# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 13:12:48 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  58  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  CR16  0  -0.325  -3.9286  -1.8651   1.6616
 D0L  C2   C  CR6   0   0.136  -3.8187  -1.8167   0.2754
 D0L  C15  C  CH2   0  -0.261   2.0313   0.6126   0.7002
 D0L  C14  C  CH2   0  -0.265   1.7102   2.7305   1.8787
 D0L  C7   C  CH2   0  -0.568  -4.1812  -0.5701  -0.4841
 D0L  C12  C  CH2   0  -0.438  -0.6679   2.9781   1.4840
 D0L  C10  C  C     0   0.563  -0.8869   1.1327  -0.1995
 D0L  C3   C  CR16  0  -0.298  -3.3443  -2.9409  -0.3988
 D0L  C13  C  CH2   0  -0.489   0.4575   3.4519   2.4019
 D0L  C11  C  CH1   0  -0.181  -0.1717   1.5949   1.0573
 D0L  C6   C  CR16  0  -0.239  -3.5676  -3.0089   2.3641
 D0L  C8   C  CH1   0  -0.151  -2.9381   0.1459  -1.0382
 D0L  C5   C  CR16  0  -0.268  -3.0930  -4.1209   1.6840
 D0L  C9   C  C     0   0.536  -3.3823   1.3786  -1.8119
 D0L  C4   C  CR16  0  -0.239  -2.9843  -4.0843   0.2984
 D0L  O2   O  O     0  -0.429  -3.4691   2.4816  -1.3411
 D0L  O3   O  O     0  -0.481  -0.4751   1.3313  -1.3303
 D0L  O1   O  OH1   0  -0.590  -3.7166   1.0691  -3.0562
 D0L  N2   N  NT    0  -0.436   1.2361   1.8118   0.8451
 D0L  C16  C  CH2   0  -0.438   3.4263   0.9014   0.1669
 D0L  C17  C  CH2   0  -0.414   4.2600  -0.3622  -0.0068
 D0L  C18  C  CH2   0  -0.410   5.6590  -0.0783  -0.5384
 D0L  C19  C  CH2   0  -0.406   6.5131  -1.3300  -0.6988
 D0L  C20  C  CH2   0  -0.419   7.9086  -1.0386  -1.2367
 D0L  C21  C  CH3   0  -0.661   8.7639  -2.2900  -1.3815
 D0L  N1   N  NH1   0  -0.646  -2.0600   0.5148   0.0343
 D0L  H1   H  HCR6  0   0.256  -4.3085  -1.0033   2.1988
 D0L  H2   H  HCH2  0   0.185   2.1111   0.0700   1.6597
 D0L  H3   H  HCH2  0   0.227   1.5270  -0.0618   0.0034
 D0L  H4   H  HCH2  0   0.226   2.4456   3.4255   1.4670
 D0L  H5   H  HCH2  0   0.203   2.2070   2.1898   2.6965
 D0L  H6   H  HCH2  0   0.288  -4.8365  -0.8183  -1.3209
 D0L  H7   H  HCH2  0   0.276  -4.7356   0.1161   0.1610
 D0L  H8   H  HCH2  0   0.247  -1.6402   2.9438   1.9738
 D0L  H9   H  HCH2  0   0.240  -0.7526   3.6232   0.6069
 D0L  H10  H  HCR6  0   0.252  -3.2577  -2.9237  -1.4794
 D0L  H11  H  HCH2  0   0.238   0.2530   3.1508   3.4299
 D0L  H12  H  HCH2  0   0.247   0.5650   4.5360   2.3981
 D0L  H13  H  HCH1  0   0.230  -0.3749   0.8701   1.8680
 D0L  H14  H  HCR6  0   0.257  -3.6591  -3.0289   3.4424
 D0L  H15  H  HCH1  0   0.291  -2.4229  -0.5309  -1.7260
 D0L  H16  H  HCR6  0   0.257  -2.8106  -5.0130   2.2278
 D0L  H17  H  HCR6  0   0.257  -2.6199  -4.9503  -0.2390
 D0L  H18  H  HOH1  0   0.485  -4.0559   1.8510  -3.5178
 D0L  H20  H  HCH2  0   0.214   3.3357   1.4202  -0.7926
 D0L  H21  H  HCH2  0   0.220   3.9522   1.5848   0.8413
 D0L  H22  H  HCH2  0   0.209   4.3351  -0.8835   0.9541
 D0L  H23  H  HCH2  0   0.209   3.7455  -1.0507  -0.6862
 D0L  H24  H  HCH2  0   0.207   5.5824   0.4336  -1.5042
 D0L  H25  H  HCH2  0   0.207   6.1660   0.6216   0.1351
 D0L  H26  H  HCH2  0   0.205   6.5957  -1.8384   0.2685
 D0L  H27  H  HCH2  0   0.206   6.0067  -2.0343  -1.3684
 D0L  H28  H  HCH2  0   0.210   7.8242  -0.5392  -2.2072
 D0L  H29  H  HCH2  0   0.210   8.4100  -0.3271  -0.5731
 D0L  H30  H  HCH3  0   0.215   8.8970  -2.7895  -0.4200
 D0L  H31  H  HCH3  0   0.215   8.3022  -3.0076  -2.0626
 D0L  H32  H  HCH3  0   0.225   9.7550  -2.0558  -1.7719
 D0L  H33  H  HNH1  0   0.403  -2.3779   0.4079   0.9845

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    1.524  0.020  1.524
 D0L  C18  C17  single    1.523  0.020  1.523
 D0L  C14  N2   single    1.462  0.020  1.462
 D0L  C14  C13  single    1.537  0.020  1.537
 D0L  C17  C16  single    1.524  0.020  1.524
 D0L  C15  N2   single    1.446  0.020  1.446
 D0L  C15  C16  single    1.521  0.020  1.521
 D0L  N2   C11  single    1.440  0.020  1.440
 D0L  C13  C12  single    1.528  0.020  1.528
 D0L  O2   C9   double    1.202  0.020  1.202
 D0L  C11  C12  single    1.530  0.020  1.530
 D0L  C11  C10  single    1.518  0.020  1.518
 D0L  C5   C4   aromatic  1.390  0.020  1.390
 D0L  C5   C6   aromatic  1.387  0.020  1.387
 D0L  C4   C3   aromatic  1.387  0.020  1.387
 D0L  C6   C1   aromatic  1.390  0.020  1.390
 D0L  N1   C10  single    1.346  0.020  1.346
 D0L  N1   C8   single    1.434  0.020  1.434
 D0L  C9   O1   single    1.325  0.020  1.325
 D0L  C9   C8   single    1.522  0.020  1.522
 D0L  C10  O3   double    1.220  0.020  1.220
 D0L  C3   C2   aromatic  1.394  0.020  1.394
 D0L  C1   C2   aromatic  1.391  0.020  1.391
 D0L  C8   C7   single    1.538  0.020  1.538
 D0L  C2   C7   single    1.504  0.020  1.504
 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  O1   H18  single    0.850  0.020  0.980
 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    0.860  0.020  1.020

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   119.65  3.000
 D0L  H1   C1   C2   119.58  3.000
 D0L  C6   C1   C2   120.77  3.000
 D0L  C3   C2   C7   120.41  3.000
 D0L  C7   C2   C1   120.85  3.000
 D0L  C3   C2   C1   118.73  3.000
 D0L  H3   C15  H2   106.49  3.000
 D0L  H3   C15  C16  108.47  3.000
 D0L  H2   C15  C16  109.35  3.000
 D0L  H3   C15  N2   108.77  3.000
 D0L  H2   C15  N2   111.09  3.000
 D0L  C16  C15  N2   112.45  3.000
 D0L  H5   C14  H4   106.80  3.000
 D0L  H5   C14  N2   111.32  3.000
 D0L  H4   C14  N2   110.60  3.000
 D0L  H5   C14  C13  110.24  3.000
 D0L  H4   C14  C13  112.22  3.000
 D0L  N2   C14  C13  105.74  3.000
 D0L  H7   C7   H6   106.90  3.000
 D0L  H7   C7   C8   109.29  3.000
 D0L  H6   C7   C8   108.36  3.000
 D0L  H7   C7   C2   110.15  3.000
 D0L  H6   C7   C2   110.08  3.000
 D0L  C8   C7   C2   111.90  3.000
 D0L  H9   C12  H8   108.09  3.000
 D0L  H9   C12  C11  109.58  3.000
 D0L  H8   C12  C11  112.73  3.000
 D0L  H9   C12  C13  110.88  3.000
 D0L  H8   C12  C13  113.40  3.000
 D0L  C11  C12  C13  102.06  3.000
 D0L  N1   C10  O3   122.00  3.000
 D0L  O3   C10  C11  123.98  3.000
 D0L  N1   C10  C11  113.98  3.000
 D0L  H10  C3   C4   119.57  3.000
 D0L  H10  C3   C2   119.76  3.000
 D0L  C4   C3   C2   120.67  3.000
 D0L  H12  C13  H11  107.25  3.000
 D0L  H12  C13  C12  112.29  3.000
 D0L  H11  C13  C12  110.03  3.000
 D0L  H12  C13  C14  112.67  3.000
 D0L  H11  C13  C14  110.12  3.000
 D0L  C12  C13  C14  104.49  3.000
 D0L  H13  C11  N2   112.72  3.000
 D0L  H13  C11  C10  108.70  3.000
 D0L  N2   C11  C10  112.61  3.000
 D0L  H13  C11  C12  109.17  3.000
 D0L  C10  C11  C12  110.69  3.000
 D0L  N2   C11  C12  102.83  3.000
 D0L  H14  C6   C5   120.17  3.000
 D0L  H14  C6   C1   119.78  3.000
 D0L  C5   C6   C1   120.05  3.000
 D0L  H15  C8   N1   109.93  3.000
 D0L  H15  C8   C9   108.60  3.000
 D0L  N1   C8   C9   110.52  3.000
 D0L  H15  C8   C7   108.61  3.000
 D0L  C9   C8   C7   108.93  3.000
 D0L  N1   C8   C7   110.20  3.000
 D0L  H16  C5   C4   120.13  3.000
 D0L  H16  C5   C6   120.25  3.000
 D0L  C4   C5   C6   119.62  3.000
 D0L  O1   C9   O2   124.31  3.000
 D0L  O1   C9   C8   111.22  3.000
 D0L  O2   C9   C8   124.41  3.000
 D0L  H17  C4   C5   120.00  3.000
 D0L  H17  C4   C3   119.83  3.000
 D0L  C5   C4   C3   120.16  3.000
 D0L  H18  O1   C9   110.31  3.000
 D0L  C11  N2   C14  107.91  3.000
 D0L  C11  N2   C15  115.31  3.000
 D0L  C14  N2   C15  114.43  3.000
 D0L  H21  C16  H20  106.49  3.000
 D0L  H21  C16  C17  108.97  3.000
 D0L  H20  C16  C17  109.78  3.000
 D0L  H21  C16  C15  110.07  3.000
 D0L  H20  C16  C15  108.75  3.000
 D0L  C17  C16  C15  112.60  3.000
 D0L  H23  C17  H22  106.09  3.000
 D0L  H23  C17  C18  109.39  3.000
 D0L  H22  C17  C18  109.37  3.000
 D0L  H23  C17  C16  109.56  3.000
 D0L  H22  C17  C16  109.39  3.000
 D0L  C18  C17  C16  112.81  3.000
 D0L  H25  C18  H24  106.00  3.000
 D0L  H25  C18  C19  109.27  3.000
 D0L  H24  C18  C19  109.28  3.000
 D0L  H25  C18  C17  109.24  3.000
 D0L  H24  C18  C17  109.29  3.000
 D0L  C19  C18  C17  113.48  3.000
 D0L  H27  C19  H26  106.02  3.000
 D0L  H27  C19  C20  109.30  3.000
 D0L  H26  C19  C20  109.34  3.000
 D0L  H27  C19  C18  109.47  3.000
 D0L  H26  C19  C18  109.29  3.000
 D0L  C20  C19  C18  113.17  3.000
 D0L  H29  C20  H28  106.04  3.000
 D0L  H29  C20  C21  109.55  3.000
 D0L  H28  C20  C21  109.51  3.000
 D0L  H29  C20  C19  109.26  3.000
 D0L  H28  C20  C19  109.24  3.000
 D0L  C21  C20  C19  113.01  3.000
 D0L  H32  C21  H31  107.58  3.000
 D0L  H32  C21  H30  107.62  3.000
 D0L  H31  C21  H30  107.48  3.000
 D0L  H32  C21  C20  111.59  3.000
 D0L  H31  C21  C20  111.22  3.000
 D0L  H30  C21  C20  111.15  3.000
 D0L  H33  N1   C8   118.99  3.000
 D0L  H33  N1   C10  119.17  3.000
 D0L  C8   N1   C10  121.44  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  CONST_17  H18  O1   C9   C8    180.00   0.0  0
 D0L  Var_01    C11  C12  C13  C14    28.04  30.0  1
 D0L  Var_02    N2   C14  C13  C12    -6.12  30.0  1
 D0L  Var_03    C11  N2   C14  C13   -20.22  30.0  1
 D0L  Var_04    C8   C7   C2   C1    108.11  30.0  2
 D0L  Var_05    C16  C15  N2   C14   -67.14  30.0  1
 D0L  Var_06    C17  C16  C15  N2   -179.14  30.0  3
 D0L  Var_07    C18  C17  C16  C15  -179.90  30.0  1
 D0L  Var_08    C19  C18  C17  C16   179.17  30.0  1
 D0L  Var_09    C20  C19  C18  C17   179.75  30.0  1
 D0L  Var_10    C21  C20  C19  C18   179.38  30.0  1
 D0L  Var_11    H30  C21  C20  C19   -60.11  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
 D0L  plan-3  H18  0.020

