# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 17:08:26 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-1-heptanoylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc2ccccc2)C(O)=O
#
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
 OPF  OPF  '(2~{S})-2-[[(2~{S})-1-heptanoylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid'  ligand  56  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OPF
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
 OPF  O54  O  OC    -1  -0.598  32.9406  28.8615   6.1444
 OPF  C55  C  C      0   0.419  33.0198  29.0039   4.9061
 OPF  O53  O  O      0  -0.585  34.0295  29.2696   4.2354
 OPF  C56  C  CH1    0  -0.180  31.6883  28.8705   4.1270
 OPF  C36  C  CH2    0  -0.524  31.0236  30.2518   3.9507
 OPF  C35  C  CR6    0   0.156  31.7693  31.1785   3.0359
 OPF  C34  C  CR16   0  -0.311  31.7245  30.9872   1.6556
 OPF  C33  C  CR16   0  -0.239  32.4075  31.8341   0.7943
 OPF  C32  C  CR16   0  -0.274  33.1474  32.8954   1.3018
 OPF  C31  C  CR16   0  -0.242  33.1956  33.0994   2.6744
 OPF  C30  C  CR16   0  -0.308  32.5119  32.2465   3.5312
 OPF  N52  N  NH1    0  -0.630  30.8083  27.9907   4.8602
 OPF  C51  C  C      0   0.538  29.8083  27.2977   4.3180
 OPF  O49  O  O      0  -0.511  29.5050  27.3445   3.1303
 OPF  C50  C  CH1    0  -0.172  28.9806  26.4304   5.2645
 OPF  C48  C  CH2    0  -0.481  27.6453  27.1088   5.5995
 OPF  C47  C  CH2    0  -0.476  27.9571  27.8835   6.8743
 OPF  C46  C  CH2    0  -0.278  28.8677  26.9304   7.6380
 OPF  N45  N  NT     0  -0.496  29.5745  26.2194   6.5732
 OPF  C44  C  C      0   0.553  30.5824  25.3351   6.7466
 OPF  O43  O  O      0  -0.488  31.0988  24.7699   5.7922
 OPF  C42  C  CH2    0  -0.597  31.0478  25.1223   8.1719
 OPF  C41  C  CH2    0  -0.413  31.8928  23.8724   8.3702
 OPF  C40  C  CH2    0  -0.412  31.1092  22.5749   8.2149
 OPF  C39  C  CH2    0  -0.405  31.9494  21.3356   8.4921
 OPF  C38  C  CH2    0  -0.416  31.1783  20.0355   8.3059
 OPF  C37  C  CH3    0  -0.659  32.0203  18.8009   8.5949
 OPF  H2   H  HCH1   0   0.235  31.8802  28.4419   3.1406
 OPF  H3   H  HCH2   0   0.240  30.9037  30.7095   4.9361
 OPF  H4   H  HCH2   0   0.252  30.0172  30.0925   3.5544
 OPF  H5   H  HCR6   0   0.242  31.1432  30.1659   1.2510
 OPF  H6   H  HCR6   0   0.248  32.3581  31.6696  -0.2747
 OPF  H7   H  HCR6   0   0.249  33.6787  33.5597   0.6324
 OPF  H8   H  HCR6   0   0.248  33.7669  33.9250   3.0799
 OPF  H9   H  HCR6   0   0.241  32.5564  32.4129   4.6013
 OPF  H10  H  HNH1   0   0.391  31.0274  27.9026   5.8422
 OPF  H11  H  HCH1   0   0.279  28.8212  25.4784   4.7541
 OPF  H12  H  HCH2   0   0.262  27.2770  27.7313   4.7854
 OPF  H13  H  HCH2   0   0.254  26.8914  26.3437   5.7952
 OPF  H14  H  HCH2   0   0.243  28.4857  28.8095   6.6393
 OPF  H15  H  HCH2   0   0.258  27.0681  28.1450   7.4461
 OPF  H16  H  HCH2   0   0.247  28.2832  26.2347   8.2471
 OPF  H17  H  HCH2   0   0.259  29.5616  27.4526   8.2973
 OPF  H18  H  HCH2   0   0.280  31.6191  26.0117   8.4622
 OPF  H19  H  HCH2   0   0.257  30.1885  25.0971   8.8477
 OPF  H20  H  HCH2   0   0.225  32.3178  23.9116   9.3769
 OPF  H21  H  HCH2   0   0.219  32.7423  23.8796   7.6828
 OPF  H22  H  HCH2   0   0.205  30.2500  22.5889   8.8950
 OPF  H23  H  HCH2   0   0.216  30.6960  22.5090   7.2049
 OPF  H24  H  HCH2   0   0.206  32.8241  21.3339   7.8319
 OPF  H25  H  HCH2   0   0.205  32.3425  21.3812   9.5137
 OPF  H26  H  HCH2   0   0.209  30.7956  19.9878   7.2818
 OPF  H27  H  HCH2   0   0.209  30.2982  20.0403   8.9564
 OPF  H28  H  HCH3   0   0.224  31.4499  17.8823   8.4530
 OPF  H29  H  HCH3   0   0.214  32.8897  18.7550   7.9364
 OPF  H30  H  HCH3   0   0.214  32.3876  18.8065   9.6227

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
 OPF  C33  C34  aromatic  1.388  0.020  1.388
 OPF  C33  C32  aromatic  1.390  0.020  1.390
 OPF  C34  C35  aromatic  1.394  0.020  1.394
 OPF  C32  C31  aromatic  1.388  0.020  1.388
 OPF  O49  C51  double    1.227  0.020  1.227
 OPF  C35  C30  aromatic  1.392  0.020  1.392
 OPF  C35  C36  single    1.501  0.020  1.501
 OPF  C31  C30  aromatic  1.389  0.020  1.389
 OPF  O53  C55  deloc     1.241  0.020  1.241
 OPF  C56  C36  single    1.543  0.020  1.543
 OPF  C56  C55  single    1.549  0.020  1.549
 OPF  C56  N52  single    1.444  0.020  1.444
 OPF  C51  N52  single    1.332  0.020  1.332
 OPF  C51  C50  single    1.527  0.020  1.527
 OPF  C55  O54  deloc     1.249  0.020  1.249
 OPF  C50  C48  single    1.535  0.020  1.535
 OPF  C50  N45  single    1.453  0.020  1.453
 OPF  C48  C47  single    1.524  0.020  1.524
 OPF  O43  C44  double    1.224  0.020  1.224
 OPF  N45  C44  single    1.352  0.020  1.352
 OPF  N45  C46  single    1.463  0.020  1.463
 OPF  C44  C42  single    1.514  0.020  1.514
 OPF  C47  C46  single    1.523  0.020  1.523
 OPF  C40  C41  single    1.524  0.020  1.524
 OPF  C40  C39  single    1.523  0.020  1.523
 OPF  C42  C41  single    1.522  0.020  1.522
 OPF  C37  C38  single    1.522  0.020  1.522
 OPF  C38  C39  single    1.523  0.020  1.523
 OPF  C56  H2   single    0.970  0.020  1.090
 OPF  C36  H3   single    0.970  0.020  1.090
 OPF  C36  H4   single    0.970  0.020  1.090
 OPF  C34  H5   single    0.930  0.020  1.080
 OPF  C33  H6   single    0.930  0.020  1.080
 OPF  C32  H7   single    0.930  0.020  1.080
 OPF  C31  H8   single    0.930  0.020  1.080
 OPF  C30  H9   single    0.930  0.020  1.080
 OPF  N52  H10  single    0.860  0.020  1.020
 OPF  C50  H11  single    0.970  0.020  1.090
 OPF  C48  H12  single    0.970  0.020  1.090
 OPF  C48  H13  single    0.970  0.020  1.090
 OPF  C47  H14  single    0.970  0.020  1.090
 OPF  C47  H15  single    0.970  0.020  1.090
 OPF  C46  H16  single    0.970  0.020  1.090
 OPF  C46  H17  single    0.970  0.020  1.090
 OPF  C42  H18  single    0.970  0.020  1.090
 OPF  C42  H19  single    0.970  0.020  1.090
 OPF  C41  H20  single    0.970  0.020  1.090
 OPF  C41  H21  single    0.970  0.020  1.090
 OPF  C40  H22  single    0.970  0.020  1.090
 OPF  C40  H23  single    0.970  0.020  1.090
 OPF  C39  H24  single    0.970  0.020  1.090
 OPF  C39  H25  single    0.970  0.020  1.090
 OPF  C38  H26  single    0.970  0.020  1.090
 OPF  C38  H27  single    0.970  0.020  1.090
 OPF  C37  H28  single    0.970  0.020  1.090
 OPF  C37  H29  single    0.970  0.020  1.090
 OPF  C37  H30  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
 OPF  C56  C55  O53  116.50  3.000
 OPF  C56  C55  O54  115.75  3.000
 OPF  O53  C55  O54  127.73  3.000
 OPF  H2   C56  N52  109.05  3.000
 OPF  H2   C56  C36  108.89  3.000
 OPF  N52  C56  C36  109.93  3.000
 OPF  H2   C56  C55  109.70  3.000
 OPF  N52  C56  C55  108.72  3.000
 OPF  C36  C56  C55  110.54  3.000
 OPF  H4   C36  H3   106.66  3.000
 OPF  H4   C36  C35  109.05  3.000
 OPF  H3   C36  C35  110.21  3.000
 OPF  H4   C36  C56  107.91  3.000
 OPF  H3   C36  C56  108.61  3.000
 OPF  C35  C36  C56  114.11  3.000
 OPF  C30  C35  C34  118.34  3.000
 OPF  C30  C35  C36  121.47  3.000
 OPF  C34  C35  C36  120.19  3.000
 OPF  H5   C34  C33  119.64  3.000
 OPF  H5   C34  C35  119.37  3.000
 OPF  C33  C34  C35  120.99  3.000
 OPF  H6   C33  C32  120.06  3.000
 OPF  H6   C33  C34  119.84  3.000
 OPF  C32  C33  C34  120.10  3.000
 OPF  H7   C32  C31  120.27  3.000
 OPF  H7   C32  C33  120.27  3.000
 OPF  C31  C32  C33  119.45  3.000
 OPF  H8   C31  C30  119.79  3.000
 OPF  H8   C31  C32  120.04  3.000
 OPF  C30  C31  C32  120.16  3.000
 OPF  H9   C30  C31  119.64  3.000
 OPF  H9   C30  C35  119.41  3.000
 OPF  C31  C30  C35  120.95  3.000
 OPF  H10  N52  C51  120.88  3.000
 OPF  H10  N52  C56  114.49  3.000
 OPF  C51  N52  C56  124.59  3.000
 OPF  C50  C51  O49  119.19  3.000
 OPF  C50  C51  N52  116.75  3.000
 OPF  O49  C51  N52  124.04  3.000
 OPF  H11  C50  N45  110.74  3.000
 OPF  H11  C50  C48  111.13  3.000
 OPF  N45  C50  C48  102.90  3.000
 OPF  H11  C50  C51  106.53  3.000
 OPF  N45  C50  C51  114.78  3.000
 OPF  C48  C50  C51  110.84  3.000
 OPF  H13  C48  H12  107.51  3.000
 OPF  H13  C48  C47  110.34  3.000
 OPF  H12  C48  C47  113.83  3.000
 OPF  H13  C48  C50  109.28  3.000
 OPF  H12  C48  C50  112.57  3.000
 OPF  C47  C48  C50  103.26  3.000
 OPF  H15  C47  H14  107.73  3.000
 OPF  H15  C47  C46  112.03  3.000
 OPF  H14  C47  C46  110.44  3.000
 OPF  H15  C47  C48  113.22  3.000
 OPF  H14  C47  C48  110.49  3.000
 OPF  C46  C47  C48  102.92  3.000
 OPF  H17  C46  H16  107.94  3.000
 OPF  H17  C46  N45  111.44  3.000
 OPF  H16  C46  N45  110.76  3.000
 OPF  H17  C46  C47  112.57  3.000
 OPF  H16  C46  C47  110.96  3.000
 OPF  N45  C46  C47  103.18  3.000
 OPF  C44  N45  C46  125.79  3.000
 OPF  C46  N45  C50  112.82  3.000
 OPF  C44  N45  C50  121.02  3.000
 OPF  C42  C44  O43  122.66  3.000
 OPF  C42  C44  N45  116.21  3.000
 OPF  O43  C44  N45  121.11  3.000
 OPF  H19  C42  H18  105.35  3.000
 OPF  H19  C42  C41  109.69  3.000
 OPF  H18  C42  C41  110.03  3.000
 OPF  H19  C42  C44  110.08  3.000
 OPF  H18  C42  C44  107.18  3.000
 OPF  C41  C42  C44  114.12  3.000
 OPF  H21  C41  H20  106.07  3.000
 OPF  H21  C41  C40  109.95  3.000
 OPF  H20  C41  C40  108.92  3.000
 OPF  H21  C41  C42  110.14  3.000
 OPF  H20  C41  C42  107.84  3.000
 OPF  C40  C41  C42  113.62  3.000
 OPF  H23  C40  H22  106.13  3.000
 OPF  H23  C40  C39  109.13  3.000
 OPF  H22  C40  C39  109.27  3.000
 OPF  H23  C40  C41  109.86  3.000
 OPF  H22  C40  C41  109.21  3.000
 OPF  C39  C40  C41  113.00  3.000
 OPF  H25  C39  H24  105.99  3.000
 OPF  H25  C39  C38  109.34  3.000
 OPF  H24  C39  C38  109.22  3.000
 OPF  H25  C39  C40  109.50  3.000
 OPF  H24  C39  C40  109.39  3.000
 OPF  C38  C39  C40  113.15  3.000
 OPF  H27  C38  H26  105.97  3.000
 OPF  H27  C38  C37  109.61  3.000
 OPF  H26  C38  C37  109.62  3.000
 OPF  H27  C38  C39  109.32  3.000
 OPF  H26  C38  C39  109.19  3.000
 OPF  C37  C38  C39  112.90  3.000
 OPF  H30  C37  H29  107.47  3.000
 OPF  H30  C37  H28  107.63  3.000
 OPF  H29  C37  H28  107.62  3.000
 OPF  H30  C37  C38  111.15  3.000
 OPF  H29  C37  C38  111.11  3.000
 OPF  H28  C37  C38  111.67  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
 OPF  CONST_01  C32  C33  C34  C35     0.00   0.0  0
 OPF  CONST_02  C32  C31  C30  C35     0.00   0.0  0
 OPF  CONST_03  C31  C32  C33  C34     0.00   0.0  0
 OPF  CONST_04  C31  C30  C35  C34     0.00   0.0  0
 OPF  CONST_05  C30  C35  C34  C33     0.00   0.0  0
 OPF  CONST_06  C30  C31  C32  C33     0.00   0.0  0
 OPF  CONST_07  C33  C34  C35  C36   180.00   0.0  0
 OPF  CONST_08  C31  C30  C35  C36   180.00   0.0  0
 OPF  CONST_09  H6   C33  C34  C35   180.00   0.0  0
 OPF  CONST_10  H8   C31  C30  C35   180.00   0.0  0
 OPF  CONST_11  H7   C32  C33  C34   180.00   0.0  0
 OPF  CONST_12  H9   C30  C35  C34   180.00   0.0  0
 OPF  CONST_13  H5   C34  C33  C32   180.00   0.0  0
 OPF  CONST_14  O43  C44  N45  C50     0.00   0.0  0
 OPF  CONST_15  C42  C44  N45  C50   180.00   0.0  0
 OPF  CONST_16  O43  C44  N45  C46   180.00   0.0  0
 OPF  CONST_17  C42  C44  N45  C46     0.00   0.0  0
 OPF  CONST_18  C50  C51  N52  C56   180.00   0.0  0
 OPF  CONST_19  H10  N52  C51  C50     0.00   0.0  0
 OPF  CONST_20  O49  C51  N52  C56     0.00   0.0  0
 OPF  Var_01    C46  C47  C48  C50   -38.89  30.0  1
 OPF  Var_02    C47  C46  N45  C50   -12.76  30.0  1
 OPF  Var_03    N45  C46  C47  C48    31.60  30.0  1
 OPF  Var_04    C34  C35  C36  C56    75.22  30.0  2
 OPF  Var_05    C41  C42  C44  N45   164.07  30.0  3
 OPF  Var_06    C40  C41  C42  C44   -69.12  30.0  3
 OPF  Var_07    C39  C40  C41  C42  -176.80  30.0  1
 OPF  Var_08    C38  C39  C40  C41  -178.64  30.0  3
 OPF  Var_09    C37  C38  C39  C40  -179.55  30.0  2
 OPF  Var_10    H28  C37  C38  C39  -179.85  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
 OPF  chir_01  C56  C36  C55  N52  negativ
 OPF  chir_02  C50  N45  C51  C48  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
 OPF  plan-1  C36  0.020
 OPF  plan-1  C35  0.020
 OPF  plan-1  C34  0.020
 OPF  plan-1  C33  0.020
 OPF  plan-1  C32  0.020
 OPF  plan-1  C31  0.020
 OPF  plan-1  C30  0.020
 OPF  plan-1  H5   0.020
 OPF  plan-1  H6   0.020
 OPF  plan-1  H7   0.020
 OPF  plan-1  H8   0.020
 OPF  plan-1  H9   0.020
 OPF  plan-2  C50  0.020
 OPF  plan-2  C46  0.020
 OPF  plan-2  N45  0.020
 OPF  plan-2  C44  0.020
 OPF  plan-2  O43  0.020
 OPF  plan-2  C42  0.020
 OPF  plan-3  C56  0.020
 OPF  plan-3  N52  0.020
 OPF  plan-3  C51  0.020
 OPF  plan-3  O49  0.020
 OPF  plan-3  C50  0.020
 OPF  plan-3  H10  0.020
 OPF  plan-4  O54  0.020
 OPF  plan-4  C55  0.020
 OPF  plan-4  O53  0.020
 OPF  plan-4  C56  0.020

