# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:54:54 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (2R,4R)-2-carboxy-4-hydroxy-1,1-dimethylpyrrolidinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+]1(C)C[C@H](O)C[C@@H]1C(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
 4OP  4OP  (2R,4R)-2-carboxy-4-hydroxy-1,1-dimethylpyrrolidinium  D-peptide  24  11  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4OP
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
 4OP  CN1  C  CH3    0  -0.551  29.8512  58.6057  7.9166
 4OP  N    N  NT     1  -0.388  29.7155  59.3612  6.6381
 4OP  CD   C  CH2    0  -0.344  31.0335  59.9711  6.2606
 4OP  CG   C  CH1    0   0.034  31.1782  61.2343  7.0997
 4OP  CB   C  CH2    0  -0.501  29.7297  61.5985  7.4840
 4OP  CA   C  CH1    0  -0.245  28.8334  60.5895  6.7737
 4OP  C    C  C      0   0.448  27.4256  60.3943  7.3873
 4OP  OXT  O  OC    -1  -0.569  26.9095  61.4592  7.7550
 4OP  O    O  O      0  -0.570  26.9410  59.2511  7.4057
 4OP  OG   O  OH1    0  -0.659  32.0082  60.9663  8.2050
 4OP  CN2  C  CH3    0  -0.540  29.2540  58.4331  5.5748
 4OP  H1   H  HCH3   0   0.288  30.1799  59.2650  8.7136
 4OP  H2   H  HCH3   0   0.291  28.8940  58.1667  8.1697
 4OP  H3   H  HCH3   0   0.281  30.5946  57.8260  7.7701
 4OP  H4   H  HCH2   0   0.307  31.8338  59.2465  6.4021
 4OP  H5   H  HCH2   0   0.309  30.9708  60.2249  5.2029
 4OP  H6   H  HCH1   0   0.253  31.6170  62.0177  6.4732
 4OP  H7   H  HCH2   0   0.277  29.4672  62.6091  7.1807
 4OP  H8   H  HCH2   0   0.264  29.6067  61.5429  8.5670
 4OP  H9   H  HCH1   0   0.308  28.6852  60.9196  5.7395
 4OP  H11  H  HOH1   0   0.455  32.0841  61.7720  8.7267
 4OP  H12  H  HCH3   0   0.293  28.3069  57.9995  5.8728
 4OP  H13  H  HCH3   0   0.281  29.1352  58.9862  4.6463
 4OP  H14  H  HCH3   0   0.280  30.0015  57.6545  5.4426

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
 4OP  CN2  N    single  1.485  0.020  1.485
 4OP  CD   N    single  1.473  0.014  1.473
 4OP  CD   CG   single  1.523  0.020  1.523
 4OP  N    CA   single  1.458  0.019  1.458
 4OP  N    CN1  single  1.491  0.020  1.491
 4OP  CA   CB   single  1.521  0.033  1.521
 4OP  CA   C    single  1.525  0.021  1.525
 4OP  CG   CB   single  1.542  0.020  1.542
 4OP  CG   OG   single  1.408  0.020  1.408
 4OP  O    C    deloc   1.231  0.020  1.231
 4OP  C    OXT  deloc   1.239  0.020  1.239
 4OP  CN1  H1   single  0.970  0.020  1.090
 4OP  CN1  H2   single  0.970  0.020  1.090
 4OP  CN1  H3   single  0.970  0.020  1.090
 4OP  CD   H4   single  0.970  0.020  1.090
 4OP  CD   H5   single  0.970  0.020  1.090
 4OP  CG   H6   single  0.970  0.020  1.090
 4OP  CB   H7   single  0.970  0.020  1.090
 4OP  CB   H8   single  0.970  0.020  1.090
 4OP  CA   H9   single  0.970  0.020  1.090
 4OP  OG   H11  single  0.850  0.020  0.980
 4OP  CN2  H12  single  0.970  0.020  1.090
 4OP  CN2  H13  single  0.970  0.020  1.090
 4OP  CN2  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
 4OP  H3   CN1  H2   110.19  3.000
 4OP  H3   CN1  H1   109.12  3.000
 4OP  H2   CN1  H1   110.01  3.000
 4OP  H3   CN1  N    108.06  3.000
 4OP  H2   CN1  N    108.98  3.000
 4OP  H1   CN1  N    110.45  3.000
 4OP  CN2  N    CA   112.90  3.000
 4OP  CA   N    CD   101.77  3.000
 4OP  CN2  N    CD   110.30  3.000
 4OP  CA   N    CN1  112.71  3.000
 4OP  CD   N    CN1  109.98  3.000
 4OP  CN2  N    CN1  109.00  3.000
 4OP  H5   CD   H4   108.88  3.000
 4OP  H5   CD   CG   110.30  3.000
 4OP  H4   CD   CG   114.23  3.000
 4OP  H5   CD   N    106.76  3.000
 4OP  H4   CD   N    110.03  3.000
 4OP  CG   CD   N    103.20  1.500
 4OP  H6   CG   OG   110.44  3.000
 4OP  H6   CG   CB   110.48  3.000
 4OP  OG   CG   CB   113.76  3.000
 4OP  H6   CG   CD   108.44  3.000
 4OP  OG   CG   CD   109.31  3.000
 4OP  CB   CG   CD   104.12  3.000
 4OP  H8   CB   H7   107.28  3.000
 4OP  H8   CB   CA   111.23  3.000
 4OP  H7   CB   CA   110.06  3.000
 4OP  H8   CB   CG   109.94  3.000
 4OP  H7   CB   CG   112.14  3.000
 4OP  CA   CB   CG   106.24  3.000
 4OP  H9   CA   C    106.80  3.000
 4OP  H9   CA   CB   108.65  3.000
 4OP  C    CA   CB   110.50  1.500
 4OP  H9   CA   N    103.77  3.000
 4OP  C    CA   N    111.00  2.800
 4OP  CB   CA   N    110.40  1.500
 4OP  O    C    OXT  128.62  3.000
 4OP  OXT  C    CA   120.80  1.700
 4OP  O    C    CA   120.80  1.700
 4OP  H11  OG   CG   108.22  3.000
 4OP  H14  CN2  H13  109.60  3.000
 4OP  H14  CN2  H12  110.36  3.000
 4OP  H13  CN2  H12  110.05  3.000
 4OP  H14  CN2  N    108.72  3.000
 4OP  H13  CN2  N    109.12  3.000
 4OP  H12  CN2  N    108.96  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
 4OP  Var_01  CA   N    CD  CG   39.73  30.0  1
 4OP  Var_02  H12  CN2  N   CD  179.52  30.0  3
 4OP  Var_03  H1   CN1  N   CD   59.46  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
 4OP  chir_01  CG  CD  CB  OG  negativ
 4OP  chir_02  CA  N   CB  C   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
 4OP  plan-1  CA   0.020
 4OP  plan-1  C    0.020
 4OP  plan-1  OXT  0.020
 4OP  plan-1  O    0.020

