# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 09:28:59 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: (3S,4R)-1-acetyl-4-phenylpyrrolidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1C[C@H]([C@@H](C1)c2ccccc2)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
 VXG  VXG  '(3S,4R)-1-acetyl-4-phenylpyrrolidine-3-carboxylic acid'  ligand  31  17  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VXG
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
 VXG  N1   N  NT     0  -0.460  -30.3630  13.5445  -21.2108
 VXG  C4   C  CR6    0   0.198  -29.5046  16.8233  -22.6862
 VXG  C5   C  CR16   0  -0.332  -29.7714  18.1530  -22.3713
 VXG  C6   C  CR16   0  -0.236  -29.0612  19.1882  -22.9669
 VXG  C7   C  CR16   0  -0.273  -28.0664  18.9055  -23.8918
 VXG  C8   C  CR16   0  -0.235  -27.7902  17.5826  -24.2155
 VXG  C10  C  CH2    0  -0.223  -29.4787  14.6975  -21.2628
 VXG  C13  C  CH2    0  -0.252  -31.4798  13.6643  -22.1449
 VXG  O1   O  O      0  -0.597  -32.2876  15.7229  -24.8902
 VXG  C1   C  C      0   0.413  -32.2906  15.5947  -23.6517
 VXG  C2   C  CH1    0  -0.365  -31.0945  14.8473  -23.0251
 VXG  C3   C  CH1    0  -0.388  -30.2989  15.7216  -22.0466
 VXG  C9   C  CR16   0  -0.324  -28.5028  16.5529  -23.6182
 VXG  C11  C  C      0   0.503  -30.1587  12.5256  -20.3596
 VXG  C12  C  CH3    0  -0.790  -31.1878  11.4219  -20.3896
 VXG  O2   O  O      0  -0.508  -29.1911  12.4932  -19.6062
 VXG  O3   O  OC    -1  -0.599  -33.1479  16.0215  -22.8517
 VXG  H1   H  HCR6   0   0.246  -30.5469  18.3817  -21.6493
 VXG  H2   H  HCR6   0   0.251  -29.2860  20.2146  -22.7062
 VXG  H3   H  HCR6   0   0.251  -27.5103  19.7086  -24.3582
 VXG  H4   H  HCR6   0   0.250  -27.0176  17.3520  -24.9383
 VXG  H5   H  HCH2   0   0.231  -28.5429  14.4492  -21.7745
 VXG  H6   H  HCH2   0   0.248  -29.2248  15.0517  -20.2631
 VXG  H7   H  HCH2   0   0.232  -32.4131  13.8698  -21.6129
 VXG  H8   H  HCH2   0   0.247  -31.6148  12.7500  -22.7249
 VXG  H9   H  HCH1   0   0.227  -30.4252  14.4967  -23.8173
 VXG  H10  H  HCH1   0   0.255  -31.0182  16.1737  -21.3568
 VXG  H11  H  HCR6   0   0.246  -28.2772  15.5273  -23.8867
 VXG  H12  H  HCH3   0   0.262  -30.9921  10.7151  -19.5871
 VXG  H13  H  HCH3   0   0.257  -32.2019  11.8077  -20.2777
 VXG  H14  H  HCH3   0   0.263  -31.1533  10.8815  -21.3377

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
 VXG  O1   C1   deloc     1.245  0.020  1.245
 VXG  C8   C7   aromatic  1.390  0.020  1.390
 VXG  C8   C9   aromatic  1.387  0.020  1.387
 VXG  C7   C6   aromatic  1.387  0.020  1.387
 VXG  C1   C2   single    1.543  0.020  1.543
 VXG  C1   O3   deloc     1.248  0.020  1.248
 VXG  C9   C4   aromatic  1.395  0.020  1.395
 VXG  C6   C5   aromatic  1.389  0.020  1.389
 VXG  C2   C13  single    1.524  0.020  1.524
 VXG  C2   C3   single    1.535  0.020  1.535
 VXG  C4   C5   aromatic  1.392  0.020  1.392
 VXG  C4   C3   single    1.501  0.020  1.501
 VXG  C13  N1   single    1.461  0.020  1.461
 VXG  C3   C10  single    1.528  0.020  1.528
 VXG  C10  N1   single    1.454  0.020  1.454
 VXG  N1   C11  single    1.343  0.020  1.343
 VXG  C11  C12  single    1.509  0.020  1.509
 VXG  C11  O2   double    1.227  0.020  1.227
 VXG  C5   H1   single    0.930  0.020  1.080
 VXG  C6   H2   single    0.930  0.020  1.080
 VXG  C7   H3   single    0.930  0.020  1.080
 VXG  C8   H4   single    0.930  0.020  1.080
 VXG  C10  H5   single    0.970  0.020  1.090
 VXG  C10  H6   single    0.970  0.020  1.090
 VXG  C13  H7   single    0.970  0.020  1.090
 VXG  C13  H8   single    0.970  0.020  1.090
 VXG  C2   H9   single    0.970  0.020  1.090
 VXG  C3   H10  single    0.970  0.020  1.090
 VXG  C9   H11  single    0.930  0.020  1.080
 VXG  C12  H12  single    0.970  0.020  1.090
 VXG  C12  H13  single    0.970  0.020  1.090
 VXG  C12  H14  single    0.970  0.020  1.090

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
 VXG  C11  N1   C13  125.70  3.000
 VXG  C11  N1   C10  122.12  3.000
 VXG  C13  N1   C10  112.15  3.000
 VXG  C9   C4   C3   121.50  3.000
 VXG  C3   C4   C5   120.20  3.000
 VXG  C9   C4   C5   118.29  3.000
 VXG  H1   C5   C6   119.61  3.000
 VXG  H1   C5   C4   119.29  3.000
 VXG  C6   C5   C4   121.10  3.000
 VXG  H2   C6   C7   120.17  3.000
 VXG  H2   C6   C5   119.80  3.000
 VXG  C7   C6   C5   120.03  3.000
 VXG  H3   C7   C8   120.25  3.000
 VXG  H3   C7   C6   120.29  3.000
 VXG  C8   C7   C6   119.45  3.000
 VXG  H4   C8   C9   119.72  3.000
 VXG  H4   C8   C7   120.00  3.000
 VXG  C9   C8   C7   120.28  3.000
 VXG  H6   C10  H5   107.64  3.000
 VXG  H6   C10  C3   112.17  3.000
 VXG  H5   C10  C3   111.77  3.000
 VXG  H6   C10  N1   111.49  3.000
 VXG  H5   C10  N1   110.90  3.000
 VXG  C3   C10  N1   102.90  3.000
 VXG  H8   C13  H7   108.09  3.000
 VXG  H8   C13  C2   112.00  3.000
 VXG  H7   C13  C2   110.54  3.000
 VXG  H8   C13  N1   111.46  3.000
 VXG  H7   C13  N1   110.90  3.000
 VXG  C2   C13  N1   103.87  3.000
 VXG  O3   C1   C2   115.96  3.000
 VXG  O3   C1   O1   127.16  3.000
 VXG  C2   C1   O1   116.87  3.000
 VXG  H9   C2   C3   109.08  3.000
 VXG  H9   C2   C1   109.58  3.000
 VXG  C3   C2   C1   112.63  3.000
 VXG  H9   C2   C13  108.90  3.000
 VXG  C3   C2   C13  101.83  3.000
 VXG  C1   C2   C13  114.49  3.000
 VXG  H10  C3   C2   107.25  3.000
 VXG  H10  C3   C10  107.84  3.000
 VXG  C2   C3   C10  102.91  3.000
 VXG  H10  C3   C4   108.25  3.000
 VXG  C10  C3   C4   115.23  3.000
 VXG  C2   C3   C4   114.88  3.000
 VXG  H11  C9   C8   119.26  3.000
 VXG  H11  C9   C4   119.90  3.000
 VXG  C8   C9   C4   120.85  3.000
 VXG  O2   C11  C12  122.05  3.000
 VXG  O2   C11  N1   121.95  3.000
 VXG  C12  C11  N1   116.00  3.000
 VXG  H14  C12  H13  107.07  3.000
 VXG  H14  C12  H12  108.27  3.000
 VXG  H13  C12  H12  108.75  3.000
 VXG  H14  C12  C11  110.96  3.000
 VXG  H13  C12  C11  111.91  3.000
 VXG  H12  C12  C11  109.76  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
 VXG  CONST_01  C7   C8   C9   C4      0.00   0.0  0
 VXG  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 VXG  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 VXG  CONST_04  C8   C9   C4   C5      0.00   0.0  0
 VXG  CONST_05  C9   C8   C7   C6      0.00   0.0  0
 VXG  CONST_06  C9   C4   C5   C6      0.00   0.0  0
 VXG  CONST_07  C3   C4   C5   C6    180.00   0.0  0
 VXG  CONST_08  C3   C4   C9   C8    180.00   0.0  0
 VXG  CONST_09  H4   C8   C9   C4    180.00   0.0  0
 VXG  CONST_10  H2   C6   C5   C4    180.00   0.0  0
 VXG  CONST_11  H3   C7   C6   C5    180.00   0.0  0
 VXG  CONST_12  H11  C9   C4   C5    180.00   0.0  0
 VXG  CONST_13  H1   C5   C6   C7    180.00   0.0  0
 VXG  CONST_14  C12  C11  N1   C10   180.00   0.0  0
 VXG  CONST_15  O2   C11  N1   C10     0.00   0.0  0
 VXG  CONST_16  C12  C11  N1   C13     0.00   0.0  0
 VXG  CONST_17  O2   C11  N1   C13   180.00   0.0  0
 VXG  Var_01    C2   C13  N1   C10    11.76  30.0  1
 VXG  Var_02    C3   C10  N1   C13    13.65  30.0  1
 VXG  Var_03    H12  C12  C11  N1   -173.29  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
 VXG  chir_01  C2  C1  C13  C3   positiv
 VXG  chir_02  C3  C2  C4   C10  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
 VXG  plan-1  C4   0.020
 VXG  plan-1  C5   0.020
 VXG  plan-1  C6   0.020
 VXG  plan-1  C7   0.020
 VXG  plan-1  C8   0.020
 VXG  plan-1  C3   0.020
 VXG  plan-1  C9   0.020
 VXG  plan-1  H1   0.020
 VXG  plan-1  H2   0.020
 VXG  plan-1  H3   0.020
 VXG  plan-1  H4   0.020
 VXG  plan-1  H11  0.020
 VXG  plan-2  N1   0.020
 VXG  plan-2  C10  0.020
 VXG  plan-2  C13  0.020
 VXG  plan-2  C11  0.020
 VXG  plan-2  C12  0.020
 VXG  plan-2  O2   0.020
 VXG  plan-3  O1   0.020
 VXG  plan-3  C1   0.020
 VXG  plan-3  C2   0.020
 VXG  plan-3  O3   0.020

