# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 00:22:50 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (3S,5S)-3-hydroxy-5-methyl-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1C[C@H](O)[C@H](N1)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
 H5M  H5M  (3S,5S)-3-hydroxy-5-methyl-L-proline  L-peptide  20  10  .  2012-08-28  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H5M
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
 H5M  N     N  NH1    0  -0.614  1.0113  20.3528  19.6018
 H5M  CA    C  CH1    0  -0.208  1.6777  19.5957  20.6610
 H5M  C     C  C      0   0.392  1.6705  20.3305  22.0261
 H5M  O     O  O      0  -0.592  1.2455  21.5028  22.0421
 H5M  OXT   O  OC    -1  -0.604  2.1005  19.6712  22.9909
 H5M  CB    C  CH1    0   0.004  3.1195  19.3237  20.1809
 H5M  CG    C  CH2    0  -0.467  3.3299  20.4129  19.1380
 H5M  CD    C  CH1    0  -0.070  1.9504  20.5208  18.4911
 H5M  OB    O  OH1    0  -0.678  3.1608  18.0254  19.6116
 H5M  CD1   C  CH3    0  -0.674  1.7091  21.8079  17.7274
 H5M  H     H  HNH1   0   0.329  0.8161  21.2665  20.0033
 H5M  HA    H  HCH1   0   0.216  1.1881  18.6270  20.8200
 H5M  HB    H  HCH1   0   0.210  3.8399  19.3954  21.0034
 H5M  HG2   H  HCH2   0   0.215  3.5768  21.3559  19.6378
 H5M  HG3   H  HCH2   0   0.231  4.1377  20.1933  18.4348
 H5M  HD    H  HCH1   0   0.201  1.8286  19.6837  17.7929
 H5M  HOB   H  HOH1   0   0.440  4.0219  17.9125  19.1971
 H5M  HD11  H  HCH3   0   0.227  2.4035  21.8978  16.8917
 H5M  HD12  H  HCH3   0   0.228  0.6963  21.8478  17.3235
 H5M  HD13  H  HCH3   0   0.214  1.8495  22.6782  18.3734

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
 H5M  N    CA    single  1.466  0.015  1.466
 H5M  N    CD    single  1.473  0.014  1.473
 H5M  N    H     single  0.860  0.020  1.020
 H5M  CA   C     single  1.525  0.021  1.525
 H5M  CA   CB    single  1.530  0.020  1.530
 H5M  CA   HA    single  0.970  0.020  0.970
 H5M  C    O     deloc   1.231  0.020  1.231
 H5M  C    OXT   deloc   1.245  0.020  1.245
 H5M  CB   CG    single  1.523  0.020  1.523
 H5M  CB   OB    single  1.418  0.020  1.418
 H5M  CB   HB    single  0.970  0.020  1.090
 H5M  CG   CD    single  1.528  0.020  1.528
 H5M  CG   HG2   single  0.970  0.020  1.090
 H5M  CG   HG3   single  0.970  0.020  1.090
 H5M  CD   CD1   single  1.516  0.020  1.516
 H5M  CD   HD    single  0.970  0.020  1.090
 H5M  OB   HOB   single  0.850  0.020  0.980
 H5M  CD1  HD11  single  0.970  0.020  1.090
 H5M  CD1  HD12  single  0.970  0.020  1.090
 H5M  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
 H5M  H     N    CD    108.63  3.000
 H5M  H     N    CA    105.46  3.000
 H5M  CD    N    CA    108.45  3.000
 H5M  HA    CA   CB    109.00  3.000
 H5M  HA    CA   C     109.00  3.000
 H5M  CB    CA   C     110.10  1.900
 H5M  HA    CA   N     110.00  3.000
 H5M  CB    CA   N     103.00  1.100
 H5M  C     CA   N     112.10  2.500
 H5M  OXT   C    O     127.27  3.000
 H5M  OXT   C    CA    115.45  3.000
 H5M  O     C    CA    119.00  3.000
 H5M  HB    CB   OB    110.00  3.000
 H5M  HB    CB   CG    112.12  3.000
 H5M  OB    CB   CG    112.08  3.000
 H5M  HB    CB   CA    111.66  3.000
 H5M  OB    CB   CA    108.26  3.000
 H5M  CG    CB   CA    102.48  3.000
 H5M  HG3   CG   HG2   107.44  3.000
 H5M  HG3   CG   CD    114.15  3.000
 H5M  HG2   CG   CD    109.63  3.000
 H5M  HG3   CG   CB    113.52  3.000
 H5M  HG2   CG   CB    109.54  3.000
 H5M  CD    CG   CB    102.46  3.000
 H5M  HD    CD   CD1   108.03  3.000
 H5M  HD    CD   CG    108.41  3.000
 H5M  CD1   CD   CG    114.65  3.000
 H5M  HD    CD   N     108.91  3.000
 H5M  CD1   CD   N     112.18  3.000
 H5M  CG    CD   N     103.20  1.500
 H5M  HOB   OB   CB    107.84  3.000
 H5M  HD13  CD1  HD12  108.00  3.000
 H5M  HD13  CD1  HD11  107.80  3.000
 H5M  HD12  CD1  HD11  107.73  3.000
 H5M  HD13  CD1  CD    110.96  3.000
 H5M  HD12  CD1  CD    111.42  3.000
 H5M  HD11  CD1  CD    110.78  3.000

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
 H5M  chir_01  CA  N   C    CB  positiv
 H5M  chir_02  CB  OB  CA   CG  positiv
 H5M  chir_03  CD  N   CD1  CG  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
 H5M  plan-1  CA   0.020
 H5M  plan-1  C    0.020
 H5M  plan-1  O    0.020
 H5M  plan-1  OXT  0.020

