# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:48:13 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 3-[(2-amino-2-oxoethyl)selanyl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[Se]CC(N)=O)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
 SYS  SYS  3-[(2-amino-2-oxoethyl)selanyl]-L-alanine  L-peptide  20  11  .  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_SYS
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
 SYS  N    N   NH2    0  -0.799   2.1678   1.6220  -0.5500
 SYS  CA   C   CH1    0  -0.212   2.1440   0.4063   0.2396
 SYS  CB   C   CH2    0  -0.583   0.9220  -0.4938   0.0069
 SYS  SE   SE  SE     0   0.043  -0.7319   0.3821   0.6176
 SYS  C    C   C      0   0.412   3.4037  -0.4569  -0.0447
 SYS  O    O   O      0  -0.599   3.9822  -0.2729  -1.1320
 SYS  HN   H   HNH2   0   0.330   2.4533   1.3817  -1.4909
 SYS  HNA  H   HNH2   0   0.335   1.2433   2.0311  -0.6160
 SYS  HA   H   HCH1   0   0.216   2.1731   0.6732   1.3029
 SYS  HB   H   HCH2   0   0.254   0.8194  -0.7144  -1.0596
 SYS  HBA  H   HCH2   0   0.259   1.0357  -1.4368   0.5435
 SYS  O2   O   OC    -1  -0.612   3.7025  -1.2889   0.8330
 SYS  C4   C   CH2    0  -0.718  -1.9662  -0.7510  -0.3764
 SYS  C5   C   C      0   0.532  -3.3836  -0.3063  -0.0849
 SYS  N2   N   NH2    0  -0.795  -4.3325  -1.0929  -0.6075
 SYS  O3   O   O      0  -0.482  -3.6237   0.6980   0.5688
 SYS  H6   H   HCH2   0   0.304  -1.7689  -0.6709  -1.4491
 SYS  H7   H   HCH2   0   0.298  -1.8312  -1.7997  -0.1014
 SYS  H8   H   HNH2   0   0.411  -4.1103  -1.9269  -1.1233
 SYS  H9   H   HNH2   0   0.404  -5.3064  -0.8736  -0.4744

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
 SYS  N   CA   single  1.458  0.020  1.458
 SYS  N   HN   single  0.890  0.020  1.040
 SYS  N   HNA  single  0.890  0.020  1.040
 SYS  CA  CB   single  1.521  0.020  1.521
 SYS  CA  C    single  1.525  0.033  1.525
 SYS  CA  HA   single  0.939  0.021  0.939
 SYS  CB  SE   single  1.969  0.020  1.969
 SYS  CB  HB   single  0.970  0.020  1.090
 SYS  CB  HBA  single  0.970  0.020  1.090
 SYS  C   O    deloc   1.231  0.020  1.231
 SYS  C   O2   deloc   1.246  0.020  1.246
 SYS  SE  C4   single  1.948  0.020  1.948
 SYS  C4  C5   single  1.514  0.020  1.514
 SYS  C5  N2   single  1.339  0.020  1.339
 SYS  C5  O3   double  1.222  0.020  1.222
 SYS  C4  H6   single  0.970  0.020  1.090
 SYS  C4  H7   single  0.970  0.020  1.090
 SYS  N2  H8   single  0.860  0.020  1.020
 SYS  N2  H9   single  0.860  0.020  1.020

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
 SYS  HNA  N   HN  107.02  3.000
 SYS  HNA  N   CA  111.05  3.000
 SYS  HN   N   CA  108.16  3.000
 SYS  HA   CA  C   110.00  3.000
 SYS  HA   CA  CB  109.00  3.000
 SYS  C    CA  CB  110.50  1.500
 SYS  HA   CA  N   110.00  3.000
 SYS  C    CA  N   111.00  2.800
 SYS  CB   CA  N   110.40  1.500
 SYS  HBA  CB  HB  108.36  3.000
 SYS  HBA  CB  SE  108.64  3.000
 SYS  HB   CB  SE  108.26  3.000
 SYS  HBA  CB  CA  110.44  3.000
 SYS  HB   CB  CA  109.92  3.000
 SYS  SE   CB  CA  111.15  3.000
 SYS  C4   SE  CB   96.61  3.000
 SYS  O2   C   O   127.04  3.000
 SYS  O2   C   CA  115.90  3.000
 SYS  O    C   CA  120.80  1.700
 SYS  H7   C4  H6  107.15  3.000
 SYS  H7   C4  C5  110.44  3.000
 SYS  H6   C4  C5  109.65  3.000
 SYS  H7   C4  SE  110.59  3.000
 SYS  H6   C4  SE  110.10  3.000
 SYS  C5   C4  SE  108.91  3.000
 SYS  O3   C5  N2  123.53  3.000
 SYS  O3   C5  C4  121.89  3.000
 SYS  N2   C5  C4  114.57  3.000
 SYS  H9   N2  H8  117.52  3.000
 SYS  H9   N2  C5  120.39  3.000
 SYS  H8   N2  C5  122.07  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
 SYS  CONST_01  H8  N2  C5  C4     0.00   0.0  0
 SYS  CONST_02  H9  N2  C5  C4   180.00   0.0  0
 SYS  Var_01    C5  C4  SE  CB   179.49  30.0  3
 SYS  Var_02    N2  C5  C4  SE  -173.73  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
 SYS  chir_01  CA  N  CB  C  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
 SYS  plan-1  C4  0.020
 SYS  plan-1  C5  0.020
 SYS  plan-1  N2  0.020
 SYS  plan-1  O3  0.020
 SYS  plan-1  H8  0.020
 SYS  plan-1  H9  0.020
 SYS  plan-2  CA  0.020
 SYS  plan-2  C   0.020
 SYS  plan-2  O   0.020
 SYS  plan-2  O2  0.020

