# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 03:18:41 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: (5S)-5-methyl-4-oxo-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@@H](CC1=O)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
 POM  POM  (5S)-5-methyl-4-oxo-L-proline  L-peptide  18  10  .  2016-04-26  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_POM
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
 POM  N     N  NR15   0  -0.613  -5.4991  16.2558  18.1654
 POM  CA    C  CR15   0  -0.232  -5.6582  15.3362  17.0357
 POM  C     C  C      0   0.407  -6.7028  15.7664  15.9715
 POM  O     O  O      0  -0.602  -7.0155  16.9733  15.9551
 POM  OXT   O  OC    -1  -0.598  -7.0878  14.8783  15.1873
 POM  CB    C  CH2    0  -0.576  -5.9596  13.9977  17.7020
 POM  CG    C  CR5    0   0.382  -6.5798  14.3693  19.0227
 POM  CD    C  CR15   0  -0.178  -6.4057  15.8618  19.2321
 POM  OG    O  O      0  -0.399  -7.1367  13.6231  19.7908
 POM  CD1   C  CH3    0  -0.671  -7.7786  16.5418  19.2402
 POM  H     H  HNR5   0   0.341  -5.6973  17.1972  17.8489
 POM  HA    H  HCR5   0   0.237  -4.7049  15.2724  16.4964
 POM  HB2   H  HCH2   0   0.274  -6.6072  13.3475  17.1146
 POM  HB3   H  HCH2   0   0.277  -5.0448  13.4343  17.9143
 POM  HD    H  HCR5   0   0.252  -5.9435  16.0296  20.2123
 POM  HD11  H  HCH3   0   0.227  -8.3696  16.1951  20.0879
 POM  HD12  H  HCH3   0   0.237  -7.6590  17.6215  19.3362
 POM  HD13  H  HCH3   0   0.234  -8.3387  16.3482  18.3261

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
 POM  N    CA    single  1.466  0.015  1.466
 POM  N    CD    single  1.473  0.014  1.473
 POM  N    H     single  0.860  0.020  1.020
 POM  CA   C     single  1.525  0.021  1.525
 POM  CA   CB    single  1.530  0.020  1.530
 POM  CA   HA    single  0.970  0.020  0.970
 POM  C    O     deloc   1.231  0.020  1.231
 POM  C    OXT   deloc   1.246  0.020  1.246
 POM  CB   CG    single  1.506  0.020  1.506
 POM  CB   HB2   single  0.970  0.020  1.090
 POM  CB   HB3   single  0.970  0.020  1.090
 POM  CG   CD    single  1.517  0.020  1.517
 POM  CG   OG    double  1.207  0.020  1.207
 POM  CD   CD1   single  1.532  0.020  1.532
 POM  CD   HD    single  0.970  0.020  1.090
 POM  CD1  HD11  single  0.970  0.020  1.090
 POM  CD1  HD12  single  0.970  0.020  1.090
 POM  CD1  HD13  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
 POM  H     N    CD    111.04  3.000
 POM  H     N    CA    108.74  3.000
 POM  CD    N    CA    109.13  3.000
 POM  HA    CA   CB    109.00  3.000
 POM  HA    CA   C     109.00  3.000
 POM  CB    CA   C     110.10  1.900
 POM  HA    CA   N     110.00  3.000
 POM  CB    CA   N     103.00  1.100
 POM  C     CA   N     112.10  2.500
 POM  OXT   C    O     127.18  3.000
 POM  OXT   C    CA    116.23  3.000
 POM  O     C    CA    119.00  3.000
 POM  HB3   CB   HB2   107.10  3.000
 POM  HB3   CB   CG    107.52  3.000
 POM  HB2   CB   CG    112.04  3.000
 POM  HB3   CB   CA    111.79  3.000
 POM  HB2   CB   CA    113.93  3.000
 POM  CG    CB   CA    104.36  3.000
 POM  OG    CG   CD    124.98  3.000
 POM  OG    CG   CB    126.56  3.000
 POM  CD    CG   CB    108.46  3.000
 POM  HD    CD   CD1   107.76  3.000
 POM  HD    CD   CG    108.80  3.000
 POM  CD1   CD   CG    109.54  3.000
 POM  HD    CD   N     110.57  3.000
 POM  CD1   CD   N     116.25  3.000
 POM  CG    CD   N     103.20  1.500
 POM  HD13  CD1  HD12  107.83  3.000
 POM  HD13  CD1  HD11  108.50  3.000
 POM  HD12  CD1  HD11  107.81  3.000
 POM  HD13  CD1  CD    112.18  3.000
 POM  HD12  CD1  CD    109.98  3.000
 POM  HD11  CD1  CD    110.41  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
 POM  Var_01  CD  CG  CB  CA  -10.27  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
 POM  chir_01  CA  N  C   CB   positiv
 POM  chir_02  CD  N  CG  CD1  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
 POM  plan-1  CB   0.020
 POM  plan-1  CG   0.020
 POM  plan-1  CD   0.020
 POM  plan-1  OG   0.020
 POM  plan-2  CA   0.020
 POM  plan-2  C    0.020
 POM  plan-2  O    0.020
 POM  plan-2  OXT  0.020

