# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 18:31:44 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-1-(3-cyclopentylpropanoyl)piperidin-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]2CCCCN2C(=O)CCC3CCCC3
#
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
 YIC  YIC  '(2~{S})-2-[[(2~{S})-1-(3-cyclopentylpropanoyl)piperidin-2-yl]carbonylamino]-3-phenyl-propanoic acid'  ligand  61  29  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YIC
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
 YIC  O15  O  O     0  -0.484  -10.3078   6.6110  22.7029
 YIC  C14  C  C     0   0.579  -10.8542   5.9046  23.5361
 YIC  C16  C  CH2   0  -0.613  -10.5438   4.4235  23.6363
 YIC  C17  C  CH2   0  -0.408   -9.9012   3.8304  22.3865
 YIC  C18  C  CH1   0  -0.229  -10.9066   3.3980  21.3267
 YIC  C22  C  CH2   0  -0.432  -10.2595   2.7485  20.1009
 YIC  C21  C  CH2   0  -0.444  -11.3411   2.7754  19.0052
 YIC  C20  C  CH2   0  -0.446  -12.4000   3.7930  19.4874
 YIC  C19  C  CH2   0  -0.427  -11.7694   4.4899  20.6952
 YIC  N13  N  NT    0  -0.492  -11.7247   6.4324  24.4447
 YIC  C12  C  CH2   0  -0.341  -12.4827   5.6619  25.4254
 YIC  C11  C  CH2   0  -0.424  -13.9441   5.5509  25.0194
 YIC  C10  C  CH2   0  -0.453  -14.5393   6.9415  24.8335
 YIC  C9   C  CH2   0  -0.421  -13.6953   7.7703  23.8728
 YIC  C7   C  CH1   0  -0.248  -12.2158   7.7892  24.2565
 YIC  C6   C  C     0   0.560  -11.9257   8.6823  25.4648
 YIC  O8   O  O     0  -0.481  -12.6116   9.6597  25.7166
 YIC  N5   N  NH1   0  -0.641  -10.8280   8.3513  26.1662
 YIC  C1   C  CH1   0  -0.173  -10.3863   9.0727  27.3316
 YIC  C2   C  C     0   0.552   -8.8721   9.0047  27.3909
 YIC  O4   O  OH1   0  -0.572   -8.3352  10.1314  27.8156
 YIC  O3   O  O     0  -0.435   -8.2457   8.0140  27.1086
 YIC  C23  C  CH2   0  -0.526  -10.9879   8.4632  28.6167
 YIC  C24  C  CR6   0   0.126  -10.4916   9.1142  29.8757
 YIC  C29  C  CR16  0  -0.305  -11.0076  10.3393  30.2928
 YIC  C28  C  CR16  0  -0.239  -10.5265  10.9584  31.4375
 YIC  C27  C  CR16  0  -0.269   -9.5198  10.3582  32.1840
 YIC  C26  C  CR16  0  -0.239   -9.0015   9.1359  31.7790
 YIC  C25  C  CR16  0  -0.303   -9.4856   8.5201  30.6323
 YIC  H1   H  HCH2  0   0.259  -11.4419   3.8494  23.8715
 YIC  H2   H  HCH2  0   0.287   -9.8800   4.2957  24.4983
 YIC  H3   H  HCH2  0   0.230   -9.3339   2.9472  22.6924
 YIC  H4   H  HCH2  0   0.222   -9.1752   4.5248  21.9577
 YIC  H5   H  HCH1  0   0.212  -11.5836   2.6650  21.7871
 YIC  H6   H  HCH2  0   0.227   -9.8899   1.7422  20.3072
 YIC  H7   H  HCH2  0   0.214   -9.3949   3.3466  19.7960
 YIC  H8   H  HCH2  0   0.224  -11.7874   1.7896  18.8676
 YIC  H9   H  HCH2  0   0.224  -10.9178   3.0605  18.0412
 YIC  H10  H  HCH2  0   0.226  -12.6917   4.4975  18.7074
 YIC  H11  H  HCH2  0   0.220  -13.3090   3.2716  19.7956
 YIC  H12  H  HCH2  0   0.214  -11.1343   5.3182  20.3685
 YIC  H13  H  HCH2  0   0.218  -12.5185   4.9063  21.3734
 YIC  H14  H  HCH2  0   0.282  -12.0315   4.6866  25.5797
 YIC  H15  H  HCH2  0   0.247  -12.4138   6.1731  26.3907
 YIC  H16  H  HCH2  0   0.244  -14.4895   4.9955  25.7849
 YIC  H17  H  HCH2  0   0.224  -14.0186   4.9760  24.0908
 YIC  H18  H  HCH2  0   0.224  -14.5982   7.4422  25.8050
 YIC  H19  H  HCH2  0   0.245  -15.5624   6.8716  24.4600
 YIC  H20  H  HCH2  0   0.249  -14.0697   8.7914  23.8049
 YIC  H21  H  HCH2  0   0.238  -13.7651   7.3459  22.8674
 YIC  H22  H  HCH1  0   0.316  -11.6502   8.2338  23.4348
 YIC  H23  H  HNH1  0   0.404  -10.3480   7.4944  25.9350
 YIC  H24  H  HCH1  0   0.292  -10.7010  10.1124  27.2405
 YIC  H25  H  HOH1  0   0.486   -7.3730  10.0379  27.8963
 YIC  H26  H  HCH2  0   0.277  -12.0726   8.5622  28.5378
 YIC  H27  H  HCH2  0   0.263  -10.7635   7.3940  28.6291
 YIC  H28  H  HCR6  0   0.249  -11.7959  10.8114  29.7175
 YIC  H29  H  HCR6  0   0.255  -10.9399  11.9092  31.7486
 YIC  H30  H  HCR6  0   0.255   -9.1450  10.8396  33.0781
 YIC  H31  H  HCR6  0   0.255   -8.2219   8.6574  32.3579
 YIC  H32  H  HCR6  0   0.251   -9.0774   7.5637  30.3258

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
 YIC  C21  C20  single    1.546  0.020  1.546
 YIC  C21  C22  single    1.540  0.020  1.540
 YIC  C20  C19  single    1.530  0.020  1.530
 YIC  C22  C18  single    1.531  0.020  1.531
 YIC  C19  C18  single    1.528  0.020  1.528
 YIC  C18  C17  single    1.523  0.020  1.523
 YIC  C17  C16  single    1.525  0.020  1.525
 YIC  O15  C14  double    1.221  0.020  1.221
 YIC  C16  C14  single    1.517  0.020  1.517
 YIC  C14  N13  single    1.365  0.020  1.365
 YIC  C7   C9   single    1.529  0.020  1.529
 YIC  C7   N13  single    1.455  0.020  1.455
 YIC  C7   C6   single    1.530  0.020  1.530
 YIC  C9   C10  single    1.524  0.020  1.524
 YIC  N13  C12  single    1.459  0.020  1.459
 YIC  C6   O8   double    1.220  0.020  1.220
 YIC  C6   N5   single    1.344  0.020  1.344
 YIC  C10  C11  single    1.524  0.020  1.524
 YIC  C11  C12  single    1.521  0.020  1.521
 YIC  N5   C1   single    1.440  0.020  1.440
 YIC  O3   C2   double    1.206  0.020  1.206
 YIC  C1   C2   single    1.517  0.020  1.517
 YIC  C1   C23  single    1.544  0.020  1.544
 YIC  C2   O4   single    1.318  0.020  1.318
 YIC  C23  C24  single    1.502  0.020  1.502
 YIC  C24  C29  aromatic  1.393  0.020  1.393
 YIC  C24  C25  aromatic  1.392  0.020  1.392
 YIC  C29  C28  aromatic  1.387  0.020  1.387
 YIC  C25  C26  aromatic  1.389  0.020  1.389
 YIC  C28  C27  aromatic  1.390  0.020  1.390
 YIC  C26  C27  aromatic  1.388  0.020  1.388
 YIC  C16  H1   single    0.970  0.020  1.090
 YIC  C16  H2   single    0.970  0.020  1.090
 YIC  C17  H3   single    0.970  0.020  1.090
 YIC  C17  H4   single    0.970  0.020  1.090
 YIC  C18  H5   single    0.970  0.020  1.090
 YIC  C22  H6   single    0.970  0.020  1.090
 YIC  C22  H7   single    0.970  0.020  1.090
 YIC  C21  H8   single    0.970  0.020  1.090
 YIC  C21  H9   single    0.970  0.020  1.090
 YIC  C20  H10  single    0.970  0.020  1.090
 YIC  C20  H11  single    0.970  0.020  1.090
 YIC  C19  H12  single    0.970  0.020  1.090
 YIC  C19  H13  single    0.970  0.020  1.090
 YIC  C12  H14  single    0.970  0.020  1.090
 YIC  C12  H15  single    0.970  0.020  1.090
 YIC  C11  H16  single    0.970  0.020  1.090
 YIC  C11  H17  single    0.970  0.020  1.090
 YIC  C10  H18  single    0.970  0.020  1.090
 YIC  C10  H19  single    0.970  0.020  1.090
 YIC  C9   H20  single    0.970  0.020  1.090
 YIC  C9   H21  single    0.970  0.020  1.090
 YIC  C7   H22  single    0.970  0.020  1.090
 YIC  N5   H23  single    0.860  0.020  1.020
 YIC  C1   H24  single    0.970  0.020  1.090
 YIC  O4   H25  single    0.850  0.020  0.980
 YIC  C23  H26  single    0.970  0.020  1.090
 YIC  C23  H27  single    0.970  0.020  1.090
 YIC  C29  H28  single    0.930  0.020  1.080
 YIC  C28  H29  single    0.930  0.020  1.080
 YIC  C27  H30  single    0.930  0.020  1.080
 YIC  C26  H31  single    0.930  0.020  1.080
 YIC  C25  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
 YIC  N13  C14  C16  117.67  3.000
 YIC  N13  C14  O15  121.06  3.000
 YIC  C16  C14  O15  121.22  3.000
 YIC  H2   C16  H1   105.53  3.000
 YIC  H2   C16  C17  110.13  3.000
 YIC  H1   C16  C17  108.58  3.000
 YIC  H2   C16  C14  106.85  3.000
 YIC  H1   C16  C14  111.06  3.000
 YIC  C17  C16  C14  114.32  3.000
 YIC  H4   C17  H3   106.17  3.000
 YIC  H4   C17  C18  110.24  3.000
 YIC  H3   C17  C18  107.93  3.000
 YIC  H4   C17  C16  110.76  3.000
 YIC  H3   C17  C16  107.66  3.000
 YIC  C18  C17  C16  113.72  3.000
 YIC  H5   C18  C19  107.57  3.000
 YIC  H5   C18  C22  108.23  3.000
 YIC  C19  C18  C22  102.18  3.000
 YIC  H5   C18  C17  107.72  3.000
 YIC  C19  C18  C17  117.22  3.000
 YIC  C22  C18  C17  113.48  3.000
 YIC  H7   C22  H6   106.79  3.000
 YIC  H7   C22  C21  110.31  3.000
 YIC  H6   C22  C21  112.85  3.000
 YIC  H7   C22  C18  108.97  3.000
 YIC  H6   C22  C18  112.52  3.000
 YIC  C21  C22  C18  105.39  3.000
 YIC  H9   C21  H8   106.47  3.000
 YIC  H9   C21  C20  111.68  3.000
 YIC  H8   C21  C20  110.74  3.000
 YIC  H9   C21  C22  111.15  3.000
 YIC  H8   C21  C22  111.18  3.000
 YIC  C20  C21  C22  105.71  3.000
 YIC  H11  C20  H10  106.71  3.000
 YIC  H11  C20  C19  109.73  3.000
 YIC  H10  C20  C19  112.37  3.000
 YIC  H11  C20  C21  110.11  3.000
 YIC  H10  C20  C21  112.66  3.000
 YIC  C19  C20  C21  105.29  3.000
 YIC  H13  C19  H12  107.15  3.000
 YIC  H13  C19  C20  112.38  3.000
 YIC  H12  C19  C20  110.39  3.000
 YIC  H13  C19  C18  113.75  3.000
 YIC  H12  C19  C18  109.68  3.000
 YIC  C20  C19  C18  103.50  3.000
 YIC  C7   N13  C12  113.82  3.000
 YIC  C12  N13  C14  125.07  3.000
 YIC  C7   N13  C14  119.33  3.000
 YIC  H15  C12  H14  105.55  3.000
 YIC  H15  C12  C11  109.27  3.000
 YIC  H14  C12  C11  111.82  3.000
 YIC  H15  C12  N13  108.26  3.000
 YIC  H14  C12  N13  110.73  3.000
 YIC  C11  C12  N13  110.99  3.000
 YIC  H17  C11  H16  107.08  3.000
 YIC  H17  C11  C10  110.44  3.000
 YIC  H16  C11  C10  110.77  3.000
 YIC  H17  C11  C12  109.28  3.000
 YIC  H16  C11  C12  109.27  3.000
 YIC  C10  C11  C12  109.95  3.000
 YIC  H19  C10  H18  106.41  3.000
 YIC  H19  C10  C9   109.77  3.000
 YIC  H18  C10  C9   109.91  3.000
 YIC  H19  C10  C11  110.45  3.000
 YIC  H18  C10  C11  109.28  3.000
 YIC  C9   C10  C11  110.91  3.000
 YIC  H21  C9   H20  106.53  3.000
 YIC  H21  C9   C7   107.30  3.000
 YIC  H20  C9   C7   109.67  3.000
 YIC  H21  C9   C10  109.46  3.000
 YIC  H20  C9   C10  111.02  3.000
 YIC  C7   C9   C10  112.61  3.000
 YIC  H22  C7   C6   104.97  3.000
 YIC  H22  C7   C9   108.51  3.000
 YIC  C6   C7   C9   112.89  3.000
 YIC  H22  C7   N13  107.58  3.000
 YIC  C6   C7   N13  112.21  3.000
 YIC  C9   C7   N13  110.34  3.000
 YIC  N5   C6   O8   123.27  3.000
 YIC  N5   C6   C7   115.04  3.000
 YIC  O8   C6   C7   121.59  3.000
 YIC  H23  N5   C1   117.71  3.000
 YIC  H23  N5   C6   118.55  3.000
 YIC  C1   N5   C6   123.33  3.000
 YIC  H24  C1   C23  109.48  3.000
 YIC  H24  C1   C2   109.52  3.000
 YIC  C23  C1   C2   109.79  3.000
 YIC  H24  C1   N5   108.76  3.000
 YIC  C23  C1   N5   110.87  3.000
 YIC  C2   C1   N5   108.38  3.000
 YIC  O3   C2   O4   124.47  3.000
 YIC  O4   C2   C1   112.38  3.000
 YIC  O3   C2   C1   123.12  3.000
 YIC  H25  O4   C2   110.39  3.000
 YIC  H27  C23  H26  107.07  3.000
 YIC  H27  C23  C24  110.29  3.000
 YIC  H26  C23  C24  110.46  3.000
 YIC  H27  C23  C1   108.40  3.000
 YIC  H26  C23  C1   106.92  3.000
 YIC  C24  C23  C1   113.44  3.000
 YIC  C25  C24  C29  118.70  3.000
 YIC  C25  C24  C23  120.64  3.000
 YIC  C29  C24  C23  120.65  3.000
 YIC  H28  C29  C28  119.71  3.000
 YIC  H28  C29  C24  119.56  3.000
 YIC  C28  C29  C24  120.73  3.000
 YIC  H29  C28  C27  120.11  3.000
 YIC  H29  C28  C29  119.78  3.000
 YIC  C27  C28  C29  120.11  3.000
 YIC  H30  C27  C26  120.22  3.000
 YIC  H30  C27  C28  120.17  3.000
 YIC  C26  C27  C28  119.61  3.000
 YIC  H31  C26  C25  119.78  3.000
 YIC  H31  C26  C27  120.14  3.000
 YIC  C25  C26  C27  120.08  3.000
 YIC  H32  C25  C26  119.56  3.000
 YIC  H32  C25  C24  119.67  3.000
 YIC  C26  C25  C24  120.77  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
 YIC  CONST_01  C27  C28  C29  C24    0.00   0.0  0
 YIC  CONST_02  C27  C26  C25  C24    0.00   0.0  0
 YIC  CONST_03  C26  C25  C24  C29    0.00   0.0  0
 YIC  CONST_04  C26  C27  C28  C29    0.00   0.0  0
 YIC  CONST_05  C25  C24  C29  C28    0.00   0.0  0
 YIC  CONST_06  C25  C26  C27  C28    0.00   0.0  0
 YIC  CONST_07  C28  C29  C24  C23  180.00   0.0  0
 YIC  CONST_08  C26  C25  C24  C23  180.00   0.0  0
 YIC  CONST_09  H29  C28  C29  C24  180.00   0.0  0
 YIC  CONST_10  H31  C26  C25  C24  180.00   0.0  0
 YIC  CONST_11  H32  C25  C24  C29  180.00   0.0  0
 YIC  CONST_12  H30  C27  C28  C29  180.00   0.0  0
 YIC  CONST_13  H28  C29  C28  C27  180.00   0.0  0
 YIC  CONST_14  C7   N13  C14  O15    0.00   0.0  0
 YIC  CONST_15  C12  N13  C14  O15  180.00   0.0  0
 YIC  CONST_16  C7   N13  C14  C16  180.00   0.0  0
 YIC  CONST_17  C12  N13  C14  C16    0.00   0.0  0
 YIC  CONST_18  C1   N5   C6   C7   180.00   0.0  0
 YIC  CONST_19  H23  N5   C6   C7     0.00   0.0  0
 YIC  CONST_20  C1   N5   C6   O8     0.00   0.0  0
 YIC  CONST_21  H25  O4   C2   C1   180.00   0.0  0
 YIC  Var_01    C20  C21  C22  C18   16.34  30.0  1
 YIC  Var_02    C21  C20  C19  C18  -32.64  30.0  1
 YIC  Var_03    C19  C20  C21  C22   10.02  30.0  1
 YIC  Var_04    C10  C11  C12  N13  -56.60  30.0  1
 YIC  Var_05    C9   C10  C11  C12   53.25  30.0  1
 YIC  Var_06    C7   C9   C10  C11  -51.69  30.0  1
 YIC  Var_07    C7   N13  C12  C11   59.35  30.0  1
 YIC  Var_08    C29  C24  C23  C1    78.57  30.0  2
 YIC  Var_09    C18  C17  C16  C14  -85.22  30.0  1
 YIC  Var_10    N13  C14  C16  C17  163.42  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
 YIC  chir_01  C18  C22  C19  C17  positiv
 YIC  chir_02  C7   N13  C9   C6   negativ
 YIC  chir_03  C1   N5   C2   C23  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
 YIC  plan-1  O15  0.020
 YIC  plan-1  C14  0.020
 YIC  plan-1  C16  0.020
 YIC  plan-1  N13  0.020
 YIC  plan-1  C12  0.020
 YIC  plan-1  C7   0.020
 YIC  plan-2  C23  0.020
 YIC  plan-2  C24  0.020
 YIC  plan-2  C29  0.020
 YIC  plan-2  C28  0.020
 YIC  plan-2  C27  0.020
 YIC  plan-2  C26  0.020
 YIC  plan-2  C25  0.020
 YIC  plan-2  H28  0.020
 YIC  plan-2  H29  0.020
 YIC  plan-2  H30  0.020
 YIC  plan-2  H31  0.020
 YIC  plan-2  H32  0.020
 YIC  plan-3  C7   0.020
 YIC  plan-3  C6   0.020
 YIC  plan-3  O8   0.020
 YIC  plan-3  N5   0.020
 YIC  plan-3  C1   0.020
 YIC  plan-3  H23  0.020
 YIC  plan-4  C1   0.020
 YIC  plan-4  C2   0.020
 YIC  plan-4  O4   0.020
 YIC  plan-4  O3   0.020
 YIC  plan-4  H25  0.020

