# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 04:24:15 2022
#   Inital geometry file: a 144 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-1-(3-cyclohexylpropanoyl)pyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H]2CCCN2C(=O)CCC3CCCCC3
#
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
 D0F  D0F  '(2~{S})-2-[[(2~{S})-1-(3-cyclohexylpropanoyl)pyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid'  ligand  60  29  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D0F
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
 D0F  O22  O  O      0  -0.491   3.0607   -7.8389  24.9801
 D0F  C20  C  C      0   0.532   3.1681   -6.6320  25.1606
 D0F  C21  C  CH2    0  -0.583   2.5653   -5.6325  24.2038
 D0F  C23  C  CH2    0  -0.436   1.1212   -5.3184  24.6182
 D0F  C24  C  CH1    0  -0.223   0.3257   -4.4893  23.6100
 D0F  C29  C  CH2    0  -0.420   0.0472   -5.2407  22.3080
 D0F  C28  C  CH2    0  -0.427  -0.8245   -4.4169  21.3650
 D0F  C27  C  CH2    0  -0.427  -0.2013   -3.0541  21.0816
 D0F  C26  C  CH2    0  -0.427   0.0939   -2.3006  22.3749
 D0F  C25  C  CH2    0  -0.423   0.9633   -3.1328  23.3129
 D0F  N19  N  NT     0  -0.484   3.7813   -6.1460  26.2608
 D0F  C18  C  CH2    0  -0.284   4.0273   -4.7394  26.5749
 D0F  C17  C  CH2    0  -0.476   4.4837   -4.7865  28.0270
 D0F  C16  C  CH2    0  -0.485   5.2072   -6.1252  28.1199
 D0F  C14  C  CH1    0  -0.172   4.3738   -7.0562  27.2253
 D0F  C13  C  C      0   0.537   3.3534   -7.8433  28.0448
 D0F  O15  O  O      0  -0.506   3.6745   -8.9137  28.5494
 D0F  N5   N  NH1    0  -0.635   2.1619   -7.2666  28.2085
 D0F  C1   C  CH1    0  -0.179   1.0868   -7.7983  29.0135
 D0F  C2   C  C      0   0.419  -0.2401   -7.1331  28.5691
 D0F  O4   O  OC    -1  -0.583  -1.2763   -7.7902  28.7504
 D0F  O3   O  O      0  -0.597  -0.1399   -5.9796  28.0991
 D0F  C6   C  CH2    0  -0.522   1.3595   -7.5186  30.5068
 D0F  C7   C  CR6    0   0.157   0.3828   -8.1697  31.4424
 D0F  C12  C  CR16   0  -0.311   0.3797   -9.5551  31.6042
 D0F  C11  C  CR16   0  -0.239  -0.5166  -10.1712  32.4651
 D0F  C10  C  CR16   0  -0.274  -1.4257   -9.4086  33.1895
 D0F  C9   C  CR16   0  -0.240  -1.4273   -8.0283  33.0438
 D0F  C8   C  CR16   0  -0.316  -0.5297   -7.4176  32.1765
 D0F  H1   H  HCH2   0   0.264   2.5849   -6.0833  23.2109
 D0F  H2   H  HCH2   0   0.259   3.1579   -4.7180  24.1550
 D0F  H3   H  HCH2   0   0.234   1.1273   -4.7926  25.5778
 D0F  H4   H  HCH2   0   0.234   0.5915   -6.2595  24.7936
 D0F  H5   H  HCH1   0   0.216  -0.6472   -4.2934  24.0805
 D0F  H6   H  HCH2   0   0.222  -0.4349   -6.1975  22.5287
 D0F  H7   H  HCH2   0   0.208   0.9909   -5.4760  21.8040
 D0F  H8   H  HCH2   0   0.207  -1.8125   -4.2763  21.8172
 D0F  H9   H  HCH2   0   0.223  -0.9865   -4.9606  20.4311
 D0F  H10  H  HCH2   0   0.223  -0.8591   -2.4626  20.4398
 D0F  H11  H  HCH2   0   0.206   0.7323   -3.1925  20.5250
 D0F  H12  H  HCH2   0   0.223   0.5834   -1.3487  22.1542
 D0F  H13  H  HCH2   0   0.207  -0.8492   -2.0561  22.8759
 D0F  H14  H  HCH2   0   0.210   1.9444   -3.2790  22.8471
 D0F  H15  H  HCH2   0   0.222   1.1418   -2.5930  24.2479
 D0F  H16  H  HCH2   0   0.249   4.8084   -4.3278  25.9292
 D0F  H17  H  HCH2   0   0.261   3.1298   -4.1344  26.4469
 D0F  H18  H  HCH2   0   0.259   5.1195   -3.9405  28.2831
 D0F  H19  H  HCH2   0   0.243   3.6206   -4.7674  28.6950
 D0F  H20  H  HCH2   0   0.264   5.3046   -6.4982  29.1391
 D0F  H21  H  HCH2   0   0.255   6.2138   -6.0391  27.7069
 D0F  H22  H  HCH1   0   0.276   5.0096   -7.7920  26.7290
 D0F  H23  H  HNH1   0   0.392   1.9459   -6.3867  27.7613
 D0F  H24  H  HCH1   0   0.235   1.0213   -8.8782  28.8621
 D0F  H26  H  HCH2   0   0.253   2.3657   -7.8780  30.7364
 D0F  H27  H  HCH2   0   0.240   1.3673   -6.4368  30.6625
 D0F  H28  H  HCR6   0   0.243   1.0899  -10.1584  31.0495
 D0F  H29  H  HCR6   0   0.248  -0.5037  -11.2483  32.5752
 D0F  H30  H  HCR6   0   0.249  -2.1246   -9.8875  33.8633
 D0F  H31  H  HCR6   0   0.248  -2.1288   -7.4239  33.6050
 D0F  H32  H  HCR6   0   0.242  -0.5397   -6.3393  32.0670

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
 D0F  C27  C26  single    1.526  0.020  1.526
 D0F  C27  C28  single    1.525  0.020  1.525
 D0F  C26  C25  single    1.526  0.020  1.526
 D0F  C28  C29  single    1.526  0.020  1.526
 D0F  C25  C24  single    1.528  0.020  1.528
 D0F  C29  C24  single    1.529  0.020  1.529
 D0F  C24  C23  single    1.529  0.020  1.529
 D0F  C23  C21  single    1.535  0.020  1.535
 D0F  C21  C20  single    1.509  0.020  1.509
 D0F  C20  O22  double    1.225  0.020  1.225
 D0F  C20  N19  single    1.350  0.020  1.350
 D0F  N19  C14  single    1.452  0.020  1.452
 D0F  N19  C18  single    1.462  0.020  1.462
 D0F  C14  C13  single    1.527  0.020  1.527
 D0F  C14  C16  single    1.537  0.020  1.537
 D0F  C18  C17  single    1.523  0.020  1.523
 D0F  C13  O15  double    1.226  0.020  1.226
 D0F  C13  N5   single    1.334  0.020  1.334
 D0F  N5   C1   single    1.444  0.020  1.444
 D0F  C16  C17  single    1.525  0.020  1.525
 D0F  O3   C2   deloc     1.250  0.020  1.250
 D0F  C1   C2   single    1.549  0.020  1.549
 D0F  C1   C6   single    1.544  0.020  1.544
 D0F  C2   O4   deloc     1.240  0.020  1.240
 D0F  C6   C7   single    1.501  0.020  1.501
 D0F  C7   C12  aromatic  1.395  0.020  1.395
 D0F  C7   C8   aromatic  1.392  0.020  1.392
 D0F  C12  C11  aromatic  1.387  0.020  1.387
 D0F  C8   C9   aromatic  1.390  0.020  1.390
 D0F  C11  C10  aromatic  1.390  0.020  1.390
 D0F  C9   C10  aromatic  1.388  0.020  1.388
 D0F  C21  H1   single    0.970  0.020  1.090
 D0F  C21  H2   single    0.970  0.020  1.090
 D0F  C23  H3   single    0.970  0.020  1.090
 D0F  C23  H4   single    0.970  0.020  1.090
 D0F  C24  H5   single    0.970  0.020  1.090
 D0F  C29  H6   single    0.970  0.020  1.090
 D0F  C29  H7   single    0.970  0.020  1.090
 D0F  C28  H8   single    0.970  0.020  1.090
 D0F  C28  H9   single    0.970  0.020  1.090
 D0F  C27  H10  single    0.970  0.020  1.090
 D0F  C27  H11  single    0.970  0.020  1.090
 D0F  C26  H12  single    0.970  0.020  1.090
 D0F  C26  H13  single    0.970  0.020  1.090
 D0F  C25  H14  single    0.970  0.020  1.090
 D0F  C25  H15  single    0.970  0.020  1.090
 D0F  C18  H16  single    0.970  0.020  1.090
 D0F  C18  H17  single    0.970  0.020  1.090
 D0F  C17  H18  single    0.970  0.020  1.090
 D0F  C17  H19  single    0.970  0.020  1.090
 D0F  C16  H20  single    0.970  0.020  1.090
 D0F  C16  H21  single    0.970  0.020  1.090
 D0F  C14  H22  single    0.970  0.020  1.090
 D0F  N5   H23  single    0.860  0.020  1.020
 D0F  C1   H24  single    0.970  0.020  1.090
 D0F  C6   H26  single    0.970  0.020  1.090
 D0F  C6   H27  single    0.970  0.020  1.090
 D0F  C12  H28  single    0.930  0.020  1.080
 D0F  C11  H29  single    0.930  0.020  1.080
 D0F  C10  H30  single    0.930  0.020  1.080
 D0F  C9   H31  single    0.930  0.020  1.080
 D0F  C8   H32  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
 D0F  N19  C20  C21  117.37  3.000
 D0F  N19  C20  O22  120.97  3.000
 D0F  C21  C20  O22  121.60  3.000
 D0F  H2   C21  H1   107.22  3.000
 D0F  H2   C21  C23  110.59  3.000
 D0F  H1   C21  C23  110.33  3.000
 D0F  H2   C21  C20  111.50  3.000
 D0F  H1   C21  C20  107.23  3.000
 D0F  C23  C21  C20  109.88  3.000
 D0F  H4   C23  H3   105.98  3.000
 D0F  H4   C23  C24  108.68  3.000
 D0F  H3   C23  C24  108.71  3.000
 D0F  H4   C23  C21  108.83  3.000
 D0F  H3   C23  C21  109.27  3.000
 D0F  C24  C23  C21  114.99  3.000
 D0F  H5   C24  C25  107.13  3.000
 D0F  H5   C24  C29  106.92  3.000
 D0F  C25  C24  C29  110.29  3.000
 D0F  H5   C24  C23  105.97  3.000
 D0F  C29  C24  C23  112.95  3.000
 D0F  C25  C24  C23  113.11  3.000
 D0F  H7   C29  H6   106.53  3.000
 D0F  H7   C29  C28  108.89  3.000
 D0F  H6   C29  C28  110.19  3.000
 D0F  H7   C29  C24  109.91  3.000
 D0F  H6   C29  C24  109.78  3.000
 D0F  C28  C29  C24  111.41  3.000
 D0F  H9   C28  H8   106.44  3.000
 D0F  H9   C28  C27  110.26  3.000
 D0F  H8   C28  C27  109.30  3.000
 D0F  H9   C28  C29  110.14  3.000
 D0F  H8   C28  C29  109.24  3.000
 D0F  C27  C28  C29  111.34  3.000
 D0F  H11  C27  H10  106.43  3.000
 D0F  H11  C27  C26  109.16  3.000
 D0F  H10  C27  C26  110.30  3.000
 D0F  H11  C27  C28  109.25  3.000
 D0F  H10  C27  C28  110.29  3.000
 D0F  C26  C27  C28  111.28  3.000
 D0F  H13  C26  H12  106.48  3.000
 D0F  H13  C26  C25  109.33  3.000
 D0F  H12  C26  C25  110.12  3.000
 D0F  H13  C26  C27  109.35  3.000
 D0F  H12  C26  C27  110.22  3.000
 D0F  C25  C26  C27  111.22  3.000
 D0F  H15  C25  H14  106.43  3.000
 D0F  H15  C25  C26  110.44  3.000
 D0F  H14  C25  C26  108.76  3.000
 D0F  H15  C25  C24  109.87  3.000
 D0F  H14  C25  C24  109.74  3.000
 D0F  C26  C25  C24  111.47  3.000
 D0F  C14  N19  C18  113.06  3.000
 D0F  C18  N19  C20  126.71  3.000
 D0F  C14  N19  C20  120.06  3.000
 D0F  H17  C18  H16  108.05  3.000
 D0F  H17  C18  C17  112.08  3.000
 D0F  H16  C18  C17  111.13  3.000
 D0F  H17  C18  N19  111.73  3.000
 D0F  H16  C18  N19  110.82  3.000
 D0F  C17  C18  N19  103.03  3.000
 D0F  H19  C17  H18  107.71  3.000
 D0F  H19  C17  C16  110.69  3.000
 D0F  H18  C17  C16  113.01  3.000
 D0F  H19  C17  C18  110.24  3.000
 D0F  H18  C17  C18  112.04  3.000
 D0F  C16  C17  C18  103.15  3.000
 D0F  H21  C16  H20  107.37  3.000
 D0F  H21  C16  C14  109.12  3.000
 D0F  H20  C16  C14  112.68  3.000
 D0F  H21  C16  C17  110.20  3.000
 D0F  H20  C16  C17  113.58  3.000
 D0F  C14  C16  C17  103.84  3.000
 D0F  H22  C14  C13  106.60  3.000
 D0F  H22  C14  C16  110.92  3.000
 D0F  C13  C14  C16  111.23  3.000
 D0F  H22  C14  N19  110.98  3.000
 D0F  C16  C14  N19  103.19  3.000
 D0F  C13  C14  N19  114.00  3.000
 D0F  N5   C13  O15  124.12  3.000
 D0F  N5   C13  C14  116.10  3.000
 D0F  O15  C13  C14  119.72  3.000
 D0F  H23  N5   C1   114.09  3.000
 D0F  H23  N5   C13  120.87  3.000
 D0F  C1   N5   C13  125.04  3.000
 D0F  H24  C1   C6   108.89  3.000
 D0F  H24  C1   C2   109.47  3.000
 D0F  C6   C1   C2   110.54  3.000
 D0F  H24  C1   N5   109.35  3.000
 D0F  C6   C1   N5   109.93  3.000
 D0F  C2   C1   N5   108.63  3.000
 D0F  O3   C2   O4   127.66  3.000
 D0F  O4   C2   C1   116.49  3.000
 D0F  O3   C2   C1   115.82  3.000
 D0F  H27  C6   H26  106.79  3.000
 D0F  H27  C6   C7   110.20  3.000
 D0F  H26  C6   C7   109.00  3.000
 D0F  H27  C6   C1   108.57  3.000
 D0F  H26  C6   C1   107.83  3.000
 D0F  C7   C6   C1   114.17  3.000
 D0F  C8   C7   C12  118.30  3.000
 D0F  C8   C7   C6   121.39  3.000
 D0F  C12  C7   C6   120.30  3.000
 D0F  H28  C12  C11  119.57  3.000
 D0F  H28  C12  C7   119.46  3.000
 D0F  C11  C12  C7   120.97  3.000
 D0F  H29  C11  C10  120.03  3.000
 D0F  H29  C11  C12  119.81  3.000
 D0F  C10  C11  C12  120.16  3.000
 D0F  H30  C10  C9   120.30  3.000
 D0F  H30  C10  C11  120.26  3.000
 D0F  C9   C10  C11  119.44  3.000
 D0F  H31  C9   C8   119.78  3.000
 D0F  H31  C9   C10  120.10  3.000
 D0F  C8   C9   C10  120.12  3.000
 D0F  H32  C8   C9   119.63  3.000
 D0F  H32  C8   C7   119.36  3.000
 D0F  C9   C8   C7   121.01  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
 D0F  CONST_01  C10  C11  C12  C7      0.00   0.0  0
 D0F  CONST_02  C10  C9   C8   C7      0.00   0.0  0
 D0F  CONST_03  C9   C8   C7   C12     0.00   0.0  0
 D0F  CONST_04  C9   C10  C11  C12     0.00   0.0  0
 D0F  CONST_05  C8   C7   C12  C11     0.00   0.0  0
 D0F  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 D0F  CONST_07  C11  C12  C7   C6    180.00   0.0  0
 D0F  CONST_08  C9   C8   C7   C6    180.00   0.0  0
 D0F  CONST_09  H29  C11  C12  C7    180.00   0.0  0
 D0F  CONST_10  H31  C9   C8   C7    180.00   0.0  0
 D0F  CONST_11  H32  C8   C7   C12   180.00   0.0  0
 D0F  CONST_12  H30  C10  C11  C12   180.00   0.0  0
 D0F  CONST_13  H28  C12  C11  C10   180.00   0.0  0
 D0F  CONST_14  C14  N19  C20  O22     0.00   0.0  0
 D0F  CONST_15  C18  N19  C20  O22   180.00   0.0  0
 D0F  CONST_16  C14  N19  C20  C21   180.00   0.0  0
 D0F  CONST_17  C18  N19  C20  C21     0.00   0.0  0
 D0F  CONST_18  C1   N5   C13  C14   180.00   0.0  0
 D0F  CONST_19  H23  N5   C13  C14     0.00   0.0  0
 D0F  CONST_20  C1   N5   C13  O15     0.00   0.0  0
 D0F  Var_01    C27  C26  C25  C24   -55.86  30.0  1
 D0F  Var_02    C27  C28  C29  C24    55.74  30.0  1
 D0F  Var_03    C26  C27  C28  C29   -54.84  30.0  1
 D0F  Var_04    C25  C26  C27  C28    54.85  30.0  1
 D0F  Var_05    C16  C17  C18  N19    32.16  30.0  1
 D0F  Var_06    C14  C16  C17  C18   -37.18  30.0  1
 D0F  Var_07    C14  N19  C18  C17   -15.68  30.0  1
 D0F  Var_08    C12  C7   C6   C1     69.58  30.0  2
 D0F  Var_09    C24  C23  C21  C20  -170.84  30.0  1
 D0F  Var_10    N19  C20  C21  C23   -88.44  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
 D0F  chir_01  C24  C25  C29  C23  negativ
 D0F  chir_02  C14  N19  C13  C16  positiv
 D0F  chir_03  C1   N5   C2   C6   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
 D0F  plan-1  O22  0.020
 D0F  plan-1  C20  0.020
 D0F  plan-1  C21  0.020
 D0F  plan-1  N19  0.020
 D0F  plan-1  C18  0.020
 D0F  plan-1  C14  0.020
 D0F  plan-2  C6   0.020
 D0F  plan-2  C7   0.020
 D0F  plan-2  C12  0.020
 D0F  plan-2  C11  0.020
 D0F  plan-2  C10  0.020
 D0F  plan-2  C9   0.020
 D0F  plan-2  C8   0.020
 D0F  plan-2  H28  0.020
 D0F  plan-2  H29  0.020
 D0F  plan-2  H30  0.020
 D0F  plan-2  H31  0.020
 D0F  plan-2  H32  0.020
 D0F  plan-3  C14  0.020
 D0F  plan-3  C13  0.020
 D0F  plan-3  O15  0.020
 D0F  plan-3  N5   0.020
 D0F  plan-3  C1   0.020
 D0F  plan-3  H23  0.020
 D0F  plan-4  C1   0.020
 D0F  plan-4  C2   0.020
 D0F  plan-4  O4   0.020
 D0F  plan-4  O3   0.020

