# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:53:35 2020
#   Inital geometry file: a 40 line input string
#   Ligand name: 3-(sulfanylselanyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[Se]S)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
 PSW  PSW  3-(sulfanylselanyl)-L-alanine  L-peptide  14  8  .  2022-07-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_PSW
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
 PSW  N     N   NH2    0  -0.782   1.4450   1.6592  -0.4033
 PSW  C     C   C      0   0.396   2.8022  -0.4549   0.0310
 PSW  O     O   O      0  -0.598   3.6415  -0.0012  -0.7686
 PSW  CA    C   CH1    0  -0.212   1.4820   0.3367   0.2009
 PSW  CB    C   CH2    0  -0.562   0.3350  -0.4746  -0.3919
 PSW  SE    SE  SE     0   0.031  -1.1752   0.7840  -0.5336
 PSW  SD    S   S2     0  -0.357  -2.8380  -0.6856  -0.6782
 PSW  OXT   O   OC    -1  -0.614   2.8864  -1.5044   0.6986
 PSW  HN1   H   HNH2   0   0.356   1.9536   2.3204   0.1698
 PSW  HN2   H   HNH2   0   0.342   1.9385   1.6294  -1.2889
 PSW  HA    H   HCH1   0   0.240   1.2874   0.4587   1.2703
 PSW  HB1C  H   HCH2   0   0.260   0.5717  -0.8452  -1.3922
 PSW  HB2C  H   HCH2   0   0.271   0.0514  -1.3195   0.2335
 PSW  HD    H   HSH1   0   0.228  -3.0598  -0.9147   0.6246

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
 PSW  N   CA    single  1.458  0.020  1.458
 PSW  C   O     deloc   1.231  0.020  1.231
 PSW  C   CA    single  1.525  0.033  1.525
 PSW  C   OXT   deloc   1.247  0.020  1.247
 PSW  CA  CB    single  1.521  0.020  1.521
 PSW  CB  SE    single  1.971  0.020  1.971
 PSW  SE  SD    single  2.224  0.020  2.224
 PSW  N   HN1   single  0.890  0.020  1.040
 PSW  N   HN2   single  0.890  0.020  1.040
 PSW  CA  HA    single  0.939  0.021  0.939
 PSW  CB  HB1C  single  0.970  0.020  1.090
 PSW  CB  HB2C  single  0.970  0.020  1.090
 PSW  SD  HD    single  1.200  0.020  1.300

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
 PSW  HN2   N   HN1   105.61  3.000
 PSW  HN2   N   CA    108.88  3.000
 PSW  HN1   N   CA    110.25  3.000
 PSW  OXT   C   CA    114.20  3.000
 PSW  OXT   C   O     127.25  3.000
 PSW  CA    C   O     120.80  1.700
 PSW  HA    CA  CB    109.00  3.000
 PSW  HA    CA  C     110.00  3.000
 PSW  CB    CA  C     110.50  1.500
 PSW  HA    CA  N     110.00  3.000
 PSW  CB    CA  N     110.40  1.500
 PSW  C     CA  N     111.00  2.800
 PSW  HB2C  CB  HB1C  108.61  3.000
 PSW  HB2C  CB  SE    109.71  3.000
 PSW  HB1C  CB  SE    108.47  3.000
 PSW  HB2C  CB  CA    112.67  3.000
 PSW  HB1C  CB  CA    111.92  3.000
 PSW  SE    CB  CA    105.34  3.000
 PSW  SD    SE  CB     98.95  3.000
 PSW  HD    SD  SE     99.98  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
 PSW  Var_01  HB1C  CB  SE  SD  79.49  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
 PSW  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
 PSW  plan-1  C    0.020
 PSW  plan-1  O    0.020
 PSW  plan-1  CA   0.020
 PSW  plan-1  OXT  0.020

