# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 02:03:05 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: N-methyl-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](CO)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
 5JP  5JP  'N-methyl-L-serine        '  ligand  16  8  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5JP
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
 5JP  O    O  O      0  -0.602   1.2661  -1.1520   1.0864
 5JP  C    C  C      0   0.406   1.1916  -0.5120   0.0217
 5JP  CA   C  CH1    0  -0.236  -0.2166  -0.1880  -0.5378
 5JP  CB   C  CH2    0  -0.169  -0.3910   1.3266  -0.6033
 5JP  OG   O  OH1    0  -0.677  -0.3328   1.8472   0.7094
 5JP  N    N  NH1    0  -0.584  -1.2471  -0.9060   0.1846
 5JP  CN   C  CH3    0  -0.521  -2.6059  -0.6202  -0.2164
 5JP  OXT  O  OC    -1  -0.624   2.1481  -0.0835  -0.6561
 5JP  HA   H  HCH1   0   0.215  -0.2407  -0.5297  -1.5816
 5JP  HB2  H  HCH2   0   0.193   0.3981   1.7393  -1.2423
 5JP  HB3  H  HCH2   0   0.193  -1.3468   1.5753  -1.0826
 5JP  HG   H  HOH1   0   0.449  -0.4759   2.7961   0.6615
 5JP  H    H  HNH1   0   0.330  -1.1303  -0.7507   1.1760
 5JP  H7   H  HCH3   0   0.190  -2.9491   0.4079  -0.0384
 5JP  H8   H  HCH3   0   0.212  -2.7273  -0.8186  -1.2840
 5JP  H9   H  HCH3   0   0.225  -3.2906  -1.2845   0.3137

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
 5JP  CN  N    single  1.445  0.020  1.445
 5JP  N   CA   single  1.449  0.020  1.449
 5JP  O   C    deloc   1.244  0.020  1.244
 5JP  CA  C    single  1.550  0.020  1.550
 5JP  CA  CB   single  1.526  0.020  1.526
 5JP  CB  OG   single  1.413  0.020  1.413
 5JP  C   OXT  deloc   1.248  0.020  1.248
 5JP  CA  HA   single  0.970  0.020  1.090
 5JP  CB  HB2  single  0.970  0.020  1.090
 5JP  CB  HB3  single  0.970  0.020  1.090
 5JP  OG  HG   single  0.850  0.020  0.980
 5JP  N   H    single  0.860  0.020  1.020
 5JP  CN  H7   single  0.970  0.020  1.090
 5JP  CN  H8   single  0.970  0.020  1.090
 5JP  CN  H9   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
 5JP  OXT  C   CA   115.38  3.000
 5JP  OXT  C   O    126.53  3.000
 5JP  CA   C   O    118.09  3.000
 5JP  HA   CA  N    107.70  3.000
 5JP  HA   CA  CB   105.39  3.000
 5JP  N    CA  CB   115.59  3.000
 5JP  HA   CA  C    107.34  3.000
 5JP  CB   CA  C    109.08  3.000
 5JP  N    CA  C    111.27  3.000
 5JP  HB3  CB  HB2  106.68  3.000
 5JP  HB3  CB  OG   110.97  3.000
 5JP  HB2  CB  OG   111.91  3.000
 5JP  HB3  CB  CA   110.06  3.000
 5JP  HB2  CB  CA   108.45  3.000
 5JP  OG   CB  CA   108.72  3.000
 5JP  HG   OG  CB   108.14  3.000
 5JP  H    N   CN   110.52  3.000
 5JP  H    N   CA   109.32  3.000
 5JP  CN   N   CA   115.62  3.000
 5JP  H9   CN  H8   107.12  3.000
 5JP  H9   CN  H7   107.16  3.000
 5JP  H8   CN  H7   107.07  3.000
 5JP  H9   CN  N    109.56  3.000
 5JP  H8   CN  N    109.86  3.000
 5JP  H7   CN  N    115.71  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
 5JP  Var_01  H7  CN  N  CA  -64.61  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
 5JP  chir_01  CA  N  C  CB  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
 5JP  plan-1  O    0.020
 5JP  plan-1  C    0.020
 5JP  plan-1  CA   0.020
 5JP  plan-1  OXT  0.020

