# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 14:23:18 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[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]2OCCNCCc3cccc(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
 JRR  JRR  6-{[(3R,4R)-4-(2-{[2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  56  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JRR
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
 JRR  C1    C  CH2   0  -0.161   0.2276   2.9203   1.2147
 JRR  O1    O  O2    0  -0.493  -0.7289   2.0846   0.6116
 JRR  C2    C  CH2   0  -0.294   1.4810   2.1111   1.4618
 JRR  N2    N  NH1   0  -0.601   2.0681   1.6448   0.2212
 JRR  C3    C  CH2   0  -0.246   3.2082   0.7783   0.4377
 JRR  C4    C  CH2   0  -0.532   3.7868   0.2964  -0.8902
 JRR  N1'   N  NH1   0  -0.603  -2.6825   2.8621  -1.8828
 JRR  C11   C  CR6   0   0.140   4.9362  -0.6462  -0.6762
 JRR  C12   C  CR16  0  -0.467   6.2447  -0.1708  -0.6621
 JRR  C13   C  CR6   0   0.539   7.2817  -1.0519  -0.4227
 JRR  F13   F  F     0  -0.319   8.5405  -0.5788  -0.4186
 JRR  C14   C  CR16  0  -0.426   7.0755  -2.3973  -0.1906
 JRR  C15   C  CR16  0  -0.225   5.7680  -2.8658  -0.2034
 JRR  C16   C  CR16  0  -0.317   4.7094  -2.0019  -0.4431
 JRR  N1A   N  N     0  -0.486  -5.1339  -0.4051   0.8389
 JRR  C2'   C  CH2   0  -0.305  -2.0708   3.6083  -0.7738
 JRR  C2A   C  CR6   0   0.285  -3.8911  -0.7480   0.4908
 JRR  C3'   C  CH1   0   0.023  -2.0038   2.6627   0.4449
 JRR  C3A   C  CR16  0  -0.438  -3.5976  -1.9384  -0.1496
 JRR  C4'   C  CH1   0  -0.278  -2.9935   1.5564   0.0791
 JRR  C4A   C  CR6   0   0.206  -4.6377  -2.8260  -0.4498
 JRR  C5'   C  CH2   0  -0.287  -2.8318   1.4804  -1.4383
 JRR  C5A   C  CR16  0  -0.450  -5.9198  -2.4700  -0.0871
 JRR  C6A   C  CR6   0   0.439  -6.1286  -1.2402   0.5626
 JRR  N6A   N  NH2   0  -0.839  -7.3777  -0.8794   0.9797
 JRR  C7A   C  CH2   0  -0.489  -2.8090   0.2405   0.8250
 JRR  C8A   C  CH3   0  -0.726  -4.3545  -4.1266  -1.1374
 JRR  H1    H  HCH2  0   0.198   0.4661   3.7851   0.5809
 JRR  H1A   H  HCH2  0   0.205  -0.1460   3.3121   2.1711
 JRR  H2    H  HCH2  0   0.226   2.2020   2.7533   1.9759
 JRR  H2A   H  HCH2  0   0.194   1.2469   1.2899   2.1587
 JRR  HN2   H  HNH1  0   0.340   1.3644   1.1289  -0.2947
 JRR  H3    H  HCH2  0   0.224   3.9748   1.3375   0.9836
 JRR  H3A   H  HCH2  0   0.198   2.9618  -0.0952   1.0629
 JRR  H4    H  HCH2  0   0.247   3.0014  -0.2069  -1.4610
 JRR  H4A   H  HCH2  0   0.248   4.1076   1.1594  -1.4778
 JRR  HN1'  H  HNH1  0   0.348  -3.6020   3.2407  -2.0613
 JRR  H12   H  HCR6  0   0.270   6.4532   0.8774  -0.8409
 JRR  H14   H  HCR6  0   0.277   7.9102  -3.0614  -0.0090
 JRR  H15   H  HCR6  0   0.266   5.5790  -3.9167  -0.0282
 JRR  H16   H  HCR6  0   0.252   3.6954  -2.3836  -0.4526
 JRR  H2'   H  HCH2  0   0.223  -1.0672   3.9546  -1.0393
 JRR  H2'A  H  HCH2  0   0.231  -2.6585   4.4986  -0.5433
 JRR  H3'   H  HCH1  0   0.224  -2.2967   3.1758   1.3710
 JRR  H3AA  H  HCR6  0   0.242  -2.5756  -2.1763  -0.4170
 JRR  H4'   H  HCH1  0   0.243  -3.9971   1.9394   0.2932
 JRR  H5'   H  HCH2  0   0.236  -3.6772   1.0083  -1.9398
 JRR  H5'A  H  HCH2  0   0.210  -1.9385   0.8976  -1.6926
 JRR  H5A   H  HCR6  0   0.253  -6.7590  -3.1226  -0.2970
 JRR  HN6A  H  HNH2  0   0.379  -7.5189   0.0990   1.1701
 JRR  HN6B  H  HNH2  0   0.387  -8.1636  -1.3312   0.5431
 JRR  H7A   H  HCH2  0   0.244  -2.8236   0.4276   1.9032
 JRR  H7AA  H  HCH2  0   0.241  -1.8357  -0.1914   0.5892
 JRR  H8A   H  HCH3  0   0.252  -3.7627  -4.7807  -0.4949
 JRR  H8AA  H  HCH3  0   0.246  -5.2705  -4.6536  -1.3998
 JRR  H8AB  H  HCH3  0   0.249  -3.7775  -3.9697  -2.0496

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
 JRR  C2   C1    single    1.512  0.020  1.512
 JRR  C1   O1    single    1.406  0.020  1.406
 JRR  C1   H1    single    0.970  0.020  1.090
 JRR  C1   H1A   single    0.970  0.020  1.090
 JRR  O1   C3'   single    1.410  0.020  1.410
 JRR  C2   N2    single    1.450  0.020  1.450
 JRR  C2   H2    single    0.970  0.020  1.090
 JRR  C2   H2A   single    0.970  0.020  1.090
 JRR  C3   N2    single    1.448  0.020  1.448
 JRR  N2   HN2   single    0.890  0.020  1.040
 JRR  C3   C4    single    1.527  0.020  1.527
 JRR  C3   H3    single    0.970  0.020  1.090
 JRR  C3   H3A   single    0.970  0.020  1.090
 JRR  C11  C4    single    1.502  0.020  1.502
 JRR  C4   H4    single    0.970  0.020  1.090
 JRR  C4   H4A   single    0.970  0.020  1.090
 JRR  C2'  N1'   single    1.470  0.020  1.470
 JRR  C5'  N1'   single    1.459  0.020  1.459
 JRR  N1'  HN1'  single    0.890  0.020  1.040
 JRR  C12  C11   aromatic  1.392  0.020  1.392
 JRR  C11  C16   aromatic  1.394  0.020  1.394
 JRR  C13  C12   aromatic  1.382  0.020  1.382
 JRR  C12  H12   single    0.930  0.020  1.080
 JRR  F13  C13   single    1.345  0.020  1.345
 JRR  C13  C14   aromatic  1.381  0.020  1.381
 JRR  C14  C15   aromatic  1.389  0.020  1.389
 JRR  C14  H14   single    0.930  0.020  1.080
 JRR  C15  C16   aromatic  1.387  0.020  1.387
 JRR  C15  H15   single    0.930  0.020  1.080
 JRR  C16  H16   single    0.930  0.020  1.080
 JRR  C2A  N1A   aromatic  1.335  0.020  1.335
 JRR  N1A  C6A   aromatic  1.328  0.020  1.328
 JRR  C3'  C2'   single    1.544  0.020  1.544
 JRR  C2'  H2'   single    0.970  0.020  1.090
 JRR  C2'  H2'A  single    0.970  0.020  1.090
 JRR  C7A  C2A   single    1.503  0.020  1.503
 JRR  C2A  C3A   aromatic  1.383  0.020  1.383
 JRR  C3'  C4'   single    1.529  0.020  1.529
 JRR  C3'  H3'   single    0.970  0.020  1.090
 JRR  C3A  C4A   aromatic  1.400  0.020  1.400
 JRR  C3A  H3AA  single    0.930  0.020  1.080
 JRR  C7A  C4'   single    1.524  0.020  1.524
 JRR  C4'  C5'   single    1.528  0.020  1.528
 JRR  C4'  H4'   single    0.970  0.020  1.090
 JRR  C4A  C5A   aromatic  1.379  0.020  1.379
 JRR  C4A  C8A   single    1.498  0.020  1.498
 JRR  C5'  H5'   single    0.970  0.020  1.090
 JRR  C5'  H5'A  single    0.970  0.020  1.090
 JRR  C6A  C5A   aromatic  1.406  0.020  1.406
 JRR  C5A  H5A   single    0.930  0.020  1.080
 JRR  N6A  C6A   single    1.365  0.020  1.365
 JRR  N6A  HN6A  single    0.890  0.020  1.040
 JRR  N6A  HN6B  single    0.890  0.020  1.040
 JRR  C7A  H7A   single    0.970  0.020  1.090
 JRR  C7A  H7AA  single    0.970  0.020  1.090
 JRR  C8A  H8A   single    0.970  0.020  1.090
 JRR  C8A  H8AA  single    0.970  0.020  1.090
 JRR  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
 JRR  H1A   C1   H1    107.17  3.000
 JRR  H1A   C1   C2    109.29  3.000
 JRR  H1    C1   C2    109.61  3.000
 JRR  H1A   C1   O1    110.73  3.000
 JRR  H1    C1   O1    111.60  3.000
 JRR  C2    C1   O1    108.42  3.000
 JRR  C3'   O1   C1    114.98  3.000
 JRR  H2A   C2   H2    106.28  3.000
 JRR  H2A   C2   N2    112.80  3.000
 JRR  H2    C2   N2    108.91  3.000
 JRR  H2A   C2   C1    109.02  3.000
 JRR  H2    C2   C1    108.00  3.000
 JRR  N2    C2   C1    111.59  3.000
 JRR  HN2   N2   C3    108.55  3.000
 JRR  HN2   N2   C2    108.55  3.000
 JRR  C3    N2   C2    112.54  3.000
 JRR  H3A   C3   H3    106.17  3.000
 JRR  H3A   C3   C4    109.15  3.000
 JRR  H3    C3   C4    109.25  3.000
 JRR  H3A   C3   N2    112.52  3.000
 JRR  H3    C3   N2    108.68  3.000
 JRR  C4    C3   N2    110.93  3.000
 JRR  H4A   C4   H4    107.09  3.000
 JRR  H4A   C4   C11   110.35  3.000
 JRR  H4    C4   C11   109.59  3.000
 JRR  H4A   C4   C3    109.26  3.000
 JRR  H4    C4   C3    109.09  3.000
 JRR  C11   C4   C3    111.36  3.000
 JRR  HN1'  N1'  C5'   108.40  3.000
 JRR  HN1'  N1'  C2'   108.77  3.000
 JRR  C5'   N1'  C2'   107.07  3.000
 JRR  C16   C11  C12   118.90  3.000
 JRR  C16   C11  C4    120.64  3.000
 JRR  C12   C11  C4    120.43  3.000
 JRR  H12   C12  C13   120.07  3.000
 JRR  H12   C12  C11   120.63  3.000
 JRR  C13   C12  C11   119.30  3.000
 JRR  C14   C13  F13   118.82  3.000
 JRR  C14   C13  C12   122.58  3.000
 JRR  F13   C13  C12   118.60  3.000
 JRR  H14   C14  C15   121.38  3.000
 JRR  H14   C14  C13   120.74  3.000
 JRR  C15   C14  C13   117.88  3.000
 JRR  H15   C15  C16   119.96  3.000
 JRR  H15   C15  C14   119.38  3.000
 JRR  C16   C15  C14   120.66  3.000
 JRR  H16   C16  C15   119.75  3.000
 JRR  H16   C16  C11   119.57  3.000
 JRR  C15   C16  C11   120.68  3.000
 JRR  C6A   N1A  C2A   118.78  3.000
 JRR  H2'A  C2'  H2'   106.68  3.000
 JRR  H2'A  C2'  C3'   110.87  3.000
 JRR  H2'   C2'  C3'   110.21  3.000
 JRR  H2'A  C2'  N1'   110.45  3.000
 JRR  H2'   C2'  N1'   111.05  3.000
 JRR  C3'   C2'  N1'   107.61  3.000
 JRR  C7A   C2A  C3A   121.07  3.000
 JRR  C3A   C2A  N1A   122.63  3.000
 JRR  C7A   C2A  N1A   116.30  3.000
 JRR  H3'   C3'  C4'   111.54  3.000
 JRR  H3'   C3'  C2'   111.58  3.000
 JRR  C4'   C3'  C2'   103.08  3.000
 JRR  H3'   C3'  O1    109.45  3.000
 JRR  C4'   C3'  O1    108.49  3.000
 JRR  C2'   C3'  O1    112.56  3.000
 JRR  H3AA  C3A  C4A   120.60  3.000
 JRR  H3AA  C3A  C2A   120.24  3.000
 JRR  C4A   C3A  C2A   119.16  3.000
 JRR  H4'   C4'  C7A   108.50  3.000
 JRR  H4'   C4'  C5'   107.97  3.000
 JRR  C7A   C4'  C5'   115.49  3.000
 JRR  H4'   C4'  C3'   107.06  3.000
 JRR  C5'   C4'  C3'   101.83  3.000
 JRR  C7A   C4'  C3'   115.43  3.000
 JRR  C8A   C4A  C5A   121.37  3.000
 JRR  C8A   C4A  C3A   120.55  3.000
 JRR  C5A   C4A  C3A   118.07  3.000
 JRR  H5'A  C5'  H5'   107.14  3.000
 JRR  H5'A  C5'  C4'   110.06  3.000
 JRR  H5'   C5'  C4'   113.34  3.000
 JRR  H5'A  C5'  N1'   110.45  3.000
 JRR  H5'   C5'  N1'   110.44  3.000
 JRR  C4'   C5'  N1'   105.44  3.000
 JRR  H5A   C5A  C6A   120.08  3.000
 JRR  H5A   C5A  C4A   120.90  3.000
 JRR  C6A   C5A  C4A   119.03  3.000
 JRR  N6A   C6A  C5A   120.53  3.000
 JRR  N6A   C6A  N1A   117.10  3.000
 JRR  C5A   C6A  N1A   122.33  3.000
 JRR  HN6B  N6A  HN6A  114.14  3.000
 JRR  HN6B  N6A  C6A   117.60  3.000
 JRR  HN6A  N6A  C6A   116.29  3.000
 JRR  H7AA  C7A  H7A   107.01  3.000
 JRR  H7AA  C7A  C4'   110.14  3.000
 JRR  H7A   C7A  C4'   109.45  3.000
 JRR  H7AA  C7A  C2A   109.51  3.000
 JRR  H7A   C7A  C2A   108.77  3.000
 JRR  C4'   C7A  C2A   111.83  3.000
 JRR  H8AB  C8A  H8AA  108.25  3.000
 JRR  H8AB  C8A  H8A   106.97  3.000
 JRR  H8AA  C8A  H8A   107.94  3.000
 JRR  H8AB  C8A  C4A   111.04  3.000
 JRR  H8AA  C8A  C4A   111.82  3.000
 JRR  H8A   C8A  C4A   110.65  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
 JRR  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 JRR  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 JRR  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 JRR  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 JRR  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 JRR  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 JRR  CONST_07  C4A   C3A  C2A  N1A     0.00   0.0  0
 JRR  CONST_08  C4A   C5A  C6A  N1A     0.00   0.0  0
 JRR  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 JRR  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 JRR  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 JRR  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 JRR  CONST_13  C13   C12  C11  C4    180.00   0.0  0
 JRR  CONST_14  C15   C16  C11  C4    180.00   0.0  0
 JRR  CONST_15  F13   C13  C12  C11   180.00   0.0  0
 JRR  CONST_16  C15   C14  C13  F13   180.00   0.0  0
 JRR  CONST_17  N6A   C6A  N1A  C2A   180.00   0.0  0
 JRR  CONST_18  C8A   C4A  C3A  C2A   180.00   0.0  0
 JRR  CONST_19  C7A   C2A  C3A  C4A   180.00   0.0  0
 JRR  CONST_20  N6A   C6A  C5A  C4A   180.00   0.0  0
 JRR  CONST_21  C7A   C2A  N1A  C6A   180.00   0.0  0
 JRR  CONST_22  C8A   C4A  C5A  C6A   180.00   0.0  0
 JRR  CONST_23  H15   C15  C16  C11   180.00   0.0  0
 JRR  CONST_24  H16   C16  C11  C12   180.00   0.0  0
 JRR  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 JRR  CONST_26  H12   C12  C13  C14   180.00   0.0  0
 JRR  CONST_27  H3AA  C3A  C2A  N1A   180.00   0.0  0
 JRR  CONST_28  H5A   C5A  C6A  N1A   180.00   0.0  0
 JRR  Var_01    C4'   C5'  N1'  C2'    28.66  30.0  1
 JRR  Var_02    C5'   N1'  C2'  C3'    -6.77  30.0  1
 JRR  Var_03    C4'   C7A  C2A  N1A   -63.47  30.0  2
 JRR  Var_04    C12   C11  C4   C3    -93.94  30.0  2
 JRR  Var_05    H8A   C8A  C4A  C3A    65.95  30.0  2
 JRR  Var_06    C11   C4   C3   N2   -177.76  30.0  3
 JRR  Var_07    H1    C1   O1   C3'   -65.45  30.0  1
 JRR  Var_08    C3    N2   C2   C1   -175.35  30.0  3
 JRR  Var_09    N2    C2   C1   O1     63.11  30.0  2
 JRR  Var_10    C4    C3   N2   C2    179.33  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
 JRR  chir_01  C3'  O1   C2'  C4'  negativ
 JRR  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
 JRR  plan-1  C4    0.020
 JRR  plan-1  C11   0.020
 JRR  plan-1  C12   0.020
 JRR  plan-1  C13   0.020
 JRR  plan-1  F13   0.020
 JRR  plan-1  C14   0.020
 JRR  plan-1  C15   0.020
 JRR  plan-1  C16   0.020
 JRR  plan-1  H12   0.020
 JRR  plan-1  H14   0.020
 JRR  plan-1  H15   0.020
 JRR  plan-1  H16   0.020
 JRR  plan-2  N1A   0.020
 JRR  plan-2  C2A   0.020
 JRR  plan-2  C3A   0.020
 JRR  plan-2  C4A   0.020
 JRR  plan-2  C5A   0.020
 JRR  plan-2  C6A   0.020
 JRR  plan-2  N6A   0.020
 JRR  plan-2  C7A   0.020
 JRR  plan-2  C8A   0.020
 JRR  plan-2  H3AA  0.020
 JRR  plan-2  H5A   0.020
 JRR  plan-3  C6A   0.020
 JRR  plan-3  N6A   0.020
 JRR  plan-3  HN6A  0.020
 JRR  plan-3  HN6B  0.020

