# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:12:35 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3S,4S)-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
 JSS  JSS  6-{[(3S,4S)-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_JSS
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
 JSS  C1    C  CH2   0  -0.159  -0.1008   3.5084  -0.5035
 JSS  O1    O  O2    0  -0.493  -0.9819   2.4755  -0.1284
 JSS  C2    C  CH2   0  -0.298   1.2851   3.1584  -0.0099
 JSS  N2    N  NH1   0  -0.602   1.7728   1.9450  -0.6347
 JSS  C3    C  CH2   0  -0.245   3.0624   1.5286  -0.1259
 JSS  C4    C  CH2   0  -0.531   3.5225   0.2406  -0.8052
 JSS  N1'   N  NH1   0  -0.614  -4.3965   2.9203   0.2131
 JSS  C11   C  CR6   0   0.138   4.8500  -0.2177  -0.2735
 JSS  C12   C  CR16  0  -0.462   4.9118  -0.9780   0.8926
 JSS  C13   C  CR6   0   0.538   6.1437  -1.3529   1.3911
 JSS  F13   F  F     0  -0.319   6.1870  -2.0891   2.5155
 JSS  C14   C  CR16  0  -0.426   7.3316  -1.0033   0.7786
 JSS  C15   C  CR16  0  -0.224   7.2642  -0.2466  -0.3832
 JSS  C16   C  CR16  0  -0.322   6.0382   0.1437  -0.9045
 JSS  N1A   N  N     0  -0.477  -3.4470  -1.6049   1.0093
 JSS  C2'   C  CH2   0  -0.304  -3.1528   3.6168  -0.0841
 JSS  C2A   C  CR6   0   0.268  -2.9661  -1.2580  -0.1846
 JSS  C3'   C  CH1   0   0.049  -2.2501   2.5421  -0.7325
 JSS  C3A   C  CR16  0  -0.427  -3.2288  -1.9841  -1.3356
 JSS  C4'   C  CH1   0  -0.278  -3.0173   1.2211  -0.5106
 JSS  C4A   C  CR6   0   0.202  -4.0305  -3.1249  -1.2540
 JSS  C5'   C  CH2   0  -0.271  -4.0072   1.5742   0.5945
 JSS  C5A   C  CR16  0  -0.443  -4.5379  -3.4750  -0.0171
 JSS  C6A   C  CR6   0   0.440  -4.2197  -2.6844   1.0977
 JSS  N6A   N  NH2   0  -0.839  -4.7381  -2.9737   2.3294
 JSS  C7A   C  CH2   0  -0.496  -2.1423  -0.0022  -0.2452
 JSS  C8A   C  CH3   0  -0.726  -4.3032  -3.9602  -2.4675
 JSS  H1    H  HCH2  0   0.200  -0.0872   3.6240  -1.5963
 JSS  H1A   H  HCH2  0   0.208  -0.4080   4.4728  -0.0777
 JSS  H2    H  HCH2  0   0.228   1.9535   3.9846  -0.2684
 JSS  H2A   H  HCH2  0   0.197   1.2772   3.1003   1.0907
 JSS  HN2   H  HNH1  0   0.341   1.1020   1.2041  -0.4663
 JSS  H3    H  HCH2  0   0.224   3.7913   2.3207  -0.3258
 JSS  H3A   H  HCH2  0   0.198   3.0617   1.3806   0.9661
 JSS  H4    H  HCH2  0   0.245   2.7699  -0.5372  -0.6459
 JSS  H4A   H  HCH2  0   0.248   3.5864   0.4076  -1.8823
 JSS  HN1'  H  HNH1  0   0.350  -4.9180   3.3888   0.9419
 JSS  H12   H  HCR6  0   0.270   4.0058  -1.2783   1.4063
 JSS  H14   H  HCR6  0   0.277   8.2811  -1.3123   1.1953
 JSS  H15   H  HCR6  0   0.266   8.1798   0.0363  -0.8857
 JSS  H16   H  HCR6  0   0.252   6.0043   0.7329  -1.8130
 JSS  H2'   H  HCH2  0   0.227  -3.3276   4.4756  -0.7354
 JSS  H2'A  H  HCH2  0   0.207  -2.6465   3.9858   0.8199
 JSS  H3'   H  HCH1  0   0.219  -2.1256   2.7290  -1.8072
 JSS  H3AA  H  HCR6  0   0.241  -2.8146  -1.6675  -2.2852
 JSS  H4'   H  HCH1  0   0.253  -3.5965   1.0332  -1.4202
 JSS  H5'   H  HCH2  0   0.192  -3.5100   1.5217   1.5763
 JSS  H5'A  H  HCH2  0   0.231  -4.8693   0.9067   0.6268
 JSS  H5A   H  HCR6  0   0.253  -5.1708  -4.3471   0.0984
 JSS  HN6A  H  HNH2  0   0.377  -4.2680  -2.5542   3.1149
 JSS  HN6B  H  HNH2  0   0.386  -5.0394  -3.9197   2.4940
 JSS  H7A   H  HCH2  0   0.238  -1.6015   0.1121   0.6954
 JSS  H7AA  H  HCH2  0   0.244  -1.3982  -0.0959  -1.0398
 JSS  H8A   H  HCH3  0   0.255  -3.4979  -4.6818  -2.6197
 JSS  H8AA  H  HCH3  0   0.247  -5.2306  -4.5228  -2.3700
 JSS  H8AB  H  HCH3  0   0.247  -4.3630  -3.3492  -3.3675

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
 JSS  O1   C1    single    1.409  0.020  1.409
 JSS  C2   C1    single    1.512  0.020  1.512
 JSS  C1   H1    single    0.970  0.020  1.090
 JSS  C1   H1A   single    0.970  0.020  1.090
 JSS  O1   C3'   single    1.406  0.020  1.406
 JSS  N2   C2    single    1.449  0.020  1.449
 JSS  C2   H2    single    0.970  0.020  1.090
 JSS  C2   H2A   single    0.970  0.020  1.090
 JSS  C3   N2    single    1.448  0.020  1.448
 JSS  N2   HN2   single    0.890  0.020  1.040
 JSS  C4   C3    single    1.527  0.020  1.527
 JSS  C3   H3    single    0.970  0.020  1.090
 JSS  C3   H3A   single    0.970  0.020  1.090
 JSS  C11  C4    single    1.502  0.020  1.502
 JSS  C4   H4    single    0.970  0.020  1.090
 JSS  C4   H4A   single    0.970  0.020  1.090
 JSS  C2'  N1'   single    1.456  0.020  1.456
 JSS  N1'  C5'   single    1.452  0.020  1.452
 JSS  N1'  HN1'  single    0.890  0.020  1.040
 JSS  C16  C11   aromatic  1.393  0.020  1.393
 JSS  C11  C12   aromatic  1.393  0.020  1.393
 JSS  C13  C12   aromatic  1.381  0.020  1.381
 JSS  C12  H12   single    0.930  0.020  1.080
 JSS  C14  C13   aromatic  1.381  0.020  1.381
 JSS  C13  F13   single    1.345  0.020  1.345
 JSS  C15  C14   aromatic  1.388  0.020  1.388
 JSS  C14  H14   single    0.930  0.020  1.080
 JSS  C15  C16   aromatic  1.388  0.020  1.388
 JSS  C15  H15   single    0.930  0.020  1.080
 JSS  C16  H16   single    0.930  0.020  1.080
 JSS  N1A  C2A   aromatic  1.333  0.020  1.333
 JSS  N1A  C6A   aromatic  1.331  0.020  1.331
 JSS  C2'  C3'   single    1.546  0.020  1.546
 JSS  C2'  H2'   single    0.970  0.020  1.090
 JSS  C2'  H2'A  single    0.970  0.020  1.090
 JSS  C7A  C2A   single    1.503  0.020  1.503
 JSS  C2A  C3A   aromatic  1.386  0.020  1.386
 JSS  C3'  C4'   single    1.544  0.020  1.544
 JSS  C3'  H3'   single    0.970  0.020  1.090
 JSS  C3A  C4A   aromatic  1.397  0.020  1.397
 JSS  C3A  H3AA  single    0.930  0.020  1.080
 JSS  C5'  C4'   single    1.525  0.020  1.525
 JSS  C7A  C4'   single    1.527  0.020  1.527
 JSS  C4'  H4'   single    0.970  0.020  1.090
 JSS  C5A  C4A   aromatic  1.382  0.020  1.382
 JSS  C4A  C8A   single    1.498  0.020  1.498
 JSS  C5'  H5'   single    0.970  0.020  1.090
 JSS  C5'  H5'A  single    0.970  0.020  1.090
 JSS  C6A  C5A   aromatic  1.403  0.020  1.403
 JSS  C5A  H5A   single    0.930  0.020  1.080
 JSS  N6A  C6A   single    1.367  0.020  1.367
 JSS  N6A  HN6A  single    0.890  0.020  1.040
 JSS  N6A  HN6B  single    0.890  0.020  1.040
 JSS  C7A  H7A   single    0.970  0.020  1.090
 JSS  C7A  H7AA  single    0.970  0.020  1.090
 JSS  C8A  H8A   single    0.970  0.020  1.090
 JSS  C8A  H8AA  single    0.970  0.020  1.090
 JSS  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
 JSS  H1A   C1   H1    107.26  3.000
 JSS  H1A   C1   C2    109.46  3.000
 JSS  H1    C1   C2    109.73  3.000
 JSS  H1A   C1   O1    111.45  3.000
 JSS  H1    C1   O1    110.46  3.000
 JSS  C2    C1   O1    108.46  3.000
 JSS  C3'   O1   C1    114.52  3.000
 JSS  H2A   C2   H2    106.28  3.000
 JSS  H2A   C2   N2    112.88  3.000
 JSS  H2    C2   N2    108.96  3.000
 JSS  H2A   C2   C1    109.36  3.000
 JSS  H2    C2   C1    107.94  3.000
 JSS  N2    C2   C1    111.19  3.000
 JSS  HN2   N2   C3    108.72  3.000
 JSS  HN2   N2   C2    108.52  3.000
 JSS  C3    N2   C2    112.90  3.000
 JSS  H3A   C3   H3    106.18  3.000
 JSS  H3A   C3   C4    109.13  3.000
 JSS  H3    C3   C4    109.17  3.000
 JSS  H3A   C3   N2    112.73  3.000
 JSS  H3    C3   N2    108.71  3.000
 JSS  C4    C3   N2    110.77  3.000
 JSS  H4A   C4   H4    107.01  3.000
 JSS  H4A   C4   C11   110.14  3.000
 JSS  H4    C4   C11   109.85  3.000
 JSS  H4A   C4   C3    109.12  3.000
 JSS  H4    C4   C3    109.12  3.000
 JSS  C11   C4   C3    111.48  3.000
 JSS  HN1'  N1'  C5'   112.24  3.000
 JSS  HN1'  N1'  C2'   111.47  3.000
 JSS  C5'   N1'  C2'   105.54  3.000
 JSS  C16   C11  C12   118.87  3.000
 JSS  C12   C11  C4    120.14  3.000
 JSS  C16   C11  C4    120.96  3.000
 JSS  H12   C12  C13   119.96  3.000
 JSS  H12   C12  C11   120.71  3.000
 JSS  C13   C12  C11   119.33  3.000
 JSS  C14   C13  F13   118.79  3.000
 JSS  F13   C13  C12   118.63  3.000
 JSS  C14   C13  C12   122.58  3.000
 JSS  H14   C14  C15   121.37  3.000
 JSS  H14   C14  C13   120.77  3.000
 JSS  C15   C14  C13   117.86  3.000
 JSS  H15   C15  C16   119.96  3.000
 JSS  H15   C15  C14   119.35  3.000
 JSS  C16   C15  C14   120.69  3.000
 JSS  H16   C16  C15   119.70  3.000
 JSS  H16   C16  C11   119.62  3.000
 JSS  C15   C16  C11   120.68  3.000
 JSS  C6A   N1A  C2A   118.70  3.000
 JSS  H2'A  C2'  H2'   107.46  3.000
 JSS  H2'A  C2'  C3'   108.01  3.000
 JSS  H2'   C2'  C3'   112.96  3.000
 JSS  H2'A  C2'  N1'   112.70  3.000
 JSS  H2'   C2'  N1'   111.18  3.000
 JSS  C3'   C2'  N1'   104.59  3.000
 JSS  C7A   C2A  C3A   120.54  3.000
 JSS  C3A   C2A  N1A   122.62  3.000
 JSS  C7A   C2A  N1A   116.82  3.000
 JSS  H3'   C3'  C4'   110.05  3.000
 JSS  H3'   C3'  C2'   111.00  3.000
 JSS  C4'   C3'  C2'   104.15  3.000
 JSS  H3'   C3'  O1    109.04  3.000
 JSS  C4'   C3'  O1    110.24  3.000
 JSS  C2'   C3'  O1    112.29  3.000
 JSS  H3AA  C3A  C4A   120.62  3.000
 JSS  H3AA  C3A  C2A   120.16  3.000
 JSS  C4A   C3A  C2A   119.22  3.000
 JSS  H4'   C4'  C7A   108.07  3.000
 JSS  H4'   C4'  C5'   107.36  3.000
 JSS  C7A   C4'  C5'   115.56  3.000
 JSS  H4'   C4'  C3'   106.88  3.000
 JSS  C7A   C4'  C3'   115.20  3.000
 JSS  C5'   C4'  C3'   103.22  3.000
 JSS  C8A   C4A  C5A   121.12  3.000
 JSS  C8A   C4A  C3A   120.83  3.000
 JSS  C5A   C4A  C3A   118.03  3.000
 JSS  H5'A  C5'  H5'   107.52  3.000
 JSS  H5'A  C5'  C4'   113.13  3.000
 JSS  H5'   C5'  C4'   109.98  3.000
 JSS  H5'A  C5'  N1'   111.30  3.000
 JSS  H5'   C5'  N1'   113.52  3.000
 JSS  C4'   C5'  N1'   101.44  3.000
 JSS  H5A   C5A  C6A   120.08  3.000
 JSS  H5A   C5A  C4A   120.91  3.000
 JSS  C6A   C5A  C4A   119.02  3.000
 JSS  N6A   C6A  C5A   120.70  3.000
 JSS  N6A   C6A  N1A   116.85  3.000
 JSS  C5A   C6A  N1A   122.41  3.000
 JSS  HN6B  N6A  HN6A  113.82  3.000
 JSS  HN6B  N6A  C6A   117.37  3.000
 JSS  HN6A  N6A  C6A   115.95  3.000
 JSS  H7AA  C7A  H7A   107.36  3.000
 JSS  H7AA  C7A  C4'   109.42  3.000
 JSS  H7A   C7A  C4'   110.48  3.000
 JSS  H7AA  C7A  C2A   109.32  3.000
 JSS  H7A   C7A  C2A   108.93  3.000
 JSS  C4'   C7A  C2A   111.24  3.000
 JSS  H8AB  C8A  H8AA  108.47  3.000
 JSS  H8AB  C8A  H8A   107.22  3.000
 JSS  H8AA  C8A  H8A   107.40  3.000
 JSS  H8AB  C8A  C4A   111.49  3.000
 JSS  H8AA  C8A  C4A   111.75  3.000
 JSS  H8A   C8A  C4A   110.31  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
 JSS  CONST_01  C14   C15  C16  C11     0.00   0.0  0
 JSS  CONST_02  C14   C13  C12  C11     0.00   0.0  0
 JSS  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 JSS  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 JSS  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 JSS  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 JSS  CONST_07  C4A   C3A  C2A  N1A     0.00   0.0  0
 JSS  CONST_08  C4A   C5A  C6A  N1A     0.00   0.0  0
 JSS  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 JSS  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 JSS  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 JSS  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 JSS  CONST_13  C15   C16  C11  C4    180.00   0.0  0
 JSS  CONST_14  C13   C12  C11  C4    180.00   0.0  0
 JSS  CONST_15  F13   C13  C12  C11   180.00   0.0  0
 JSS  CONST_16  C15   C14  C13  F13   180.00   0.0  0
 JSS  CONST_17  N6A   C6A  N1A  C2A   180.00   0.0  0
 JSS  CONST_18  C8A   C4A  C3A  C2A   180.00   0.0  0
 JSS  CONST_19  C7A   C2A  C3A  C4A   180.00   0.0  0
 JSS  CONST_20  N6A   C6A  C5A  C4A   180.00   0.0  0
 JSS  CONST_21  C7A   C2A  N1A  C6A   180.00   0.0  0
 JSS  CONST_22  C8A   C4A  C5A  C6A   180.00   0.0  0
 JSS  CONST_23  H15   C15  C16  C11   180.00   0.0  0
 JSS  CONST_24  H16   C16  C11  C12   180.00   0.0  0
 JSS  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 JSS  CONST_26  H12   C12  C13  C14   180.00   0.0  0
 JSS  CONST_27  H3AA  C3A  C2A  N1A   180.00   0.0  0
 JSS  CONST_28  H5A   C5A  C6A  N1A   180.00   0.0  0
 JSS  Var_01    C4'   C5'  N1'  C2'   -46.94  30.0  1
 JSS  Var_02    C5'   N1'  C2'  C3'    35.59  30.0  1
 JSS  Var_03    C4'   C7A  C2A  N1A   -89.59  30.0  3
 JSS  Var_04    C16   C11  C4   C3    -93.68  30.0  2
 JSS  Var_05    H8A   C8A  C4A  C3A    85.04  30.0  2
 JSS  Var_06    C11   C4   C3   N2   -179.11  30.0  1
 JSS  Var_07    H1    C1   O1   C3'   -48.38  30.0  3
 JSS  Var_08    C3    N2   C2   C1   -176.31  30.0  1
 JSS  Var_09    N2    C2   C1   O1     62.89  30.0  2
 JSS  Var_10    C4    C3   N2   C2    179.41  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
 JSS  chir_01  C3'  O1   C2'  C4'  positiv
 JSS  chir_02  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
 JSS  plan-1  C4    0.020
 JSS  plan-1  C11   0.020
 JSS  plan-1  C12   0.020
 JSS  plan-1  C13   0.020
 JSS  plan-1  F13   0.020
 JSS  plan-1  C14   0.020
 JSS  plan-1  C15   0.020
 JSS  plan-1  C16   0.020
 JSS  plan-1  H12   0.020
 JSS  plan-1  H14   0.020
 JSS  plan-1  H15   0.020
 JSS  plan-1  H16   0.020
 JSS  plan-2  N1A   0.020
 JSS  plan-2  C2A   0.020
 JSS  plan-2  C3A   0.020
 JSS  plan-2  C4A   0.020
 JSS  plan-2  C5A   0.020
 JSS  plan-2  C6A   0.020
 JSS  plan-2  N6A   0.020
 JSS  plan-2  C7A   0.020
 JSS  plan-2  C8A   0.020
 JSS  plan-2  H3AA  0.020
 JSS  plan-2  H5A   0.020
 JSS  plan-3  C6A   0.020
 JSS  plan-3  N6A   0.020
 JSS  plan-3  HN6A  0.020
 JSS  plan-3  HN6B  0.020

