# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:36:37 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 2-methyl-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(CCCN1)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
 3WX  3WX  '2-methyl-L-proline       '  peptide  19  9  .  2016-04-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3WX
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
 3WX  CB   C  CH2    0  -0.414  7.2673  87.2825  107.5762
 3WX  CA   C  CT     0  -0.055  6.6350  88.6670  107.8019
 3WX  CG   C  CH2    0  -0.486  6.0857  86.4375  107.0976
 3WX  C    C  C      0   0.421  6.4884  89.4141  106.4407
 3WX  N    N  NH1    0  -0.572  5.3335  88.3507  108.3947
 3WX  O    O  O      0  -0.592  5.3569  89.7979  106.0923
 3WX  C39  C  CH3    0  -0.663  7.4445  89.5351  108.7562
 3WX  CD   C  CH2    0  -0.300  4.8516  87.1534  107.7063
 3WX  HB2  H  HCH2   0   0.205  7.6452  86.9025  108.5319
 3WX  HB3  H  HCH2   0   0.218  8.1052  87.2903  106.8800
 3WX  HG2  H  HCH2   0   0.222  6.0297  86.4316  106.0072
 3WX  HG3  H  HCH2   0   0.225  6.1608  85.3971  107.4169
 3WX  H    H  HNH1   0   0.325  5.5031  88.0975  109.3623
 3WX  H55  H  HCH3   0   0.211  7.5848  89.0299  109.7160
 3WX  H56  H  HCH3   0   0.224  8.4307  89.7483  108.3471
 3WX  H57  H  HCH3   0   0.221  6.9463  90.4874  108.9499
 3WX  HD2  H  HCH2   0   0.208  4.1477  87.4288  106.9191
 3WX  HD3  H  HCH2   0   0.216  4.3101  86.5157  108.4064
 3WX  OXT  O  OC    -1  -0.614  7.5543  89.5830  105.8109

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
 3WX  O    C    deloc   1.231  0.020  1.231
 3WX  C    CA   single  1.525  0.021  1.525
 3WX  CG   CB   single  1.529  0.020  1.529
 3WX  CG   CD   single  1.551  0.020  1.551
 3WX  CB   CA   single  1.530  0.020  1.530
 3WX  CA   N    single  1.466  0.015  1.466
 3WX  CA   C39  single  1.523  0.020  1.523
 3WX  CD   N    single  1.473  0.014  1.473
 3WX  CB   HB2  single  0.970  0.020  1.090
 3WX  CB   HB3  single  0.970  0.020  1.090
 3WX  CG   HG2  single  0.970  0.020  1.090
 3WX  CG   HG3  single  0.970  0.020  1.090
 3WX  N    H    single  0.860  0.020  1.020
 3WX  C39  H55  single  0.970  0.020  1.090
 3WX  C39  H56  single  0.970  0.020  1.090
 3WX  C39  H57  single  0.970  0.020  1.090
 3WX  CD   HD2  single  0.970  0.020  1.090
 3WX  CD   HD3  single  0.970  0.020  1.090
 3WX  C    OXT  deloc   1.250  0.020  1.250

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
 3WX  HB3  CB   HB2  107.13  3.000
 3WX  HB3  CB   CG   113.46  3.000
 3WX  HB2  CB   CG   110.35  3.000
 3WX  HB3  CB   CA   113.79  3.000
 3WX  HB2  CB   CA   109.02  3.000
 3WX  CG   CB   CA   103.03  3.000
 3WX  C39  CA   N    109.99  3.000
 3WX  C39  CA   C    108.89  3.000
 3WX  N    CA   C    112.10  2.500
 3WX  C39  CA   CB   112.73  3.000
 3WX  N    CA   CB   103.00  1.100
 3WX  C    CA   CB   110.10  1.900
 3WX  HG3  CG   HG2  106.90  3.000
 3WX  HG3  CG   CD   112.34  3.000
 3WX  HG2  CG   CD   110.71  3.000
 3WX  HG3  CG   CB   112.46  3.000
 3WX  HG2  CG   CB   110.80  3.000
 3WX  CD   CG   CB   103.70  3.000
 3WX  OXT  C    O    126.35  3.000
 3WX  OXT  C    CA   115.12  3.000
 3WX  O    C    CA   119.00  3.000
 3WX  H    N    CD   107.43  3.000
 3WX  H    N    CA   106.94  3.000
 3WX  CD   N    CA   106.20  3.000
 3WX  H57  C39  H56  108.00  3.000
 3WX  H57  C39  H55  107.80  3.000
 3WX  H56  C39  H55  107.70  3.000
 3WX  H57  C39  CA   111.45  3.000
 3WX  H56  C39  CA   110.95  3.000
 3WX  H55  C39  CA   110.78  3.000
 3WX  HD3  CD   HD2  106.87  3.000
 3WX  HD3  CD   N    109.88  3.000
 3WX  HD2  CD   N    110.20  3.000
 3WX  HD3  CD   CG   112.15  3.000
 3WX  HD2  CD   CG   110.27  3.000
 3WX  N    CD   CG   103.20  1.500

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
 3WX  Var_01  N   CD  CG  CB    3.31  30.0  1
 3WX  Var_02  CD  CG  CB  CA  -25.65  30.0  1
 3WX  Var_03  CG  CD  N   CA   21.89  30.0  1

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
 3WX  chir_01  CA  CB  N  C39  negativ

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
 3WX  plan-1  CA   0.020
 3WX  plan-1  C    0.020
 3WX  plan-1  O    0.020
 3WX  plan-1  OXT  0.020

