# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 11:13:27 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: O-methyl-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@H](N)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
 7C9  7C9  'O-methyl-L-serine        '  L-peptide  16  8  .  2022-07-23  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_7C9
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
 7C9  O20  O  O2     0  -0.489   2.1205   0.0525  -0.2996
 7C9  N03  N  NH2    0  -0.798  -0.1762   1.7901  -0.3926
 7C9  C04  C  CH1    0  -0.247  -0.2509   0.3427  -0.4782
 7C9  C05  C  C      0   0.397  -1.5835  -0.1949   0.0955
 7C9  O18  O  O      0  -0.600  -2.2605   0.5785   0.7985
 7C9  C19  C  CH2    0  -0.136   0.8901  -0.3819   0.2327
 7C9  C21  C  CH3    0  -0.392   3.2237  -0.5072   0.3619
 7C9  H5   H  HNH2   0   0.327  -0.4760   2.0748   0.5312
 7C9  H6   H  HCH1   0   0.212  -0.2071   0.0550  -1.5362
 7C9  H13  H  HCH2   0   0.195   0.7796  -1.4672   0.1105
 7C9  H14  H  HCH2   0   0.185   0.8481  -0.1709   1.3137
 7C9  H15  H  HCH3   0   0.201   3.2289  -0.2642   1.4317
 7C9  H16  H  HCH3   0   0.201   3.2494  -1.6000   0.2704
 7C9  H17  H  HCH3   0   0.230   4.1311  -0.1038  -0.0874
 7C9  H2   H  HNH2   0   0.331   0.7841   2.0928  -0.4986
 7C9  OXT  O  OC    -1  -0.616  -1.8472  -1.3844  -0.1723

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
 7C9  C19  O20  single  1.409  0.020  1.409
 7C9  C19  C04  single  1.527  0.020  1.527
 7C9  N03  C04  single  1.452  0.020  1.452
 7C9  C21  O20  single  1.403  0.020  1.403
 7C9  C04  C05  single  1.547  0.020  1.547
 7C9  C05  O18  deloc   1.245  0.020  1.245
 7C9  N03  H5   single  0.890  0.020  1.040
 7C9  C04  H6   single  0.970  0.020  1.090
 7C9  C19  H13  single  0.970  0.020  1.090
 7C9  C19  H14  single  0.970  0.020  1.090
 7C9  C21  H15  single  0.970  0.020  1.090
 7C9  C21  H16  single  0.970  0.020  1.090
 7C9  C21  H17  single  0.970  0.020  1.090
 7C9  N03  H2   single  0.890  0.020  1.040
 7C9  C05  OXT  deloc   1.247  0.020  1.247

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
 7C9  C21  O20  C19  112.67  3.000
 7C9  H2   N03  H5   107.00  3.000
 7C9  H2   N03  C04  109.93  3.000
 7C9  H5   N03  C04  108.60  3.000
 7C9  H6   C04  C19  107.13  3.000
 7C9  H6   C04  C05  107.51  3.000
 7C9  C19  C04  C05  107.83  3.000
 7C9  H6   C04  N03  108.43  3.000
 7C9  C05  C04  N03  111.65  3.000
 7C9  C19  C04  N03  114.02  3.000
 7C9  OXT  C05  O18  126.76  3.000
 7C9  OXT  C05  C04  115.71  3.000
 7C9  O18  C05  C04  117.50  3.000
 7C9  H14  C19  H13  107.13  3.000
 7C9  H14  C19  C04  109.71  3.000
 7C9  H13  C19  C04  110.00  3.000
 7C9  H14  C19  O20  110.16  3.000
 7C9  H13  C19  O20  110.53  3.000
 7C9  C04  C19  O20  109.29  3.000
 7C9  H17  C21  H16  108.35  3.000
 7C9  H17  C21  H15  108.42  3.000
 7C9  H16  C21  H15  107.58  3.000
 7C9  H17  C21  O20  108.22  3.000
 7C9  H16  C21  O20  112.12  3.000
 7C9  H15  C21  O20  112.04  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
 7C9  Var_01  H15  C21  O20  C19  -59.00  30.0  3
 7C9  Var_02  H13  C19  O20  C21  -62.58  30.0  1

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
 7C9  chir_01  C04  C19  N03  C05  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
 7C9  plan-1  C04  0.020
 7C9  plan-1  C05  0.020
 7C9  plan-1  O18  0.020
 7C9  plan-1  OXT  0.020

