# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 16:21:47 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3R,4R)-4-{2-[(2,2-difluoro-2-phenylethyl)amino]ethoxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@@H]2CNC[C@@H]2OCCNCC(F)(F)c3ccccc3)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
 3XD  3XD  6-{[(3R,4R)-4-{2-[(2,2-difluoro-2-phenylethyl)amino]ethoxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  56  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_3XD
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
 3XD  C1    C  CH2   0  -0.160   0.2902   2.6125   1.4270
 3XD  O1    O  O2    0  -0.492  -0.6766   1.8216   0.7819
 3XD  C2    C  CH2   0  -0.300   1.5112   1.7631   1.6935
 3XD  N2    N  NH1   0  -0.611   2.1310   1.3301   0.4549
 3XD  C3    C  CH2   0  -0.361   3.2869   0.4985   0.6840
 3XD  C4    C  CT    0   0.770   4.0906   0.2731  -0.5814
 3XD  F5    F  F     0  -0.350   3.2836  -0.2881  -1.5363
 3XD  F6    F  F     0  -0.342   4.4831   1.4715  -1.1020
 3XD  N1'   N  NH1   0  -0.595  -2.5372   2.7547  -1.8532
 3XD  C11   C  CR6   0  -0.094   5.2921  -0.6032  -0.3546
 3XD  C12   C  CR16  0  -0.291   6.5127  -0.0380   0.0011
 3XD  C13   C  CR16  0  -0.238   7.6065  -0.8511   0.2632
 3XD  C14   C  CR16  0  -0.256   7.4891  -2.2313   0.1733
 3XD  C15   C  CR16  0  -0.238   6.2709  -2.7967  -0.1777
 3XD  C16   C  CR16  0  -0.291   5.1751  -1.9868  -0.4410
 3XD  N1A   N  N     0  -0.486  -5.2672  -0.2662   0.8164
 3XD  C2'   C  CH2   0  -0.317  -1.7468   3.3797  -0.7881
 3XD  C2A   C  CR6   0   0.287  -4.0532  -0.7356   0.5172
 3XD  C3'   C  CH1   0   0.035  -1.8751   2.5023   0.4835
 3XD  C3A   C  CR16  0  -0.439  -3.8558  -1.9701  -0.0741
 3XD  C4'   C  CH1   0  -0.281  -2.9535   1.4822   0.1064
 3XD  C4A   C  CR6   0   0.206  -4.9660  -2.7698  -0.3712
 3XD  C5'   C  CH2   0  -0.297  -2.8033   1.3915  -1.4124
 3XD  C5A   C  CR16  0  -0.450  -6.2180  -2.2831  -0.0588
 3XD  C6A   C  CR6   0   0.438  -6.3281  -1.0138   0.5368
 3XD  N6A   N  NH2   0  -0.839  -7.5502  -0.5205   0.8974
 3XD  C7A   C  CH2   0  -0.489  -2.8909   0.1562   0.8556
 3XD  C8A   C  CH3   0  -0.726  -4.7886  -4.1131  -1.0102
 3XD  H1    H  HCH2  0   0.199   0.5770   3.4801   0.8172
 3XD  H1A   H  HCH2  0   0.207  -0.0975   3.0001   2.3797
 3XD  H2    H  HCH2  0   0.233   2.2290   2.3701   2.2520
 3XD  H2A   H  HCH2  0   0.202   1.2331   0.9246   2.3511
 3XD  HN2   H  HNH1  0   0.348   1.4454   0.8188  -0.0868
 3XD  H3    H  HCH2  0   0.256   3.9452   0.9931   1.4038
 3XD  H3A   H  HCH2  0   0.234   3.0524  -0.4863   1.1160
 3XD  HN1'  H  HNH1  0   0.346  -3.4222   3.2398  -1.9229
 3XD  H12   H  HCR6  0   0.263   6.6236   1.0354   0.0807
 3XD  H13   H  HCR6  0   0.263   8.5520  -0.4028   0.5384
 3XD  H14   H  HCR6  0   0.262   8.3427  -2.8640   0.3791
 3XD  H15   H  HCR6  0   0.263   6.1704  -3.8717  -0.2481
 3XD  H16   H  HCR6  0   0.263   4.2326  -2.4453  -0.7104
 3XD  H2'   H  HCH2  0   0.224  -0.6932   3.4374  -1.0793
 3XD  H2'A  H  HCH2  0   0.235  -2.0851   4.4027  -0.6207
 3XD  H3'   H  HCH1  0   0.219  -2.1828   3.0946   1.3557
 3XD  H3AA  H  HCR6  0   0.242  -2.8535  -2.3078  -0.3060
 3XD  H4'   H  HCH1  0   0.243  -3.9231   1.9450   0.3175
 3XD  H5'   H  HCH2  0   0.239  -3.6868   0.9933  -1.9125
 3XD  H5'A  H  HCH2  0   0.214  -1.9614   0.7381  -1.6707
 3XD  H5A   H  HCR6  0   0.254  -7.1089  -2.8640  -0.2656
 3XD  HN6A  H  HNH2  0   0.378  -7.5970   0.4741   1.0491
 3XD  HN6B  H  HNH2  0   0.387  -8.3575  -0.8998   0.4311
 3XD  H7A   H  HCH2  0   0.244  -2.8976   0.3472   1.9335
 3XD  H7AA  H  HCH2  0   0.241  -1.9583  -0.3628   0.6320
 3XD  H8A   H  HCH3  0   0.251  -4.1594  -4.7562  -0.3934
 3XD  H8AA  H  HCH3  0   0.246  -5.7415  -4.6175  -1.1627
 3XD  H8AB  H  HCH3  0   0.251  -4.2956  -4.0201  -1.9792

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
 3XD  C2   C1    single    1.511  0.020  1.511
 3XD  C1   O1    single    1.406  0.020  1.406
 3XD  C1   H1    single    0.970  0.020  1.090
 3XD  C1   H1A   single    0.970  0.020  1.090
 3XD  O1   C3'   single    1.410  0.020  1.410
 3XD  C2   N2    single    1.451  0.020  1.451
 3XD  C2   H2    single    0.970  0.020  1.090
 3XD  C2   H2A   single    0.970  0.020  1.090
 3XD  C3   N2    single    1.442  0.020  1.442
 3XD  N2   HN2   single    0.890  0.020  1.040
 3XD  C4   C3    single    1.516  0.020  1.516
 3XD  C3   H3    single    0.970  0.020  1.090
 3XD  C3   H3A   single    0.970  0.020  1.090
 3XD  F5   C4    single    1.370  0.020  1.370
 3XD  C11  C4    single    1.504  0.020  1.504
 3XD  C4   F6    single    1.364  0.020  1.364
 3XD  C2'  N1'   single    1.466  0.020  1.466
 3XD  C5'  N1'   single    1.457  0.020  1.457
 3XD  N1'  HN1'  single    0.890  0.020  1.040
 3XD  C12  C11   aromatic  1.391  0.020  1.391
 3XD  C11  C16   aromatic  1.391  0.020  1.391
 3XD  C13  C12   aromatic  1.388  0.020  1.388
 3XD  C12  H12   single    0.930  0.020  1.080
 3XD  C13  C14   aromatic  1.388  0.020  1.388
 3XD  C13  H13   single    0.930  0.020  1.080
 3XD  C14  C15   aromatic  1.388  0.020  1.388
 3XD  C14  H14   single    0.930  0.020  1.080
 3XD  C15  C16   aromatic  1.388  0.020  1.388
 3XD  C15  H15   single    0.930  0.020  1.080
 3XD  C16  H16   single    0.930  0.020  1.080
 3XD  N1A  C2A   aromatic  1.336  0.020  1.336
 3XD  N1A  C6A   aromatic  1.328  0.020  1.328
 3XD  C3'  C2'   single    1.550  0.020  1.550
 3XD  C2'  H2'   single    0.970  0.020  1.090
 3XD  C2'  H2'A  single    0.970  0.020  1.090
 3XD  C7A  C2A   single    1.504  0.020  1.504
 3XD  C2A  C3A   aromatic  1.383  0.020  1.383
 3XD  C3'  C4'   single    1.532  0.020  1.532
 3XD  C3'  H3'   single    0.970  0.020  1.090
 3XD  C3A  C4A   aromatic  1.400  0.020  1.400
 3XD  C3A  H3AA  single    0.930  0.020  1.080
 3XD  C7A  C4'   single    1.524  0.020  1.524
 3XD  C4'  C5'   single    1.529  0.020  1.529
 3XD  C4'  H4'   single    0.970  0.020  1.090
 3XD  C5A  C4A   aromatic  1.379  0.020  1.379
 3XD  C4A  C8A   single    1.498  0.020  1.498
 3XD  C5'  H5'   single    0.970  0.020  1.090
 3XD  C5'  H5'A  single    0.970  0.020  1.090
 3XD  C6A  C5A   aromatic  1.406  0.020  1.406
 3XD  C5A  H5A   single    0.930  0.020  1.080
 3XD  N6A  C6A   single    1.366  0.020  1.366
 3XD  N6A  HN6A  single    0.890  0.020  1.040
 3XD  N6A  HN6B  single    0.890  0.020  1.040
 3XD  C7A  H7A   single    0.970  0.020  1.090
 3XD  C7A  H7AA  single    0.970  0.020  1.090
 3XD  C8A  H8A   single    0.970  0.020  1.090
 3XD  C8A  H8AA  single    0.970  0.020  1.090
 3XD  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
 3XD  H1A   C1   H1    107.14  3.000
 3XD  H1A   C1   C2    109.29  3.000
 3XD  H1    C1   C2    109.32  3.000
 3XD  H1A   C1   O1    110.71  3.000
 3XD  H1    C1   O1    111.66  3.000
 3XD  C2    C1   O1    108.69  3.000
 3XD  C3'   O1   C1    114.20  3.000
 3XD  H2A   C2   H2    106.47  3.000
 3XD  H2A   C2   N2    112.98  3.000
 3XD  H2    C2   N2    108.74  3.000
 3XD  H2A   C2   C1    109.22  3.000
 3XD  H2    C2   C1    107.97  3.000
 3XD  N2    C2   C1    111.24  3.000
 3XD  HN2   N2   C3    109.67  3.000
 3XD  HN2   N2   C2    108.55  3.000
 3XD  C3    N2   C2    112.26  3.000
 3XD  H3A   C3   H3    105.94  3.000
 3XD  H3A   C3   C4    107.91  3.000
 3XD  H3    C3   C4    107.31  3.000
 3XD  H3A   C3   N2    114.04  3.000
 3XD  H3    C3   N2    109.04  3.000
 3XD  C4    C3   N2    112.21  3.000
 3XD  C11   C4   F6    109.84  3.000
 3XD  F6    C4   F5    105.26  3.000
 3XD  C11   C4   F5    109.69  3.000
 3XD  F6    C4   C3    109.91  3.000
 3XD  C11   C4   C3    112.59  3.000
 3XD  F5    C4   C3    109.29  3.000
 3XD  HN1'  N1'  C5'   108.04  3.000
 3XD  HN1'  N1'  C2'   108.49  3.000
 3XD  C5'   N1'  C2'   106.11  3.000
 3XD  C16   C11  C12   119.58  3.000
 3XD  C16   C11  C4    120.18  3.000
 3XD  C12   C11  C4    120.17  3.000
 3XD  H12   C12  C13   119.12  3.000
 3XD  H12   C12  C11   120.77  3.000
 3XD  C13   C12  C11   120.11  3.000
 3XD  H13   C13  C14   120.15  3.000
 3XD  H13   C13  C12   119.60  3.000
 3XD  C14   C13  C12   120.24  3.000
 3XD  H14   C14  C15   120.14  3.000
 3XD  H14   C14  C13   120.15  3.000
 3XD  C15   C14  C13   119.70  3.000
 3XD  H15   C15  C16   119.61  3.000
 3XD  H15   C15  C14   120.17  3.000
 3XD  C16   C15  C14   120.21  3.000
 3XD  H16   C16  C15   119.19  3.000
 3XD  H16   C16  C11   120.67  3.000
 3XD  C15   C16  C11   120.15  3.000
 3XD  C6A   N1A  C2A   118.77  3.000
 3XD  H2'A  C2'  H2'   106.86  3.000
 3XD  H2'A  C2'  C3'   112.29  3.000
 3XD  H2'   C2'  C3'   109.13  3.000
 3XD  H2'A  C2'  N1'   110.13  3.000
 3XD  H2'   C2'  N1'   110.37  3.000
 3XD  C3'   C2'  N1'   108.06  3.000
 3XD  C7A   C2A  C3A   121.02  3.000
 3XD  C3A   C2A  N1A   122.63  3.000
 3XD  C7A   C2A  N1A   116.35  3.000
 3XD  H3'   C3'  C4'   110.95  3.000
 3XD  H3'   C3'  C2'   111.68  3.000
 3XD  C4'   C3'  C2'   103.49  3.000
 3XD  H3'   C3'  O1    109.29  3.000
 3XD  C4'   C3'  O1    109.21  3.000
 3XD  C2'   C3'  O1    112.11  3.000
 3XD  H3AA  C3A  C4A   120.69  3.000
 3XD  H3AA  C3A  C2A   120.14  3.000
 3XD  C4A   C3A  C2A   119.17  3.000
 3XD  H4'   C4'  C7A   108.01  3.000
 3XD  H4'   C4'  C5'   107.67  3.000
 3XD  C7A   C4'  C5'   115.64  3.000
 3XD  H4'   C4'  C3'   107.13  3.000
 3XD  C5'   C4'  C3'   102.41  3.000
 3XD  C7A   C4'  C3'   115.43  3.000
 3XD  C8A   C4A  C5A   121.37  3.000
 3XD  C8A   C4A  C3A   120.58  3.000
 3XD  C5A   C4A  C3A   118.05  3.000
 3XD  H5'A  C5'  H5'   107.23  3.000
 3XD  H5'A  C5'  C4'   110.17  3.000
 3XD  H5'   C5'  C4'   113.43  3.000
 3XD  H5'A  C5'  N1'   110.24  3.000
 3XD  H5'   C5'  N1'   110.54  3.000
 3XD  C4'   C5'  N1'   105.25  3.000
 3XD  H5A   C5A  C6A   120.02  3.000
 3XD  H5A   C5A  C4A   120.93  3.000
 3XD  C6A   C5A  C4A   119.04  3.000
 3XD  N6A   C6A  C5A   120.51  3.000
 3XD  N6A   C6A  N1A   117.11  3.000
 3XD  C5A   C6A  N1A   122.34  3.000
 3XD  HN6B  N6A  HN6A  113.87  3.000
 3XD  HN6B  N6A  C6A   117.33  3.000
 3XD  HN6A  N6A  C6A   115.97  3.000
 3XD  H7AA  C7A  H7A   106.87  3.000
 3XD  H7AA  C7A  C4'   110.39  3.000
 3XD  H7A   C7A  C4'   109.39  3.000
 3XD  H7AA  C7A  C2A   109.43  3.000
 3XD  H7A   C7A  C2A   108.69  3.000
 3XD  C4'   C7A  C2A   111.93  3.000
 3XD  H8AB  C8A  H8AA  108.09  3.000
 3XD  H8AB  C8A  H8A   106.96  3.000
 3XD  H8AA  C8A  H8A   108.11  3.000
 3XD  H8AB  C8A  C4A   110.85  3.000
 3XD  H8AA  C8A  C4A   111.81  3.000
 3XD  H8A   C8A  C4A   110.84  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
 3XD  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 3XD  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 3XD  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 3XD  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 3XD  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 3XD  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 3XD  CONST_07  C4A   C3A  C2A  N1A     0.00   0.0  0
 3XD  CONST_08  C4A   C5A  C6A  N1A     0.00   0.0  0
 3XD  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 3XD  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 3XD  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 3XD  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 3XD  CONST_13  C13   C12  C11  C4    180.00   0.0  0
 3XD  CONST_14  C15   C16  C11  C4    180.00   0.0  0
 3XD  CONST_15  N6A   C6A  N1A  C2A   180.00   0.0  0
 3XD  CONST_16  C8A   C4A  C3A  C2A   180.00   0.0  0
 3XD  CONST_17  C7A   C2A  C3A  C4A   180.00   0.0  0
 3XD  CONST_18  N6A   C6A  C5A  C4A   180.00   0.0  0
 3XD  CONST_19  C7A   C2A  N1A  C6A   180.00   0.0  0
 3XD  CONST_20  C8A   C4A  C5A  C6A   180.00   0.0  0
 3XD  CONST_21  H13   C13  C12  C11   180.00   0.0  0
 3XD  CONST_22  H15   C15  C16  C11   180.00   0.0  0
 3XD  CONST_23  H16   C16  C11  C12   180.00   0.0  0
 3XD  CONST_24  H14   C14  C13  C12   180.00   0.0  0
 3XD  CONST_25  H12   C12  C13  C14   180.00   0.0  0
 3XD  CONST_26  H3AA  C3A  C2A  N1A   180.00   0.0  0
 3XD  CONST_27  H5A   C5A  C6A  N1A   180.00   0.0  0
 3XD  Var_01    C4'   C5'  N1'  C2'    34.17  30.0  1
 3XD  Var_02    C5'   N1'  C2'  C3'   -15.84  30.0  1
 3XD  Var_03    C4'   C7A  C2A  N1A   -61.34  30.0  1
 3XD  Var_04    C12   C11  C4   C3    -89.87  30.0  2
 3XD  Var_05    H8A   C8A  C4A  C3A    58.40  30.0  2
 3XD  Var_06    C11   C4   C3   N2   -179.51  30.0  2
 3XD  Var_07    H1    C1   O1   C3'   -59.67  30.0  2
 3XD  Var_08    C3    N2   C2   C1   -179.03  30.0  3
 3XD  Var_09    N2    C2   C1   O1     64.37  30.0  1
 3XD  Var_10    C4    C3   N2   C2   -168.67  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
 3XD  chir_01  C3'  O1   C2'  C4'  negativ
 3XD  chir_02  C4'  C3'  C7A  C5'  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
 3XD  plan-1  C4    0.020
 3XD  plan-1  C11   0.020
 3XD  plan-1  C12   0.020
 3XD  plan-1  C13   0.020
 3XD  plan-1  C14   0.020
 3XD  plan-1  C15   0.020
 3XD  plan-1  C16   0.020
 3XD  plan-1  H12   0.020
 3XD  plan-1  H13   0.020
 3XD  plan-1  H14   0.020
 3XD  plan-1  H15   0.020
 3XD  plan-1  H16   0.020
 3XD  plan-2  N1A   0.020
 3XD  plan-2  C2A   0.020
 3XD  plan-2  C3A   0.020
 3XD  plan-2  C4A   0.020
 3XD  plan-2  C5A   0.020
 3XD  plan-2  C6A   0.020
 3XD  plan-2  N6A   0.020
 3XD  plan-2  C7A   0.020
 3XD  plan-2  C8A   0.020
 3XD  plan-2  H3AA  0.020
 3XD  plan-2  H5A   0.020
 3XD  plan-3  C6A   0.020
 3XD  plan-3  N6A   0.020
 3XD  plan-3  HN6A  0.020
 3XD  plan-3  HN6B  0.020

