# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:34:17 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: (3S)-N-benzylpyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@@H](CN1)NCc2ccccc2
#
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
 WM7  WM7  (3S)-N-benzylpyrrolidin-3-amine  ligand  29  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WM7
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
 WM7  C10  C  CR16  0  -0.241  -35.1405  21.8299  -3.7263
 WM7  C13  C  CR16  0  -0.315  -34.4913  22.9089  -1.2606
 WM7  C01  C  CH2   0  -0.320  -36.4608  21.7840  -0.1638
 WM7  C03  C  CR15  0  -0.110  -38.7482  21.5346   0.6410
 WM7  C04  C  CH2   0  -0.497  -38.6969  22.4232   1.9028
 WM7  C05  C  CH2   0  -0.309  -39.8971  23.3928   1.7532
 WM7  C07  C  CH2   0  -0.330  -40.2154  21.6810   0.2240
 WM7  C08  C  CR6   0   0.093  -35.6154  22.0965  -1.3712
 WM7  C09  C  CR16  0  -0.290  -35.9340  21.5640  -2.6200
 WM7  C11  C  CR16  0  -0.272  -34.0157  22.6384  -3.6038
 WM7  C12  C  CR16  0  -0.241  -33.6933  23.1778  -2.3668
 WM7  N02  N  NH1   0  -0.587  -37.8723  21.9410  -0.4478
 WM7  N06  N  NR15  0  -0.589  -40.5816  23.0635   0.5007
 WM7  H1   H  HCR6  0   0.252  -35.3992  21.4059  -4.6885
 WM7  H2   H  HCR6  0   0.247  -34.2360  23.3383  -0.2986
 WM7  H3   H  HCH2  0   0.237  -36.2974  20.7412   0.1297
 WM7  H4   H  HCH2  0   0.213  -36.1064  22.3904   0.6831
 WM7  H5   H  HCR5  0   0.235  -38.5049  20.4954   0.8783
 WM7  H7   H  HCH2  0   0.241  -37.7454  22.9506   1.9882
 WM7  H8   H  HCH2  0   0.234  -39.5943  24.4397   1.7500
 WM7  H9   H  HCH2  0   0.221  -40.5866  23.2634   2.5910
 WM7  H10  H  HCH2  0   0.239  -40.3859  21.4262  -0.8227
 WM7  H11  H  HCH2  0   0.228  -40.8347  21.0161   0.8346
 WM7  H12  H  HCR6  0   0.244  -36.8128  20.9399  -2.7235
 WM7  H13  H  HCR6  0   0.253  -33.3978  22.8466  -4.4679
 WM7  H14  H  HCR6  0   0.253  -32.8234  23.8136  -2.2608
 WM7  H15  H  HNH1  0   0.334  -38.0517  22.9076  -0.6974
 WM7  H17  H  HNR5  0   0.342  -40.2250  23.6540  -0.2400
 WM7  H6   H  HCH2  0   0.236  -38.8021  21.8159   2.8035

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
 WM7  C10  C11  aromatic  1.391  0.020  1.391
 WM7  C10  C09  aromatic  1.387  0.020  1.387
 WM7  C11  C12  aromatic  1.388  0.020  1.388
 WM7  C09  C08  aromatic  1.394  0.020  1.394
 WM7  C12  C13  aromatic  1.390  0.020  1.390
 WM7  C08  C13  aromatic  1.391  0.020  1.391
 WM7  C08  C01  single    1.507  0.020  1.507
 WM7  N02  C01  single    1.448  0.020  1.448
 WM7  N02  C03  single    1.455  0.020  1.455
 WM7  C07  C03  single    1.532  0.020  1.532
 WM7  C07  N06  single    1.457  0.020  1.457
 WM7  C03  C04  single    1.544  0.020  1.544
 WM7  N06  C05  single    1.465  0.020  1.465
 WM7  C05  C04  single    1.550  0.020  1.550
 WM7  C10  H1   single    0.930  0.020  1.080
 WM7  C13  H2   single    0.930  0.020  1.080
 WM7  C01  H3   single    0.970  0.020  1.090
 WM7  C01  H4   single    0.970  0.020  1.090
 WM7  C03  H5   single    0.970  0.020  1.090
 WM7  C04  H6   single    0.970  0.020  1.090
 WM7  C04  H7   single    0.970  0.020  1.090
 WM7  C05  H8   single    0.970  0.020  1.090
 WM7  C05  H9   single    0.970  0.020  1.090
 WM7  C07  H10  single    0.970  0.020  1.090
 WM7  C07  H11  single    0.970  0.020  1.090
 WM7  C09  H12  single    0.930  0.020  1.080
 WM7  C11  H13  single    0.930  0.020  1.080
 WM7  C12  H14  single    0.930  0.020  1.080
 WM7  N02  H15  single    0.890  0.020  1.040
 WM7  N06  H17  single    0.890  0.020  1.040

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
 WM7  H1   C10  C11  119.95  3.000
 WM7  H1   C10  C09  119.80  3.000
 WM7  C11  C10  C09  120.25  3.000
 WM7  H2   C13  C12  119.63  3.000
 WM7  H2   C13  C08  119.48  3.000
 WM7  C12  C13  C08  120.90  3.000
 WM7  H4   C01  H3   105.69  3.000
 WM7  H4   C01  N02  113.90  3.000
 WM7  H3   C01  N02  107.52  3.000
 WM7  H4   C01  C08  108.77  3.000
 WM7  H3   C01  C08  109.17  3.000
 WM7  N02  C01  C08  111.54  3.000
 WM7  H5   C03  N02  107.09  3.000
 WM7  H5   C03  C07  111.28  3.000
 WM7  N02  C03  C07  110.24  3.000
 WM7  H5   C03  C04  111.24  3.000
 WM7  C07  C03  C04  101.49  3.000
 WM7  N02  C03  C04  115.51  3.000
 WM7  H7   C04  H6   106.76  3.000
 WM7  H7   C04  C05  112.35  3.000
 WM7  H6   C04  C05  110.68  3.000
 WM7  H7   C04  C03  111.78  3.000
 WM7  H6   C04  C03  110.55  3.000
 WM7  C05  C04  C03  104.79  3.000
 WM7  H9   C05  H8   106.93  3.000
 WM7  H9   C05  N06  109.52  3.000
 WM7  H8   C05  N06  110.08  3.000
 WM7  H9   C05  C04  109.90  3.000
 WM7  H8   C05  C04  112.71  3.000
 WM7  N06  C05  C04  107.68  3.000
 WM7  H11  C07  H10  107.75  3.000
 WM7  H11  C07  N06  109.16  3.000
 WM7  H10  C07  N06  111.39  3.000
 WM7  H11  C07  C03  109.38  3.000
 WM7  H10  C07  C03  112.87  3.000
 WM7  N06  C07  C03  106.24  3.000
 WM7  C09  C08  C01  120.68  3.000
 WM7  C01  C08  C13  120.71  3.000
 WM7  C09  C08  C13  118.60  3.000
 WM7  H12  C09  C08  119.41  3.000
 WM7  H12  C09  C10  119.90  3.000
 WM7  C08  C09  C10  120.69  3.000
 WM7  H13  C11  C12  120.28  3.000
 WM7  H13  C11  C10  120.21  3.000
 WM7  C12  C11  C10  119.51  3.000
 WM7  H14  C12  C11  120.15  3.000
 WM7  H14  C12  C13  119.80  3.000
 WM7  C11  C12  C13  120.05  3.000
 WM7  H15  N02  C03  110.11  3.000
 WM7  H15  N02  C01  108.90  3.000
 WM7  C03  N02  C01  114.18  3.000
 WM7  H17  N06  C07  109.03  3.000
 WM7  H17  N06  C05  109.26  3.000
 WM7  C07  N06  C05  104.97  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
 WM7  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 WM7  CONST_02  C13  C08  C09  C10    0.00   0.0  0
 WM7  CONST_03  C11  C10  C09  C08    0.00   0.0  0
 WM7  CONST_04  C11  C12  C13  C08    0.00   0.0  0
 WM7  CONST_05  C12  C11  C10  C09    0.00   0.0  0
 WM7  CONST_06  C12  C13  C08  C09    0.00   0.0  0
 WM7  CONST_07  C01  C08  C09  C10  180.00   0.0  0
 WM7  CONST_08  C12  C13  C08  C01  180.00   0.0  0
 WM7  CONST_09  H14  C12  C11  C10  180.00   0.0  0
 WM7  CONST_10  H13  C11  C12  C13  180.00   0.0  0
 WM7  CONST_11  H12  C09  C08  C13  180.00   0.0  0
 WM7  CONST_12  H1   C10  C09  C08  180.00   0.0  0
 WM7  CONST_13  H2   C13  C08  C09  180.00   0.0  0
 WM7  Var_01    C05  N06  C07  C03  -38.00  30.0  1
 WM7  Var_02    N06  C05  C04  C03    0.47  30.0  1
 WM7  Var_03    C07  N06  C05  C04   22.82  30.0  1
 WM7  Var_04    N02  C01  C08  C13  133.67  30.0  2
 WM7  Var_05    C08  C01  N02  C03  174.60  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
 WM7  chir_01  C03  N02  C07  C04  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
 WM7  plan-1  C10  0.020
 WM7  plan-1  C13  0.020
 WM7  plan-1  C01  0.020
 WM7  plan-1  C08  0.020
 WM7  plan-1  C09  0.020
 WM7  plan-1  C11  0.020
 WM7  plan-1  C12  0.020
 WM7  plan-1  H1   0.020
 WM7  plan-1  H2   0.020
 WM7  plan-1  H12  0.020
 WM7  plan-1  H13  0.020
 WM7  plan-1  H14  0.020

