# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:19:35 2021
#   Inital geometry file: a 137 line input string
#   Ligand name: (2~{S})-~{N}-[[4-(aminomethyl)phenyl]methyl]-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H](N)Cc3ccccc3)cc1
#
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
 K73  K73  (2~{S})-~{N}-[[4-(aminomethyl)phenyl]methyl]-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]pyrrolidine-2-carboxamide  ligand  56  28  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K73
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
 K73  N    N  NH2   0  -0.793  53.8909  -12.5698  167.3841
 K73  C    C  CH2   0  -0.337  54.2513  -11.2437  166.9141
 K73  O    O  O     0  -0.487  59.9927  -13.6844  162.3642
 K73  C1   C  CR6   0   0.076  55.3395  -11.2878  165.8711
 K73  C10  C  CH2   0  -0.279  63.3060  -14.8154  163.5260
 K73  C11  C  C     0   0.593  61.2584  -15.0389  164.9779
 K73  C12  C  CH1   0  -0.211  61.6252  -16.4600  165.3838
 K73  C13  C  CH2   0  -0.524  62.1566  -16.4342  166.8346
 K73  C14  C  CR6   0   0.105  63.3819  -15.5789  166.9936
 K73  C15  C  CR16  0  -0.310  64.6495  -16.1076  166.7561
 K73  C16  C  CR16  0  -0.241  65.7814  -15.3065  166.8249
 K73  C17  C  CR16  0  -0.269  65.6627  -13.9583  167.1364
 K73  C18  C  CR16  0  -0.241  64.4060  -13.4214  167.3837
 K73  C19  C  CR16  0  -0.287  63.2773  -14.2264  167.3137
 K73  C2   C  CR16  0  -0.276  56.3799  -12.2114  165.9462
 K73  C20  C  CR16  0  -0.292  56.3697  -10.3795  163.8797
 K73  C21  C  CR16  0  -0.296  55.3481  -10.3768  164.8198
 K73  C3   C  CR16  0  -0.300  57.3995  -12.2193  165.0052
 K73  C4   C  CR6   0   0.071  57.4066  -11.3026  163.9569
 K73  C5   C  CH2   0  -0.342  58.4850  -11.3181  162.9000
 K73  C6   C  C     0   0.568  60.4072  -12.8426  163.1432
 K73  C7   C  CH1   0  -0.182  61.7594  -12.9839  163.8285
 K73  C8   C  CH2   0  -0.477  62.9025  -12.5570  162.8950
 K73  C9   C  CH2   0  -0.469  64.0342  -13.5063  163.2684
 K73  N1   N  NH1   0  -0.634  59.7775  -11.6885  163.4183
 K73  N2   N  NT    0  -0.470  62.0574  -14.3697  164.1375
 K73  N3   N  NH2   0  -0.781  60.4531  -17.2933  165.1951
 K73  O1   O  O     0  -0.505  60.2568  -14.5159  165.4583
 K73  H1   H  HNH2  0   0.353  53.2285  -12.4874  168.1442
 K73  H2   H  HNH2  0   0.343  53.4126  -13.0723  166.6471
 K73  H4   H  HCH2  0   0.239  54.6158  -10.6737  167.7745
 K73  H5   H  HCH2  0   0.213  53.4065  -10.6671  166.5132
 K73  H6   H  HCH2  0   0.246  63.1075  -15.3507  162.5932
 K73  H7   H  HCH2  0   0.262  63.8695  -15.4692  164.1860
 K73  H8   H  HCH1  0   0.260  62.4113  -16.8600  164.7414
 K73  H9   H  HCH2  0   0.247  61.3560  -16.0828  167.4909
 K73  H10  H  HCH2  0   0.256  62.3782  -17.4653  167.1209
 K73  H11  H  HCR6  0   0.250  64.7526  -17.1594  166.5133
 K73  H12  H  HCR6  0   0.253  66.7568  -15.7365  166.6360
 K73  H13  H  HCR6  0   0.253  66.5434  -13.3315  167.1925
 K73  H14  H  HCR6  0   0.253  64.3031  -12.3729  167.6330
 K73  H15  H  HCR6  0   0.246  62.3020  -13.7976  167.5124
 K73  H16  H  HCR6  0   0.243  56.3878  -12.9354  166.7508
 K73  H17  H  HCR6  0   0.247  56.3547   -9.6531  163.0751
 K73  H18  H  HCR6  0   0.245  54.5493   -9.6491  164.7326
 K73  H19  H  HCR6  0   0.269  58.2001  -12.9437  165.0985
 K73  H20  H  HCH2  0   0.262  58.5497  -10.3355  162.4273
 K73  H21  H  HCH2  0   0.267  58.2260  -12.0256  162.1115
 K73  H22  H  HCH1  0   0.270  61.7784  -12.3869  164.7470
 K73  H23  H  HCH2  0   0.265  63.1543  -11.5058  163.0244
 K73  H24  H  HCH2  0   0.250  62.6206  -12.7092  161.8507
 K73  H25  H  HCH2  0   0.256  64.7890  -13.5971  162.4886
 K73  H26  H  HCH2  0   0.245  64.5276  -13.1751  164.1849
 K73  H27  H  HNH1  0   0.400  60.1860  -11.0761  164.1066
 K73  H28  H  HNH2  0   0.353  60.6808  -18.2476  165.4448
 K73  H29  H  HNH2  0   0.343  59.7184  -17.0000  165.8280

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
 K73  O    C6   double    1.219  0.020  1.219
 K73  C8   C9   single    1.524  0.020  1.524
 K73  C8   C7   single    1.536  0.020  1.536
 K73  C5   N1   single    1.441  0.020  1.441
 K73  C5   C4   single    1.510  0.020  1.510
 K73  C9   C10  single    1.520  0.020  1.520
 K73  C6   N1   single    1.343  0.020  1.343
 K73  C6   C7   single    1.523  0.020  1.523
 K73  C10  N2   single    1.460  0.020  1.460
 K73  C7   N2   single    1.451  0.020  1.451
 K73  C4   C3   aromatic  1.393  0.020  1.393
 K73  C4   C20  aromatic  1.390  0.020  1.390
 K73  N2   C11  single    1.339  0.020  1.339
 K73  C3   C2   aromatic  1.387  0.020  1.387
 K73  C20  C21  aromatic  1.388  0.020  1.388
 K73  C11  O1   double    1.228  0.020  1.228
 K73  C11  C12  single    1.523  0.020  1.523
 K73  C2   C1   aromatic  1.393  0.020  1.393
 K73  C21  C1   aromatic  1.391  0.020  1.391
 K73  N3   C12  single    1.450  0.020  1.450
 K73  C12  C13  single    1.545  0.020  1.545
 K73  C1   C    single    1.508  0.020  1.508
 K73  C15  C16  aromatic  1.388  0.020  1.388
 K73  C15  C14  aromatic  1.394  0.020  1.394
 K73  C16  C17  aromatic  1.389  0.020  1.389
 K73  N    C    single    1.452  0.020  1.452
 K73  C13  C14  single    1.503  0.020  1.503
 K73  C14  C19  aromatic  1.394  0.020  1.394
 K73  C17  C18  aromatic  1.389  0.020  1.389
 K73  C19  C18  aromatic  1.388  0.020  1.388
 K73  N    H1   single    0.890  0.020  1.040
 K73  N    H2   single    0.890  0.020  1.040
 K73  C    H4   single    0.970  0.020  1.090
 K73  C    H5   single    0.970  0.020  1.090
 K73  C10  H6   single    0.970  0.020  1.090
 K73  C10  H7   single    0.970  0.020  1.090
 K73  C12  H8   single    0.970  0.020  1.090
 K73  C13  H9   single    0.970  0.020  1.090
 K73  C13  H10  single    0.970  0.020  1.090
 K73  C15  H11  single    0.930  0.020  1.080
 K73  C16  H12  single    0.930  0.020  1.080
 K73  C17  H13  single    0.930  0.020  1.080
 K73  C18  H14  single    0.930  0.020  1.080
 K73  C19  H15  single    0.930  0.020  1.080
 K73  C2   H16  single    0.930  0.020  1.080
 K73  C20  H17  single    0.930  0.020  1.080
 K73  C21  H18  single    0.930  0.020  1.080
 K73  C3   H19  single    0.930  0.020  1.080
 K73  C5   H20  single    0.970  0.020  1.090
 K73  C5   H21  single    0.970  0.020  1.090
 K73  C7   H22  single    0.970  0.020  1.090
 K73  C8   H23  single    0.970  0.020  1.090
 K73  C8   H24  single    0.970  0.020  1.090
 K73  C9   H25  single    0.970  0.020  1.090
 K73  C9   H26  single    0.970  0.020  1.090
 K73  N1   H27  single    0.860  0.020  1.020
 K73  N3   H28  single    0.890  0.020  1.040
 K73  N3   H29  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
 K73  H2   N    H1   106.14  3.000
 K73  H2   N    C    109.57  3.000
 K73  H1   N    C    109.34  3.000
 K73  H5   C    H4   105.64  3.000
 K73  H5   C    C1   108.53  3.000
 K73  H4   C    C1   108.58  3.000
 K73  H5   C    N    113.99  3.000
 K73  H4   C    N    107.69  3.000
 K73  C1   C    N    112.10  3.000
 K73  C21  C1   C2   118.05  3.000
 K73  C21  C1   C    120.53  3.000
 K73  C2   C1   C    121.40  3.000
 K73  H7   C10  H6   108.52  3.000
 K73  H7   C10  N2   111.89  3.000
 K73  H6   C10  N2   110.58  3.000
 K73  H7   C10  C9   111.88  3.000
 K73  H6   C10  C9   111.35  3.000
 K73  N2   C10  C9   102.58  3.000
 K73  O1   C11  N2   121.30  3.000
 K73  O1   C11  C12  119.32  3.000
 K73  N2   C11  C12  119.34  3.000
 K73  H8   C12  N3   107.16  3.000
 K73  H8   C12  C13  108.12  3.000
 K73  N3   C12  C13  114.18  3.000
 K73  H8   C12  C11  111.02  3.000
 K73  C13  C12  C11  108.51  3.000
 K73  N3   C12  C11  107.87  3.000
 K73  H10  C13  H9   107.13  3.000
 K73  H10  C13  C14  110.12  3.000
 K73  H9   C13  C14  110.53  3.000
 K73  H10  C13  C12  107.45  3.000
 K73  H9   C13  C12  108.49  3.000
 K73  C14  C13  C12  112.91  3.000
 K73  C19  C14  C15  118.39  3.000
 K73  C19  C14  C13  121.03  3.000
 K73  C15  C14  C13  120.50  3.000
 K73  H11  C15  C16  119.55  3.000
 K73  H11  C15  C14  119.51  3.000
 K73  C16  C15  C14  120.94  3.000
 K73  H12  C16  C17  120.11  3.000
 K73  H12  C16  C15  119.79  3.000
 K73  C17  C16  C15  120.10  3.000
 K73  H13  C17  C18  120.21  3.000
 K73  H13  C17  C16  120.28  3.000
 K73  C18  C17  C16  119.51  3.000
 K73  H14  C18  C19  119.73  3.000
 K73  H14  C18  C17  120.10  3.000
 K73  C19  C18  C17  120.17  3.000
 K73  H15  C19  C18  119.54  3.000
 K73  H15  C19  C14  119.57  3.000
 K73  C18  C19  C14  120.88  3.000
 K73  H16  C2   C3   119.67  3.000
 K73  H16  C2   C1   119.27  3.000
 K73  C3   C2   C1   121.06  3.000
 K73  H17  C20  C4   119.76  3.000
 K73  H17  C20  C21  119.41  3.000
 K73  C4   C20  C21  120.82  3.000
 K73  H18  C21  C20  119.27  3.000
 K73  H18  C21  C1   119.73  3.000
 K73  C20  C21  C1   121.00  3.000
 K73  H19  C3   C4   120.07  3.000
 K73  H19  C3   C2   119.23  3.000
 K73  C4   C3   C2   120.70  3.000
 K73  C5   C4   C3   121.59  3.000
 K73  C3   C4   C20  118.36  3.000
 K73  C5   C4   C20  120.03  3.000
 K73  H21  C5   H20  106.55  3.000
 K73  H21  C5   N1   107.84  3.000
 K73  H20  C5   N1   109.50  3.000
 K73  H21  C5   C4   110.07  3.000
 K73  H20  C5   C4   109.63  3.000
 K73  N1   C5   C4   113.04  3.000
 K73  N1   C6   C7   113.82  3.000
 K73  C7   C6   O    121.69  3.000
 K73  N1   C6   O    124.38  3.000
 K73  H22  C7   N2   109.77  3.000
 K73  H22  C7   C8   110.19  3.000
 K73  N2   C7   C8   104.00  3.000
 K73  H22  C7   C6   110.01  3.000
 K73  N2   C7   C6   111.53  3.000
 K73  C8   C7   C6   111.20  3.000
 K73  H24  C8   H23  107.93  3.000
 K73  H24  C8   C9   109.83  3.000
 K73  H23  C8   C9   113.62  3.000
 K73  H24  C8   C7   110.49  3.000
 K73  H23  C8   C7   111.60  3.000
 K73  C9   C8   C7   103.34  3.000
 K73  H26  C9   H25  108.24  3.000
 K73  H26  C9   C8   110.62  3.000
 K73  H25  C9   C8   113.03  3.000
 K73  H26  C9   C10  109.60  3.000
 K73  H25  C9   C10  112.43  3.000
 K73  C8   C9   C10  102.84  3.000
 K73  H27  N1   C6   118.17  3.000
 K73  H27  N1   C5   116.93  3.000
 K73  C6   N1   C5   124.59  3.000
 K73  C7   N2   C11  119.25  3.000
 K73  C11  N2   C10  128.37  3.000
 K73  C7   N2   C10  112.21  3.000
 K73  H29  N3   H28  106.37  3.000
 K73  H29  N3   C12  109.78  3.000
 K73  H28  N3   C12  109.13  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
 K73  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 K73  CONST_02  C4   C20  C21  C1     0.00   0.0  0
 K73  CONST_03  C17  C16  C15  C14    0.00   0.0  0
 K73  CONST_04  C17  C18  C19  C14    0.00   0.0  0
 K73  CONST_05  C18  C17  C16  C15    0.00   0.0  0
 K73  CONST_06  C18  C19  C14  C15    0.00   0.0  0
 K73  CONST_07  C19  C14  C15  C16    0.00   0.0  0
 K73  CONST_08  C19  C18  C17  C16    0.00   0.0  0
 K73  CONST_09  C20  C4   C3   C2     0.00   0.0  0
 K73  CONST_10  C20  C21  C1   C2     0.00   0.0  0
 K73  CONST_11  C3   C4   C20  C21    0.00   0.0  0
 K73  CONST_12  C3   C2   C1   C21    0.00   0.0  0
 K73  CONST_13  C3   C2   C1   C    180.00   0.0  0
 K73  CONST_14  C20  C21  C1   C    180.00   0.0  0
 K73  CONST_15  C16  C15  C14  C13  180.00   0.0  0
 K73  CONST_16  C18  C19  C14  C13  180.00   0.0  0
 K73  CONST_17  C5   C4   C3   C2   180.00   0.0  0
 K73  CONST_18  C5   C4   C20  C21  180.00   0.0  0
 K73  CONST_19  H19  C3   C2   C1   180.00   0.0  0
 K73  CONST_20  H17  C20  C21  C1   180.00   0.0  0
 K73  CONST_21  H12  C16  C15  C14  180.00   0.0  0
 K73  CONST_22  H14  C18  C19  C14  180.00   0.0  0
 K73  CONST_23  H13  C17  C16  C15  180.00   0.0  0
 K73  CONST_24  H15  C19  C14  C15  180.00   0.0  0
 K73  CONST_25  H11  C15  C16  C17  180.00   0.0  0
 K73  CONST_26  H18  C21  C1   C2   180.00   0.0  0
 K73  CONST_27  H16  C2   C1   C21  180.00   0.0  0
 K73  CONST_28  O1   C11  N2   C10  180.00   0.0  0
 K73  CONST_29  C12  C11  N2   C10    0.00   0.0  0
 K73  CONST_30  C7   N2   C11  C12  180.00   0.0  0
 K73  CONST_31  O1   C11  N2   C7     0.00   0.0  0
 K73  CONST_32  C7   C6   N1   C5   180.00   0.0  0
 K73  CONST_33  H27  N1   C6   C7     0.00   0.0  0
 K73  CONST_34  C5   N1   C6   O      0.00   0.0  0
 K73  Var_01    C7   C8   C9   C10   37.76  30.0  1
 K73  Var_02    C9   C10  N2   C7    21.15  30.0  1
 K73  Var_03    N2   C10  C9   C8   -35.87  30.0  1
 K73  Var_04    C2   C1   C    N    -36.79  30.0  2
 K73  Var_05    C15  C14  C13  C12  -86.31  30.0  2
 K73  Var_06    N1   C5   C4   C20  146.41  30.0  3
 K73  Var_07    C6   N1   C5   C4   110.46  30.0  3
 K73  Var_08    H1   N    C    C1   174.37  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
 K73  chir_01  C12  C11  N3  C13  positiv
 K73  chir_02  C7   N2   C6  C8   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
 K73  plan-1  C13  0.020
 K73  plan-1  C14  0.020
 K73  plan-1  C15  0.020
 K73  plan-1  C16  0.020
 K73  plan-1  C17  0.020
 K73  plan-1  C18  0.020
 K73  plan-1  C19  0.020
 K73  plan-1  H11  0.020
 K73  plan-1  H12  0.020
 K73  plan-1  H13  0.020
 K73  plan-1  H14  0.020
 K73  plan-1  H15  0.020
 K73  plan-2  C    0.020
 K73  plan-2  C1   0.020
 K73  plan-2  C2   0.020
 K73  plan-2  C20  0.020
 K73  plan-2  C21  0.020
 K73  plan-2  C3   0.020
 K73  plan-2  C4   0.020
 K73  plan-2  C5   0.020
 K73  plan-2  H16  0.020
 K73  plan-2  H17  0.020
 K73  plan-2  H18  0.020
 K73  plan-2  H19  0.020
 K73  plan-3  O    0.020
 K73  plan-3  C5   0.020
 K73  plan-3  C6   0.020
 K73  plan-3  C7   0.020
 K73  plan-3  N1   0.020
 K73  plan-3  H27  0.020
 K73  plan-4  C10  0.020
 K73  plan-4  C11  0.020
 K73  plan-4  C12  0.020
 K73  plan-4  C7   0.020
 K73  plan-4  N2   0.020
 K73  plan-4  O1   0.020

