# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 01:22:53 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3R,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
 JSR  JSR  6-{[(3R,4S)-4-(2-{[2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  56  27  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JSR
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
 JSR  C1    C  CH2   0  -0.162   0.1870   3.5526  -0.0607
 JSR  O1    O  O2    0  -0.499  -0.7342   2.6018   0.4230
 JSR  C2    C  CH2   0  -0.295   1.5867   3.0415   0.2005
 JSR  N2    N  NH1   0  -0.601   1.8456   1.8368  -0.5628
 JSR  C3    C  CH2   0  -0.245   3.1527   1.2676  -0.3100
 JSR  C4    C  CH2   0  -0.530   3.3772   0.0359  -1.1847
 JSR  N1'   N  NH1   0  -0.610  -3.8459   3.1719   1.3848
 JSR  C11   C  CR6   0   0.139   4.7126  -0.5985  -0.9219
 JSR  C12   C  CR16  0  -0.464   4.8532  -1.5428   0.0925
 JSR  C13   C  CR6   0   0.539   6.0972  -2.0885   0.3411
 JSR  F13   F  F     0  -0.319   6.2144  -3.0034   1.3197
 JSR  C14   C  CR16  0  -0.426   7.2220  -1.7353  -0.3788
 JSR  C15   C  CR16  0  -0.225   7.0771  -0.7908  -1.3862
 JSR  C16   C  CR16  0  -0.321   5.8376  -0.2267  -1.6549
 JSR  N1A   N  N     0  -0.485  -2.9521  -1.5557   0.4962
 JSR  C2'   C  CH2   0  -0.311  -2.8814   3.8562   0.5346
 JSR  C2A   C  CR6   0   0.284  -3.5285  -0.8543  -0.4822
 JSR  C3'   C  CH1   0   0.066  -2.0405   2.7217  -0.0864
 JSR  C3A   C  CR16  0  -0.435  -4.7108  -1.2448  -1.0853
 JSR  C4'   C  CH1   0  -0.273  -2.8167   1.4403   0.2492
 JSR  C4A   C  CR6   0   0.204  -5.3349  -2.4227  -0.6593
 JSR  C5'   C  CH2   0  -0.271  -4.1883   1.9549   0.6688
 JSR  C5A   C  CR16  0  -0.446  -4.7374  -3.1449   0.3537
 JSR  C6A   C  CR6   0   0.436  -3.5363  -2.6740   0.9108
 JSR  N6A   N  NH2   0  -0.839  -2.8948  -3.3862   1.8857
 JSR  C7A   C  CH2   0  -0.504  -2.8279   0.4153  -0.8776
 JSR  C8A   C  CH3   0  -0.724  -6.6028  -2.8934  -1.3043
 JSR  H1    H  HCH2  0   0.200   0.0524   3.7081  -1.1399
 JSR  H1A   H  HCH2  0   0.207   0.0515   4.5266   0.4277
 JSR  H2    H  HCH2  0   0.227   2.2924   3.8170  -0.1104
 JSR  H2A   H  HCH2  0   0.198   1.7332   2.9059   1.2844
 JSR  HN2   H  HNH1  0   0.339   1.1413   1.1483  -0.3233
 JSR  H3    H  HCH2  0   0.223   3.9136   2.0189  -0.5450
 JSR  H3A   H  HCH2  0   0.199   3.3040   0.9975   0.7474
 JSR  H4    H  HCH2  0   0.245   2.5800  -0.6890  -0.9969
 JSR  H4A   H  HCH2  0   0.248   3.2996   0.3281  -2.2341
 JSR  HN1'  H  HNH1  0   0.350  -4.6584   3.7470   1.5627
 JSR  H12   H  HCR6  0   0.269   3.9986  -1.8551   0.6811
 JSR  H14   H  HCR6  0   0.277   8.1811  -2.1875  -0.1633
 JSR  H15   H  HCR6  0   0.266   7.9411  -0.4988  -1.9686
 JSR  H16   H  HCR6  0   0.253   5.7410   0.5072  -2.4453
 JSR  H2'   H  HCH2  0   0.205  -3.3606   4.4260  -0.2733
 JSR  H2'A  H  HCH2  0   0.230  -2.2737   4.5611   1.1080
 JSR  H3'   H  HCH1  0   0.214  -1.9883   2.8678  -1.1748
 JSR  H3AA  H  HCR6  0   0.241  -5.1493  -0.6400  -1.8692
 JSR  H4'   H  HCH1  0   0.246  -2.3437   0.9893   1.1269
 JSR  H5'   H  HCH2  0   0.233  -4.7237   1.2520   1.3102
 JSR  H5'A  H  HCH2  0   0.192  -4.8165   2.1323  -0.2198
 JSR  H5A   H  HCR6  0   0.254  -5.1849  -4.0612   0.7198
 JSR  HN6A  H  HNH2  0   0.387  -3.4483  -4.0330   2.4223
 JSR  HN6B  H  HNH2  0   0.378  -2.2248  -2.8725   2.4343
 JSR  H7A   H  HCH2  0   0.250  -1.7960   0.1769  -1.1523
 JSR  H7AA  H  HCH2  0   0.239  -3.3015   0.8438  -1.7648
 JSR  H8A   H  HCH3  0   0.254  -6.3853  -3.3920  -2.2509
 JSR  H8AA  H  HCH3  0   0.246  -7.1376  -3.6021  -0.6738
 JSR  H8AB  H  HCH3  0   0.247  -7.2685  -2.0595  -1.5271

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
 JSR  O1   C1    single    1.409  0.020  1.409
 JSR  C2   C1    single    1.513  0.020  1.513
 JSR  C1   H1    single    0.970  0.020  1.090
 JSR  C1   H1A   single    0.970  0.020  1.090
 JSR  O1   C3'   single    1.407  0.020  1.407
 JSR  C2   N2    single    1.449  0.020  1.449
 JSR  C2   H2    single    0.970  0.020  1.090
 JSR  C2   H2A   single    0.970  0.020  1.090
 JSR  N2   C3    single    1.448  0.020  1.448
 JSR  N2   HN2   single    0.890  0.020  1.040
 JSR  C3   C4    single    1.527  0.020  1.527
 JSR  C3   H3    single    0.970  0.020  1.090
 JSR  C3   H3A   single    0.970  0.020  1.090
 JSR  C4   C11   single    1.502  0.020  1.502
 JSR  C4   H4    single    0.970  0.020  1.090
 JSR  C4   H4A   single    0.970  0.020  1.090
 JSR  C5'  N1'   single    1.453  0.020  1.453
 JSR  C2'  N1'   single    1.456  0.020  1.456
 JSR  N1'  HN1'  single    0.890  0.020  1.040
 JSR  C11  C12   aromatic  1.393  0.020  1.393
 JSR  C11  C16   aromatic  1.393  0.020  1.393
 JSR  C12  C13   aromatic  1.381  0.020  1.381
 JSR  C12  H12   single    0.930  0.020  1.080
 JSR  C13  F13   single    1.345  0.020  1.345
 JSR  C13  C14   aromatic  1.381  0.020  1.381
 JSR  C15  C14   aromatic  1.388  0.020  1.388
 JSR  C14  H14   single    0.930  0.020  1.080
 JSR  C16  C15   aromatic  1.388  0.020  1.388
 JSR  C15  H15   single    0.930  0.020  1.080
 JSR  C16  H16   single    0.930  0.020  1.080
 JSR  C6A  N1A   aromatic  1.328  0.020  1.328
 JSR  C2A  N1A   aromatic  1.335  0.020  1.335
 JSR  C3'  C2'   single    1.543  0.020  1.543
 JSR  C2'  H2'   single    0.970  0.020  1.090
 JSR  C2'  H2'A  single    0.970  0.020  1.090
 JSR  C3A  C2A   aromatic  1.384  0.020  1.384
 JSR  C2A  C7A   single    1.503  0.020  1.503
 JSR  C4'  C3'   single    1.535  0.020  1.535
 JSR  C3'  H3'   single    0.970  0.020  1.090
 JSR  C4A  C3A   aromatic  1.399  0.020  1.399
 JSR  C3A  H3AA  single    0.930  0.020  1.080
 JSR  C7A  C4'   single    1.523  0.020  1.523
 JSR  C4'  C5'   single    1.524  0.020  1.524
 JSR  C4'  H4'   single    0.970  0.020  1.090
 JSR  C8A  C4A   single    1.498  0.020  1.498
 JSR  C4A  C5A   aromatic  1.380  0.020  1.380
 JSR  C5'  H5'   single    0.970  0.020  1.090
 JSR  C5'  H5'A  single    0.970  0.020  1.090
 JSR  C5A  C6A   aromatic  1.405  0.020  1.405
 JSR  C5A  H5A   single    0.930  0.020  1.080
 JSR  C6A  N6A   single    1.367  0.020  1.367
 JSR  N6A  HN6A  single    0.890  0.020  1.040
 JSR  N6A  HN6B  single    0.890  0.020  1.040
 JSR  C7A  H7A   single    0.970  0.020  1.090
 JSR  C7A  H7AA  single    0.970  0.020  1.090
 JSR  C8A  H8A   single    0.970  0.020  1.090
 JSR  C8A  H8AA  single    0.970  0.020  1.090
 JSR  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
 JSR  H1A   C1   H1    107.24  3.000
 JSR  H1A   C1   C2    109.70  3.000
 JSR  H1    C1   C2    109.31  3.000
 JSR  H1A   C1   O1    111.42  3.000
 JSR  H1    C1   O1    110.64  3.000
 JSR  C2    C1   O1    108.51  3.000
 JSR  C3'   O1   C1    115.15  3.000
 JSR  H2A   C2   H2    106.32  3.000
 JSR  H2A   C2   N2    113.07  3.000
 JSR  H2    C2   N2    108.93  3.000
 JSR  H2A   C2   C1    109.53  3.000
 JSR  H2    C2   C1    107.96  3.000
 JSR  N2    C2   C1    110.80  3.000
 JSR  HN2   N2   C3    108.60  3.000
 JSR  HN2   N2   C2    108.42  3.000
 JSR  C3    N2   C2    113.33  3.000
 JSR  H3A   C3   H3    106.18  3.000
 JSR  H3A   C3   C4    109.38  3.000
 JSR  H3    C3   C4    109.17  3.000
 JSR  H3A   C3   N2    112.83  3.000
 JSR  H3    C3   N2    108.67  3.000
 JSR  C4    C3   N2    110.47  3.000
 JSR  H4A   C4   H4    106.89  3.000
 JSR  H4A   C4   C11   110.15  3.000
 JSR  H4    C4   C11   109.76  3.000
 JSR  H4A   C4   C3    108.91  3.000
 JSR  H4    C4   C3    109.20  3.000
 JSR  C11   C4   C3    111.79  3.000
 JSR  HN1'  N1'  C5'   111.95  3.000
 JSR  HN1'  N1'  C2'   111.56  3.000
 JSR  C5'   N1'  C2'   105.19  3.000
 JSR  C16   C11  C12   118.85  3.000
 JSR  C16   C11  C4    120.88  3.000
 JSR  C12   C11  C4    120.24  3.000
 JSR  H12   C12  C13   119.92  3.000
 JSR  H12   C12  C11   120.75  3.000
 JSR  C13   C12  C11   119.33  3.000
 JSR  C14   C13  F13   118.84  3.000
 JSR  C14   C13  C12   122.59  3.000
 JSR  F13   C13  C12   118.57  3.000
 JSR  H14   C14  C15   121.41  3.000
 JSR  H14   C14  C13   120.74  3.000
 JSR  C15   C14  C13   117.85  3.000
 JSR  H15   C15  C16   119.94  3.000
 JSR  H15   C15  C14   119.39  3.000
 JSR  C16   C15  C14   120.67  3.000
 JSR  H16   C16  C15   119.76  3.000
 JSR  H16   C16  C11   119.52  3.000
 JSR  C15   C16  C11   120.71  3.000
 JSR  C6A   N1A  C2A   118.78  3.000
 JSR  H2'A  C2'  H2'   107.09  3.000
 JSR  H2'A  C2'  C3'   112.47  3.000
 JSR  H2'   C2'  C3'   108.86  3.000
 JSR  H2'A  C2'  N1'   111.40  3.000
 JSR  H2'   C2'  N1'   112.59  3.000
 JSR  C3'   C2'  N1'   104.50  3.000
 JSR  C7A   C2A  C3A   121.47  3.000
 JSR  C7A   C2A  N1A   115.81  3.000
 JSR  C3A   C2A  N1A   122.70  3.000
 JSR  H3'   C3'  C4'   110.56  3.000
 JSR  H3'   C3'  C2'   109.06  3.000
 JSR  C4'   C3'  C2'   104.49  3.000
 JSR  H3'   C3'  O1    109.00  3.000
 JSR  C4'   C3'  O1    108.60  3.000
 JSR  C2'   C3'  O1    115.03  3.000
 JSR  H3AA  C3A  C4A   120.66  3.000
 JSR  H3AA  C3A  C2A   120.26  3.000
 JSR  C4A   C3A  C2A   119.08  3.000
 JSR  H4'   C4'  C7A   108.61  3.000
 JSR  H4'   C4'  C5'   107.90  3.000
 JSR  C7A   C4'  C5'   115.10  3.000
 JSR  H4'   C4'  C3'   107.50  3.000
 JSR  C5'   C4'  C3'   103.49  3.000
 JSR  C7A   C4'  C3'   113.81  3.000
 JSR  C8A   C4A  C5A   121.19  3.000
 JSR  C5A   C4A  C3A   118.09  3.000
 JSR  C8A   C4A  C3A   120.71  3.000
 JSR  H5'A  C5'  H5'   107.31  3.000
 JSR  H5'A  C5'  C4'   110.20  3.000
 JSR  H5'   C5'  C4'   112.69  3.000
 JSR  H5'A  C5'  N1'   113.37  3.000
 JSR  H5'   C5'  N1'   111.43  3.000
 JSR  C4'   C5'  N1'   101.92  3.000
 JSR  H5A   C5A  C6A   120.16  3.000
 JSR  H5A   C5A  C4A   120.78  3.000
 JSR  C6A   C5A  C4A   119.06  3.000
 JSR  N6A   C6A  C5A   120.61  3.000
 JSR  N6A   C6A  N1A   117.05  3.000
 JSR  C5A   C6A  N1A   122.30  3.000
 JSR  HN6B  N6A  HN6A  113.78  3.000
 JSR  HN6B  N6A  C6A   115.79  3.000
 JSR  HN6A  N6A  C6A   117.19  3.000
 JSR  H7AA  C7A  H7A   106.87  3.000
 JSR  H7AA  C7A  C4'   109.86  3.000
 JSR  H7A   C7A  C4'   108.99  3.000
 JSR  H7AA  C7A  C2A   110.04  3.000
 JSR  H7A   C7A  C2A   108.76  3.000
 JSR  C4'   C7A  C2A   112.16  3.000
 JSR  H8AB  C8A  H8AA  108.44  3.000
 JSR  H8AB  C8A  H8A   107.09  3.000
 JSR  H8AA  C8A  H8A   107.62  3.000
 JSR  H8AB  C8A  C4A   111.37  3.000
 JSR  H8AA  C8A  C4A   111.76  3.000
 JSR  H8A   C8A  C4A   110.37  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
 JSR  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 JSR  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 JSR  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 JSR  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 JSR  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 JSR  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 JSR  CONST_07  C4A   C5A  C6A  N1A     0.00   0.0  0
 JSR  CONST_08  C4A   C3A  C2A  N1A     0.00   0.0  0
 JSR  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 JSR  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 JSR  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 JSR  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 JSR  CONST_13  C13   C12  C11  C4    180.00   0.0  0
 JSR  CONST_14  C15   C16  C11  C4    180.00   0.0  0
 JSR  CONST_15  F13   C13  C12  C11   180.00   0.0  0
 JSR  CONST_16  C15   C14  C13  F13   180.00   0.0  0
 JSR  CONST_17  N6A   C6A  N1A  C2A   180.00   0.0  0
 JSR  CONST_18  C8A   C4A  C3A  C2A   180.00   0.0  0
 JSR  CONST_19  C7A   C2A  C3A  C4A   180.00   0.0  0
 JSR  CONST_20  N6A   C6A  C5A  C4A   180.00   0.0  0
 JSR  CONST_21  C7A   C2A  N1A  C6A   180.00   0.0  0
 JSR  CONST_22  C8A   C4A  C5A  C6A   180.00   0.0  0
 JSR  CONST_23  H15   C15  C16  C11   180.00   0.0  0
 JSR  CONST_24  H16   C16  C11  C12   180.00   0.0  0
 JSR  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 JSR  CONST_26  H12   C12  C13  C14   180.00   0.0  0
 JSR  CONST_27  H5A   C5A  C6A  N1A   180.00   0.0  0
 JSR  CONST_28  H3AA  C3A  C2A  N1A   180.00   0.0  0
 JSR  Var_01    C4'   C5'  N1'  C2'    46.32  30.0  1
 JSR  Var_02    C5'   N1'  C2'  C3'   -36.46  30.0  1
 JSR  Var_03    C4'   C7A  C2A  N1A   -64.71  30.0  2
 JSR  Var_04    C12   C11  C4   C3     86.96  30.0  2
 JSR  Var_05    H8A   C8A  C4A  C3A    79.55  30.0  2
 JSR  Var_06    C11   C4   C3   N2   -178.61  30.0  3
 JSR  Var_07    H1    C1   O1   C3'   -41.84  30.0  3
 JSR  Var_08    C3    N2   C2   C1   -177.51  30.0  3
 JSR  Var_09    N2    C2   C1   O1     64.90  30.0  1
 JSR  Var_10    C4    C3   N2   C2   -177.82  30.0  3

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
 JSR  chir_01  C3'  O1   C2'  C4'  positiv
 JSR  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
 JSR  plan-1  C4    0.020
 JSR  plan-1  C11   0.020
 JSR  plan-1  C12   0.020
 JSR  plan-1  C13   0.020
 JSR  plan-1  F13   0.020
 JSR  plan-1  C14   0.020
 JSR  plan-1  C15   0.020
 JSR  plan-1  C16   0.020
 JSR  plan-1  H12   0.020
 JSR  plan-1  H14   0.020
 JSR  plan-1  H15   0.020
 JSR  plan-1  H16   0.020
 JSR  plan-2  N1A   0.020
 JSR  plan-2  C2A   0.020
 JSR  plan-2  C3A   0.020
 JSR  plan-2  C4A   0.020
 JSR  plan-2  C5A   0.020
 JSR  plan-2  C6A   0.020
 JSR  plan-2  N6A   0.020
 JSR  plan-2  C7A   0.020
 JSR  plan-2  C8A   0.020
 JSR  plan-2  H3AA  0.020
 JSR  plan-2  H5A   0.020
 JSR  plan-3  C6A   0.020
 JSR  plan-3  N6A   0.020
 JSR  plan-3  HN6A  0.020
 JSR  plan-3  HN6B  0.020

