# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:12:42 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  17  8  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.434   1.3195  -1.1790   1.0435
 5JP  C    C  C     0   0.544   1.1107  -0.5471   0.0409
 5JP  CA   C  CH1   0  -0.240  -0.2631  -0.1493  -0.4731
 5JP  CB   C  CH2   0  -0.167  -0.3592   1.3761  -0.5372
 5JP  OG   O  OH1   0  -0.670  -0.0719   1.8730   0.7499
 5JP  N    N  NH1   0  -0.585  -1.2800  -0.8037   0.3145
 5JP  CN   C  CH3   0  -0.522  -2.5952  -0.7943  -0.2923
 5JP  OXT  O  OH1   0  -0.596   2.0763  -0.1090  -0.7595
 5JP  HA   H  HCH1  0   0.283  -0.3446  -0.5176  -1.5025
 5JP  HB2  H  HCH2  0   0.213   0.3335   1.7624  -1.2932
 5JP  HB3  H  HCH2  0   0.221  -1.3686   1.6498  -0.8660
 5JP  HG   H  HOH1  0   0.461  -0.1764   2.8287   0.7406
 5JP  H    H  HNH1  0   0.347  -1.3210  -0.3959   1.2394
 5JP  H7   H  HCH3  0   0.200  -3.0078   0.1998  -0.5073
 5JP  H8   H  HCH3  0   0.225  -2.5684  -1.3469  -1.2337
 5JP  H9   H  HCH3  0   0.237  -3.2975  -1.3037   0.3670
 5JP  HXT  H  HOH1  0   0.481   2.9413  -0.3600  -0.4025

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  1.448  0.020  1.448
 5JP  N    CA   single  1.443  0.020  1.443
 5JP  O    C    double  1.203  0.020  1.203
 5JP  CA   C    single  1.520  0.020  1.520
 5JP  CA   CB   single  1.530  0.020  1.530
 5JP  CB   OG   single  1.409  0.020  1.409
 5JP  C    OXT  single  1.328  0.020  1.328
 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
 5JP  OXT  HXT  single  0.850  0.020  0.980

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   111.53  3.000
 5JP  OXT  C    O    123.30  3.000
 5JP  CA   C    O    125.17  3.000
 5JP  HA   CA   N    107.92  3.000
 5JP  HA   CA   CB   106.91  3.000
 5JP  N    CA   CB   115.52  3.000
 5JP  HA   CA   C    107.26  3.000
 5JP  CB   CA   C    109.39  3.000
 5JP  N    CA   C    109.49  3.000
 5JP  HB3  CB   HB2  106.68  3.000
 5JP  HB3  CB   OG   111.93  3.000
 5JP  HB2  CB   OG   112.15  3.000
 5JP  HB3  CB   CA   108.62  3.000
 5JP  HB2  CB   CA   109.93  3.000
 5JP  OG   CB   CA   107.49  3.000
 5JP  HG   OG   CB   108.64  3.000
 5JP  H    N    CN   110.09  3.000
 5JP  H    N    CA   110.16  3.000
 5JP  CN   N    CA   114.10  3.000
 5JP  H9   CN   H8   107.51  3.000
 5JP  H9   CN   H7   107.43  3.000
 5JP  H8   CN   H7   107.37  3.000
 5JP  H9   CN   N    109.20  3.000
 5JP  H8   CN   N    109.61  3.000
 5JP  H7   CN   N    115.42  3.000
 5JP  HXT  OXT  C    109.96  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  CONST_01  HXT  OXT  C  O     0.00   0.0  0
 5JP  Var_01    H7   CN   N  CA  -58.72  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
 5JP  plan-1  HXT  0.020

