  1.388
 3XE  C13  H13   single    0.930  0.020  1.080
 3XE  C15  C14   aromatic  1.388  0.020  1.388
 3XE  C14  H14   single    0.930  0.020  1.080
 3XE  C16  C15   aromatic  1.388  0.020  1.388
 3XE  C15  H15   single    0.930  0.020  1.080
 3XE  C16  H16   single    0.930  0.020  1.080
 3XE  C6A  N1A   double    1.272  0.020  1.272
 3XE  C2A  N1A   single    1.447  0.020  1.447
 3XE  C2'  C3'   single    1.545  0.020  1.545
 3XE  C2'  H2'   single    0.970  0.020  1.090
 3XE  C2'  H2'A  single    0.970  0.020  1.090
 3XE  C3A  C2A   single    1.527  0.020  1.527
 3XE  C2A  C7A   single    1.530  0.020  1.530
 3XE  C2A  H2AA  single    0.970  0.020  1.090
 3XE  C4'  C3'   single    1.545  0.020  1.545
 3XE  C3'  H3'   single    0.970  0.020  1.090
 3XE  C4A  C3A   single    1.520  0.020  1.520
 3XE  C3A  H3AA  single    0.970  0.020  1.090
 3XE  C3A  H3AB  single    0.970  0.020  1.090
 3XE  C5'  C4'   single    1.525  0.020  1.525
 3XE  C4'  C7A   single    1.523  0.020  1.523
 3XE  C4'  H4'   single    0.970  0.020  1.090
 3XE  C8A  C4A   single    1.521  0.020  1.521
 3XE  C4A  C5A   single    1.522  0.020  1.522
 3XE  C4A  H4A   single    0.970  0.020  1.090
 3XE  C5'  H5'   single    0.970  0.020  1.090
 3XE  C5'  H5'A  single    0.970  0.020  1.090
 3XE  C5A  C6A   single    1.509  0.020  1.509
 3XE  C5A  H5A   single    0.970  0.020  1.090
 3XE  C5A  H5AA  single    0.970  0.020  1.090
 3XE  C6A  N6A   single    1.372  0.020  1.372
 3XE  N6A  HN6A  single    0.890  0.020  1.040
 3XE  N6A  HN6B  single    0.890  0.020  1.040
 3XE  C7A  H7A   single    0.970  0.020  1.090
 3XE  C7A  H7AA  single    0.970  0.020  1.090
 3XE  C8A  H8A   single    0.970  0.020  1.090
 3XE  C8A  H8AA  single    0.970  0.020  1.090
 3XE  C8A  H8AB  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
 3XE  H1A   C1   H1    107.15  3.000
 3XE  H1A   C1   C2    109.27  3.000
 3XE  H1    C1   C2    109.45  3.000
 3XE  H1A   C1   O1    110.72  3.000
 3XE  H1    C1   O1    111.52  3.000
 3XE  C2    C1   O1    108.70  3.000
 3XE  C3'   O1   C1    114.02  3.000
 3XE  H2A   C2   H2    106.51  3.000
 3XE  H2A   C2   N2    112.97  3.000
 3XE  H2    C2   N2    108.75  3.000
 3XE  H2A   C2   C1    109.12  3.000
 3XE  H2    C2   C1    107.97  3.000
 3XE  N2    C2   C1    111.29  3.000
 3XE  HN2   N2   C3    109.59  3.000
 3XE  HN2   N2   C2    108.59  3.000
 3XE  C3    N2   C2    112.26  3.000
 3XE  H3A   C3   H3    105.99  3.000
 3XE  H3A   C3   C4    107.96  3.000
 3XE  H3    C3   C4    107.28  3.000
 3XE  H3A   C3   N2    114.02  3.000
 3XE  H3    C3   N2    109.01  3.000
 3XE  C4    C3   N2    112.20  3.000
 3XE  C11   C4   F6    109.85  3.000
 3XE  C11   C4   F5    109.68  3.000
 3XE  F6    C4   F5    105.27  3.000
 3XE  F5    C4   C3    109.30  3.000
 3XE  C11   C4   C3    112.62  3.000
 3XE  F6    C4   C3    109.86  3.000
 3XE  HN1'  N1'  C5'   112.20  3.000
 3XE  HN1'  N1'  C2'   111.37  3.000
 3XE  C5'   N1'  C2'   106.27  3.000
 3XE  C16   C11  C12   119.60  3.000
 3XE  C12   C11  C4    120.17  3.000
 3XE  C16   C11  C4    120.17  3.000
 3XE  H12   C12  C13   119.18  3.000
 3XE  H12   C12  C11   120.69  3.000
 3XE  C13   C12  C11   120.13  3.000
 3XE  H13   C13  C14   120.16  3.000
 3XE  H13   C13  C12   119.62  3.000
 3XE  C14   C13  C12   120.21  3.000
 3XE  H14   C14  C15   120.18  3.000
 3XE  H14   C14  C13   120.10  3.000
 3XE  C15   C14  C13   119.72  3.000
 3XE  H15   C15  C16   119.61  3.000
 3XE  H15   C15  C14   120.16  3.000
 3XE  C16   C15  C14   120.23  3.000
 3XE  H16   C16  C15   119.17  3.000
 3XE  H16   C16  C11   120.72  3.000
 3XE  C15   C16  C11   120.11  3.000
 3XE  C6A   N1A  C2A   121.02  3.000
 3XE  H2'A  C2'  H2'   107.18  3.000
 3XE  H2'A  C2'  C3'   112.77  3.000
 3XE  H2'   C2'  C3'   108.43  3.000
 3XE  H2'A  C2'  N1'   110.93  3.000
 3XE  H2'   C2'  N1'   112.80  3.000
 3XE  C3'   C2'  N1'   104.81  3.000
 3XE  H2AA  C2A  C7A   106.82  3.000
 3XE  H2AA  C2A  C3A   107.56  3.000
 3XE  C7A   C2A  C3A   109.96  3.000
 3XE  H2AA  C2A  N1A   107.22  3.000
 3XE  C7A   C2A  N1A   110.43  3.000
 3XE  C3A   C2A  N1A   114.49  3.000
 3XE  H3'   C3'  C4'   109.92  3.000
 3XE  H3'   C3'  C2'   111.07  3.000
 3XE  C4'   C3'  C2'   104.56  3.000
 3XE  H3'   C3'  O1    108.80  3.000
 3XE  C4'   C3'  O1    110.20  3.000
 3XE  C2'   C3'  O1    112.24  3.000
 3XE  H3AB  C3A  H3AA  106.63  3.000
 3XE  H3AB  C3A  C4A   110.75  3.000
 3XE  H3AA  C3A  C4A   109.05  3.000
 3XE  H3AB  C3A  C2A   109.33  3.000
 3XE  H3AA  C3A  C2A   109.72  3.000
 3XE  C4A   C3A  C2A   111.26  3.000
 3XE  H4'   C4'  C7A   108.15  3.000
 3XE  H4'   C4'  C5'   107.43  3.000
 3XE  C7A   C4'  C5'   116.83  3.000
 3XE  H4'   C4'  C3'   106.39  3.000
 3XE  C7A   C4'  C3'   114.47  3.000
 3XE  C5'   C4'  C3'   102.91  3.000
 3XE  H4A   C4A  C8A   108.45  3.000
 3XE  H4A   C4A  C5A   108.31  3.000
 3XE  C8A   C4A  C5A   111.46  3.000
 3XE  H4A   C4A  C3A   108.20  3.000
 3XE  C5A   C4A  C3A   107.87  3.000
 3XE  C8A   C4A  C3A   112.42  3.000
 3XE  H5'A  C5'  H5'   107.31  3.000
 3XE  H5'A  C5'  C4'   109.67  3.000
 3XE  H5'   C5'  C4'   112.73  3.000
 3XE  H5'A  C5'  N1'   113.73  3.000
 3XE  H5'   C5'  N1'   111.49  3.000
 3XE  C4'   C5'  N1'   101.98  3.000
 3XE  H5AA  C5A  H5A   106.06  3.000
 3XE  H5AA  C5A  C6A   109.26  3.000
 3XE  H5A   C5A  C6A   108.33  3.000
 3XE  H5AA  C5A  C4A   111.00  3.000
 3XE  H5A   C5A  C4A   109.91  3.000
 3XE  C6A   C5A  C4A   112.07  3.000
 3XE  N6A   C6A  C5A   114.19  3.000
 3XE  N6A   C6A  N1A   119.47  3.000
 3XE  C5A   C6A  N1A   126.28  3.000
 3XE  HN6B  N6A  HN6A  113.50  3.000
 3XE  HN6B  N6A  C6A   115.47  3.000
 3XE  HN6A  N6A  C6A   117.03  3.000
 3XE  H7AA  C7A  H7A   106.17  3.000
 3XE  H7AA  C7A  C4'   110.44  3.000
 3XE  H7A   C7A  C4'   108.93  3.000
 3XE  H7AA  C7A  C2A   108.76  3.000
 3XE  H7A   C7A  C2A   107.10  3.000
 3XE  C4'   C7A  C2A   115.02  3.000
 3XE  H8AB  C8A  H8AA  107.70  3.000
 3XE  H8AB  C8A  H8A   107.74  3.000
 3XE  H8AA  C8A  H8A   107.61  3.000
 3XE  H8AB  C8A  C4A   110.87  3.000
 3XE  H8AA  C8A  C4A   111.62  3.000
 3XE  H8A   C8A  C4A   111.12  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
 3XE  CONST_01  C14  C15  C16  C11     0.00   0.0  0
 3XE  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 3XE  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 3XE  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 3XE  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 3XE  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 3XE  CONST_07  C5A  C6A  N1A  C2A     0.00   0.0  0
 3XE  CONST_08  C15  C16  C11  C4    180.00   0.0  0
 3XE  CONST_09  C13  C12  C11  C4    180.00   0.0  0
 3XE  CONST_10  N6A  C6A  N1A  C2A   180.00   0.0  0
 3XE  CONST_11  H15  C15  C16  C11   180.00   0.0  0
 3XE  CONST_12  H13  C13  C12  C11   180.00   0.0  0
 3XE  CONST_13  H16  C16  C11  C12   180.00   0.0  0
 3XE  CONST_14  H14  C14  C13  C12   180.00   0.0  0
 3XE  CONST_15  H12  C12  C13  C14   180.00   0.0  0
 3XE  Var_01    C4A  C5A  C6A  N1A    14.56  30.0  1
 3XE  Var_02    C4'  C5'  N1'  C2'    45.08  30.0  1
 3XE  Var_03    C5'  N1'  C2'  C3'   -32.64  30.0  1
 3XE  Var_04    C16  C11  C4   C3    -89.82  30.0  2
 3XE  Var_05    C11  C4   C3   N2   -179.37  30.0  3
 3XE  Var_06    H1   C1   O1   C3'   -62.77  30.0  3
 3XE  Var_07    C3   N2   C2   C1   -179.74  30.0  1
 3XE  Var_08    N2   C2   C1   O1     64.05  30.0  3
 3XE  Var_09    C4   C3   N2   C2   -168.59  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
 3XE  chir_01  C2A  N1A  C3A  C7A  negativ
 3XE  chir_02  C3'  O1   C2'  C4'  negativ
 3XE  chir_03  C4'  C3'  C5'  C7A  negativ
 3XE  chir_04  C4A  C5A  C8A  C3A  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
 3XE  plan-1  C4    0.020
 3XE  plan-1  C11   0.020
 3XE  plan-1  C12   0.020
 3XE  plan-1  C13   0.020
 3XE  plan-1  C14   0.020
 3XE  plan-1  C15   0.020
 3XE  plan-1  C16   0.020
 3XE  plan-1  H12   0.020
 3XE  plan-1  H13   0.020
 3XE  plan-1  H14   0.020
 3XE  plan-1  H15   0.020
 3XE  plan-1  H16   0.020
 3XE  plan-2  N1A   0.020
 3XE  plan-2  C2A   0.020
 3XE  plan-2  C5A   0.020
 3XE  plan-2  C6A   0.020
 3XE  plan-2  N6A   0.020
 3XE  plan-2  HN6A  0.020
 3XE  plan-2  HN6B  0.020

