# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 02:52:51 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: methyl L-prolinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H]1CCCN1
#
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
 PLJ  PLJ  'methyl L-prolinate       '  L-peptide  20  9  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_PLJ
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
 PLJ  CM   C  CH3   0  -0.434  -39.6153  2.6697  67.3686
 PLJ  O    O  O     0  -0.429  -43.0532  2.1100  67.8001
 PLJ  CG   C  CH2   0  -0.453  -40.5798  6.0698  67.1463
 PLJ  CB   C  CH2   0  -0.507  -41.5998  5.0723  66.5905
 PLJ  CD   C  CH2   0  -0.320  -40.9580  6.1567  68.6247
 PLJ  OXT  O  O2    0  -0.427  -40.9071  2.0937  67.5370
 PLJ  C    C  C     0   0.538  -42.0430  2.7624  67.7297
 PLJ  CA   C  CH1   0  -0.219  -42.0842  4.2788  67.8453
 PLJ  N    N  NH1   0  -0.596  -41.3815  4.8148  69.0120
 PLJ  HM1  H  HCH3  0   0.272  -38.9529  1.8384  67.1416
 PLJ  HM2  H  HCH3  0   0.248  -39.5762  3.3727  66.5396
 PLJ  HM3  H  HCH3  0   0.238  -39.2515  3.1530  68.2738
 PLJ  HG2  H  HCH2  0   0.233  -39.5606  5.6919  67.0400
 PLJ  HG3  H  HCH2  0   0.243  -40.6247  7.0343  66.6403
 PLJ  HB2  H  HCH2  0   0.262  -42.4539  5.5936  66.1586
 PLJ  HB3  H  HCH2  0   0.254  -41.1906  4.4468  65.7972
 PLJ  HD2  H  HCH2  0   0.246  -40.1460  6.4963  69.2672
 PLJ  HD3  H  HCH2  0   0.227  -41.7942  6.8499  68.7585
 PLJ  HA   H  HCH1  0   0.270  -43.1459  4.4953  67.9746
 PLJ  H    H  HNH1  0   0.356  -40.5661  4.2694  69.2546

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
 PLJ  CM   OXT  single  1.424  0.020  1.424
 PLJ  O    C    double  1.231  0.020  1.231
 PLJ  CG   CB   single  1.531  0.020  1.531
 PLJ  CG   CD   single  1.528  0.020  1.528
 PLJ  CB   CA   single  1.530  0.020  1.530
 PLJ  CD   N    single  1.473  0.014  1.473
 PLJ  OXT  C    single  1.332  0.020  1.332
 PLJ  C    CA   single  1.525  0.021  1.525
 PLJ  CA   N    single  1.466  0.015  1.466
 PLJ  CM   HM1  single  0.970  0.020  1.090
 PLJ  CM   HM2  single  0.970  0.020  1.090
 PLJ  CM   HM3  single  0.970  0.020  1.090
 PLJ  CG   HG2  single  0.970  0.020  1.090
 PLJ  CG   HG3  single  0.970  0.020  1.090
 PLJ  CB   HB2  single  0.970  0.020  1.090
 PLJ  CB   HB3  single  0.970  0.020  1.090
 PLJ  CD   HD2  single  0.970  0.020  1.090
 PLJ  CD   HD3  single  0.970  0.020  1.090
 PLJ  CA   HA   single  0.970  0.020  0.970
 PLJ  N    H    single  0.860  0.020  1.020

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
 PLJ  HM3  CM   HM2  109.55  3.000
 PLJ  HM3  CM   HM1  108.04  3.000
 PLJ  HM2  CM   HM1  108.26  3.000
 PLJ  HM3  CM   OXT  112.59  3.000
 PLJ  HM2  CM   OXT  112.58  3.000
 PLJ  HM1  CM   OXT  105.55  3.000
 PLJ  HG3  CG   HG2  107.41  3.000
 PLJ  HG3  CG   CD   112.86  3.000
 PLJ  HG2  CG   CD   110.16  3.000
 PLJ  HG3  CG   CB   112.36  3.000
 PLJ  HG2  CG   CB   111.16  3.000
 PLJ  CD   CG   CB   102.91  3.000
 PLJ  HB3  CB   HB2  106.28  3.000
 PLJ  HB3  CB   CA   114.18  3.000
 PLJ  HB2  CB   CA   108.57  3.000
 PLJ  HB3  CB   CG   112.83  3.000
 PLJ  HB2  CB   CG   110.75  3.000
 PLJ  CA   CB   CG   104.24  3.000
 PLJ  HD3  CD   HD2  107.45  3.000
 PLJ  HD3  CD   N    109.17  3.000
 PLJ  HD2  CD   N    110.26  3.000
 PLJ  HD3  CD   CG   110.08  3.000
 PLJ  HD2  CD   CG   113.80  3.000
 PLJ  N    CD   CG   103.20  1.500
 PLJ  C    OXT  CM   125.97  3.000
 PLJ  CA   C    OXT  122.31  3.000
 PLJ  CA   C    O    119.00  3.000
 PLJ  OXT  C    O    116.85  3.000
 PLJ  HA   CA   N    110.00  3.000
 PLJ  HA   CA   C    109.00  3.000
 PLJ  N    CA   C    112.10  2.500
 PLJ  HA   CA   CB   109.00  3.000
 PLJ  N    CA   CB   103.00  1.100
 PLJ  C    CA   CB   110.10  1.900
 PLJ  H    N    CA   112.40  3.000
 PLJ  H    N    CD   109.01  3.000
 PLJ  CA   N    CD   105.33  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
 PLJ  Var_01  CA   N   CD   CG   -36.39  30.0  1
 PLJ  Var_02  N    CD  CG   CB    36.03  30.0  1
 PLJ  Var_03  CA   CB  CG   CD   -21.35  30.0  1
 PLJ  Var_04  CA   C   OXT  CM    -2.28  30.0  3
 PLJ  Var_05  HM1  CM  OXT  C   -174.70  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
 PLJ  chir_01  CA  CB  C  N  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
 PLJ  plan-1  O    0.020
 PLJ  plan-1  OXT  0.020
 PLJ  plan-1  C    0.020
 PLJ  plan-1  CA   0.020

