# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 23:45:57 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-{[(3S,4S)-4-{2-[(2-fluorobenzyl)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]2OCCNCc3ccccc3F)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
 AXW  AXW  6-{[(3S,4S)-4-{2-[(2-fluorobenzyl)amino]ethoxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  53  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AXW
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
 AXW  F22  F  F     0  -0.315  -1.7516  -0.7631  -1.7798
 AXW  C22  C  CR6   0   0.513  -2.6122  -1.1585  -0.8220
 AXW  C23  C  CR16  0  -0.394  -2.5432  -2.4662  -0.3826
 AXW  C24  C  CR16  0  -0.252  -3.4205  -2.8803   0.6100
 AXW  C25  C  CR16  0  -0.255  -4.3407  -1.9863   1.1406
 AXW  C26  C  CR16  0  -0.281  -4.3785  -0.6779   0.6784
 AXW  C21  C  CR6   0  -0.096  -3.5154  -0.2323  -0.3192
 AXW  C13  C  CH2   0  -0.326  -3.5082   1.2019  -0.7754
 AXW  N12  N  NH1   0  -0.609  -2.4692   1.9322  -0.0679
 AXW  C11  C  CH2   0  -0.299  -2.2356   3.2705  -0.5739
 AXW  C10  C  CH2   0  -0.164  -1.0168   3.8631   0.1066
 AXW  O09  O  O2    0  -0.503   0.1002   3.0548  -0.1955
 AXW  C4'  C  CH1   0   0.033   1.0557   2.8935   0.8284
 AXW  C5'  C  CH2   0  -0.325   2.1407   4.0010   0.8023
 AXW  N1'  N  NH1   0  -0.592   3.4315   3.3671   0.5366
 AXW  C2'  C  CH2   0  -0.301   3.1161   2.0965  -0.1034
 AXW  C3'  C  CH1   0  -0.280   1.8525   1.5950   0.6013
 AXW  C08  C  CH2   0  -0.503   1.0686   0.4879  -0.0999
 AXW  C06  C  CR6   0   0.291   1.7470  -0.8509  -0.0488
 AXW  N01  N  N     0  -0.473   2.8834  -0.9819  -0.7352
 AXW  C02  C  CR6   0   0.447   3.5140  -2.1515  -0.7080
 AXW  N02  N  NH2   0  -0.841   4.7055  -2.2270  -1.3700
 AXW  C03  C  CR16  0  -0.450   3.0132  -3.2610  -0.0049
 AXW  C05  C  CR16  0  -0.438   1.1912  -1.8883   0.6807
 AXW  C04  C  CR6   0   0.208   1.8339  -3.1299   0.7000
 AXW  C07  C  CH3   0  -0.724   1.2592  -4.2742   1.4774
 AXW  H1   H  HCR6  0   0.275  -1.8165  -3.1444  -0.8110
 AXW  H2   H  HCR6  0   0.267  -3.3812  -3.9015   0.9651
 AXW  H3   H  HCR6  0   0.260  -5.0260  -2.3057   1.9143
 AXW  H4   H  HCR6  0   0.261  -5.0936   0.0193   1.0982
 AXW  H5   H  HCH2  0   0.215  -3.3967   1.2550  -1.8683
 AXW  H6   H  HCH2  0   0.240  -4.4777   1.6495  -0.5440
 AXW  H7   H  HNH1  0   0.359  -1.6005   1.4228  -0.1635
 AXW  H9   H  HCH2  0   0.200  -2.1012   3.2974  -1.6673
 AXW  H10  H  HCH2  0   0.228  -3.0983   3.9053  -0.3518
 AXW  H11  H  HCH2  0   0.214  -0.8630   4.8956  -0.2298
 AXW  H12  H  HCH2  0   0.204  -1.1893   3.8942   1.1897
 AXW  H13  H  HCH1  0   0.225   0.5419   2.8609   1.7975
 AXW  H14  H  HCH2  0   0.224   1.8994   4.7075   0.0017
 AXW  H15  H  HCH2  0   0.237   2.1812   4.5699   1.7316
 AXW  H16  H  HNH1  0   0.344   3.8834   3.1691   1.4205
 AXW  H18  H  HCH2  0   0.210   2.9145   2.2586  -1.1685
 AXW  H19  H  HCH2  0   0.244   3.9545   1.4061  -0.0349
 AXW  H20  H  HCH1  0   0.244   2.1518   1.2323   1.5918
 AXW  H21  H  HCH2  0   0.237   0.0888   0.3832   0.3719
 AXW  H22  H  HCH2  0   0.239   0.8939   0.7602  -1.1436
 AXW  H23  H  HNH2  0   0.379   4.8758  -1.5194  -2.0653
 AXW  H24  H  HNH2  0   0.387   5.0541  -3.1393  -1.6108
 AXW  H25  H  HCR6  0   0.254   3.5454  -4.2047  -0.0273
 AXW  H26  H  HCR6  0   0.237   0.2608  -1.7391   1.2142
 AXW  H27  H  HCH3  0   0.255   1.4523  -4.1482   2.5444
 AXW  H28  H  HCH3  0   0.242   0.1773  -4.3311   1.3536
 AXW  H29  H  HCH3  0   0.247   1.6896  -5.2271   1.1732

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
 AXW  C07  C04  single    1.498  0.020  1.498
 AXW  C04  C03  aromatic  1.380  0.020  1.380
 AXW  C04  C05  aromatic  1.398  0.020  1.398
 AXW  C03  C02  aromatic  1.406  0.020  1.406
 AXW  C05  C06  aromatic  1.385  0.020  1.385
 AXW  C02  N02  single    1.365  0.020  1.365
 AXW  C02  N01  aromatic  1.329  0.020  1.329
 AXW  C3'  C2'  single    1.531  0.020  1.531
 AXW  C3'  C08  single    1.527  0.020  1.527
 AXW  C3'  C4'  single    1.540  0.020  1.540
 AXW  C06  N01  aromatic  1.334  0.020  1.334
 AXW  C06  C08  single    1.502  0.020  1.502
 AXW  C2'  N1'  single    1.457  0.020  1.457
 AXW  C10  O09  single    1.411  0.020  1.411
 AXW  C10  C11  single    1.517  0.020  1.517
 AXW  C4'  O09  single    1.410  0.020  1.410
 AXW  C4'  C5'  single    1.551  0.020  1.551
 AXW  N1'  C5'  single    1.462  0.020  1.462
 AXW  C11  N12  single    1.450  0.020  1.450
 AXW  N12  C13  single    1.454  0.020  1.454
 AXW  C26  C25  aromatic  1.388  0.020  1.388
 AXW  C26  C21  aromatic  1.392  0.020  1.392
 AXW  C25  C24  aromatic  1.388  0.020  1.388
 AXW  C13  C21  single    1.505  0.020  1.505
 AXW  C21  C22  aromatic  1.388  0.020  1.388
 AXW  C24  C23  aromatic  1.388  0.020  1.388
 AXW  C22  C23  aromatic  1.381  0.020  1.381
 AXW  C22  F22  single    1.347  0.020  1.347
 AXW  C23  H1   single    0.930  0.020  1.080
 AXW  C24  H2   single    0.930  0.020  1.080
 AXW  C25  H3   single    0.930  0.020  1.080
 AXW  C26  H4   single    0.930  0.020  1.080
 AXW  C13  H5   single    0.970  0.020  1.090
 AXW  C13  H6   single    0.970  0.020  1.090
 AXW  N12  H7   single    0.890  0.020  1.040
 AXW  C11  H9   single    0.970  0.020  1.090
 AXW  C11  H10  single    0.970  0.020  1.090
 AXW  C10  H11  single    0.970  0.020  1.090
 AXW  C10  H12  single    0.970  0.020  1.090
 AXW  C4'  H13  single    0.970  0.020  1.090
 AXW  C5'  H14  single    0.970  0.020  1.090
 AXW  C5'  H15  single    0.970  0.020  1.090
 AXW  N1'  H16  single    0.890  0.020  1.040
 AXW  C2'  H18  single    0.970  0.020  1.090
 AXW  C2'  H19  single    0.970  0.020  1.090
 AXW  C3'  H20  single    0.970  0.020  1.090
 AXW  C08  H21  single    0.970  0.020  1.090
 AXW  C08  H22  single    0.970  0.020  1.090
 AXW  N02  H23  single    0.890  0.020  1.040
 AXW  N02  H24  single    0.890  0.020  1.040
 AXW  C03  H25  single    0.930  0.020  1.080
 AXW  C05  H26  single    0.930  0.020  1.080
 AXW  C07  H27  single    0.970  0.020  1.090
 AXW  C07  H28  single    0.970  0.020  1.090
 AXW  C07  H29  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
 AXW  C21  C22  C23  123.30  3.000
 AXW  C23  C22  F22  118.18  3.000
 AXW  C21  C22  F22  118.52  3.000
 AXW  H1   C23  C24  121.37  3.000
 AXW  H1   C23  C22  120.05  3.000
 AXW  C24  C23  C22  118.58  3.000
 AXW  H2   C24  C25  120.43  3.000
 AXW  H2   C24  C23  119.56  3.000
 AXW  C25  C24  C23  120.01  3.000
 AXW  H3   C25  C26  119.94  3.000
 AXW  H3   C25  C24  120.20  3.000
 AXW  C26  C25  C24  119.85  3.000
 AXW  H4   C26  C21  118.74  3.000
 AXW  H4   C26  C25  119.71  3.000
 AXW  C21  C26  C25  121.55  3.000
 AXW  C13  C21  C26  121.67  3.000
 AXW  C13  C21  C22  121.53  3.000
 AXW  C26  C21  C22  116.71  3.000
 AXW  H6   C13  H5   106.29  3.000
 AXW  H6   C13  N12  108.98  3.000
 AXW  H5   C13  N12  112.76  3.000
 AXW  H6   C13  C21  108.78  3.000
 AXW  H5   C13  C21  110.35  3.000
 AXW  N12  C13  C21  109.55  3.000
 AXW  H7   N12  C11  107.07  3.000
 AXW  H7   N12  C13  108.35  3.000
 AXW  C11  N12  C13  114.15  3.000
 AXW  H10  C11  H9   106.47  3.000
 AXW  H10  C11  C10  108.42  3.000
 AXW  H9   C11  C10  109.73  3.000
 AXW  H10  C11  N12  109.74  3.000
 AXW  H9   C11  N12  112.86  3.000
 AXW  C10  C11  N12  109.49  3.000
 AXW  H12  C10  H11  107.34  3.000
 AXW  H12  C10  O09  110.60  3.000
 AXW  H11  C10  O09  111.26  3.000
 AXW  H12  C10  C11  109.13  3.000
 AXW  H11  C10  C11  110.06  3.000
 AXW  O09  C10  C11  108.43  3.000
 AXW  C4'  O09  C10  116.52  3.000
 AXW  H13  C4'  C3'  110.32  3.000
 AXW  H13  C4'  C5'  111.33  3.000
 AXW  C3'  C4'  C5'  103.75  3.000
 AXW  H13  C4'  O09  109.11  3.000
 AXW  C5'  C4'  O09  112.36  3.000
 AXW  C3'  C4'  O09  109.88  3.000
 AXW  H15  C5'  H14  107.15  3.000
 AXW  H15  C5'  N1'  110.38  3.000
 AXW  H14  C5'  N1'  109.96  3.000
 AXW  H15  C5'  C4'  112.60  3.000
 AXW  H14  C5'  C4'  108.60  3.000
 AXW  N1'  C5'  C4'  108.12  3.000
 AXW  H16  N1'  C2'  108.03  3.000
 AXW  H16  N1'  C5'  108.67  3.000
 AXW  C2'  N1'  C5'  105.47  3.000
 AXW  H19  C2'  H18  107.26  3.000
 AXW  H19  C2'  C3'  113.52  3.000
 AXW  H18  C2'  C3'  110.11  3.000
 AXW  H19  C2'  N1'  111.03  3.000
 AXW  H18  C2'  N1'  109.73  3.000
 AXW  C3'  C2'  N1'  105.19  3.000
 AXW  H20  C3'  C08  108.37  3.000
 AXW  H20  C3'  C2'  107.38  3.000
 AXW  C08  C3'  C2'  116.73  3.000
 AXW  H20  C3'  C4'  106.68  3.000
 AXW  C08  C3'  C4'  114.42  3.000
 AXW  C2'  C3'  C4'  102.63  3.000
 AXW  H22  C08  H21  107.04  3.000
 AXW  H22  C08  C06  109.08  3.000
 AXW  H21  C08  C06  107.76  3.000
 AXW  H22  C08  C3'  109.88  3.000
 AXW  H21  C08  C3'  109.37  3.000
 AXW  C06  C08  C3'  113.50  3.000
 AXW  C05  C06  N01  122.64  3.000
 AXW  N01  C06  C08  117.06  3.000
 AXW  C05  C06  C08  120.30  3.000
 AXW  C02  N01  C06  118.69  3.000
 AXW  C03  C02  N02  120.66  3.000
 AXW  N02  C02  N01  116.93  3.000
 AXW  C03  C02  N01  122.39  3.000
 AXW  H24  N02  H23  114.43  3.000
 AXW  H24  N02  C02  117.95  3.000
 AXW  H23  N02  C02  116.35  3.000
 AXW  H25  C03  C04  120.86  3.000
 AXW  H25  C03  C02  120.13  3.000
 AXW  C04  C03  C02  119.01  3.000
 AXW  H26  C05  C04  120.70  3.000
 AXW  H26  C05  C06  120.08  3.000
 AXW  C04  C05  C06  119.21  3.000
 AXW  C07  C04  C05  120.61  3.000
 AXW  C05  C04  C03  118.04  3.000
 AXW  C07  C04  C03  121.35  3.000
 AXW  H29  C07  H28  108.35  3.000
 AXW  H29  C07  H27  107.70  3.000
 AXW  H28  C07  H27  107.01  3.000
 AXW  H29  C07  C04  111.83  3.000
 AXW  H28  C07  C04  111.20  3.000
 AXW  H27  C07  C04  110.56  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
 AXW  CONST_01  C25  C26  C21  C22     0.00   0.0  0
 AXW  CONST_02  C25  C24  C23  C22     0.00   0.0  0
 AXW  CONST_03  C26  C25  C24  C23     0.00   0.0  0
 AXW  CONST_04  C26  C21  C22  C23     0.00   0.0  0
 AXW  CONST_05  C21  C26  C25  C24     0.00   0.0  0
 AXW  CONST_06  C21  C22  C23  C24     0.00   0.0  0
 AXW  CONST_07  C03  C04  C05  C06     0.00   0.0  0
 AXW  CONST_08  C03  C02  N01  C06     0.00   0.0  0
 AXW  CONST_09  C04  C03  C02  N01     0.00   0.0  0
 AXW  CONST_10  C04  C05  C06  N01     0.00   0.0  0
 AXW  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 AXW  CONST_12  C05  C06  N01  C02     0.00   0.0  0
 AXW  CONST_13  C26  C21  C22  F22   180.00   0.0  0
 AXW  CONST_14  C24  C23  C22  F22   180.00   0.0  0
 AXW  CONST_15  C13  C21  C22  C23   180.00   0.0  0
 AXW  CONST_16  C13  C21  C26  C25   180.00   0.0  0
 AXW  CONST_17  C04  C05  C06  C08   180.00   0.0  0
 AXW  CONST_18  C02  N01  C06  C08   180.00   0.0  0
 AXW  CONST_19  C07  C04  C05  C06   180.00   0.0  0
 AXW  CONST_20  N02  C02  N01  C06   180.00   0.0  0
 AXW  CONST_21  C07  C04  C03  C02   180.00   0.0  0
 AXW  CONST_22  C04  C03  C02  N02   180.00   0.0  0
 AXW  CONST_23  H4   C26  C21  C22   180.00   0.0  0
 AXW  CONST_24  H2   C24  C23  C22   180.00   0.0  0
 AXW  CONST_25  H3   C25  C24  C23   180.00   0.0  0
 AXW  CONST_26  H1   C23  C24  C25   180.00   0.0  0
 AXW  CONST_27  H25  C03  C02  N01   180.00   0.0  0
 AXW  CONST_28  H26  C05  C06  N01   180.00   0.0  0
 AXW  Var_01    C2'  N1'  C5'  C4'    21.91  30.0  1
 AXW  Var_02    C3'  C2'  N1'  C5'   -37.29  30.0  1
 AXW  Var_03    C05  C06  C08  C3'   112.74  30.0  2
 AXW  Var_04    N12  C13  C21  C22   -80.79  30.0  3
 AXW  Var_05    H27  C07  C04  C03   102.74  30.0  2
 AXW  Var_06    C11  N12  C13  C21   171.03  30.0  1
 AXW  Var_07    H11  C10  O09  C4'    95.06  30.0  2
 AXW  Var_08    C10  C11  N12  C13  -172.37  30.0  1
 AXW  Var_09    O09  C10  C11  N12    61.12  30.0  1

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
 AXW  chir_01  C4'  C3'  O09  C5'  positiv
 AXW  chir_02  C3'  C4'  C08  C2'  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
 AXW  plan-1  F22  0.020
 AXW  plan-1  C22  0.020
 AXW  plan-1  C23  0.020
 AXW  plan-1  C24  0.020
 AXW  plan-1  C25  0.020
 AXW  plan-1  C26  0.020
 AXW  plan-1  C21  0.020
 AXW  plan-1  C13  0.020
 AXW  plan-1  H1   0.020
 AXW  plan-1  H2   0.020
 AXW  plan-1  H3   0.020
 AXW  plan-1  H4   0.020
 AXW  plan-2  C08  0.020
 AXW  plan-2  C06  0.020
 AXW  plan-2  N01  0.020
 AXW  plan-2  C02  0.020
 AXW  plan-2  N02  0.020
 AXW  plan-2  C03  0.020
 AXW  plan-2  C05  0.020
 AXW  plan-2  C04  0.020
 AXW  plan-2  C07  0.020
 AXW  plan-2  H25  0.020
 AXW  plan-2  H26  0.020
 AXW  plan-3  C02  0.020
 AXW  plan-3  N02  0.020
 AXW  plan-3  H23  0.020
 AXW  plan-3  H24  0.020

