# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 09:06:14 2022
#   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  60  29  .  2022-03-29  2022-03-29
;
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  -0.486  -10.4115   6.6761  22.6832
 YIC  C14  C  C      0   0.578  -10.9244   5.9376  23.5114
 YIC  C16  C  CH2    0  -0.614  -10.5893   4.4576  23.5606
 YIC  C17  C  CH2    0  -0.407   -9.9168   3.9166  22.3023
 YIC  C18  C  CH1    0  -0.229  -10.8972   3.4710  21.2253
 YIC  C22  C  CH2    0  -0.430  -10.2213   2.8727  19.9896
 YIC  C21  C  CH2    0  -0.443  -11.3004   2.8825  18.8919
 YIC  C20  C  CH2    0  -0.445  -12.3917   3.8607  19.3862
 YIC  C19  C  CH2    0  -0.427  -11.7910   4.5489  20.6142
 YIC  N13  N  NT     0  -0.484  -11.7770   6.4224  24.4560
 YIC  C12  C  CH2    0  -0.331  -12.4823   5.6184  25.4464
 YIC  C11  C  CH2    0  -0.424  -13.9752   5.5809  25.1596
 YIC  C10  C  CH2    0  -0.452  -14.5325   6.9972  25.0891
 YIC  C9   C  CH2    0  -0.418  -13.7411   7.8328  24.0909
 YIC  C7   C  CH1    0  -0.242  -12.2390   7.7995  24.3695
 YIC  C6   C  C      0   0.546  -11.8451   8.6302  25.5974
 YIC  O8   O  O      0  -0.500  -12.4919   9.6215  25.9159
 YIC  N5   N  NH1    0  -0.635  -10.7302   8.2405  26.2191
 YIC  C1   C  CH1    0  -0.178  -10.1528   8.8973  27.3692
 YIC  C2   C  C      0   0.418   -8.6486   8.5349  27.4423
 YIC  O4   O  OC    -1  -0.586   -7.8930   9.3901  27.9297
 YIC  O3   O  O      0  -0.599   -8.3494   7.3948  27.0301
 YIC  C23  C  CH2    0  -0.527  -10.8779   8.4418  28.6541
 YIC  C24  C  CR6    0   0.152  -10.4942   9.2237  29.8761
 YIC  C29  C  CR16   0  -0.310  -11.0207  10.4978  30.0833
 YIC  C28  C  CR16   0  -0.239  -10.6757  11.2402  31.2039
 YIC  C27  C  CR16   0  -0.273   -9.7946  10.7167  32.1423
 YIC  C26  C  CR16   0  -0.241   -9.2665   9.4471  31.9494
 YIC  C25  C  CR16   0  -0.306   -9.6137   8.7101  30.8242
 YIC  H1   H  HCH2   0   0.260  -11.4825   3.8627  23.7622
 YIC  H2   H  HCH2   0   0.282   -9.9375   4.3084  24.4283
 YIC  H3   H  HCH2   0   0.228   -9.3144   3.0511  22.5903
 YIC  H4   H  HCH2   0   0.220   -9.2199   4.6495  21.8901
 YIC  H5   H  HCH1   0   0.210  -11.5524   2.7044  21.6623
 YIC  H6   H  HCH2   0   0.226   -9.8130   1.8774  20.1750
 YIC  H7   H  HCH2   0   0.212   -9.3800   3.5104  19.6992
 YIC  H8   H  HCH2   0   0.222  -11.7159   1.8853  18.7398
 YIC  H9   H  HCH2   0   0.223  -10.8839   3.1926  17.9326
 YIC  H10  H  HCH2   0   0.225  -12.6954   4.5725  18.6176
 YIC  H11  H  HCH2   0   0.219  -13.2889   3.3089  19.6751
 YIC  H12  H  HCH2   0   0.211  -11.1778   5.4030  20.3124
 YIC  H13  H  HCH2   0   0.224  -12.5542   4.9248  21.2996
 YIC  H14  H  HCH2   0   0.275  -12.0652   4.6176  25.4901
 YIC  H15  H  HCH2   0   0.246  -12.3126   6.0561  26.4355
 YIC  H16  H  HCH2   0   0.239  -14.4747   5.0047  25.9412
 YIC  H17  H  HCH2   0   0.224  -14.1493   5.0595  24.2130
 YIC  H18  H  HCH2   0   0.221  -14.4849   7.4574  26.0811
 YIC  H19  H  HCH2   0   0.239  -15.5866   6.9794  24.8057
 YIC  H20  H  HCH2   0   0.243  -14.0893   8.8650  24.0800
 YIC  H21  H  HCH2   0   0.234  -13.8967   7.4374  23.0828
 YIC  H22  H  HCH1   0   0.304  -11.7225   8.2657  23.5281
 YIC  H23  H  HNH1   0   0.391  -10.2438   7.4071  25.9201
 YIC  H24  H  HCH1   0   0.234  -10.2696   9.9775  27.2611
 YIC  H26  H  HCH2   0   0.252  -11.9532   8.5443  28.4882
 YIC  H27  H  HCH2   0   0.239  -10.6813   7.3773  28.8050
 YIC  H28  H  HCR6   0   0.242  -11.7159  10.9105  29.3604
 YIC  H29  H  HCR6   0   0.248  -11.0985  12.2266  31.3479
 YIC  H30  H  HCR6   0   0.249   -9.5261  11.2917  33.0192
 YIC  H31  H  HCR6   0   0.248   -8.5822   9.0282  32.6765
 YIC  H32  H  HCR6   0   0.242   -9.1968   7.7199  30.6815

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    1.547  0.020  1.547
 YIC  C21  C22  single    1.539  0.020  1.539
 YIC  C20  C19  single    1.530  0.020  1.530
 YIC  C22  C18  single    1.530  0.020  1.530
 YIC  C19  C18  single    1.528  0.020  1.528
 YIC  C18  C17  single    1.523  0.020  1.523
 YIC  C17  C16  single    1.526  0.020  1.526
 YIC  O15  C14  double    1.222  0.020  1.222
 YIC  C16  C14  single    1.518  0.020  1.518
 YIC  C14  N13  single    1.362  0.020  1.362
 YIC  C7   C9   single    1.528  0.020  1.528
 YIC  C7   N13  single    1.455  0.020  1.455
 YIC  C7   C6   single    1.534  0.020  1.534
 YIC  C9   C10  single    1.523  0.020  1.523
 YIC  N13  C12  single    1.458  0.020  1.458
 YIC  C6   O8   double    1.226  0.020  1.226
 YIC  C6   N5   single    1.335  0.020  1.335
 YIC  C10  C11  single    1.524  0.020  1.524
 YIC  C11  C12  single    1.521  0.020  1.521
 YIC  N5   C1   single    1.445  0.020  1.445
 YIC  O3   C2   deloc     1.249  0.020  1.249
 YIC  C1   C2   single    1.549  0.020  1.549
 YIC  C1   C23  single    1.544  0.020  1.544
 YIC  C2   O4   deloc     1.241  0.020  1.241
 YIC  C23  C24  single    1.501  0.020  1.501
 YIC  C24  C29  aromatic  1.394  0.020  1.394
 YIC  C24  C25  aromatic  1.392  0.020  1.392
 YIC  C29  C28  aromatic  1.388  0.020  1.388
 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  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  117.57  3.000
 YIC  N13  C14  O15  121.17  3.000
 YIC  C16  C14  O15  121.22  3.000
 YIC  H2   C16  H1   105.44  3.000
 YIC  H2   C16  C17  110.04  3.000
 YIC  H1   C16  C17  108.64  3.000
 YIC  H2   C16  C14  106.84  3.000
 YIC  H1   C16  C14  110.89  3.000
 YIC  C17  C16  C14  114.59  3.000
 YIC  H4   C17  H3   106.21  3.000
 YIC  H4   C17  C18  109.89  3.000
 YIC  H3   C17  C18  108.02  3.000
 YIC  H4   C17  C16  110.77  3.000
 YIC  H3   C17  C16  107.84  3.000
 YIC  C18  C17  C16  113.77  3.000
 YIC  H5   C18  C19  107.60  3.000
 YIC  H5   C18  C22  108.16  3.000
 YIC  C19  C18  C22  102.20  3.000
 YIC  H5   C18  C17  107.86  3.000
 YIC  C19  C18  C17  116.93  3.000
 YIC  C22  C18  C17  113.64  3.000
 YIC  H7   C22  H6   106.78  3.000
 YIC  H7   C22  C21  110.23  3.000
 YIC  H6   C22  C21  112.90  3.000
 YIC  H7   C22  C18  109.02  3.000
 YIC  H6   C22  C18  112.61  3.000
 YIC  C21  C22  C18  105.29  3.000
 YIC  H9   C21  H8   106.42  3.000
 YIC  H9   C21  C20  111.76  3.000
 YIC  H8   C21  C20  110.73  3.000
 YIC  H9   C21  C22  111.17  3.000
 YIC  H8   C21  C22  111.14  3.000
 YIC  C20  C21  C22  105.71  3.000
 YIC  H11  C20  H10  106.70  3.000
 YIC  H11  C20  C19  109.72  3.000
 YIC  H10  C20  C19  112.41  3.000
 YIC  H11  C20  C21  110.15  3.000
 YIC  H10  C20  C21  112.58  3.000
 YIC  C19  C20  C21  105.30  3.000
 YIC  H13  C19  H12  107.23  3.000
 YIC  H13  C19  C20  112.58  3.000
 YIC  H12  C19  C20  110.47  3.000
 YIC  H13  C19  C18  113.60  3.000
 YIC  H12  C19  C18  109.47  3.000
 YIC  C20  C19  C18  103.49  3.000
 YIC  C7   N13  C12  114.13  3.000
 YIC  C12  N13  C14  125.30  3.000
 YIC  C7   N13  C14  119.64  3.000
 YIC  H15  C12  H14  105.83  3.000
 YIC  H15  C12  C11  109.42  3.000
 YIC  H14  C12  C11  111.23  3.000
 YIC  H15  C12  N13  108.56  3.000
 YIC  H14  C12  N13  110.49  3.000
 YIC  C11  C12  N13  111.13  3.000
 YIC  H17  C11  H16  107.15  3.000
 YIC  H17  C11  C10  110.16  3.000
 YIC  H16  C11  C10  110.87  3.000
 YIC  H17  C11  C12  109.33  3.000
 YIC  H16  C11  C12  109.09  3.000
 YIC  C10  C11  C12  110.17  3.000
 YIC  H19  C10  H18  106.50  3.000
 YIC  H19  C10  C9   109.91  3.000
 YIC  H18  C10  C9   109.91  3.000
 YIC  H19  C10  C11  110.49  3.000
 YIC  H18  C10  C11  109.45  3.000
 YIC  C9   C10  C11  110.50  3.000
 YIC  H21  C9   H20  106.72  3.000
 YIC  H21  C9   C7   107.46  3.000
 YIC  H20  C9   C7   109.67  3.000
 YIC  H21  C9   C10  109.37  3.000
 YIC  H20  C9   C10  111.11  3.000
 YIC  C7   C9   C10  112.29  3.000
 YIC  H22  C7   C6   105.31  3.000
 YIC  H22  C7   C9   108.37  3.000
 YIC  C6   C7   C9   112.74  3.000
 YIC  H22  C7   N13  107.44  3.000
 YIC  C6   C7   N13  112.55  3.000
 YIC  C9   C7   N13  110.09  3.000
 YIC  N5   C6   O8   123.77  3.000
 YIC  N5   C6   C7   115.42  3.000
 YIC  O8   C6   C7   120.70  3.000
 YIC  H23  N5   C1   114.72  3.000
 YIC  H23  N5   C6   120.34  3.000
 YIC  C1   N5   C6   124.89  3.000
 YIC  H24  C1   C23  108.90  3.000
 YIC  H24  C1   C2   109.87  3.000
 YIC  C23  C1   C2   110.35  3.000
 YIC  H24  C1   N5   109.16  3.000
 YIC  C23  C1   N5   109.92  3.000
 YIC  C2   C1   N5   108.62  3.000
 YIC  O3   C2   O4   127.81  3.000
 YIC  O4   C2   C1   116.66  3.000
 YIC  O3   C2   C1   115.51  3.000
 YIC  H27  C23  H26  106.82  3.000
 YIC  H27  C23  C24  110.43  3.000
 YIC  H26  C23  C24  109.05  3.000
 YIC  H27  C23  C1   108.52  3.000
 YIC  H26  C23  C1   107.94  3.000
 YIC  C24  C23  C1   113.82  3.000
 YIC  C25  C24  C29  118.34  3.000
 YIC  C25  C24  C23  121.61  3.000
 YIC  C29  C24  C23  120.05  3.000
 YIC  H28  C29  C28  119.60  3.000
 YIC  H28  C29  C24  119.39  3.000
 YIC  C28  C29  C24  121.01  3.000
 YIC  H29  C28  C27  120.07  3.000
 YIC  H29  C28  C29  119.85  3.000
 YIC  C27  C28  C29  120.09  3.000
 YIC  H30  C27  C26  120.26  3.000
 YIC  H30  C27  C28  120.28  3.000
 YIC  C26  C27  C28  119.46  3.000
 YIC  H31  C26  C25  119.78  3.000
 YIC  H31  C26  C27  120.06  3.000
 YIC  C25  C26  C27  120.17  3.000
 YIC  H32  C25  C26  119.68  3.000
 YIC  H32  C25  C24  119.38  3.000
 YIC  C26  C25  C24  120.93  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  Var_01    C20  C21  C22  C18   16.92  30.0  1
 YIC  Var_02    C21  C20  C19  C18  -32.31  30.0  1
 YIC  Var_03    C19  C20  C21  C22    9.46  30.0  1
 YIC  Var_04    C10  C11  C12  N13  -55.85  30.0  1
 YIC  Var_05    C9   C10  C11  C12   53.68  30.0  1
 YIC  Var_06    C7   C9   C10  C11  -53.05  30.0  1
 YIC  Var_07    C7   N13  C12  C11   58.34  30.0  1
 YIC  Var_08    C29  C24  C23  C1    77.55  30.0  2
 YIC  Var_09    C18  C17  C16  C14  -86.73  30.0  1
 YIC  Var_10    N13  C14  C16  C17  165.86  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

