# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 16:27:00 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 6-({(3S,4S)-4-[2-({2,2-difluoro-2-[(2R)-piperidin-2-yl]ethyl}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)[C@H]3CCCCN3)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
 3XF  3XF  6-({(3S,4S)-4-[2-({2,2-difluoro-2-[(2R)-piperidin-2-yl]ethyl}amino)ethoxy]pyrrolidin-3-yl}methyl)-4-methylpyridin-2-amine  ligand  61  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_3XF
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
 3XF  O1    O  O2    0  -0.494  -1.0580  -2.4864   0.0017
 3XF  C2    C  CH2   0  -0.156  -0.0900  -3.4569   0.3285
 3XF  C3    C  CH2   0  -0.297   1.2096  -3.0862  -0.3522
 3XF  N4    N  NH1   0  -0.616   1.6907  -1.8101   0.1380
 3XF  C5    C  CH2   0  -0.348   2.9337  -1.3993  -0.4698
 3XF  C6    C  CT    0   0.768   3.4893  -0.1614   0.2047
 3XF  F7    F  F     0  -0.363   2.5245   0.8169   0.1995
 3XF  F8    F  F     0  -0.357   3.7198  -0.4226   1.5302
 3XF  N1'   N  NH1   0  -0.614  -4.4611  -2.9748   0.5511
 3XF  N11   N  NH1   0  -0.596   5.7811  -0.6286  -0.4313
 3XF  C12   C  CH1   0  -0.218   4.7525   0.4010  -0.4319
 3XF  C13   C  CH2   0  -0.442   5.2181   1.7197   0.1925
 3XF  C14   C  CH2   0  -0.444   6.4827   2.2016  -0.5160
 3XF  C15   C  CH2   0  -0.441   7.5557   1.1188  -0.5248
 3XF  C16   C  CH2   0  -0.313   6.9971  -0.1792  -1.0981
 3XF  N1A   N  N     0  -0.475  -3.9398   1.2757  -1.2444
 3XF  C2'   C  CH2   0  -0.305  -3.1548  -3.6126   0.6010
 3XF  C2A   C  CR6   0   0.269  -3.1350   1.1897  -0.1839
 3XF  C3'   C  CH1   0   0.051  -2.1694  -2.4521   0.8619
 3XF  C3A   C  CR16  0  -0.425  -3.1094   2.1506   0.8134
 3XF  C4'   C  CH1   0  -0.281  -3.0096  -1.1780   0.6139
 3XF  C4A   C  CR6   0   0.204  -3.9647   3.2523   0.7201
 3XF  C5'   C  CH2   0  -0.270  -4.2437  -1.7029  -0.1149
 3XF  C5A   C  CR16  0  -0.447  -4.8023   3.3342  -0.3747
 3XF  C6A   C  CR6   0   0.440  -4.7573   2.3192  -1.3445
 3XF  N6A   N  NH2   0  -0.839  -5.5323   2.3916  -2.4688
 3XF  C7A   C  CH2   0  -0.494  -2.2734  -0.0386  -0.0893
 3XF  C8A   C  CH3   0  -0.727  -3.9548   4.3182   1.7731
 3XF  H2    H  HCH2  0   0.200   0.0661  -3.4933   1.4153
 3XF  H2A   H  HCH2  0   0.210  -0.4018  -4.4596   0.0084
 3XF  H3    H  HCH2  0   0.232   1.9467  -3.8595  -0.1192
 3XF  H3A   H  HCH2  0   0.202   1.0722  -3.1066  -1.4450
 3XF  HN4   H  HNH1  0   0.346   0.9785  -1.1138  -0.0413
 3XF  H5    H  HCH2  0   0.251   3.6702  -2.1979  -0.3673
 3XF  H5A   H  HCH2  0   0.220   2.8553  -1.1922  -1.5483
 3XF  HN1'  H  HNH1  0   0.350  -5.1354  -3.5501   0.0643
 3XF  HN11  H  HNH1  0   0.341   6.0159  -0.8640   0.5277
 3XF  H12   H  HCH1  0   0.248   4.5007   0.5973  -1.4817
 3XF  H13   H  HCH2  0   0.239   4.4401   2.4816   0.1204
 3XF  H13A  H  HCH2  0   0.223   5.4295   1.5727   1.2563
 3XF  H14   H  HCH2  0   0.216   6.2344   2.4737  -1.5475
 3XF  H14A  H  HCH2  0   0.236   6.8540   3.1096  -0.0365
 3XF  H15   H  HCH2  0   0.229   8.4247   1.4407  -1.1045
 3XF  H15A  H  HCH2  0   0.215   7.9077   0.9396   0.4971
 3XF  H16   H  HCH2  0   0.239   7.7365  -0.9795  -1.0358
 3XF  H16A  H  HCH2  0   0.219   6.7710  -0.0429  -2.1610
 3XF  H2'   H  HCH2  0   0.228  -3.1201  -4.3815   1.3755
 3XF  H2'A  H  HCH2  0   0.206  -2.8763  -4.0884  -0.3510
 3XF  H3'   H  HCH1  0   0.219  -1.8158  -2.4666   1.9014
 3XF  H3AA  H  HCR6  0   0.241  -2.4369   2.0451   1.6560
 3XF  H4'   H  HCH1  0   0.253  -3.3359  -0.8157   1.5939
 3XF  H5'   H  HCH2  0   0.192  -4.0323  -1.8020  -1.1916
 3XF  H5'A  H  HCH2  0   0.230  -5.1090  -1.0469  -0.0108
 3XF  H5AA  H  HCR6  0   0.254  -5.4868   4.1661  -0.4905
 3XF  HN6A  H  HNH2  0   0.378  -5.6750   1.5220  -2.9562
 3XF  HN6B  H  HNH2  0   0.386  -6.3553   2.9695  -2.4246
 3XF  H7A   H  HCH2  0   0.239  -1.9752  -0.3428  -1.0935
 3XF  H7AA  H  HCH2  0   0.241  -1.3621   0.2018   0.4629
 3XF  H8A   H  HCH3  0   0.254  -3.0509   4.9251   1.6961
 3XF  H8AA  H  HCH3  0   0.246  -4.8113   4.9839   1.6821
 3XF  H8AB  H  HCH3  0   0.248  -3.9631   3.8843   2.7733

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
 3XF  O1   C3'   single    1.406  0.020  1.406
 3XF  O1   C2    single    1.409  0.020  1.409
 3XF  C3   C2    single    1.513  0.020  1.513
 3XF  C2   H2    single    0.970  0.020  1.090
 3XF  C2   H2A   single    0.970  0.020  1.090
 3XF  N4   C3    single    1.449  0.020  1.449
 3XF  C3   H3    single    0.970  0.020  1.090
 3XF  C3   H3A   single    0.970  0.020  1.090
 3XF  C5   N4    single    1.443  0.020  1.443
 3XF  N4   HN4   single    0.890  0.020  1.040
 3XF  C6   C5    single    1.515  0.020  1.515
 3XF  C5   H5    single    0.970  0.020  1.090
 3XF  C5   H5A   single    0.970  0.020  1.090
 3XF  F7   C6    single    1.374  0.020  1.374
 3XF  F8   C6    single    1.371  0.020  1.371
 3XF  C6   C12   single    1.522  0.020  1.522
 3XF  C2'  N1'   single    1.455  0.020  1.455
 3XF  N1'  C5'   single    1.452  0.020  1.452
 3XF  N1'  HN1'  single    0.890  0.020  1.040
 3XF  C12  N11   single    1.455  0.020  1.455
 3XF  N11  C16   single    1.458  0.020  1.458
 3XF  N11  HN11  single    0.890  0.020  1.040
 3XF  C13  C12   single    1.532  0.020  1.532
 3XF  C12  H12   single    0.970  0.020  1.090
 3XF  C13  C14   single    1.528  0.020  1.528
 3XF  C13  H13   single    0.970  0.020  1.090
 3XF  C13  H13A  single    0.970  0.020  1.090
 3XF  C14  C15   single    1.524  0.020  1.524
 3XF  C14  H14   single    0.970  0.020  1.090
 3XF  C14  H14A  single    0.970  0.020  1.090
 3XF  C15  C16   single    1.525  0.020  1.525
 3XF  C15  H15   single    0.970  0.020  1.090
 3XF  C15  H15A  single    0.970  0.020  1.090
 3XF  C16  H16   single    0.970  0.020  1.090
 3XF  C16  H16A  single    0.970  0.020  1.090
 3XF  N1A  C2A   aromatic  1.334  0.020  1.334
 3XF  N1A  C6A   aromatic  1.329  0.020  1.329
 3XF  C2'  C3'   single    1.545  0.020  1.545
 3XF  C2'  H2'   single    0.970  0.020  1.090
 3XF  C2'  H2'A  single    0.970  0.020  1.090
 3XF  C7A  C2A   single    1.503  0.020  1.503
 3XF  C2A  C3A   aromatic  1.385  0.020  1.385
 3XF  C3'  C4'   single    1.546  0.020  1.546
 3XF  C3'  H3'   single    0.970  0.020  1.090
 3XF  C3A  C4A   aromatic  1.398  0.020  1.398
 3XF  C3A  H3AA  single    0.930  0.020  1.080
 3XF  C5'  C4'   single    1.526  0.020  1.526
 3XF  C7A  C4'   single    1.528  0.020  1.528
 3XF  C4'  H4'   single    0.970  0.020  1.090
 3XF  C5A  C4A   aromatic  1.381  0.020  1.381
 3XF  C4A  C8A   single    1.498  0.020  1.498
 3XF  C5'  H5'   single    0.970  0.020  1.090
 3XF  C5'  H5'A  single    0.970  0.020  1.090
 3XF  C6A  C5A   aromatic  1.404  0.020  1.404
 3XF  C5A  H5AA  single    0.930  0.020  1.080
 3XF  N6A  C6A   single    1.367  0.020  1.367
 3XF  N6A  HN6A  single    0.890  0.020  1.040
 3XF  N6A  HN6B  single    0.890  0.020  1.040
 3XF  C7A  H7A   single    0.970  0.020  1.090
 3XF  C7A  H7AA  single    0.970  0.020  1.090
 3XF  C8A  H8A   single    0.970  0.020  1.090
 3XF  C8A  H8AA  single    0.970  0.020  1.090
 3XF  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
 3XF  C3'   O1   C2    114.71  3.000
 3XF  H2A   C2   H2    107.37  3.000
 3XF  H2A   C2   C3    109.67  3.000
 3XF  H2    C2   C3    109.34  3.000
 3XF  H2A   C2   O1    111.49  3.000
 3XF  H2    C2   O1    110.47  3.000
 3XF  C3    C2   O1    108.48  3.000
 3XF  H3A   C3   H3    106.40  3.000
 3XF  H3A   C3   N4    113.16  3.000
 3XF  H3    C3   N4    109.08  3.000
 3XF  H3A   C3   C2    109.55  3.000
 3XF  H3    C3   C2    108.05  3.000
 3XF  N4    C3   C2    110.41  3.000
 3XF  HN4   N4   C5    109.61  3.000
 3XF  HN4   N4   C3    108.19  3.000
 3XF  C5    N4   C3    113.21  3.000
 3XF  H5A   C5   H5    106.12  3.000
 3XF  H5A   C5   C6    107.97  3.000
 3XF  H5    C5   C6    107.98  3.000
 3XF  H5A   C5   N4    113.87  3.000
 3XF  H5    C5   N4    109.48  3.000
 3XF  C6    C5   N4    111.15  3.000
 3XF  C12   C6   F8    109.59  3.000
 3XF  C12   C6   F7    108.55  3.000
 3XF  F8    C6   F7    104.92  3.000
 3XF  C12   C6   C5    114.83  3.000
 3XF  F8    C6   C5    109.66  3.000
 3XF  F7    C6   C5    108.82  3.000
 3XF  HN1'  N1'  C5'   112.17  3.000
 3XF  HN1'  N1'  C2'   111.46  3.000
 3XF  C5'   N1'  C2'   105.39  3.000
 3XF  HN11  N11  C16   108.10  3.000
 3XF  HN11  N11  C12   109.15  3.000
 3XF  C16   N11  C12   111.79  3.000
 3XF  H12   C12  C13   107.81  3.000
 3XF  H12   C12  N11   106.81  3.000
 3XF  C13   C12  N11   113.21  3.000
 3XF  H12   C12  C6    106.01  3.000
 3XF  C13   C12  C6    113.57  3.000
 3XF  N11   C12  C6    108.97  3.000
 3XF  H13A  C13  H13   107.19  3.000
 3XF  H13A  C13  C14   109.47  3.000
 3XF  H13   C13  C14   109.83  3.000
 3XF  H13A  C13  C12   109.84  3.000
 3XF  H13   C13  C12   110.95  3.000
 3XF  C14   C13  C12   109.52  3.000
 3XF  H14A  C14  H14   106.50  3.000
 3XF  H14A  C14  C15   110.72  3.000
 3XF  H14   C14  C15   109.30  3.000
 3XF  H14A  C14  C13   109.89  3.000
 3XF  H14   C14  C13   109.12  3.000
 3XF  C15   C14  C13   111.18  3.000
 3XF  H15A  C15  H15   106.70  3.000
 3XF  H15A  C15  C16   109.21  3.000
 3XF  H15   C15  C16   110.03  3.000
 3XF  H15A  C15  C14   109.69  3.000
 3XF  H15   C15  C14   110.70  3.000
 3XF  C16   C15  C14   110.42  3.000
 3XF  H16A  C16  H16   106.65  3.000
 3XF  H16A  C16  C15   109.54  3.000
 3XF  H16   C16  C15   110.76  3.000
 3XF  H16A  C16  N11   108.06  3.000
 3XF  H16   C16  N11   108.24  3.000
 3XF  C15   C16  N11   113.33  3.000
 3XF  C6A   N1A  C2A   118.78  3.000
 3XF  H2'A  C2'  H2'   107.53  3.000
 3XF  H2'A  C2'  C3'   108.03  3.000
 3XF  H2'   C2'  C3'   112.89  3.000
 3XF  H2'A  C2'  N1'   112.79  3.000
 3XF  H2'   C2'  N1'   111.20  3.000
 3XF  C3'   C2'  N1'   104.43  3.000
 3XF  C7A   C2A  C3A   120.72  3.000
 3XF  C3A   C2A  N1A   122.60  3.000
 3XF  C7A   C2A  N1A   116.65  3.000
 3XF  H3'   C3'  C4'   109.73  3.000
 3XF  H3'   C3'  C2'   110.82  3.000
 3XF  C4'   C3'  C2'   104.21  3.000
 3XF  H3'   C3'  O1    108.93  3.000
 3XF  C4'   C3'  O1    110.58  3.000
 3XF  C2'   C3'  O1    112.50  3.000
 3XF  H3AA  C3A  C4A   120.57  3.000
 3XF  H3AA  C3A  C2A   120.27  3.000
 3XF  C4A   C3A  C2A   119.17  3.000
 3XF  H4'   C4'  C7A   107.99  3.000
 3XF  H4'   C4'  C5'   107.48  3.000
 3XF  C7A   C4'  C5'   115.23  3.000
 3XF  H4'   C4'  C3'   106.92  3.000
 3XF  C7A   C4'  C3'   115.25  3.000
 3XF  C5'   C4'  C3'   103.44  3.000
 3XF  C8A   C4A  C5A   121.27  3.000
 3XF  C8A   C4A  C3A   120.64  3.000
 3XF  C5A   C4A  C3A   118.09  3.000
 3XF  H5'A  C5'  H5'   107.43  3.000
 3XF  H5'A  C5'  C4'   112.89  3.000
 3XF  H5'   C5'  C4'   110.03  3.000
 3XF  H5'A  C5'  N1'   111.35  3.000
 3XF  H5'   C5'  N1'   113.46  3.000
 3XF  C4'   C5'  N1'   101.73  3.000
 3XF  H5AA  C5A  C6A   120.09  3.000
 3XF  H5AA  C5A  C4A   120.90  3.000
 3XF  C6A   C5A  C4A   119.02  3.000
 3XF  N6A   C6A  C5A   120.75  3.000
 3XF  N6A   C6A  N1A   116.87  3.000
 3XF  C5A   C6A  N1A   122.35  3.000
 3XF  HN6B  N6A  HN6A  113.65  3.000
 3XF  HN6B  N6A  C6A   117.24  3.000
 3XF  HN6A  N6A  C6A   115.63  3.000
 3XF  H7AA  C7A  H7A   107.37  3.000
 3XF  H7AA  C7A  C4'   109.48  3.000
 3XF  H7A   C7A  C4'   110.33  3.000
 3XF  H7AA  C7A  C2A   109.28  3.000
 3XF  H7A   C7A  C2A   109.06  3.000
 3XF  C4'   C7A  C2A   111.23  3.000
 3XF  H8AB  C8A  H8AA  108.30  3.000
 3XF  H8AB  C8A  H8A   106.99  3.000
 3XF  H8AA  C8A  H8A   107.79  3.000
 3XF  H8AB  C8A  C4A   111.20  3.000
 3XF  H8AA  C8A  C4A   111.78  3.000
 3XF  H8A   C8A  C4A   110.58  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
 3XF  CONST_01  C4A   C3A  C2A  N1A     0.00   0.0  0
 3XF  CONST_02  C4A   C5A  C6A  N1A     0.00   0.0  0
 3XF  CONST_03  C5A   C6A  N1A  C2A     0.00   0.0  0
 3XF  CONST_04  C5A   C4A  C3A  C2A     0.00   0.0  0
 3XF  CONST_05  C6A   N1A  C2A  C3A     0.00   0.0  0
 3XF  CONST_06  C6A   C5A  C4A  C3A     0.00   0.0  0
 3XF  CONST_07  N6A   C6A  N1A  C2A   180.00   0.0  0
 3XF  CONST_08  C8A   C4A  C3A  C2A   180.00   0.0  0
 3XF  CONST_09  C7A   C2A  C3A  C4A   180.00   0.0  0
 3XF  CONST_10  N6A   C6A  C5A  C4A   180.00   0.0  0
 3XF  CONST_11  C7A   C2A  N1A  C6A   180.00   0.0  0
 3XF  CONST_12  C8A   C4A  C5A  C6A   180.00   0.0  0
 3XF  CONST_13  H3AA  C3A  C2A  N1A   180.00   0.0  0
 3XF  CONST_14  H5AA  C5A  C6A  N1A   180.00   0.0  0
 3XF  Var_01    C14   C15  C16  N11   -53.74  30.0  1
 3XF  Var_02    C15   C16  N11  C12    54.92  30.0  1
 3XF  Var_03    C15   C14  C13  C12   -53.67  30.0  1
 3XF  Var_04    C16   C15  C14  C13    53.20  30.0  1
 3XF  Var_05    C4'   C5'  N1'  C2'   -46.85  30.0  1
 3XF  Var_06    C5'   N1'  C2'  C3'    37.35  30.0  1
 3XF  Var_07    C4'   C7A  C2A  N1A   -87.31  30.0  2
 3XF  Var_08    H8A   C8A  C4A  C3A    72.45  30.0  2
 3XF  Var_09    C12   C6   C5   N4   -176.03  30.0  1
 3XF  Var_10    H2    C2   O1   C3'   -41.40  30.0  3
 3XF  Var_11    N4    C3   C2   O1     62.50  30.0  2
 3XF  Var_12    C5    N4   C3   C2    179.79  30.0  1
 3XF  Var_13    C6    C5   N4   C3   -172.33  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
 3XF  chir_01  C12  C6   N11  C13  positiv
 3XF  chir_02  C3'  O1   C2'  C4'  positiv
 3XF  chir_03  C4'  C3'  C5'  C7A  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
 3XF  plan-1  C6A   0.020
 3XF  plan-1  N6A   0.020
 3XF  plan-1  HN6A  0.020
 3XF  plan-1  HN6B  0.020
 3XF  plan-2  N1A   0.020
 3XF  plan-2  C2A   0.020
 3XF  plan-2  C3A   0.020
 3XF  plan-2  C4A   0.020
 3XF  plan-2  C5A   0.020
 3XF  plan-2  C6A   0.020
 3XF  plan-2  N6A   0.020
 3XF  plan-2  C7A   0.020
 3XF  plan-2  C8A   0.020
 3XF  plan-2  H3AA  0.020
 3XF  plan-2  H5AA  0.020

