# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 07:12:18 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(C[C@@H]2CNC[C@@H]2OCCNCCc3cccc(F)c3)n1
#
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
 59R  59R  6-{[(3R,4R)-4-(2-{[2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}pyridin-2-amine  ligand  53  26  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_59R
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
 59R  C1    C  CH2   0  -0.161   0.0456  -2.7335   1.1473
 59R  O1    O  O2    0  -0.491   0.9796  -1.8072   0.6441
 59R  C2    C  CH2   0  -0.296  -1.2475  -2.0068   1.4390
 59R  N2    N  NH1   0  -0.602  -1.8587  -1.5011   0.2260
 59R  C3    C  CH2   0  -0.245  -3.0529  -0.7225   0.4836
 59R  C4    C  CH2   0  -0.529  -3.6726  -0.2353  -0.8239
 59R  N1'   N  NH1   0  -0.585   3.4442  -2.8859  -1.6305
 59R  C11   C  CR6   0   0.140  -4.8856   0.6149  -0.5750
 59R  C12   C  CR16  0  -0.463  -6.1037   0.0169  -0.2575
 59R  C13   C  CR6   0   0.539  -7.1981   0.8134   0.0136
 59R  F13   F  F     0  -0.319  -8.3671   0.2203   0.3134
 59R  C14   C  CR16  0  -0.427  -7.1394   2.1937  -0.0132
 59R  C15   C  CR16  0  -0.224  -5.9255   2.7842  -0.3357
 59R  C16   C  CR16  0  -0.325  -4.8107   2.0050  -0.6156
 59R  N1A   N  N     0  -0.477   5.0583   1.0736   0.8272
 59R  C2'   C  CH2   0  -0.345   2.3170  -3.2936  -0.8016
 59R  C2A   C  CR6   0   0.271   3.9277   1.1785   0.1277
 59R  C3'   C  CH1   0   0.063   2.2598  -2.3470   0.4268
 59R  C3A   C  CR16  0  -0.391   3.7498   2.1374  -0.8579
 59R  C4'   C  CH1   0  -0.298   3.2749  -1.2356   0.0816
 59R  C4A   C  CR16  0  -0.147   4.8010   3.0137  -1.1186
 59R  C5'   C  CH2   0  -0.305   3.5516  -1.4514  -1.4106
 59R  C5A   C  CR16  0  -0.394   5.9728   2.9121  -0.4032
 59R  C6A   C  CR6   0   0.427   6.0594   1.9129   0.5823
 59R  N6A   N  NH2   0  -0.836   7.1701   1.7977   1.3690
 59R  C7A   C  CH2   0  -0.485   2.8495   0.1824   0.4500
 59R  H1    H  HCH2  0   0.202  -0.1420  -3.5422   0.4281
 59R  H1A   H  HCH2  0   0.206   0.4197  -3.1996   2.0699
 59R  H2    H  HCH2  0   0.227  -1.9328  -2.7173   1.9101
 59R  H2A   H  HCH2  0   0.196  -1.0581  -1.2194   2.1868
 59R  HN2   H  HNH1  0   0.340  -1.1869  -0.9143  -0.2556
 59R  H3    H  HCH2  0   0.223  -3.7726  -1.3567   1.0109
 59R  H3A   H  HCH2  0   0.198  -2.8618   0.1418   1.1396
 59R  H4    H  HCH2  0   0.246  -2.9292   0.3398  -1.3818
 59R  H4A   H  HCH2  0   0.247  -3.9387  -1.1005  -1.4359
 59R  HN1'  H  HNH1  0   0.345   4.2849  -3.3268  -1.2758
 59R  H12   H  HCR6  0   0.270  -6.1996  -1.0622  -0.2276
 59R  H14   H  HCR6  0   0.277  -8.0164   2.7893   0.2031
 59R  H15   H  HCR6  0   0.266  -5.8522   3.8631  -0.3710
 59R  H16   H  HCR6  0   0.253  -3.8720   2.4827  -0.8682
 59R  H2'   H  HCH2  0   0.225   1.3897  -3.1746  -1.3731
 59R  H2'A  H  HCH2  0   0.242   2.4023  -4.3463  -0.5316
 59R  H3'   H  HCH1  0   0.210   2.5846  -2.8733   1.3351
 59R  H3AA  H  HCR6  0   0.248   2.8188   2.1990  -1.4052
 59R  H4'   H  HCH1  0   0.247   4.1983  -1.4593   0.6240
 59R  H4AA  H  HCR6  0   0.263   4.7019   3.7729  -1.8840
 59R  H5'   H  HCH2  0   0.241   4.5265  -1.0791  -1.7257
 59R  H5'A  H  HCH2  0   0.217   2.7953  -0.9339  -2.0134
 59R  H5A   H  HCR6  0   0.262   6.8045   3.5794  -0.5892
 59R  HN6A  H  HNH2  0   0.379   7.2885   0.9138   1.8367
 59R  HN6B  H  HNH2  0   0.387   8.0287   2.1939   1.0248
 59R  H7A   H  HCH2  0   0.246   2.6225   0.2355   1.5184
 59R  H7AA  H  HCH2  0   0.239   1.9355   0.4553  -0.0798

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
 59R  C1   C2    single    1.512  0.020  1.512
 59R  C1   O1    single    1.408  0.020  1.408
 59R  C1   H1    single    0.970  0.020  1.090
 59R  C1   H1A   single    0.970  0.020  1.090
 59R  O1   C3'   single    1.406  0.020  1.406
 59R  N2   C2    single    1.449  0.020  1.449
 59R  C2   H2    single    0.970  0.020  1.090
 59R  C2   H2A   single    0.970  0.020  1.090
 59R  C3   N2    single    1.449  0.020  1.449
 59R  N2   HN2   single    0.890  0.020  1.040
 59R  C3   C4    single    1.527  0.020  1.527
 59R  C3   H3    single    0.970  0.020  1.090
 59R  C3   H3A   single    0.970  0.020  1.090
 59R  C11  C4    single    1.502  0.020  1.502
 59R  C4   H4    single    0.970  0.020  1.090
 59R  C4   H4A   single    0.970  0.020  1.090
 59R  C2'  N1'   single    1.457  0.020  1.457
 59R  C5'  N1'   single    1.455  0.020  1.455
 59R  N1'  HN1'  single    0.890  0.020  1.040
 59R  C12  C11   aromatic  1.394  0.020  1.394
 59R  C11  C16   aromatic  1.393  0.020  1.393
 59R  C13  C12   aromatic  1.380  0.020  1.380
 59R  C12  H12   single    0.930  0.020  1.080
 59R  F13  C13   single    1.345  0.020  1.345
 59R  C13  C14   aromatic  1.382  0.020  1.382
 59R  C14  C15   aromatic  1.388  0.020  1.388
 59R  C14  H14   single    0.930  0.020  1.080
 59R  C15  C16   aromatic  1.389  0.020  1.389
 59R  C15  H15   single    0.930  0.020  1.080
 59R  C16  H16   single    0.930  0.020  1.080
 59R  C2A  N1A   aromatic  1.334  0.020  1.334
 59R  N1A  C6A   aromatic  1.329  0.020  1.329
 59R  C3'  C2'   single    1.552  0.020  1.552
 59R  C2'  H2'   single    0.970  0.020  1.090
 59R  C2'  H2'A  single    0.970  0.020  1.090
 59R  C7A  C2A   single    1.503  0.020  1.503
 59R  C2A  C3A   aromatic  1.387  0.020  1.387
 59R  C3'  C4'   single    1.544  0.020  1.544
 59R  C3'  H3'   single    0.970  0.020  1.090
 59R  C3A  C4A   aromatic  1.393  0.020  1.393
 59R  C3A  H3AA  single    0.930  0.020  1.080
 59R  C7A  C4'   single    1.526  0.020  1.526
 59R  C4'  C5'   single    1.533  0.020  1.533
 59R  C4'  H4'   single    0.970  0.020  1.090
 59R  C4A  C5A   aromatic  1.377  0.020  1.377
 59R  C4A  H4AA  single    0.930  0.020  1.080
 59R  C5'  H5'   single    0.970  0.020  1.090
 59R  C5'  H5'A  single    0.970  0.020  1.090
 59R  C6A  C5A   aromatic  1.406  0.020  1.406
 59R  C5A  H5A   single    0.930  0.020  1.080
 59R  C6A  N6A   single    1.366  0.020  1.366
 59R  N6A  HN6A  single    0.890  0.020  1.040
 59R  N6A  HN6B  single    0.890  0.020  1.040
 59R  C7A  H7A   single    0.970  0.020  1.090
 59R  C7A  H7AA  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
 59R  H1A   C1   H1    107.19  3.000
 59R  H1A   C1   C2    109.45  3.000
 59R  H1    C1   C2    109.53  3.000
 59R  H1A   C1   O1    110.67  3.000
 59R  H1    C1   O1    111.32  3.000
 59R  C2    C1   O1    108.67  3.000
 59R  C3'   O1   C1    113.99  3.000
 59R  H2A   C2   H2    106.23  3.000
 59R  H2A   C2   N2    113.01  3.000
 59R  H2    C2   N2    108.84  3.000
 59R  H2A   C2   C1    109.11  3.000
 59R  H2    C2   C1    107.86  3.000
 59R  N2    C2   C1    111.53  3.000
 59R  HN2   N2   C3    108.65  3.000
 59R  HN2   N2   C2    108.67  3.000
 59R  C3    N2   C2    112.73  3.000
 59R  H3A   C3   H3    106.36  3.000
 59R  H3A   C3   C4    109.27  3.000
 59R  H3    C3   C4    109.30  3.000
 59R  H3A   C3   N2    112.61  3.000
 59R  H3    C3   N2    108.44  3.000
 59R  C4    C3   N2    110.72  3.000
 59R  H4A   C4   H4    107.24  3.000
 59R  H4A   C4   C11   110.14  3.000
 59R  H4    C4   C11   109.63  3.000
 59R  H4A   C4   C3    109.02  3.000
 59R  H4    C4   C3    109.21  3.000
 59R  C11   C4   C3    111.50  3.000
 59R  HN1'  N1'  C5'   108.35  3.000
 59R  HN1'  N1'  C2'   108.71  3.000
 59R  C5'   N1'  C2'   104.30  3.000
 59R  C16   C11  C12   118.81  3.000
 59R  C16   C11  C4    121.12  3.000
 59R  C12   C11  C4    120.04  3.000
 59R  H12   C12  C13   119.93  3.000
 59R  H12   C12  C11   120.72  3.000
 59R  C13   C12  C11   119.34  3.000
 59R  C14   C13  F13   118.80  3.000
 59R  C14   C13  C12   122.61  3.000
 59R  F13   C13  C12   118.59  3.000
 59R  H14   C14  C15   121.41  3.000
 59R  H14   C14  C13   120.77  3.000
 59R  C15   C14  C13   117.82  3.000
 59R  H15   C15  C16   119.91  3.000
 59R  H15   C15  C14   119.41  3.000
 59R  C16   C15  C14   120.68  3.000
 59R  H16   C16  C15   119.69  3.000
 59R  H16   C16  C11   119.57  3.000
 59R  C15   C16  C11   120.74  3.000
 59R  C6A   N1A  C2A   119.48  3.000
 59R  H2'A  C2'  H2'   107.47  3.000
 59R  H2'A  C2'  C3'   113.32  3.000
 59R  H2'   C2'  C3'   108.39  3.000
 59R  H2'A  C2'  N1'   110.52  3.000
 59R  H2'   C2'  N1'   109.11  3.000
 59R  C3'   C2'  N1'   107.94  3.000
 59R  C7A   C2A  C3A   121.25  3.000
 59R  C3A   C2A  N1A   122.42  3.000
 59R  C7A   C2A  N1A   116.33  3.000
 59R  H3'   C3'  C4'   109.58  3.000
 59R  H3'   C3'  C2'   110.56  3.000
 59R  C4'   C3'  C2'   103.76  3.000
 59R  H3'   C3'  O1    108.97  3.000
 59R  C4'   C3'  O1    110.90  3.000
 59R  C2'   C3'  O1    112.96  3.000
 59R  H3AA  C3A  C4A   121.26  3.000
 59R  H3AA  C3A  C2A   120.63  3.000
 59R  C4A   C3A  C2A   118.11  3.000
 59R  H4'   C4'  C7A   107.80  3.000
 59R  H4'   C4'  C5'   107.55  3.000
 59R  C7A   C4'  C5'   114.59  3.000
 59R  H4'   C4'  C3'   107.27  3.000
 59R  C5'   C4'  C3'   103.59  3.000
 59R  C7A   C4'  C3'   115.57  3.000
 59R  H4AA  C4A  C5A   119.80  3.000
 59R  H4AA  C4A  C3A   120.29  3.000
 59R  C5A   C4A  C3A   119.91  3.000
 59R  H5'A  C5'  H5'   107.26  3.000
 59R  H5'A  C5'  C4'   110.13  3.000
 59R  H5'   C5'  C4'   113.25  3.000
 59R  H5'A  C5'  N1'   109.34  3.000
 59R  H5'   C5'  N1'   111.03  3.000
 59R  C4'   C5'  N1'   105.81  3.000
 59R  H5A   C5A  C6A   120.74  3.000
 59R  H5A   C5A  C4A   121.29  3.000
 59R  C6A   C5A  C4A   117.97  3.000
 59R  N6A   C6A  C5A   120.91  3.000
 59R  N6A   C6A  N1A   116.94  3.000
 59R  C5A   C6A  N1A   122.10  3.000
 59R  HN6B  N6A  HN6A  113.84  3.000
 59R  HN6B  N6A  C6A   117.62  3.000
 59R  HN6A  N6A  C6A   115.92  3.000
 59R  H7AA  C7A  H7A   106.75  3.000
 59R  H7AA  C7A  C4'   110.42  3.000
 59R  H7A   C7A  C4'   109.81  3.000
 59R  H7AA  C7A  C2A   109.34  3.000
 59R  H7A   C7A  C2A   109.05  3.000
 59R  C4'   C7A  C2A   111.36  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
 59R  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 59R  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 59R  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 59R  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 59R  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 59R  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 59R  CONST_07  C4A   C3A  C2A  N1A     0.00   0.0  0
 59R  CONST_08  C4A   C5A  C6A  N1A     0.00   0.0  0
 59R  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 59R  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 59R  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 59R  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 59R  CONST_13  C13   C12  C11  C4    180.00   0.0  0
 59R  CONST_14  C15   C16  C11  C4    180.00   0.0  0
 59R  CONST_15  F13   C13  C12  C11   180.00   0.0  0
 59R  CONST_16  C15   C14  C13  F13   180.00   0.0  0
 59R  CONST_17  N6A   C6A  N1A  C2A   180.00   0.0  0
 59R  CONST_18  C7A   C2A  C3A  C4A   180.00   0.0  0
 59R  CONST_19  N6A   C6A  C5A  C4A   180.00   0.0  0
 59R  CONST_20  C7A   C2A  N1A  C6A   180.00   0.0  0
 59R  CONST_21  H15   C15  C16  C11   180.00   0.0  0
 59R  CONST_22  H16   C16  C11  C12   180.00   0.0  0
 59R  CONST_23  H14   C14  C13  C12   180.00   0.0  0
 59R  CONST_24  H12   C12  C13  C14   180.00   0.0  0
 59R  CONST_25  H3AA  C3A  C2A  N1A   180.00   0.0  0
 59R  CONST_26  H5A   C5A  C6A  N1A   180.00   0.0  0
 59R  CONST_27  H4AA  C4A  C3A  C2A   180.00   0.0  0
 59R  Var_01    C4'   C5'  N1'  C2'    39.33  30.0  1
 59R  Var_02    C5'   N1'  C2'  C3'   -30.51  30.0  1
 59R  Var_03    C4'   C7A  C2A  N1A   -65.63  30.0  2
 59R  Var_04    C12   C11  C4   C3    -78.49  30.0  2
 59R  Var_05    C11   C4   C3   N2   -178.00  30.0  3
 59R  Var_06    H1    C1   O1   C3'   -63.77  30.0  1
 59R  Var_07    C3    N2   C2   C1   -176.10  30.0  1
 59R  Var_08    N2    C2   C1   O1     65.44  30.0  3
 59R  Var_09    C4    C3   N2   C2   -178.94  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
 59R  chir_01  C3'  O1   C2'  C4'  negativ
 59R  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
 59R  plan-1  C4    0.020
 59R  plan-1  C11   0.020
 59R  plan-1  C12   0.020
 59R  plan-1  C13   0.020
 59R  plan-1  F13   0.020
 59R  plan-1  C14   0.020
 59R  plan-1  C15   0.020
 59R  plan-1  C16   0.020
 59R  plan-1  H12   0.020
 59R  plan-1  H14   0.020
 59R  plan-1  H15   0.020
 59R  plan-1  H16   0.020
 59R  plan-2  N1A   0.020
 59R  plan-2  C2A   0.020
 59R  plan-2  C3A   0.020
 59R  plan-2  C4A   0.020
 59R  plan-2  C5A   0.020
 59R  plan-2  C6A   0.020
 59R  plan-2  N6A   0.020
 59R  plan-2  C7A   0.020
 59R  plan-2  H3AA  0.020
 59R  plan-2  H4AA  0.020
 59R  plan-2  H5A   0.020
 59R  plan-3  C6A   0.020
 59R  plan-3  N6A   0.020
 59R  plan-3  HN6A  0.020
 59R  plan-3  HN6B  0.020

