# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:07:41 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-1-heptylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCN1CCC[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
 D0L  D0L  '(2~{S})-2-[[(2~{S})-1-heptylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid'  ligand  57  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D0L
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
 D0L  C1   C  C1     0  -0.326  -3.4361  -2.1306   1.6149
 D0L  C2   C  C      0   0.164  -3.5986  -1.9353   0.2460
 D0L  C15  C  CH2    0  -0.256   1.9637   0.7195   0.7636
 D0L  C14  C  CH2    0  -0.282   1.6058   2.9145   1.7792
 D0L  C7   C  CH2    0  -0.562  -4.1778  -0.6584  -0.2945
 D0L  C12  C  CH2    0  -0.470  -0.7748   3.0995   1.4649
 D0L  C10  C  C      0   0.538  -0.9632   1.1732  -0.1589
 D0L  C3   C  C1     0  -0.308  -3.1807  -2.9439  -0.6210
 D0L  C13  C  CH2    0  -0.452   0.4800   3.9388   1.7540
 D0L  C11  C  CR15   0  -0.180  -0.2232   1.7138   1.0544
 D0L  C6   C  C1     0  -0.240  -2.8705  -3.3001   2.1083
 D0L  C8   C  CH1    0  -0.175  -3.1118   0.2787  -0.8746
 D0L  C5   C  C1     0  -0.275  -2.4567  -4.2956   1.2344
 D0L  C9   C  C      0   0.411  -3.7826   1.5411  -1.4812
 D0L  C4   C  C1     0  -0.239  -2.6151  -4.1138  -0.1346
 D0L  O2   O  O      0  -0.584  -3.5883   2.6291  -0.9147
 D0L  O3   O  O      0  -0.498  -0.5349   1.2717  -1.2990
 D0L  O1   O  OC    -1  -0.616  -4.4827   1.3246  -2.4903
 D0L  N2   N  NR5    0  -0.426   1.1807   1.9352   0.7962
 D0L  C16  C  CH2    0  -0.443   3.4025   0.9451   0.3223
 D0L  C17  C  CH2    0  -0.414   4.1453  -0.3655   0.0936
 D0L  C18  C  CH2    0  -0.411   5.6047  -0.1662  -0.2954
 D0L  C19  C  CH2    0  -0.406   6.3333  -1.4732  -0.5814
 D0L  C20  C  CH2    0  -0.419   7.7987  -1.2803  -0.9520
 D0L  C21  C  CH3    0  -0.662   8.5093  -2.5929  -1.2525
 D0L  N1   N  NH1    0  -0.619  -2.1347   0.5887   0.1382
 D0L  H1   H  H      0   0.244  -3.7610  -1.3610   2.3065
 D0L  H2   H  HCH2   0   0.182   1.9583   0.2133   1.7465
 D0L  H3   H  HCH2   0   0.225   1.4917   0.0285   0.0605
 D0L  H4   H  HCH2   0   0.236   2.5743   3.3452   1.5207
 D0L  H5   H  HCH2   0   0.187   1.7027   2.4710   2.7858
 D0L  H6   H  HCH2   0   0.262  -4.8951  -0.8726  -1.0874
 D0L  H7   H  HCH2   0   0.248  -4.7309  -0.1392   0.4950
 D0L  H8   H  HCH2   0   0.240  -1.4165   3.0035   2.3398
 D0L  H9   H  HCH2   0   0.254  -1.3826   3.5390   0.6740
 D0L  H10  H  H      0   0.246  -3.3024  -2.8118  -1.6903
 D0L  H11  H  HCH2   0   0.236   0.4101   4.4957   2.6879
 D0L  H12  H  HCH2   0   0.233   0.6484   4.6613   0.9545
 D0L  H13  H  HCR5   0   0.226  -0.3676   1.0092   1.8938
 D0L  H14  H  H      0   0.252  -2.7544  -3.4329   3.1765
 D0L  H15  H  HCH1   0   0.241  -2.6021  -0.2517  -1.6839
 D0L  H16  H  H      0   0.253  -2.0176  -5.2082   1.6160
 D0L  H17  H  H      0   0.252  -2.3007  -4.8872  -0.8240
 D0L  H20  H  HCH2   0   0.214   3.4018   1.5327  -0.6010
 D0L  H21  H  HCH2   0   0.218   3.9400   1.5382   1.0689
 D0L  H22  H  HCH2   0   0.209   4.0933  -0.9813   0.9984
 D0L  H23  H  HCH2   0   0.209   3.6365  -0.9374  -0.6905
 D0L  H24  H  HCH2   0   0.207   5.6604   0.4798  -1.1785
 D0L  H25  H  HCH2   0   0.207   6.1232   0.3722   0.5060
 D0L  H26  H  HCH2   0   0.206   6.2648  -2.1274   0.2949
 D0L  H27  H  HCH2   0   0.206   5.8223  -2.0029  -1.3937
 D0L  H28  H  HCH2   0   0.210   7.8679  -0.6180  -1.8207
 D0L  H29  H  HCH2   0   0.210   8.3138  -0.7635  -0.1362
 D0L  H30  H  HCH3   0   0.215   8.4697  -3.2662  -0.3944
 D0L  H31  H  HCH3   0   0.215   8.0451  -3.1089  -2.0954
 D0L  H32  H  HCH3   0   0.225   9.5596  -2.4353  -1.5005
 D0L  H33  H  HNH1   0   0.383  -2.4623   0.6714   1.0887

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
 D0L  C21  C20  single    1.523  0.020  1.523
 D0L  C20  C19  single    1.524  0.020  1.524
 D0L  C19  C18  single    1.523  0.020  1.523
 D0L  C18  C17  single    1.524  0.020  1.524
 D0L  C14  N2   single    1.451  0.020  1.451
 D0L  C14  C13  single    1.522  0.020  1.522
 D0L  C17  C16  single    1.524  0.020  1.524
 D0L  C15  N2   single    1.446  0.020  1.446
 D0L  C15  C16  single    1.522  0.020  1.522
 D0L  N2   C11  single    1.445  0.020  1.445
 D0L  C13  C12  single    1.537  0.020  1.537
 D0L  O2   C9   deloc     1.242  0.020  1.242
 D0L  C11  C12  single    1.547  0.020  1.547
 D0L  C11  C10  single    1.520  0.020  1.520
 D0L  C5   C4   aromatic  1.390  0.020  1.390
 D0L  C5   C6   aromatic  1.388  0.020  1.388
 D0L  C4   C3   aromatic  1.387  0.020  1.387
 D0L  C6   C1   aromatic  1.390  0.020  1.390
 D0L  N1   C10  single    1.343  0.020  1.343
 D0L  N1   C8   single    1.441  0.020  1.441
 D0L  C9   O1   deloc     1.247  0.020  1.247
 D0L  C9   C8   single    1.553  0.020  1.553
 D0L  C10  O3   double    1.222  0.020  1.222
 D0L  C3   C2   aromatic  1.394  0.020  1.394
 D0L  C1   C2   aromatic  1.392  0.020  1.392
 D0L  C8   C7   single    1.533  0.020  1.533
 D0L  C2   C7   single    1.503  0.020  1.503
 D0L  C1   H1   single    0.930  0.020  1.080
 D0L  C15  H2   single    0.970  0.020  1.090
 D0L  C15  H3   single    0.970  0.020  1.090
 D0L  C14  H4   single    0.970  0.020  1.090
 D0L  C14  H5   single    0.970  0.020  1.090
 D0L  C7   H6   single    0.970  0.020  1.090
 D0L  C7   H7   single    0.970  0.020  1.090
 D0L  C12  H8   single    0.970  0.020  1.090
 D0L  C12  H9   single    0.970  0.020  1.090
 D0L  C3   H10  single    0.930  0.020  1.080
 D0L  C13  H11  single    0.970  0.020  1.090
 D0L  C13  H12  single    0.970  0.020  1.090
 D0L  C11  H13  single    0.970  0.020  1.090
 D0L  C6   H14  single    0.930  0.020  1.080
 D0L  C8   H15  single    0.970  0.020  1.090
 D0L  C5   H16  single    0.930  0.020  1.080
 D0L  C4   H17  single    0.930  0.020  1.080
 D0L  C16  H20  single    0.970  0.020  1.090
 D0L  C16  H21  single    0.970  0.020  1.090
 D0L  C17  H22  single    0.970  0.020  1.090
 D0L  C17  H23  single    0.970  0.020  1.090
 D0L  C18  H24  single    0.970  0.020  1.090
 D0L  C18  H25  single    0.970  0.020  1.090
 D0L  C19  H26  single    0.970  0.020  1.090
 D0L  C19  H27  single    0.970  0.020  1.090
 D0L  C20  H28  single    0.970  0.020  1.090
 D0L  C20  H29  single    0.970  0.020  1.090
 D0L  C21  H30  single    0.970  0.020  1.090
 D0L  C21  H31  single    0.970  0.020  1.090
 D0L  C21  H32  single    0.970  0.020  1.090
 D0L  N1   H33  single    0.890  0.020  1.040

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
 D0L  H1   C1   C6   119.52  3.000
 D0L  H1   C1   C2   119.50  3.000
 D0L  C6   C1   C2   120.98  3.000
 D0L  C3   C2   C7   120.44  3.000
 D0L  C7   C2   C1   121.19  3.000
 D0L  C3   C2   C1   118.36  3.000
 D0L  H3   C15  H2   106.28  3.000
 D0L  H3   C15  C16  108.39  3.000
 D0L  H2   C15  C16  109.29  3.000
 D0L  H3   C15  N2   108.19  3.000
 D0L  H2   C15  N2   111.23  3.000
 D0L  C16  C15  N2   113.19  3.000
 D0L  H5   C14  H4   107.26  3.000
 D0L  H5   C14  N2   111.85  3.000
 D0L  H4   C14  N2   111.47  3.000
 D0L  H5   C14  C13  110.50  3.000
 D0L  H4   C14  C13  112.76  3.000
 D0L  N2   C14  C13  103.07  3.000
 D0L  H7   C7   H6   106.57  3.000
 D0L  H7   C7   C8   109.52  3.000
 D0L  H6   C7   C8   107.59  3.000
 D0L  H7   C7   C2   109.77  3.000
 D0L  H6   C7   C2   110.38  3.000
 D0L  C8   C7   C2   112.80  3.000
 D0L  H9   C12  H8   106.85  3.000
 D0L  H9   C12  C11  111.56  3.000
 D0L  H8   C12  C11  110.14  3.000
 D0L  H9   C12  C13  111.81  3.000
 D0L  H8   C12  C13  112.21  3.000
 D0L  C11  C12  C13  104.36  3.000
 D0L  N1   C10  O3   123.20  3.000
 D0L  O3   C10  C11  123.05  3.000
 D0L  N1   C10  C11  113.76  3.000
 D0L  H10  C3   C4   119.62  3.000
 D0L  H10  C3   C2   119.44  3.000
 D0L  C4   C3   C2   120.94  3.000
 D0L  H12  C13  H11  107.44  3.000
 D0L  H12  C13  C12  110.48  3.000
 D0L  H11  C13  C12  112.82  3.000
 D0L  H12  C13  C14  110.10  3.000
 D0L  H11  C13  C14  112.16  3.000
 D0L  C12  C13  C14  103.85  3.000
 D0L  H13  C11  N2   111.12  3.000
 D0L  H13  C11  C10  108.40  3.000
 D0L  N2   C11  C10  112.63  3.000
 D0L  H13  C11  C12  108.84  3.000
 D0L  C10  C11  C12  110.90  3.000
 D0L  N2   C11  C12  104.87  3.000
 D0L  H14  C6   C5   120.08  3.000
 D0L  H14  C6   C1   119.82  3.000
 D0L  C5   C6   C1   120.10  3.000
 D0L  H15  C8   N1   107.96  3.000
 D0L  H15  C8   C9   107.85  3.000
 D0L  N1   C8   C9   113.11  3.000
 D0L  H15  C8   C7   107.92  3.000
 D0L  C9   C8   C7   110.14  3.000
 D0L  N1   C8   C7   109.69  3.000
 D0L  H16  C5   C4   120.26  3.000
 D0L  H16  C5   C6   120.25  3.000
 D0L  C4   C5   C6   119.49  3.000
 D0L  O1   C9   O2   127.51  3.000
 D0L  O1   C9   C8   114.67  3.000
 D0L  O2   C9   C8   117.81  3.000
 D0L  H17  C4   C5   120.04  3.000
 D0L  H17  C4   C3   119.83  3.000
 D0L  C5   C4   C3   120.13  3.000
 D0L  C11  N2   C14  105.49  3.000
 D0L  C11  N2   C15  113.66  3.000
 D0L  C14  N2   C15  115.08  3.000
 D0L  H21  C16  H20  106.55  3.000
 D0L  H21  C16  C17  109.21  3.000
 D0L  H20  C16  C17  109.61  3.000
 D0L  H21  C16  C15  110.29  3.000
 D0L  H20  C16  C15  108.88  3.000
 D0L  C17  C16  C15  112.14  3.000
 D0L  H23  C17  H22  106.00  3.000
 D0L  H23  C17  C18  109.29  3.000
 D0L  H22  C17  C18  109.26  3.000
 D0L  H23  C17  C16  109.27  3.000
 D0L  H22  C17  C16  109.66  3.000
 D0L  C18  C17  C16  113.12  3.000
 D0L  H25  C18  H24  106.01  3.000
 D0L  H25  C18  C19  109.43  3.000
 D0L  H24  C18  C19  109.28  3.000
 D0L  H25  C18  C17  109.32  3.000
 D0L  H24  C18  C17  109.37  3.000
 D0L  C19  C18  C17  113.19  3.000
 D0L  H27  C19  H26  105.97  3.000
 D0L  H27  C19  C20  109.23  3.000
 D0L  H26  C19  C20  109.28  3.000
 D0L  H27  C19  C18  109.32  3.000
 D0L  H26  C19  C18  109.40  3.000
 D0L  C20  C19  C18  113.38  3.000
 D0L  H29  C20  H28  106.03  3.000
 D0L  H29  C20  C21  109.54  3.000
 D0L  H28  C20  C21  109.60  3.000
 D0L  H29  C20  C19  109.34  3.000
 D0L  H28  C20  C19  109.29  3.000
 D0L  C21  C20  C19  112.81  3.000
 D0L  H32  C21  H31  107.58  3.000
 D0L  H32  C21  H30  107.63  3.000
 D0L  H31  C21  H30  107.46  3.000
 D0L  H32  C21  C20  111.70  3.000
 D0L  H31  C21  C20  111.19  3.000
 D0L  H30  C21  C20  111.08  3.000
 D0L  H33  N1   C8   117.36  3.000
 D0L  H33  N1   C10  117.15  3.000
 D0L  C8   N1   C10  121.99  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
 D0L  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 D0L  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 D0L  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 D0L  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 D0L  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 D0L  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 D0L  CONST_07  C4   C3   C2   C7    180.00   0.0  0
 D0L  CONST_08  C6   C1   C2   C7    180.00   0.0  0
 D0L  CONST_09  H16  C5   C6   C1    180.00   0.0  0
 D0L  CONST_10  H10  C3   C2   C1    180.00   0.0  0
 D0L  CONST_11  H17  C4   C3   C2    180.00   0.0  0
 D0L  CONST_12  H14  C6   C1   C2    180.00   0.0  0
 D0L  CONST_13  H1   C1   C2   C3    180.00   0.0  0
 D0L  CONST_14  C8   N1   C10  C11   180.00   0.0  0
 D0L  CONST_15  H33  N1   C10  C11     0.00   0.0  0
 D0L  CONST_16  O3   C10  N1   C8      0.00   0.0  0
 D0L  Var_01    C11  C12  C13  C14   -11.58  30.0  1
 D0L  Var_02    N2   C14  C13  C12    33.44  30.0  1
 D0L  Var_03    C11  N2   C14  C13   -44.19  30.0  1
 D0L  Var_04    C8   C7   C2   C1    102.89  30.0  2
 D0L  Var_05    C16  C15  N2   C14   -65.33  30.0  1
 D0L  Var_06    C17  C16  C15  N2   -171.39  30.0  3
 D0L  Var_07    C18  C17  C16  C15  -177.71  30.0  1
 D0L  Var_08    C19  C18  C17  C16  -177.58  30.0  2
 D0L  Var_09    C20  C19  C18  C17  -179.19  30.0  1
 D0L  Var_10    C21  C20  C19  C18  -179.26  30.0  1
 D0L  Var_11    H30  C21  C20  C19   -58.95  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
 D0L  chir_01  C11  N2  C12  C10  negativ
 D0L  chir_02  C8   N1  C9   C7   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
 D0L  plan-1  C1   0.020
 D0L  plan-1  C2   0.020
 D0L  plan-1  C7   0.020
 D0L  plan-1  C3   0.020
 D0L  plan-1  C6   0.020
 D0L  plan-1  C5   0.020
 D0L  plan-1  C4   0.020
 D0L  plan-1  H1   0.020
 D0L  plan-1  H10  0.020
 D0L  plan-1  H14  0.020
 D0L  plan-1  H16  0.020
 D0L  plan-1  H17  0.020
 D0L  plan-2  C10  0.020
 D0L  plan-2  C11  0.020
 D0L  plan-2  C8   0.020
 D0L  plan-2  O3   0.020
 D0L  plan-2  N1   0.020
 D0L  plan-2  H33  0.020
 D0L  plan-3  C8   0.020
 D0L  plan-3  C9   0.020
 D0L  plan-3  O2   0.020
 D0L  plan-3  O1   0.020

