# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 16:19:18 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: N,O-dimethyl-L-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]([C@@H](C)OC)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
 OTH  OTH  'N,O-dimethyl-L-threonine '  L-peptide  22  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_OTH
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
 OTH  N     N  NH1    0  -0.596  10.3493  -21.7752  -43.2865
 OTH  C     C  C      0   0.408   9.3106  -21.0272  -45.3711
 OTH  CA    C  CH1    0  -0.224   9.0603  -21.5977  -43.9472
 OTH  O     O  O      0  -0.600   9.1238  -19.8052  -45.5419
 OTH  OG1   O  O2     0  -0.497   8.0092  -21.3445  -41.8333
 OTH  CB    C  CH1    0   0.072   8.0415  -20.7854  -43.1395
 OTH  C22   C  CH3    0  -0.393   7.5421  -20.4696  -40.8439
 OTH  CG2   C  CH3    0  -0.684   6.6592  -20.8209  -43.7772
 OTH  C24   C  CH3    0  -0.524  11.1152  -20.5669  -43.0493
 OTH  H2    H  HNH1   0   0.336  10.1883  -22.2306  -42.3983
 OTH  OXT   O  OC    -1  -0.603   9.7182  -21.8440  -46.2182
 OTH  HA    H  HCH1   0   0.203   8.6446  -22.6070  -44.0661
 OTH  HB    H  HCH1   0   0.185   8.3752  -19.7413  -43.0759
 OTH  H22   H  HCH3   0   0.226   7.6407  -20.9687  -39.8794
 OTH  H22A  H  HCH3   0   0.196   8.1256  -19.5410  -40.8094
 OTH  H22B  H  HCH3   0   0.198   6.4884  -20.1956  -40.9728
 OTH  HG1   H  HCH3   0   0.226   5.9192  -20.2913  -43.1745
 OTH  HG2   H  HCH3   0   0.230   6.6770  -20.3458  -44.7559
 OTH  HG3   H  HCH3   0   0.212   6.3143  -21.8499  -43.9032
 OTH  H24   H  HCH3   0   0.221  12.0002  -20.8246  -42.4667
 OTH  H24A  H  HCH3   0   0.218  11.4650  -20.1381  -43.9890
 OTH  H24B  H  HCH3   0   0.190  10.5865  -19.7727  -42.5058

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
 OTH  N    CA    single  1.458  0.019  1.458
 OTH  N    C24   single  1.450  0.020  1.450
 OTH  N    H2    single  0.890  0.020  1.040
 OTH  C    CA    single  1.525  0.021  1.525
 OTH  C    O     deloc   1.231  0.020  1.231
 OTH  C    OXT   deloc   1.245  0.020  1.245
 OTH  CA   CB    single  1.540  0.027  1.540
 OTH  CA   HA    single  0.970  0.020  0.970
 OTH  OG1  CB    single  1.421  0.020  1.421
 OTH  OG1  C22   single  1.401  0.020  1.401
 OTH  CB   CG2   single  1.523  0.020  1.523
 OTH  CB   HB    single  0.970  0.020  1.090
 OTH  C22  H22   single  0.970  0.020  1.090
 OTH  C22  H22A  single  0.970  0.020  1.090
 OTH  C22  H22B  single  0.970  0.020  1.090
 OTH  CG2  HG1   single  0.970  0.020  1.090
 OTH  CG2  HG2   single  0.970  0.020  1.090
 OTH  CG2  HG3   single  0.970  0.020  1.090
 OTH  C24  H24   single  0.970  0.020  1.090
 OTH  C24  H24A  single  0.970  0.020  1.090
 OTH  C24  H24B  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
 OTH  H2    N    C24   108.40  3.000
 OTH  H2    N    CA    108.17  3.000
 OTH  C24   N    CA    116.05  3.000
 OTH  OXT   C    O     126.73  3.000
 OTH  OXT   C    CA    115.79  3.000
 OTH  O     C    CA    120.80  1.700
 OTH  HA    CA   CB    109.00  3.000
 OTH  HA    CA   C     109.00  3.000
 OTH  CB    CA   C     109.10  2.200
 OTH  HA    CA   N     110.00  3.000
 OTH  CB    CA   N     111.50  1.700
 OTH  C     CA   N     111.00  2.800
 OTH  C22   OG1  CB    114.26  3.000
 OTH  HB    CB   CG2   108.81  3.000
 OTH  HB    CB   OG1   109.13  3.000
 OTH  CG2   CB   OG1   110.80  3.000
 OTH  HB    CB   CA    109.41  3.000
 OTH  CG2   CB   CA    111.73  3.000
 OTH  OG1   CB   CA    106.91  3.000
 OTH  H22B  C22  H22A  107.66  3.000
 OTH  H22B  C22  H22   107.78  3.000
 OTH  H22A  C22  H22   108.15  3.000
 OTH  H22B  C22  OG1   113.17  3.000
 OTH  H22A  C22  OG1   111.93  3.000
 OTH  H22   C22  OG1   107.98  3.000
 OTH  HG3   CG2  HG2   108.22  3.000
 OTH  HG3   CG2  HG1   107.86  3.000
 OTH  HG2   CG2  HG1   107.21  3.000
 OTH  HG3   CG2  CB    110.91  3.000
 OTH  HG2   CG2  CB    110.59  3.000
 OTH  HG1   CG2  CB    111.89  3.000
 OTH  H24B  C24  H24A  107.25  3.000
 OTH  H24B  C24  H24   107.29  3.000
 OTH  H24A  C24  H24   107.04  3.000
 OTH  H24B  C24  N     115.43  3.000
 OTH  H24A  C24  N     110.86  3.000
 OTH  H24   C24  N     108.61  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
 OTH  Var_01  H24  C24  N    CA   174.42  30.0  3
 OTH  Var_02  H22  C22  OG1  CB  -175.19  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
 OTH  chir_01  CA  N    C   CB   positiv
 OTH  chir_02  CB  OG1  CA  CG2  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
 OTH  plan-1  C    0.020
 OTH  plan-1  CA   0.020
 OTH  plan-1  O    0.020
 OTH  plan-1  OXT  0.020

