# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:52:47 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: N-methyl-D-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
 DSE  DSE  'N-methyl-D-serine        '  D-peptide  16  8  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DSE
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
 DSE  N    N  NH1    0  -0.604  50.1125  13.9662  20.2486
 DSE  CA   C  CH1    0  -0.226  50.8952  12.8288  19.7699
 DSE  C    C  C      0   0.410  50.4697  12.4946  18.3145
 DSE  O    O  O      0  -0.604  51.1471  12.9931  17.3931
 DSE  OXT  O  OC    -1  -0.609  49.4549  11.7815  18.1906
 DSE  CB   C  CH2    0  -0.151  52.3974  13.0116  19.9305
 DSE  CN   C  CH3    0  -0.520  50.3317  15.2343  19.5780
 DSE  OG   O  OH1    0  -0.674  53.0252  11.7715  19.6738
 DSE  H    H  HNH1   0   0.338  50.2889  14.0860  21.2380
 DSE  HA   H  HCH1   0   0.206  50.6033  11.9838  20.4042
 DSE  HB2  H  HCH2   0   0.182  52.7618  13.7901  19.2518
 DSE  HB3  H  HCH2   0   0.175  52.6060  13.3548  20.9557
 DSE  HN1  H  HCH3   0   0.221  49.7281  15.9973  20.0706
 DSE  HN2  H  HCH3   0   0.190  51.3689  15.5929  19.5725
 DSE  HN3  H  HCH3   0   0.221  50.0013  15.1822  18.5411
 DSE  HG   H  HOH1   0   0.445  53.9760  11.9091  19.6804

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
 DSE  N   CA   single  1.458  0.019  1.458
 DSE  N   CN   single  1.451  0.020  1.451
 DSE  N   H    single  0.860  0.020  0.860
 DSE  CA  C    single  1.525  0.021  1.525
 DSE  CA  CB   single  1.521  0.033  1.521
 DSE  CA  HA   single  0.970  0.020  0.970
 DSE  C   O    deloc   1.231  0.020  1.231
 DSE  C   OXT  deloc   1.246  0.020  1.246
 DSE  CB  OG   single  1.413  0.020  1.413
 DSE  CB  HB2  single  0.970  0.020  1.090
 DSE  CB  HB3  single  0.970  0.020  1.090
 DSE  CN  HN1  single  0.970  0.020  1.090
 DSE  CN  HN2  single  0.970  0.020  1.090
 DSE  CN  HN3  single  0.970  0.020  1.090
 DSE  OG  HG   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
 DSE  H    N   CN   108.79  3.000
 DSE  H    N   CA   114.00  3.000
 DSE  CN   N   CA   116.61  3.000
 DSE  HA   CA  CB   109.00  3.000
 DSE  HA   CA  C    110.00  3.000
 DSE  CB   CA  C    110.50  1.500
 DSE  HA   CA  N    110.00  3.000
 DSE  CB   CA  N    110.40  1.500
 DSE  C    CA  N    111.00  2.800
 DSE  OXT  C   O    126.67  3.000
 DSE  OXT  C   CA   120.80  1.700
 DSE  O    C   CA   120.80  1.700
 DSE  HB3  CB  HB2  107.01  3.000
 DSE  HB3  CB  OG   111.00  3.000
 DSE  HB2  CB  OG   111.31  3.000
 DSE  HB3  CB  CA   108.82  3.000
 DSE  HB2  CB  CA   110.39  3.000
 DSE  OG   CB  CA   108.29  3.000
 DSE  HN3  CN  HN2  107.30  3.000
 DSE  HN3  CN  HN1  107.20  3.000
 DSE  HN2  CN  HN1  107.27  3.000
 DSE  HN3  CN  N    110.62  3.000
 DSE  HN2  CN  N    115.50  3.000
 DSE  HN1  CN  N    108.60  3.000
 DSE  HG   OG  CB   108.21  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
 DSE  Var_01  HN1  CN  N  CA  -176.92  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
 DSE  chir_01  CA  N  C  CB  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
 DSE  plan-1  CA   0.020
 DSE  plan-1  C    0.020
 DSE  plan-1  O    0.020
 DSE  plan-1  OXT  0.020

