# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:09:34 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 1-methyl-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[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
 3BY  3BY  '1-methyl-L-proline       '  L-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 OK
;

data_comp_3BY
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
 3BY  O    O  O      0  -0.607  -24.2635  123.7881  383.9881
 3BY  C    C  C      0   0.394  -24.5266  122.7544  384.6337
 3BY  OXT  O  OC    -1  -0.595  -24.6810  122.6641  385.8675
 3BY  CA   C  CH1    0  -0.229  -24.7579  121.4623  383.8227
 3BY  CB   C  CH2    0  -0.444  -24.7168  120.1372  384.6061
 3BY  CG   C  CH2    0  -0.469  -24.4467  119.0777  383.5226
 3BY  CD   C  CH2    0  -0.316  -24.2100  119.9145  382.2425
 3BY  N    N  NT     0  -0.399  -23.8725  121.2644  382.6713
 3BY  CN   C  CH3    0  -0.537  -22.4637  121.3710  383.0133
 3BY  HA   H  HCH1   0   0.225  -25.7720  121.5588  383.4044
 3BY  HB3  H  HCH2   0   0.221  -25.6465  119.9568  385.1457
 3BY  HB2  H  HCH2   0   0.215  -23.9195  120.1521  385.3507
 3BY  HG3  H  HCH2   0   0.225  -25.2848  118.3922  383.3930
 3BY  HG2  H  HCH2   0   0.223  -23.5756  118.4678  383.7667
 3BY  HD3  H  HCH2   0   0.222  -25.1303  119.9502  381.6512
 3BY  HD2  H  HCH2   0   0.226  -23.4295  119.5054  381.5986
 3BY  HN1  H  HCH3   0   0.231  -22.2316  122.3902  383.3164
 3BY  HN2  H  HCH3   0   0.191  -22.1270  120.7005  383.8176
 3BY  HN3  H  HCH3   0   0.224  -21.8599  121.1466  382.1324

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
 3BY  CD  N    single  1.473  0.014  1.473
 3BY  CD  CG   single  1.548  0.020  1.548
 3BY  N   CN   single  1.454  0.020  1.454
 3BY  N   CA   single  1.466  0.015  1.466
 3BY  CG  CB   single  1.539  0.020  1.539
 3BY  CA  CB   single  1.530  0.020  1.530
 3BY  CA  C    single  1.525  0.021  1.525
 3BY  O   C    deloc   1.231  0.020  1.231
 3BY  C   OXT  deloc   1.247  0.020  1.247
 3BY  CA  HA   single  0.970  0.020  0.970
 3BY  CB  HB3  single  0.970  0.020  1.090
 3BY  CB  HB2  single  0.970  0.020  1.090
 3BY  CG  HG3  single  0.970  0.020  1.090
 3BY  CG  HG2  single  0.970  0.020  1.090
 3BY  CD  HD3  single  0.970  0.020  1.090
 3BY  CD  HD2  single  0.970  0.020  1.090
 3BY  CN  HN1  single  0.970  0.020  1.090
 3BY  CN  HN2  single  0.970  0.020  1.090
 3BY  CN  HN3  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
 3BY  CA   C   OXT  116.17  3.000
 3BY  OXT  C   O    126.77  3.000
 3BY  CA   C   O    119.00  3.000
 3BY  HA   CA  N    110.00  3.000
 3BY  HA   CA  CB   109.00  3.000
 3BY  N    CA  CB   103.00  1.100
 3BY  HA   CA  C    109.00  3.000
 3BY  CB   CA  C    110.10  1.900
 3BY  N    CA  C    112.10  2.500
 3BY  HB2  CB  HB3  106.72  3.000
 3BY  HB2  CB  CG   111.20  3.000
 3BY  HB3  CB  CG   112.60  3.000
 3BY  HB2  CB  CA   110.79  3.000
 3BY  HB3  CB  CA   111.81  3.000
 3BY  CG   CB  CA   103.82  3.000
 3BY  HG2  CG  HG3  106.79  3.000
 3BY  HG2  CG  CD   111.42  3.000
 3BY  HG3  CG  CD   111.04  3.000
 3BY  HG2  CG  CB   111.55  3.000
 3BY  HG3  CG  CB   112.43  3.000
 3BY  CD   CG  CB   103.71  3.000
 3BY  HD2  CD  HD3  107.15  3.000
 3BY  HD2  CD  N    110.82  3.000
 3BY  HD3  CD  N    108.89  3.000
 3BY  HD2  CD  CG   113.25  3.000
 3BY  HD3  CD  CG   109.63  3.000
 3BY  N    CD  CG   103.20  1.500
 3BY  CN   N   CD   111.22  3.000
 3BY  CN   N   CA   113.00  3.000
 3BY  CD   N   CA   102.50  3.000
 3BY  HN3  CN  HN2  107.19  3.000
 3BY  HN3  CN  HN1  107.43  3.000
 3BY  HN2  CN  HN1  107.57  3.000
 3BY  HN3  CN  N    109.34  3.000
 3BY  HN2  CN  N    115.09  3.000
 3BY  HN1  CN  N    109.93  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
 3BY  Var_01  CG   CD  N   CA  -38.30  30.0  1
 3BY  Var_02  CD   CG  CB  CA    5.77  30.0  1
 3BY  Var_03  N    CD  CG  CB   19.75  30.0  1
 3BY  Var_04  HN1  CN  N   CA  -66.18  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
 3BY  chir_01  CA  N  CB  C  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
 3BY  plan-1  O    0.020
 3BY  plan-1  C    0.020
 3BY  plan-1  OXT  0.020
 3BY  plan-1  CA   0.020

