# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:45:41 2021
#   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  32  17  .  2022-08-11  2022-11-18
;
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  -0.467  -30.3695  13.5398  -21.2080
 VXG  C4   C  CR6   0   0.194  -29.4825  16.8186  -22.6740
 VXG  C5   C  CR16  0  -0.326  -29.7265  18.1499  -22.3499
 VXG  C6   C  CR16  0  -0.237  -29.0019  19.1745  -22.9461
 VXG  C7   C  CR16  0  -0.270  -28.0184  18.8769  -23.8780
 VXG  C8   C  CR16  0  -0.237  -27.7673  17.5507  -24.2106
 VXG  C10  C  CH2   0  -0.221  -29.4783  14.6874  -21.2521
 VXG  C13  C  CH2   0  -0.244  -31.4975  13.6646  -22.1216
 VXG  O1   O  O     0  -0.433  -32.2795  15.8132  -24.8436
 VXG  C1   C  C     0   0.556  -32.2240  15.5861  -23.6614
 VXG  C2   C  CH1   0  -0.388  -31.0919  14.8493  -22.9977
 VXG  C3   C  CH1   0  -0.405  -30.2880  15.7306  -22.0225
 VXG  C9   C  CR16  0  -0.322  -28.4943  16.5309  -23.6146
 VXG  C11  C  C     0   0.514  -30.1452  12.4945  -20.3916
 VXG  C12  C  CH3   0  -0.797  -31.1715  11.3907  -20.4321
 VXG  O2   O  O     0  -0.508  -29.1607  12.4505  -19.6634
 VXG  O3   O  OH1   0  -0.588  -33.1461  15.9888  -22.7965
 VXG  H1   H  HCR6  0   0.253  -30.4925  18.3872  -21.6204
 VXG  H2   H  HCR6  0   0.257  -29.2074  20.2035  -22.6806
 VXG  H3   H  HCR6  0   0.257  -27.4488  19.6710  -24.3429
 VXG  H4   H  HCR6  0   0.257  -27.0013  17.3116  -24.9370
 VXG  H5   H  HCH2  0   0.245  -28.5460  14.4371  -21.7672
 VXG  H6   H  HCH2  0   0.263  -29.2232  15.0368  -20.2518
 VXG  H7   H  HCH2  0   0.257  -32.4259  13.8561  -21.5776
 VXG  H8   H  HCH2  0   0.272  -31.6351  12.7619  -22.7171
 VXG  H9   H  HCH1  0   0.296  -30.4316  14.4932  -23.7913
 VXG  H10  H  HCH1  0   0.285  -30.9884  16.1926  -21.3208
 VXG  H11  H  HCR6  0   0.253  -28.2848  15.5038  -23.8896
 VXG  H12  H  HCH3  0   0.268  -30.9548  10.6582  -19.6587
 VXG  H13  H  HCH3  0   0.262  -32.1820  11.7729  -20.2801
 VXG  H14  H  HCH3  0   0.268  -31.1607  10.8820  -21.3981
 VXG  H15  H  HOH1  0   0.487  -33.8441  16.4802  -23.2557

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   double    1.205  0.020  1.205
 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    1.505  0.020  1.505
 VXG  C1   O3   single    1.327  0.020  1.327
 VXG  C9   C4   aromatic  1.394  0.020  1.394
 VXG  C6   C5   aromatic  1.389  0.020  1.389
 VXG  C2   C13  single    1.528  0.020  1.528
 VXG  C2   C3   single    1.541  0.020  1.541
 VXG  C4   C5   aromatic  1.392  0.020  1.392
 VXG  C4   C3   single    1.502  0.020  1.502
 VXG  C13  N1   single    1.457  0.020  1.457
 VXG  C3   C10  single    1.529  0.020  1.529
 VXG  C10  N1   single    1.454  0.020  1.454
 VXG  N1   C11  single    1.345  0.020  1.345
 VXG  C11  C12  single    1.508  0.020  1.508
 VXG  C11  O2   double    1.225  0.020  1.225
 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
 VXG  O3   H15  single    0.850  0.020  0.980

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  125.18  3.000
 VXG  C11  N1   C10  121.98  3.000
 VXG  C13  N1   C10  112.84  3.000
 VXG  C9   C4   C3   121.54  3.000
 VXG  C3   C4   C5   119.85  3.000
 VXG  C9   C4   C5   118.60  3.000
 VXG  H1   C5   C6   119.73  3.000
 VXG  H1   C5   C4   119.34  3.000
 VXG  C6   C5   C4   120.94  3.000
 VXG  H2   C6   C7   120.22  3.000
 VXG  H2   C6   C5   119.79  3.000
 VXG  C7   C6   C5   119.98  3.000
 VXG  H3   C7   C8   120.14  3.000
 VXG  H3   C7   C6   120.28  3.000
 VXG  C8   C7   C6   119.57  3.000
 VXG  H4   C8   C9   119.79  3.000
 VXG  H4   C8   C7   119.95  3.000
 VXG  C9   C8   C7   120.26  3.000
 VXG  H6   C10  H5   107.82  3.000
 VXG  H6   C10  C3   111.58  3.000
 VXG  H5   C10  C3   111.72  3.000
 VXG  H6   C10  N1   111.64  3.000
 VXG  H5   C10  N1   110.86  3.000
 VXG  C3   C10  N1   103.25  3.000
 VXG  H8   C13  H7   108.05  3.000
 VXG  H8   C13  C2   111.24  3.000
 VXG  H7   C13  C2   112.01  3.000
 VXG  H8   C13  N1   111.68  3.000
 VXG  H7   C13  N1   111.14  3.000
 VXG  C2   C13  N1   102.73  3.000
 VXG  O3   C1   C2   112.57  3.000
 VXG  O3   C1   O1   123.39  3.000
 VXG  C2   C1   O1   124.02  3.000
 VXG  H9   C2   C3   109.33  3.000
 VXG  H9   C2   C1   107.10  3.000
 VXG  C3   C2   C1   113.06  3.000
 VXG  H9   C2   C13  108.92  3.000
 VXG  C3   C2   C13  102.65  3.000
 VXG  C1   C2   C13  115.64  3.000
 VXG  H10  C3   C2   108.27  3.000
 VXG  H10  C3   C10  107.70  3.000
 VXG  C2   C3   C10  101.83  3.000
 VXG  H10  C3   C4   108.40  3.000
 VXG  C10  C3   C4   115.38  3.000
 VXG  C2   C3   C4   114.80  3.000
 VXG  H11  C9   C8   119.11  3.000
 VXG  H11  C9   C4   120.25  3.000
 VXG  C8   C9   C4   120.64  3.000
 VXG  O2   C11  C12  122.45  3.000
 VXG  O2   C11  N1   121.50  3.000
 VXG  C12  C11  N1   116.05  3.000
 VXG  H14  C12  H13  107.19  3.000
 VXG  H14  C12  H12  108.28  3.000
 VXG  H13  C12  H12  108.77  3.000
 VXG  H14  C12  C11  110.98  3.000
 VXG  H13  C12  C11  111.73  3.000
 VXG  H12  C12  C11  109.78  3.000
 VXG  H15  O3   C1   110.21  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  CONST_18  H15  O3   C1   C2    180.00   0.0  0
 VXG  Var_01    C2   C13  N1   C10    12.52  30.0  1
 VXG  Var_02    C3   C10  N1   C13    13.19  30.0  1
 VXG  Var_03    H12  C12  C11  N1   -173.55  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
 VXG  plan-3  H15  0.020

