# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 11:52:07 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: (2~{S})-3-phenyl-2-[[(2~{S})-1-phenylmethoxycarbonylpyrrolidin-2-yl]carbonylamino]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H]2CCCN2C(=O)OCc3ccccc3
#
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
 ZP6  ZP6  "(2S)-3-phenyl-2-[[(2S)-1-phenylmethoxycarbonylpyrrolidin-2-yl]carbonylamino]propanoic acid"  ligand  52  29  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZP6
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
 ZP6  O5   O  OC    -1  -0.586  12.2879  29.5645  -3.7391
 ZP6  C15  C  C      0   0.419  13.1361  29.1468  -4.5426
 ZP6  O4   O  O      0  -0.599  12.9951  28.9383  -5.7657
 ZP6  C14  C  CH1    0  -0.181  14.5552  28.8886  -3.9804
 ZP6  C16  C  CH2    0  -0.520  15.4360  30.1461  -4.1416
 ZP6  C17  C  CR6    0   0.152  14.9644  31.3316  -3.3518
 ZP6  C22  C  CR16   0  -0.307  14.3027  32.3914  -3.9661
 ZP6  C21  C  CR16   0  -0.241  13.8692  33.4861  -3.2294
 ZP6  C20  C  CR16   0  -0.273  14.0906  33.5360  -1.8595
 ZP6  C19  C  CR16   0  -0.239  14.7515  32.4852  -1.2348
 ZP6  C18  C  CR16   0  -0.313  15.1849  31.3957  -1.9769
 ZP6  N2   N  NH1    0  -0.630  15.1513  27.7894  -4.7053
 ZP6  C13  C  C      0   0.539  16.1368  27.0178  -4.2480
 ZP6  O3   O  O      0  -0.508  16.6232  27.1084  -3.1259
 ZP6  C12  C  CH1    0  -0.183  16.7028  25.9881  -5.2236
 ZP6  C11  C  CH2    0  -0.474  18.0746  26.4387  -5.7423
 ZP6  C10  C  CH2    0  -0.486  17.7263  27.2331  -6.9952
 ZP6  C9   C  CH2    0  -0.264  16.5910  26.4276  -7.6146
 ZP6  N1   N  NT     0  -0.527  15.9379  25.8312  -6.4475
 ZP6  C8   C  C      0   0.757  14.8857  24.9894  -6.4955
 ZP6  O2   O  O      0  -0.500  14.4224  24.4085  -5.5363
 ZP6  O1   O  O2     0  -0.479  14.4018  24.8904  -7.7394
 ZP6  C7   C  CH2    0  -0.237  13.3782  23.9236  -7.9617
 ZP6  C5   C  CR6    0   0.059  13.9132  22.5182  -7.9482
 ZP6  C6   C  CR16   0  -0.282  15.0762  22.1967  -8.6450
 ZP6  C1   C  CR16   0  -0.239  15.5524  20.8938  -8.6548
 ZP6  C4   C  CR16   0  -0.298  13.2363  21.5133  -7.2667
 ZP6  C3   C  CR16   0  -0.240  13.7053  20.2057  -7.2845
 ZP6  C2   C  CR16   0  -0.263  14.8665  19.8931  -7.9770
 ZP6  H2   H  HCH1   0   0.235  14.4929  28.6281  -2.9223
 ZP6  H3   H  HCH2   0   0.251  16.4522  29.8879  -3.8327
 ZP6  H4   H  HCH2   0   0.239  15.4824  30.3970  -5.2045
 ZP6  H5   H  HCR6   0   0.242  14.1249  32.3595  -5.0349
 ZP6  H6   H  HCR6   0   0.248  13.3588  34.3014  -3.7267
 ZP6  H7   H  HCR6   0   0.249  13.7551  34.3889  -1.2835
 ZP6  H8   H  HCR6   0   0.248  14.9344  32.5173  -0.1681
 ZP6  H9   H  HCR6   0   0.243  15.7072  30.5836  -1.4833
 ZP6  H10  H  HNH1   0   0.392  14.8020  27.6651  -5.6445
 ZP6  H11  H  HCH1   0   0.285  16.7760  25.0421  -4.6840
 ZP6  H12  H  HCH2   0   0.255  18.6638  25.5581  -6.0054
 ZP6  H13  H  HCH2   0   0.263  18.6368  27.0061  -5.0029
 ZP6  H14  H  HCH2   0   0.259  18.5665  27.3406  -7.6793
 ZP6  H15  H  HCH2   0   0.244  17.3845  28.2358  -6.7301
 ZP6  H16  H  HCH2   0   0.256  15.9015  27.0496  -8.1843
 ZP6  H17  H  HCH2   0   0.246  16.9778  25.6498  -8.2780
 ZP6  H18  H  HCH2   0   0.265  12.9830  24.1706  -8.9476
 ZP6  H19  H  HCH2   0   0.253  12.5659  24.0385  -7.2417
 ZP6  H20  H  HCR6   0   0.254  15.6179  22.9645  -9.1846
 ZP6  H21  H  HCR6   0   0.254  16.4589  20.6576  -9.1973
 ZP6  H22  H  HCR6   0   0.252  12.3361  21.7541  -6.7135
 ZP6  H23  H  HCR6   0   0.255  13.1680  19.4340  -6.7486
 ZP6  H24  H  HCR6   0   0.255  15.2373  18.8763  -7.9879

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
 ZP6  C6   C1   aromatic  1.387  0.020  1.387
 ZP6  C6   C5   aromatic  1.393  0.020  1.393
 ZP6  C1   C2   aromatic  1.390  0.020  1.390
 ZP6  C7   C5   single    1.504  0.020  1.504
 ZP6  C7   O1   single    1.425  0.020  1.425
 ZP6  C5   C4   aromatic  1.390  0.020  1.390
 ZP6  O1   C8   single    1.338  0.020  1.338
 ZP6  C2   C3   aromatic  1.388  0.020  1.388
 ZP6  C9   C10  single    1.524  0.020  1.524
 ZP6  C9   N1   single    1.464  0.020  1.464
 ZP6  C4   C3   aromatic  1.389  0.020  1.389
 ZP6  C10  C11  single    1.524  0.020  1.524
 ZP6  C8   N1   single    1.348  0.020  1.348
 ZP6  C8   O2   double    1.213  0.020  1.213
 ZP6  N1   C12  single    1.452  0.020  1.452
 ZP6  C11  C12  single    1.534  0.020  1.534
 ZP6  O4   C15  deloc     1.249  0.020  1.249
 ZP6  C12  C13  single    1.527  0.020  1.527
 ZP6  N2   C13  single    1.333  0.020  1.333
 ZP6  N2   C14  single    1.445  0.020  1.445
 ZP6  C13  O3   double    1.226  0.020  1.226
 ZP6  C15  C14  single    1.548  0.020  1.548
 ZP6  C15  O5   deloc     1.241  0.020  1.241
 ZP6  C22  C21  aromatic  1.389  0.020  1.389
 ZP6  C22  C17  aromatic  1.392  0.020  1.392
 ZP6  C16  C14  single    1.544  0.020  1.544
 ZP6  C16  C17  single    1.501  0.020  1.501
 ZP6  C21  C20  aromatic  1.389  0.020  1.389
 ZP6  C17  C18  aromatic  1.394  0.020  1.394
 ZP6  C20  C19  aromatic  1.390  0.020  1.390
 ZP6  C18  C19  aromatic  1.388  0.020  1.388
 ZP6  C14  H2   single    0.970  0.020  1.090
 ZP6  C16  H3   single    0.970  0.020  1.090
 ZP6  C16  H4   single    0.970  0.020  1.090
 ZP6  C22  H5   single    0.930  0.020  1.080
 ZP6  C21  H6   single    0.930  0.020  1.080
 ZP6  C20  H7   single    0.930  0.020  1.080
 ZP6  C19  H8   single    0.930  0.020  1.080
 ZP6  C18  H9   single    0.930  0.020  1.080
 ZP6  N2   H10  single    0.860  0.020  1.020
 ZP6  C12  H11  single    0.970  0.020  1.090
 ZP6  C11  H12  single    0.970  0.020  1.090
 ZP6  C11  H13  single    0.970  0.020  1.090
 ZP6  C10  H14  single    0.970  0.020  1.090
 ZP6  C10  H15  single    0.970  0.020  1.090
 ZP6  C9   H16  single    0.970  0.020  1.090
 ZP6  C9   H17  single    0.970  0.020  1.090
 ZP6  C7   H18  single    0.970  0.020  1.090
 ZP6  C7   H19  single    0.970  0.020  1.090
 ZP6  C6   H20  single    0.930  0.020  1.080
 ZP6  C1   H21  single    0.930  0.020  1.080
 ZP6  C4   H22  single    0.930  0.020  1.080
 ZP6  C3   H23  single    0.930  0.020  1.080
 ZP6  C2   H24  single    0.930  0.020  1.080

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
 ZP6  C14  C15  O4   115.55  3.000
 ZP6  C14  C15  O5   116.59  3.000
 ZP6  O4   C15  O5   127.83  3.000
 ZP6  H2   C14  N2   109.16  3.000
 ZP6  H2   C14  C16  109.16  3.000
 ZP6  N2   C14  C16  109.38  3.000
 ZP6  H2   C14  C15  109.85  3.000
 ZP6  C16  C14  C15  110.44  3.000
 ZP6  N2   C14  C15  108.84  3.000
 ZP6  H4   C16  H3   106.84  3.000
 ZP6  H4   C16  C17  110.11  3.000
 ZP6  H3   C16  C17  109.27  3.000
 ZP6  H4   C16  C14  108.22  3.000
 ZP6  H3   C16  C14  107.97  3.000
 ZP6  C17  C16  C14  114.16  3.000
 ZP6  C18  C17  C22  118.39  3.000
 ZP6  C18  C17  C16  120.38  3.000
 ZP6  C22  C17  C16  121.23  3.000
 ZP6  H5   C22  C21  119.67  3.000
 ZP6  H5   C22  C17  119.38  3.000
 ZP6  C21  C22  C17  120.95  3.000
 ZP6  H6   C21  C20  120.08  3.000
 ZP6  H6   C21  C22  119.80  3.000
 ZP6  C20  C21  C22  120.12  3.000
 ZP6  H7   C20  C19  120.26  3.000
 ZP6  H7   C20  C21  120.26  3.000
 ZP6  C19  C20  C21  119.48  3.000
 ZP6  H8   C19  C18  119.83  3.000
 ZP6  H8   C19  C20  120.05  3.000
 ZP6  C18  C19  C20  120.12  3.000
 ZP6  H9   C18  C19  119.67  3.000
 ZP6  H9   C18  C17  119.39  3.000
 ZP6  C19  C18  C17  120.94  3.000
 ZP6  H10  N2   C13  120.26  3.000
 ZP6  H10  N2   C14  114.67  3.000
 ZP6  C13  N2   C14  124.98  3.000
 ZP6  C12  C13  O3   119.17  3.000
 ZP6  O3   C13  N2   124.37  3.000
 ZP6  C12  C13  N2   116.44  3.000
 ZP6  H11  C12  N1   111.00  3.000
 ZP6  H11  C12  C11  111.21  3.000
 ZP6  N1   C12  C11  102.58  3.000
 ZP6  H11  C12  C13  107.06  3.000
 ZP6  C11  C12  C13  110.44  3.000
 ZP6  N1   C12  C13  114.59  3.000
 ZP6  H13  C11  H12  107.78  3.000
 ZP6  H13  C11  C10  113.88  3.000
 ZP6  H12  C11  C10  110.23  3.000
 ZP6  H13  C11  C12  112.66  3.000
 ZP6  H12  C11  C12  109.09  3.000
 ZP6  C10  C11  C12  103.11  3.000
 ZP6  H15  C10  H14  107.66  3.000
 ZP6  H15  C10  C9   110.54  3.000
 ZP6  H14  C10  C9   111.82  3.000
 ZP6  H15  C10  C11  110.53  3.000
 ZP6  H14  C10  C11  113.06  3.000
 ZP6  C9   C10  C11  103.23  3.000
 ZP6  H17  C9   H16  108.23  3.000
 ZP6  H17  C9   N1   110.59  3.000
 ZP6  H16  C9   N1   111.54  3.000
 ZP6  H17  C9   C10  111.05  3.000
 ZP6  H16  C9   C10  112.48  3.000
 ZP6  N1   C9   C10  102.92  3.000
 ZP6  C8   N1   C9   125.02  3.000
 ZP6  C8   N1   C12  120.58  3.000
 ZP6  C9   N1   C12  113.13  3.000
 ZP6  O1   C8   O2   124.14  3.000
 ZP6  O2   C8   N1   124.66  3.000
 ZP6  O1   C8   N1   111.19  3.000
 ZP6  C7   O1   C8   117.05  3.000
 ZP6  H19  C7   H18  107.63  3.000
 ZP6  H19  C7   C5   110.93  3.000
 ZP6  H18  C7   C5   110.41  3.000
 ZP6  H19  C7   O1   111.10  3.000
 ZP6  H18  C7   O1   104.33  3.000
 ZP6  C5   C7   O1   112.14  3.000
 ZP6  C4   C5   C6   118.99  3.000
 ZP6  C4   C5   C7   120.45  3.000
 ZP6  C6   C5   C7   120.54  3.000
 ZP6  H20  C6   C1   119.37  3.000
 ZP6  H20  C6   C5   120.18  3.000
 ZP6  C1   C6   C5   120.45  3.000
 ZP6  H21  C1   C2   120.04  3.000
 ZP6  H21  C1   C6   119.73  3.000
 ZP6  C2   C1   C6   120.23  3.000
 ZP6  H22  C4   C3   119.74  3.000
 ZP6  H22  C4   C5   119.61  3.000
 ZP6  C3   C4   C5   120.65  3.000
 ZP6  H23  C3   C2   120.12  3.000
 ZP6  H23  C3   C4   119.81  3.000
 ZP6  C2   C3   C4   120.06  3.000
 ZP6  H24  C2   C3   120.22  3.000
 ZP6  H24  C2   C1   120.17  3.000
 ZP6  C3   C2   C1   119.61  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
 ZP6  CONST_01  C20  C21  C22  C17     0.00   0.0  0
 ZP6  CONST_02  C20  C19  C18  C17     0.00   0.0  0
 ZP6  CONST_03  C19  C20  C21  C22     0.00   0.0  0
 ZP6  CONST_04  C19  C18  C17  C22     0.00   0.0  0
 ZP6  CONST_05  C18  C17  C22  C21     0.00   0.0  0
 ZP6  CONST_06  C18  C19  C20  C21     0.00   0.0  0
 ZP6  CONST_07  C2   C1   C6   C5      0.00   0.0  0
 ZP6  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 ZP6  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 ZP6  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 ZP6  CONST_11  C4   C5   C6   C1      0.00   0.0  0
 ZP6  CONST_12  C4   C3   C2   C1      0.00   0.0  0
 ZP6  CONST_13  C21  C22  C17  C16   180.00   0.0  0
 ZP6  CONST_14  C19  C18  C17  C16   180.00   0.0  0
 ZP6  CONST_15  C1   C6   C5   C7    180.00   0.0  0
 ZP6  CONST_16  C3   C4   C5   C7    180.00   0.0  0
 ZP6  CONST_17  H6   C21  C22  C17   180.00   0.0  0
 ZP6  CONST_18  H8   C19  C18  C17   180.00   0.0  0
 ZP6  CONST_19  H7   C20  C21  C22   180.00   0.0  0
 ZP6  CONST_20  H9   C18  C17  C22   180.00   0.0  0
 ZP6  CONST_21  H8   C19  C20  C21   180.00   0.0  0
 ZP6  CONST_22  H5   C22  C21  C20   180.00   0.0  0
 ZP6  CONST_23  H9   C18  C19  C20   180.00   0.0  0
 ZP6  CONST_24  H6   C21  C20  C19   180.00   0.0  0
 ZP6  CONST_25  H5   C22  C17  C18   180.00   0.0  0
 ZP6  CONST_26  H7   C20  C19  C18   180.00   0.0  0
 ZP6  CONST_27  H21  C1   C6   C5    180.00   0.0  0
 ZP6  CONST_28  H23  C3   C4   C5    180.00   0.0  0
 ZP6  CONST_29  H24  C2   C1   C6    180.00   0.0  0
 ZP6  CONST_30  H22  C4   C5   C6    180.00   0.0  0
 ZP6  CONST_31  H23  C3   C2   C1    180.00   0.0  0
 ZP6  CONST_32  H20  C6   C5   C4    180.00   0.0  0
 ZP6  CONST_33  H24  C2   C3   C4    180.00   0.0  0
 ZP6  CONST_34  H21  C1   C2   C3    180.00   0.0  0
 ZP6  CONST_35  H20  C6   C1   C2    180.00   0.0  0
 ZP6  CONST_36  H22  C4   C3   C2    180.00   0.0  0
 ZP6  CONST_37  C12  C13  N2   C14   180.00   0.0  0
 ZP6  CONST_38  H10  N2   C13  C12     0.00   0.0  0
 ZP6  CONST_39  O3   C13  N2   C14     0.00   0.0  0
 ZP6  CONST_40  H10  N2   C13  O3    180.00   0.0  0
 ZP6  Var_01    C10  C9   N1   C12   -10.83  30.0  1
 ZP6  Var_02    C9   C10  C11  C12   -39.08  30.0  1
 ZP6  Var_03    N1   C9   C10  C11    30.57  30.0  1
 ZP6  Var_04    C8   N1   C9   C10  -177.96  30.0  1
 ZP6  Var_05    H16  C9   N1   C12  -131.65  30.0  1
 ZP6  Var_06    H17  C9   N1   C12   107.85  30.0  1
 ZP6  Var_07    H14  C10  C11  C12  -160.09  30.0  1
 ZP6  Var_08    H15  C10  C11  C12    79.15  30.0  1
 ZP6  Var_09    H16  C9   C10  C11   150.74  30.0  1
 ZP6  Var_10    H17  C9   C10  C11   -87.79  30.0  1
 ZP6  Var_11    H12  C11  C10  C9     77.26  30.0  1
 ZP6  Var_12    H13  C11  C10  C9   -161.47  30.0  1
 ZP6  Var_13    H14  C10  C9   N1    152.42  30.0  1
 ZP6  Var_14    H15  C10  C9   N1    -87.64  30.0  1
 ZP6  Var_15    C22  C17  C16  C14  -103.54  30.0  2
 ZP6  Var_16    C18  C17  C16  C14    76.61  30.0  2
 ZP6  Var_17    O1   C8   N1   C12  -173.87  30.0  1
 ZP6  Var_18    O2   C8   N1   C12     7.05  30.0  1
 ZP6  Var_19    O1   C8   N1   C9     -7.63  30.0  1
 ZP6  Var_20    O2   C8   N1   C9    173.29  30.0  1
 ZP6  Var_21    C6   C5   C7   O1    -45.78  30.0  2
 ZP6  Var_22    C4   C5   C7   O1    135.80  30.0  2
 ZP6  Var_23    H3   C16  C17  C22   135.46  30.0  2
 ZP6  Var_24    H4   C16  C17  C22    18.41  30.0  2
 ZP6  Var_25    H3   C16  C17  C18   -44.39  30.0  2
 ZP6  Var_26    H4   C16  C17  C18  -161.44  30.0  2
 ZP6  Var_27    H16  C9   N1   C8     61.22  30.0  1
 ZP6  Var_28    H17  C9   N1   C8    -59.28  30.0  1
 ZP6  Var_29    H18  C7   C5   C6     70.11  30.0  3
 ZP6  Var_30    H19  C7   C5   C6   -170.66  30.0  3
 ZP6  Var_31    H18  C7   C5   C4   -108.31  30.0  3
 ZP6  Var_32    H19  C7   C5   C4     10.92  30.0  3
 ZP6  Var_33    C7   O1   C8   N1    173.46  30.0  1
 ZP6  Var_34    C5   C7   O1   C8    -73.14  30.0  1
 ZP6  Var_35    C7   O1   C8   O2     -7.46  30.0  1
 ZP6  Var_36    H18  C7   O1   C8    167.35  30.0  1
 ZP6  Var_37    H19  C7   O1   C8     51.65  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
 ZP6  chir_01  C14  N2  C15  C16  positiv
 ZP6  chir_02  C12  N1  C13  C11  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
 ZP6  plan-1  C16  0.020
 ZP6  plan-1  C17  0.020
 ZP6  plan-1  C22  0.020
 ZP6  plan-1  C21  0.020
 ZP6  plan-1  C20  0.020
 ZP6  plan-1  C19  0.020
 ZP6  plan-1  C18  0.020
 ZP6  plan-1  H5   0.020
 ZP6  plan-1  H6   0.020
 ZP6  plan-1  H7   0.020
 ZP6  plan-1  H8   0.020
 ZP6  plan-1  H9   0.020
 ZP6  plan-2  C7   0.020
 ZP6  plan-2  C5   0.020
 ZP6  plan-2  C6   0.020
 ZP6  plan-2  C1   0.020
 ZP6  plan-2  C4   0.020
 ZP6  plan-2  C3   0.020
 ZP6  plan-2  C2   0.020
 ZP6  plan-2  H20  0.020
 ZP6  plan-2  H21  0.020
 ZP6  plan-2  H22  0.020
 ZP6  plan-2  H23  0.020
 ZP6  plan-2  H24  0.020
 ZP6  plan-3  C14  0.020
 ZP6  plan-3  N2   0.020
 ZP6  plan-3  C13  0.020
 ZP6  plan-3  O3   0.020
 ZP6  plan-3  C12  0.020
 ZP6  plan-3  H10  0.020
 ZP6  plan-4  O5   0.020
 ZP6  plan-4  C15  0.020
 ZP6  plan-4  O4   0.020
 ZP6  plan-4  C14  0.020
 ZP6  plan-5  N1   0.020
 ZP6  plan-5  C8   0.020
 ZP6  plan-5  O2   0.020
 ZP6  plan-5  O1   0.020

