# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:53:44 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2~{R})-1,2-dimethylpyrrolidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[C@]1(C)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
 6Y9  6Y9  '(2~{R})-1,2-dimethylpyrrolidine-2-carboxylic acid'  D-peptide  22  10  .  2017-07-04  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6Y9
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
 6Y9  CD   C  CH2    0  -0.264  3.2187  38.7915  18.1024
 6Y9  CG   C  CH2    0  -0.480  2.3101  38.5401  16.8884
 6Y9  CA   C  CT     0   0.001  2.6810  40.9155  17.2408
 6Y9  CB   C  CH2    0  -0.432  2.2445  39.8968  16.1737
 6Y9  C    C  C      0   0.406  3.2355  42.1846  16.5343
 6Y9  O    O  O      0  -0.596  4.4656  42.2799  16.3693
 6Y9  N    N  NT     0  -0.416  3.7131  40.1436  17.9288
 6Y9  C38  C  CH3    0  -0.662  1.4946  41.2684  18.1480
 6Y9  HD2  H  HCH2   0   0.180  2.6459  38.6730  19.0369
 6Y9  HD3  H  HCH2   0   0.216  4.0535  38.0861  18.1632
 6Y9  HG2  H  HCH2   0   0.227  1.3210  38.2145  17.2114
 6Y9  HG3  H  HCH2   0   0.232  2.7024  37.7601  16.2357
 6Y9  H5   H  HCH3   0   0.218  5.1322  40.1155  19.4479
 6Y9  H6   H  HCH3   0   0.227  4.6236  41.7211  18.9430
 6Y9  H7   H  HCH3   0   0.180  3.5710  40.7382  19.9776
 6Y9  HB2  H  HCH2   0   0.224  2.9466  39.9163  15.3363
 6Y9  HB3  H  HCH2   0   0.222  1.2558  40.1187  15.7712
 6Y9  H57  H  HCH3   0   0.215  1.7721  41.9857  18.9229
 6Y9  H58  H  HCH3   0   0.222  0.6820  41.7080  17.5739
 6Y9  H59  H  HCH3   0   0.211  1.0980  40.3839  18.6531
 6Y9  OXT  O  OC    -1  -0.607  2.3725  42.9963  16.1383
 6Y9  C37  C  CH3    0  -0.521  4.2708  40.7074  19.1274

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
 6Y9  CB   CG   single  1.535  0.020  1.535
 6Y9  CB   CA   single  1.530  0.020  1.530
 6Y9  C    O    deloc   1.231  0.020  1.231
 6Y9  C    CA   single  1.525  0.021  1.525
 6Y9  CG   CD   single  1.537  0.020  1.537
 6Y9  CA   N    single  1.466  0.015  1.466
 6Y9  CA   C38  single  1.535  0.020  1.535
 6Y9  N    CD   single  1.473  0.014  1.473
 6Y9  N    C37  single  1.437  0.020  1.437
 6Y9  CD   HD2  single  0.970  0.020  1.090
 6Y9  CD   HD3  single  0.970  0.020  1.090
 6Y9  CG   HG2  single  0.970  0.020  1.090
 6Y9  CG   HG3  single  0.970  0.020  1.090
 6Y9  C37  H5   single  0.970  0.020  1.090
 6Y9  C37  H6   single  0.970  0.020  1.090
 6Y9  C37  H7   single  0.970  0.020  1.090
 6Y9  CB   HB2  single  0.970  0.020  1.090
 6Y9  CB   HB3  single  0.970  0.020  1.090
 6Y9  C38  H57  single  0.970  0.020  1.090
 6Y9  C38  H58  single  0.970  0.020  1.090
 6Y9  C38  H59  single  0.970  0.020  1.090
 6Y9  C    OXT  deloc   1.249  0.020  1.249

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
 6Y9  HD3  CD   HD2  106.26  3.000
 6Y9  HD3  CD   N    110.34  3.000
 6Y9  HD2  CD   N    112.27  3.000
 6Y9  HD3  CD   CG   112.90  3.000
 6Y9  HD2  CD   CG   110.16  3.000
 6Y9  N    CD   CG   103.20  1.500
 6Y9  HG3  CG   HG2  106.87  3.000
 6Y9  HG3  CG   CB   111.66  3.000
 6Y9  HG2  CG   CB   111.30  3.000
 6Y9  HG3  CG   CD   112.16  3.000
 6Y9  HG2  CG   CD   110.56  3.000
 6Y9  CB   CG   CD   104.39  3.000
 6Y9  C38  CA   N    112.91  3.000
 6Y9  C38  CA   C    110.89  3.000
 6Y9  N    CA   C    112.10  2.500
 6Y9  C38  CA   CB   110.06  3.000
 6Y9  N    CA   CB   103.00  1.100
 6Y9  C    CA   CB   110.10  1.900
 6Y9  HB3  CB   HB2  107.22  3.000
 6Y9  HB3  CB   CA   112.24  3.000
 6Y9  HB2  CB   CA   109.72  3.000
 6Y9  HB3  CB   CG   112.99  3.000
 6Y9  HB2  CB   CG   110.19  3.000
 6Y9  CA   CB   CG   104.49  3.000
 6Y9  OXT  C    O    126.22  3.000
 6Y9  OXT  C    CA   115.35  3.000
 6Y9  O    C    CA   119.00  3.000
 6Y9  C37  N    CA   117.36  3.000
 6Y9  C37  N    CD   113.47  3.000
 6Y9  CA   N    CD   107.95  3.000
 6Y9  H59  C38  H58  107.45  3.000
 6Y9  H59  C38  H57  107.21  3.000
 6Y9  H58  C38  H57  107.39  3.000
 6Y9  H59  C38  CA   111.57  3.000
 6Y9  H58  C38  CA   111.01  3.000
 6Y9  H57  C38  CA   111.97  3.000
 6Y9  H7   C37  H6   108.09  3.000
 6Y9  H7   C37  H5   106.83  3.000
 6Y9  H6   C37  H5   107.35  3.000
 6Y9  H7   C37  N    114.09  3.000
 6Y9  H6   C37  N    110.46  3.000
 6Y9  H5   C37  N    109.74  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
 6Y9  Var_01  CA  CB   CG  CD  -19.14  30.0  1
 6Y9  Var_02  CA  N    CD  CG   31.53  30.0  1
 6Y9  Var_03  N   CD   CG  CB   -6.27  30.0  1
 6Y9  Var_04  H5  C37  N   CD   61.96  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
 6Y9  chir_01  CA  CB  N  C38  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
 6Y9  plan-1  CA   0.020
 6Y9  plan-1  C    0.020
 6Y9  plan-1  O    0.020
 6Y9  plan-1  OXT  0.020

