# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 16:35:31 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[(2R)-2-fluoro-2-(3-fluorophenyl)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]2OCCNC[C@H](F)c3cccc(F)c3)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
 8CX  8CX  6-{[(3R,4R)-4-(2-{[(2R)-2-fluoro-2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  56  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8CX
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
 8CX  C1    C  CH2   0  -0.159   0.0543   3.0307   1.2330
 8CX  O1    O  O2    0  -0.491  -0.8837   2.1161   0.7195
 8CX  C2    C  CH2   0  -0.298   1.3489   2.2967   1.4988
 8CX  N2    N  NH1   0  -0.609   1.9149   1.7579   0.2769
 8CX  C3    C  CH2   0  -0.297   3.1349   1.0207   0.5179
 8CX  C4    C  CH1   0   0.140   3.7291   0.4889  -0.7704
 8CX  F5    F  F     0  -0.377   2.8171  -0.3989  -1.3482
 8CX  N1'   N  NH1   0  -0.588  -3.2264   3.0593  -1.6238
 8CX  C11   C  CR6   0   0.053   5.0295  -0.2202  -0.5256
 8CX  C12   C  CR16  0  -0.464   5.0405  -1.5491  -0.1127
 8CX  C13   C  CR6   0   0.545   6.2548  -2.1483   0.1563
 8CX  F13   F  F     0  -0.316   6.2626  -3.4299   0.5584
 8CX  C14   C  CR16  0  -0.418   7.4594  -1.4832   0.0317
 8CX  C15   C  CR16  0  -0.224   7.4341  -0.1588  -0.3818
 8CX  C16   C  CR16  0  -0.308   6.2289   0.4697  -0.6621
 8CX  N1A   N  N     0  -0.485  -5.0510  -0.6788   0.9803
 8CX  C2'   C  CH2   0  -0.333  -2.2650   3.6127  -0.6716
 8CX  C2A   C  CR6   0   0.282  -3.8662  -0.8686   0.3957
 8CX  C3'   C  CH1   0   0.048  -2.1758   2.6490   0.5444
 8CX  C3A   C  CR16  0  -0.436  -3.6204  -1.9201  -0.4693
 8CX  C4'   C  CH1   0  -0.290  -3.1595   1.5238   0.1854
 8CX  C4A   C  CR6   0   0.205  -4.6496  -2.8253  -0.7513
 8CX  C5'   C  CH2   0  -0.303  -3.2613   1.6325  -1.3386
 8CX  C5A   C  CR16  0  -0.449  -5.8738  -2.6261  -0.1466
 8CX  C6A   C  CR6   0   0.439  -6.0349  -1.5333   0.7232
 8CX  N6A   N  NH2   0  -0.840  -7.2152  -1.3358   1.3806
 8CX  C7A   C  CH2   0  -0.488  -2.7976   0.1398   0.7148
 8CX  C8A   C  CH3   0  -0.726  -4.4145  -3.9868  -1.6678
 8CX  H1    H  HCH2  0   0.201   0.2358   3.8556   0.5310
 8CX  H1A   H  HCH2  0   0.205  -0.3084   3.4755   2.1706
 8CX  H2    H  HCH2  0   0.230   2.0557   3.0094   1.9326
 8CX  H2A   H  HCH2  0   0.200   1.1771   1.5240   2.2651
 8CX  HN2   H  HNH1  0   0.345   1.2326   1.1409  -0.1464
 8CX  H3    H  HCH2  0   0.244   3.8719   1.6938   0.9662
 8CX  H3A   H  HCH2  0   0.214   3.0104   0.1857   1.2277
 8CX  H4    H  HCH1  0   0.236   3.8712   1.3090  -1.4795
 8CX  HN1'  H  HNH1  0   0.345  -4.1410   3.4422  -1.4184
 8CX  H12   H  HCR6  0   0.279   4.1246  -2.1146   0.0042
 8CX  H14   H  HCR6  0   0.282   8.3922  -1.9867   0.2485
 8CX  H15   H  HCR6  0   0.271   8.3640   0.3824  -0.4935
 8CX  H16   H  HCR6  0   0.261   6.2230   1.5016  -0.9911
 8CX  H2'   H  HCH2  0   0.226  -1.2788   3.6742  -1.1428
 8CX  H2'A  H  HCH2  0   0.240  -2.5515   4.6258  -0.3895
 8CX  H3'   H  HCH1  0   0.215  -2.4840   3.1493   1.4727
 8CX  H3AA  H  HCR6  0   0.240  -2.6447  -2.0335  -0.9256
 8CX  H4'   H  HCH1  0   0.245  -4.1341   1.8025   0.6000
 8CX  H5'   H  HCH2  0   0.241  -4.1641   1.1768  -1.7465
 8CX  H5'A  H  HCH2  0   0.216  -2.4030   1.1400  -1.8111
 8CX  H5A   H  HCR6  0   0.253  -6.7027  -3.2983  -0.3353
 8CX  HN6A  H  HNH2  0   0.379  -7.3690  -0.4136   1.7538
 8CX  HN6B  H  HNH2  0   0.387  -8.0395  -1.7739   1.0056
 8CX  H7A   H  HCH2  0   0.244  -2.6667   0.1834   1.8000
 8CX  H7AA  H  HCH2  0   0.241  -1.8482  -0.1901   0.2917
 8CX  H8A   H  HCH3  0   0.254  -3.8373  -4.7620  -1.1603
 8CX  H8AA  H  HCH3  0   0.246  -5.3490  -4.4351  -2.0014
 8CX  H8AB  H  HCH3  0   0.248  -3.8428  -3.6875  -2.5463

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
 8CX  C2   C1    single    1.512  0.020  1.512
 8CX  C1   O1    single    1.407  0.020  1.407
 8CX  C1   H1    single    0.970  0.020  1.090
 8CX  C1   H1A   single    0.970  0.020  1.090
 8CX  O1   C3'   single    1.409  0.020  1.409
 8CX  C2   N2    single    1.450  0.020  1.450
 8CX  C2   H2    single    0.970  0.020  1.090
 8CX  C2   H2A   single    0.970  0.020  1.090
 8CX  C3   N2    single    1.446  0.020  1.446
 8CX  N2   HN2   single    0.890  0.020  1.040
 8CX  C3   C4    single    1.515  0.020  1.515
 8CX  C3   H3    single    0.970  0.020  1.090
 8CX  C3   H3A   single    0.970  0.020  1.090
 8CX  C11  C4    single    1.501  0.020  1.501
 8CX  C4   F5    single    1.398  0.020  1.398
 8CX  C4   H4    single    0.970  0.020  1.090
 8CX  C2'  N1'   single    1.462  0.020  1.462
 8CX  C5'  N1'   single    1.456  0.020  1.456
 8CX  N1'  HN1'  single    0.890  0.020  1.040
 8CX  C12  C11   aromatic  1.392  0.020  1.392
 8CX  C11  C16   aromatic  1.390  0.020  1.390
 8CX  C13  C12   aromatic  1.381  0.020  1.381
 8CX  C12  H12   single    0.930  0.020  1.080
 8CX  F13  C13   single    1.343  0.020  1.343
 8CX  C13  C14   aromatic  1.382  0.020  1.382
 8CX  C14  C15   aromatic  1.388  0.020  1.388
 8CX  C14  H14   single    0.930  0.020  1.080
 8CX  C15  C16   aromatic  1.388  0.020  1.388
 8CX  C15  H15   single    0.930  0.020  1.080
 8CX  C16  H16   single    0.930  0.020  1.080
 8CX  N1A  C2A   aromatic  1.335  0.020  1.335
 8CX  N1A  C6A   aromatic  1.328  0.020  1.328
 8CX  C3'  C2'   single    1.554  0.020  1.554
 8CX  C2'  H2'   single    0.970  0.020  1.090
 8CX  C2'  H2'A  single    0.970  0.020  1.090
 8CX  C7A  C2A   single    1.503  0.020  1.503
 8CX  C2A  C3A   aromatic  1.384  0.020  1.384
 8CX  C3'  C4'   single    1.537  0.020  1.537
 8CX  C3'  H3'   single    0.970  0.020  1.090
 8CX  C3A  C4A   aromatic  1.399  0.020  1.399
 8CX  C3A  H3AA  single    0.930  0.020  1.080
 8CX  C7A  C4'   single    1.525  0.020  1.525
 8CX  C4'  C5'   single    1.531  0.020  1.531
 8CX  C4'  H4'   single    0.970  0.020  1.090
 8CX  C5A  C4A   aromatic  1.380  0.020  1.380
 8CX  C4A  C8A   single    1.498  0.020  1.498
 8CX  C5'  H5'   single    0.970  0.020  1.090
 8CX  C5'  H5'A  single    0.970  0.020  1.090
 8CX  C6A  C5A   aromatic  1.406  0.020  1.406
 8CX  C5A  H5A   single    0.930  0.020  1.080
 8CX  N6A  C6A   single    1.365  0.020  1.365
 8CX  N6A  HN6A  single    0.890  0.020  1.040
 8CX  N6A  HN6B  single    0.890  0.020  1.040
 8CX  C7A  H7A   single    0.970  0.020  1.090
 8CX  C7A  H7AA  single    0.970  0.020  1.090
 8CX  C8A  H8A   single    0.970  0.020  1.090
 8CX  C8A  H8AA  single    0.970  0.020  1.090
 8CX  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
 8CX  H1A   C1   H1    107.21  3.000
 8CX  H1A   C1   C2    109.21  3.000
 8CX  H1    C1   C2    109.60  3.000
 8CX  H1A   C1   O1    110.75  3.000
 8CX  H1    C1   O1    111.42  3.000
 8CX  C2    C1   O1    108.63  3.000
 8CX  C3'   O1   C1    114.26  3.000
 8CX  H2A   C2   H2    106.37  3.000
 8CX  H2A   C2   N2    112.72  3.000
 8CX  H2    C2   N2    108.91  3.000
 8CX  H2A   C2   C1    109.23  3.000
 8CX  H2    C2   C1    107.87  3.000
 8CX  N2    C2   C1    111.49  3.000
 8CX  HN2   N2   C3    109.12  3.000
 8CX  HN2   N2   C2    108.39  3.000
 8CX  C3    N2   C2    112.23  3.000
 8CX  H3A   C3   H3    106.15  3.000
 8CX  H3A   C3   C4    109.01  3.000
 8CX  H3    C3   C4    107.46  3.000
 8CX  H3A   C3   N2    113.46  3.000
 8CX  H3    C3   N2    108.85  3.000
 8CX  C4    C3   N2    111.60  3.000
 8CX  H4    C4   C11   110.33  3.000
 8CX  H4    C4   F5    107.04  3.000
 8CX  C11   C4   F5    109.42  3.000
 8CX  H4    C4   C3    109.83  3.000
 8CX  F5    C4   C3    108.57  3.000
 8CX  C11   C4   C3    111.52  3.000
 8CX  HN1'  N1'  C5'   108.01  3.000
 8CX  HN1'  N1'  C2'   108.59  3.000
 8CX  C5'   N1'  C2'   105.02  3.000
 8CX  C16   C11  C12   119.75  3.000
 8CX  C16   C11  C4    119.79  3.000
 8CX  C12   C11  C4    120.42  3.000
 8CX  H12   C12  C13   119.76  3.000
 8CX  H12   C12  C11   121.61  3.000
 8CX  C13   C12  C11   118.63  3.000
 8CX  C14   C13  F13   118.76  3.000
 8CX  C14   C13  C12   122.71  3.000
 8CX  F13   C13  C12   118.53  3.000
 8CX  H14   C14  C15   121.30  3.000
 8CX  H14   C14  C13   120.64  3.000
 8CX  C15   C14  C13   118.06  3.000
 8CX  H15   C15  C16   119.94  3.000
 8CX  H15   C15  C14   119.51  3.000
 8CX  C16   C15  C14   120.54  3.000
 8CX  H16   C16  C15   119.84  3.000
 8CX  H16   C16  C11   119.86  3.000
 8CX  C15   C16  C11   120.30  3.000
 8CX  C6A   N1A  C2A   118.77  3.000
 8CX  H2'A  C2'  H2'   107.21  3.000
 8CX  H2'A  C2'  C3'   112.89  3.000
 8CX  H2'   C2'  C3'   108.65  3.000
 8CX  H2'A  C2'  N1'   110.34  3.000
 8CX  H2'   C2'  N1'   109.47  3.000
 8CX  C3'   C2'  N1'   108.22  3.000
 8CX  C7A   C2A  C3A   121.07  3.000
 8CX  C3A   C2A  N1A   122.66  3.000
 8CX  C7A   C2A  N1A   116.27  3.000
 8CX  H3'   C3'  C4'   110.56  3.000
 8CX  H3'   C3'  C2'   111.26  3.000
 8CX  C4'   C3'  C2'   103.56  3.000
 8CX  H3'   C3'  O1    108.94  3.000
 8CX  C4'   C3'  O1    109.83  3.000
 8CX  C2'   C3'  O1    112.62  3.000
 8CX  H3AA  C3A  C4A   120.66  3.000
 8CX  H3AA  C3A  C2A   120.20  3.000
 8CX  C4A   C3A  C2A   119.14  3.000
 8CX  H4'   C4'  C7A   108.10  3.000
 8CX  H4'   C4'  C5'   107.43  3.000
 8CX  C7A   C4'  C5'   115.19  3.000
 8CX  H4'   C4'  C3'   107.15  3.000
 8CX  C5'   C4'  C3'   102.88  3.000
 8CX  C7A   C4'  C3'   115.55  3.000
 8CX  C8A   C4A  C5A   121.29  3.000
 8CX  C8A   C4A  C3A   120.62  3.000
 8CX  C5A   C4A  C3A   118.09  3.000
 8CX  H5'A  C5'  H5'   107.41  3.000
 8CX  H5'A  C5'  C4'   110.18  3.000
 8CX  H5'   C5'  C4'   113.43  3.000
 8CX  H5'A  C5'  N1'   109.70  3.000
 8CX  H5'   C5'  N1'   110.86  3.000
 8CX  C4'   C5'  N1'   105.25  3.000
 8CX  H5A   C5A  C6A   120.15  3.000
 8CX  H5A   C5A  C4A   120.84  3.000
 8CX  C6A   C5A  C4A   119.01  3.000
 8CX  N6A   C6A  C5A   120.62  3.000
 8CX  N6A   C6A  N1A   117.01  3.000
 8CX  C5A   C6A  N1A   122.33  3.000
 8CX  HN6B  N6A  HN6A  114.32  3.000
 8CX  HN6B  N6A  C6A   117.77  3.000
 8CX  HN6A  N6A  C6A   116.31  3.000
 8CX  H7AA  C7A  H7A   107.02  3.000
 8CX  H7AA  C7A  C4'   110.27  3.000
 8CX  H7A   C7A  C4'   109.67  3.000
 8CX  H7AA  C7A  C2A   109.48  3.000
 8CX  H7A   C7A  C2A   108.80  3.000
 8CX  C4'   C7A  C2A   111.49  3.000
 8CX  H8AB  C8A  H8AA  108.44  3.000
 8CX  H8AB  C8A  H8A   107.01  3.000
 8CX  H8AA  C8A  H8A   107.69  3.000
 8CX  H8AB  C8A  C4A   111.25  3.000
 8CX  H8AA  C8A  C4A   111.83  3.000
 8CX  H8A   C8A  C4A   110.43  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
 8CX  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 8CX  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 8CX  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 8CX  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 8CX  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 8CX  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 8CX  CONST_07  C4A   C3A  C2A  N1A     0.00   0.0  0
 8CX  CONST_08  C4A   C5A  C6A  N1A     0.00   0.0  0
 8CX  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 8CX  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 8CX  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 8CX  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 8CX  CONST_13  C13   C12  C11  C4    180.00   0.0  0
 8CX  CONST_14  C15   C16  C11  C4    180.00   0.0  0
 8CX  CONST_15  F13   C13  C12  C11   180.00   0.0  0
 8CX  CONST_16  C15   C14  C13  F13   180.00   0.0  0
 8CX  CONST_17  N6A   C6A  N1A  C2A   180.00   0.0  0
 8CX  CONST_18  C8A   C4A  C3A  C2A   180.00   0.0  0
 8CX  CONST_19  C7A   C2A  C3A  C4A   180.00   0.0  0
 8CX  CONST_20  N6A   C6A  C5A  C4A   180.00   0.0  0
 8CX  CONST_21  C7A   C2A  N1A  C6A   180.00   0.0  0
 8CX  CONST_22  C8A   C4A  C5A  C6A   180.00   0.0  0
 8CX  CONST_23  H15   C15  C16  C11   180.00   0.0  0
 8CX  CONST_24  H16   C16  C11  C12   180.00   0.0  0
 8CX  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 8CX  CONST_26  H12   C12  C13  C14   180.00   0.0  0
 8CX  CONST_27  H3AA  C3A  C2A  N1A   180.00   0.0  0
 8CX  CONST_28  H5A   C5A  C6A  N1A   180.00   0.0  0
 8CX  Var_01    C4'   C5'  N1'  C2'    38.10  30.0  1
 8CX  Var_02    C5'   N1'  C2'  C3'   -23.56  30.0  1
 8CX  Var_03    C4'   C7A  C2A  N1A   -65.22  30.0  1
 8CX  Var_04    H8A   C8A  C4A  C3A    75.56  30.0  2
 8CX  Var_05    H1    C1   O1   C3'   -64.75  30.0  1
 8CX  Var_06    C3    N2   C2   C1   -178.40  30.0  3
 8CX  Var_07    N2    C2   C1   O1     62.60  30.0  2
 8CX  Var_08    C4    C3   N2   C2   -178.82  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
 8CX  chir_01  C4   C3   C11  F5   negativ
 8CX  chir_02  C3'  O1   C2'  C4'  negativ
 8CX  chir_03  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
 8CX  plan-1  C4    0.020
 8CX  plan-1  C11   0.020
 8CX  plan-1  C12   0.020
 8CX  plan-1  C13   0.020
 8CX  plan-1  F13   0.020
 8CX  plan-1  C14   0.020
 8CX  plan-1  C15   0.020
 8CX  plan-1  C16   0.020
 8CX  plan-1  H12   0.020
 8CX  plan-1  H14   0.020
 8CX  plan-1  H15   0.020
 8CX  plan-1  H16   0.020
 8CX  plan-2  N1A   0.020
 8CX  plan-2  C2A   0.020
 8CX  plan-2  C3A   0.020
 8CX  plan-2  C4A   0.020
 8CX  plan-2  C5A   0.020
 8CX  plan-2  C6A   0.020
 8CX  plan-2  N6A   0.020
 8CX  plan-2  C7A   0.020
 8CX  plan-2  C8A   0.020
 8CX  plan-2  H3AA  0.020
 8CX  plan-2  H5A   0.020
 8CX  plan-3  C6A   0.020
 8CX  plan-3  N6A   0.020
 8CX  plan-3  HN6A  0.020
 8CX  plan-3  HN6B  0.020

