# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 14 17:41:21 2019
#
#   Inital geometry file: a 38 line input string
#   Ligand name: 3-selanyl-L-alanine
#   Quantum optimisation: True
#   Basis set: 6-31G(d,p)
#   Method: UHF
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[SeH])C(O)=O
#   Imposed ALA values on main chain
#
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
SEC        SEC '3-selanyl-L-alanine      ' L-peptide 13 7 .
2019-03-21 2019-04-14
;
CIF prepared directly in eLBOW
;
#
data_comp_SEC
#
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
SEC         N      N   NH2    0    .      -0.7677    1.6913   -0.2616
SEC         CA     C   CH1    0    .      -0.9380    0.2433   -0.3057
SEC         CB     C   CH2    0    .       0.0462   -0.4326    0.6417
SEC        SE      SE  SE     0    .       1.9122    0.1141    0.2476
SEC         C      C   C      0    .      -2.3745   -0.2442    0.0806
SEC         O      O   O      0    .      -3.1397    0.6284    0.4978
SEC         OXT    O   OC    -1    .      -2.5507   -1.4556   -0.0569
SEC         H      H   HNH2   0    .      -1.0497    2.0732   -1.1431
SEC         H2     H   HNH2   0    .      -1.4635    2.0166    0.3861
SEC         HA     H   HCH1   0    .      -0.7284   -0.1124   -1.3096
SEC         HB2    H   HCH2   0    .      -0.1557   -0.1493    1.6657
SEC         HB3    H   HCH2   0    .      -0.0196   -1.5035    0.5448
SEC         HE     H   H      0    .       2.5322   -1.1465    0.6378
#
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
SEC   N       CA    single        1.458 0.020     1.458
SEC   N       H     single        0.868 0.019     1.013
SEC   N       H2    single        0.868 0.020     1.013
SEC   CA      CB    single        1.521 0.020     1.521
SEC   CA      C     single        1.525 0.033     1.525
SEC   CA      HA    single        0.939 0.021     1.096
SEC   CB     SE     single        1.984 0.020     1.984
SEC   CB      HB2   single        0.939 0.020     1.096
SEC   CB      HB3   single        0.939 0.020     1.096
SEC  SE       HE    single        1.444 0.020     1.000
SEC   C       O     deloc         1.231 0.020     1.231
SEC   C       OXT   deloc         1.232 0.020     1.232
#
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
SEC   H2      N       H           104.42 3.000
SEC   H2      N       CA          105.07 3.000
SEC   H       N       CA          114.00 3.000
SEC   HA      CA      C           110.00 3.000
SEC   HA      CA      CB          109.00 3.000
SEC   C       CA      CB          110.50 1.500
SEC   HA      CA      N           110.00 3.000
SEC   C       CA      N           111.00 2.800
SEC   CB      CA      N           110.40 1.500
SEC   HB3     CB      HB2         109.52 3.000
SEC   HB3     CB     SE           108.27 3.000
SEC   HB2     CB     SE           106.94 3.000
SEC   HB3     CB      CA          110.21 3.000
SEC   HB2     CB      CA          110.60 3.000
SEC  SE       CB      CA          111.20 3.000
SEC   HE     SE       CB           96.23 3.000
SEC   OXT     C       O           130.15 3.000
SEC   OXT     C       CA          114.20 3.000
SEC   O       C       CA          120.80 1.700
#
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
SEC 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
SEC plan-1     CA 0.020
SEC plan-1      C 0.020
SEC plan-1      O 0.020
SEC plan-1    OXT 0.020
