# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 13:09:05 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3S,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
 JRS  JRS  6-{[(3S,4R)-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_JRS
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
 JRS  C1    C  CH2   0  -0.164   0.3584  -2.5761  -1.3041
 JRS  O1    O  O2    0  -0.494  -0.5893  -1.7226  -0.7022
 JRS  C2    C  CH2   0  -0.298   1.6113  -1.7801  -1.5887
 JRS  N2    N  NH1   0  -0.601   2.2457  -1.3321  -0.3649
 JRS  C3    C  CH2   0  -0.245   3.4132  -0.5104  -0.6087
 JRS  C4    C  CH2   0  -0.530   4.0560  -0.0758   0.7062
 JRS  N1'   N  NH1   0  -0.604  -3.1598  -3.3922   1.2573
 JRS  C11   C  CR6   0   0.139   5.2556   0.7960   0.4681
 JRS  C12   C  CR16  0  -0.463   6.4909   0.2189   0.1810
 JRS  C13   C  CR6   0   0.539   7.5741   1.0342  -0.0807
 JRS  F13   F  F     0  -0.319   8.7597   0.4613  -0.3533
 JRS  C14   C  CR16  0  -0.426   7.4870   2.4130  -0.0715
 JRS  C15   C  CR16  0  -0.224   6.2542   2.9827   0.2160
 JRS  C16   C  CR16  0  -0.323   5.1499   2.1848   0.4830
 JRS  N1A   N  N     0  -0.477  -5.6780   0.1715  -0.4934
 JRS  C2'   C  CH2   0  -0.334  -1.7704  -3.2834   0.8347
 JRS  C2A   C  CR6   0   0.272  -4.4007   0.5349  -0.6191
 JRS  C3'   C  CH1   0   0.080  -1.8010  -2.3443  -0.3738
 JRS  C3A   C  CR16  0  -0.424  -3.9485   1.8019  -0.2917
 JRS  C4'   C  CH1   0  -0.300  -2.8284  -1.3059   0.0648
 JRS  C4A   C  CR6   0   0.204  -4.8576   2.7442   0.1985
 JRS  C5'   C  CH2   0  -0.271  -3.8329  -2.1349   0.8855
 JRS  C5A   C  CR16  0  -0.446  -6.1789   2.3648   0.3305
 JRS  C6A   C  CR6   0   0.441  -6.5521   1.0591  -0.0290
 JRS  N6A   N  NH2   0  -0.838  -7.8584   0.6612   0.0418
 JRS  C7A   C  CH2   0  -0.502  -3.4399  -0.5192  -1.0925
 JRS  C8A   C  CH3   0  -0.727  -4.4021   4.1243   0.5631
 JRS  H1    H  HCH2  0   0.203   0.6035  -3.4240  -0.6519
 JRS  H1A   H  HCH2  0   0.208  -0.0340  -2.9890  -2.2435
 JRS  H2    H  HCH2  0   0.228   2.3071  -2.4295  -2.1278
 JRS  H2A   H  HCH2  0   0.196   1.3666  -0.9532  -2.2750
 JRS  HN2   H  HNH1  0   0.340   1.5753  -0.7938   0.1716
 JRS  H3    H  HCH2  0   0.223   4.1353  -1.0955  -1.1874
 JRS  H3A   H  HCH2  0   0.198   3.1859   0.3827  -1.2129
 JRS  H4    H  HCH2  0   0.246   3.3194   0.4682   1.3035
 JRS  H4A   H  HCH2  0   0.247   4.3404  -0.9637   1.2756
 JRS  HN1'  H  HNH1  0   0.351  -3.5917  -4.1557   0.7568
 JRS  H12   H  HCR6  0   0.270   6.6074  -0.8584   0.1649
 JRS  H14   H  HCR6  0   0.277   8.3553   3.0239  -0.2801
 JRS  H15   H  HCR6  0   0.266   6.1582   4.0603   0.2331
 JRS  H16   H  HCR6  0   0.252   4.1967   2.6463   0.7109
 JRS  H2'   H  HCH2  0   0.214  -1.1568  -2.8319   1.6235
 JRS  H2'A  H  HCH2  0   0.240  -1.3584  -4.2704   0.6207
 JRS  H3'   H  HCH1  0   0.194  -2.1915  -2.9002  -1.2431
 JRS  H3AA  H  HCR6  0   0.240  -2.9017   2.0543  -0.4099
 JRS  H4'   H  HCH1  0   0.245  -2.3125  -0.6042   0.7316
 JRS  H5'   H  HCH2  0   0.228  -4.7349  -2.3460   0.3078
 JRS  H5'A  H  HCH2  0   0.217  -4.1541  -1.5830   1.7723
 JRS  H5A   H  HCR6  0   0.254  -6.9221   3.0597   0.7036
 JRS  HN6A  H  HNH2  0   0.378  -8.0096  -0.3346   0.0560
 JRS  HN6B  H  HNH2  0   0.386  -8.4605   1.1699   0.6676
 JRS  H7A   H  HCH2  0   0.237  -3.9593  -1.2112  -1.7608
 JRS  H7AA  H  HCH2  0   0.247  -2.6357  -0.0505  -1.6647
 JRS  H8A   H  HCH3  0   0.252  -4.0193   4.6503  -0.3130
 JRS  H8AA  H  HCH3  0   0.246  -5.2104   4.7190   0.9857
 JRS  H8AB  H  HCH3  0   0.250  -3.5912   4.0861   1.2914

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
 JRS  C2   C1    single    1.511  0.020  1.511
 JRS  O1   C1    single    1.410  0.020  1.410
 JRS  C1   H1    single    0.970  0.020  1.090
 JRS  C1   H1A   single    0.970  0.020  1.090
 JRS  C3'  O1    single    1.401  0.020  1.401
 JRS  N2   C2    single    1.449  0.020  1.449
 JRS  C2   H2    single    0.970  0.020  1.090
 JRS  C2   H2A   single    0.970  0.020  1.090
 JRS  C3   N2    single    1.448  0.020  1.448
 JRS  N2   HN2   single    0.890  0.020  1.040
 JRS  C4   C3    single    1.527  0.020  1.527
 JRS  C3   H3    single    0.970  0.020  1.090
 JRS  C3   H3A   single    0.970  0.020  1.090
 JRS  C4   C11   single    1.502  0.020  1.502
 JRS  C4   H4    single    0.970  0.020  1.090
 JRS  C4   H4A   single    0.970  0.020  1.090
 JRS  C2'  N1'   single    1.456  0.020  1.456
 JRS  N1'  C5'   single    1.474  0.020  1.474
 JRS  N1'  HN1'  single    0.890  0.020  1.040
 JRS  C12  C11   aromatic  1.393  0.020  1.393
 JRS  C11  C16   aromatic  1.393  0.020  1.393
 JRS  C12  C13   aromatic  1.381  0.020  1.381
 JRS  C12  H12   single    0.930  0.020  1.080
 JRS  F13  C13   single    1.345  0.020  1.345
 JRS  C13  C14   aromatic  1.382  0.020  1.382
 JRS  C14  C15   aromatic  1.388  0.020  1.388
 JRS  C14  H14   single    0.930  0.020  1.080
 JRS  C16  C15   aromatic  1.388  0.020  1.388
 JRS  C15  H15   single    0.930  0.020  1.080
 JRS  C16  H16   single    0.930  0.020  1.080
 JRS  N1A  C2A   aromatic  1.334  0.020  1.334
 JRS  N1A  C6A   aromatic  1.329  0.020  1.329
 JRS  C2'  C3'   single    1.531  0.020  1.531
 JRS  C2'  H2'   single    0.970  0.020  1.090
 JRS  C2'  H2'A  single    0.970  0.020  1.090
 JRS  C7A  C2A   single    1.503  0.020  1.503
 JRS  C2A  C3A   aromatic  1.385  0.020  1.385
 JRS  C3'  C4'   single    1.525  0.020  1.525
 JRS  C3'  H3'   single    0.970  0.020  1.090
 JRS  C3A  C4A   aromatic  1.398  0.020  1.398
 JRS  C3A  H3AA  single    0.930  0.020  1.080
 JRS  C7A  C4'   single    1.527  0.020  1.527
 JRS  C4'  C5'   single    1.539  0.020  1.539
 JRS  C4'  H4'   single    0.970  0.020  1.090
 JRS  C5A  C4A   aromatic  1.381  0.020  1.381
 JRS  C4A  C8A   single    1.498  0.020  1.498
 JRS  C5'  H5'   single    0.970  0.020  1.090
 JRS  C5'  H5'A  single    0.970  0.020  1.090
 JRS  C6A  C5A   aromatic  1.405  0.020  1.405
 JRS  C5A  H5A   single    0.930  0.020  1.080
 JRS  N6A  C6A   single    1.367  0.020  1.367
 JRS  N6A  HN6A  single    0.890  0.020  1.040
 JRS  N6A  HN6B  single    0.890  0.020  1.040
 JRS  C7A  H7A   single    0.970  0.020  1.090
 JRS  C7A  H7AA  single    0.970  0.020  1.090
 JRS  C8A  H8A   single    0.970  0.020  1.090
 JRS  C8A  H8AA  single    0.970  0.020  1.090
 JRS  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
 JRS  H1A   C1   H1    107.31  3.000
 JRS  H1A   C1   C2    109.45  3.000
 JRS  H1    C1   C2    109.49  3.000
 JRS  H1A   C1   O1    110.64  3.000
 JRS  H1    C1   O1    111.35  3.000
 JRS  C2    C1   O1    108.58  3.000
 JRS  C3'   O1   C1    114.37  3.000
 JRS  H2A   C2   H2    106.25  3.000
 JRS  H2A   C2   N2    113.02  3.000
 JRS  H2    C2   N2    108.74  3.000
 JRS  H2A   C2   C1    109.17  3.000
 JRS  H2    C2   C1    107.91  3.000
 JRS  N2    C2   C1    111.51  3.000
 JRS  HN2   N2   C3    108.73  3.000
 JRS  HN2   N2   C2    108.76  3.000
 JRS  C3    N2   C2    112.71  3.000
 JRS  H3A   C3   H3    106.22  3.000
 JRS  H3A   C3   C4    109.17  3.000
 JRS  H3    C3   C4    109.24  3.000
 JRS  H3A   C3   N2    112.70  3.000
 JRS  H3    C3   N2    108.51  3.000
 JRS  C4    C3   N2    110.85  3.000
 JRS  H4A   C4   H4    107.16  3.000
 JRS  H4A   C4   C11   110.27  3.000
 JRS  H4    C4   C11   109.63  3.000
 JRS  H4A   C4   C3    109.09  3.000
 JRS  H4    C4   C3    109.18  3.000
 JRS  C11   C4   C3    111.41  3.000
 JRS  HN1'  N1'  C5'   108.94  3.000
 JRS  HN1'  N1'  C2'   108.71  3.000
 JRS  C5'   N1'  C2'   107.38  3.000
 JRS  C16   C11  C12   118.84  3.000
 JRS  C16   C11  C4    121.09  3.000
 JRS  C12   C11  C4    120.03  3.000
 JRS  H12   C12  C13   119.99  3.000
 JRS  H12   C12  C11   120.67  3.000
 JRS  C13   C12  C11   119.34  3.000
 JRS  C14   C13  F13   118.83  3.000
 JRS  C14   C13  C12   122.58  3.000
 JRS  F13   C13  C12   118.59  3.000
 JRS  H14   C14  C15   121.39  3.000
 JRS  H14   C14  C13   120.77  3.000
 JRS  C15   C14  C13   117.84  3.000
 JRS  H15   C15  C16   119.92  3.000
 JRS  H15   C15  C14   119.39  3.000
 JRS  C16   C15  C14   120.69  3.000
 JRS  H16   C16  C15   119.70  3.000
 JRS  H16   C16  C11   119.59  3.000
 JRS  C15   C16  C11   120.70  3.000
 JRS  C6A   N1A  C2A   118.72  3.000
 JRS  H2'A  C2'  H2'   107.60  3.000
 JRS  H2'A  C2'  C3'   114.07  3.000
 JRS  H2'   C2'  C3'   109.05  3.000
 JRS  H2'A  C2'  N1'   110.47  3.000
 JRS  H2'   C2'  N1'   110.84  3.000
 JRS  C3'   C2'  N1'   104.83  3.000
 JRS  C7A   C2A  C3A   120.50  3.000
 JRS  C3A   C2A  N1A   122.67  3.000
 JRS  C7A   C2A  N1A   116.80  3.000
 JRS  H3'   C3'  C4'   109.34  3.000
 JRS  H3'   C3'  C2'   108.66  3.000
 JRS  C4'   C3'  C2'   101.78  3.000
 JRS  H3'   C3'  O1    110.18  3.000
 JRS  C4'   C3'  O1    110.36  3.000
 JRS  C2'   C3'  O1    116.11  3.000
 JRS  H3AA  C3A  C4A   120.64  3.000
 JRS  H3AA  C3A  C2A   120.20  3.000
 JRS  C4A   C3A  C2A   119.17  3.000
 JRS  H4'   C4'  C7A   108.63  3.000
 JRS  H4'   C4'  C5'   109.11  3.000
 JRS  C7A   C4'  C5'   114.84  3.000
 JRS  H4'   C4'  C3'   107.07  3.000
 JRS  C5'   C4'  C3'   103.08  3.000
 JRS  C7A   C4'  C3'   113.74  3.000
 JRS  C8A   C4A  C5A   121.38  3.000
 JRS  C8A   C4A  C3A   120.56  3.000
 JRS  C5A   C4A  C3A   118.06  3.000
 JRS  H5'A  C5'  H5'   106.51  3.000
 JRS  H5'A  C5'  C4'   110.64  3.000
 JRS  H5'   C5'  C4'   111.17  3.000
 JRS  H5'A  C5'  N1'   111.12  3.000
 JRS  H5'   C5'  N1'   110.24  3.000
 JRS  C4'   C5'  N1'   107.21  3.000
 JRS  H5A   C5A  C6A   120.13  3.000
 JRS  H5A   C5A  C4A   120.86  3.000
 JRS  C6A   C5A  C4A   119.02  3.000
 JRS  N6A   C6A  C5A   120.73  3.000
 JRS  N6A   C6A  N1A   116.87  3.000
 JRS  C5A   C6A  N1A   122.37  3.000
 JRS  HN6B  N6A  HN6A  113.65  3.000
 JRS  HN6B  N6A  C6A   117.17  3.000
 JRS  HN6A  N6A  C6A   115.58  3.000
 JRS  H7AA  C7A  H7A   107.52  3.000
 JRS  H7AA  C7A  C4'   108.85  3.000
 JRS  H7A   C7A  C4'   109.11  3.000
 JRS  H7AA  C7A  C2A   109.55  3.000
 JRS  H7A   C7A  C2A   109.44  3.000
 JRS  C4'   C7A  C2A   112.25  3.000
 JRS  H8AB  C8A  H8AA  108.17  3.000
 JRS  H8AB  C8A  H8A   106.99  3.000
 JRS  H8AA  C8A  H8A   107.99  3.000
 JRS  H8AB  C8A  C4A   110.87  3.000
 JRS  H8AA  C8A  C4A   111.83  3.000
 JRS  H8A   C8A  C4A   110.81  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
 JRS  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 JRS  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 JRS  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 JRS  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 JRS  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 JRS  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 JRS  CONST_07  C4A   C3A  C2A  N1A     0.00   0.0  0
 JRS  CONST_08  C4A   C5A  C6A  N1A     0.00   0.0  0
 JRS  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 JRS  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 JRS  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 JRS  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 JRS  CONST_13  C13   C12  C11  C4    180.00   0.0  0
 JRS  CONST_14  C15   C16  C11  C4    180.00   0.0  0
 JRS  CONST_15  F13   C13  C12  C11   180.00   0.0  0
 JRS  CONST_16  C15   C14  C13  F13   180.00   0.0  0
 JRS  CONST_17  N6A   C6A  N1A  C2A   180.00   0.0  0
 JRS  CONST_18  C8A   C4A  C3A  C2A   180.00   0.0  0
 JRS  CONST_19  C7A   C2A  C3A  C4A   180.00   0.0  0
 JRS  CONST_20  N6A   C6A  C5A  C4A   180.00   0.0  0
 JRS  CONST_21  C7A   C2A  N1A  C6A   180.00   0.0  0
 JRS  CONST_22  C8A   C4A  C5A  C6A   180.00   0.0  0
 JRS  CONST_23  H15   C15  C16  C11   180.00   0.0  0
 JRS  CONST_24  H16   C16  C11  C12   180.00   0.0  0
 JRS  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 JRS  CONST_26  H12   C12  C13  C14   180.00   0.0  0
 JRS  CONST_27  H3AA  C3A  C2A  N1A   180.00   0.0  0
 JRS  CONST_28  H5A   C5A  C6A  N1A   180.00   0.0  0
 JRS  Var_01    C4'   C5'  N1'  C2'     6.42  30.0  1
 JRS  Var_02    C5'   N1'  C2'  C3'   -28.84  30.0  1
 JRS  Var_03    C4'   C7A  C2A  N1A   -90.07  30.0  1
 JRS  Var_04    C12   C11  C4   C3    -82.53  30.0  2
 JRS  Var_05    H8A   C8A  C4A  C3A    63.01  30.0  2
 JRS  Var_06    C11   C4   C3   N2   -179.08  30.0  1
 JRS  Var_07    H1    C1   O1   C3'   -58.82  30.0  3
 JRS  Var_08    C3    N2   C2   C1   -177.14  30.0  1
 JRS  Var_09    N2    C2   C1   O1     65.18  30.0  2
 JRS  Var_10    C4    C3   N2   C2   -179.36  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
 JRS  chir_01  C3'  O1   C2'  C4'  negativ
 JRS  chir_02  C4'  C3'  C7A  C5'  negativ

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
 JRS  plan-1  C4    0.020
 JRS  plan-1  C11   0.020
 JRS  plan-1  C12   0.020
 JRS  plan-1  C13   0.020
 JRS  plan-1  F13   0.020
 JRS  plan-1  C14   0.020
 JRS  plan-1  C15   0.020
 JRS  plan-1  C16   0.020
 JRS  plan-1  H12   0.020
 JRS  plan-1  H14   0.020
 JRS  plan-1  H15   0.020
 JRS  plan-1  H16   0.020
 JRS  plan-2  N1A   0.020
 JRS  plan-2  C2A   0.020
 JRS  plan-2  C3A   0.020
 JRS  plan-2  C4A   0.020
 JRS  plan-2  C5A   0.020
 JRS  plan-2  C6A   0.020
 JRS  plan-2  N6A   0.020
 JRS  plan-2  C7A   0.020
 JRS  plan-2  C8A   0.020
 JRS  plan-2  H3AA  0.020
 JRS  plan-2  H5A   0.020
 JRS  plan-3  C6A   0.020
 JRS  plan-3  N6A   0.020
 JRS  plan-3  HN6A  0.020
 JRS  plan-3  HN6B  0.020

