# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 08:10:55 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (2S)-2-(dimethylamino)-4-(methylselanyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Se]CC[C@H](N(C)C)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
 6KY  6KY  '(2S)-2-(dimethylamino)-4-(methylselanyl)butanoic acid'  L-peptide  25  11  .  2022-03-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6KY
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
 6KY  N    N   NT     0  -0.405  -1.8738  -1.2734   0.1224
 6KY  CA   C   CH1    0  -0.185  -1.6774   0.1358   0.4109
 6KY  C    C   C      0   0.398  -2.7687   1.1327  -0.0665
 6KY  O    O   O      0  -0.587  -3.6833   0.7106  -0.7980
 6KY  CB   C   CH2    0  -0.455  -0.2969   0.6198  -0.0546
 6KY  CG   C   CH2    0  -0.559   0.8289  -0.2335   0.5062
 6KY  SE   SE  SE     0   0.004   2.5713   0.4614  -0.0722
 6KY  CE   C   CH3    0  -0.803   3.6812  -0.8539   0.8486
 6KY  CN1  C   CH3    0  -0.507  -2.9608  -1.8714   0.8578
 6KY  CN2  C   CH3    0  -0.514  -1.8803  -1.6664  -1.2684
 6KY  HA   H   HCH1   0   0.216  -1.6656   0.2100   1.5076
 6KY  HB1  H   HCH2   0   0.224  -0.2458   0.6446  -1.1476
 6KY  HG1  H   HCH2   0   0.249   0.7979  -0.2279   1.5987
 6KY  OXT  O   OC    -1  -0.623  -2.6315   2.3064   0.3409
 6KY  H1   H   HCH2   0   0.241  -0.1840   1.6526   0.2774
 6KY  H2   H   HCH2   0   0.262   0.7399  -1.2689   0.1767
 6KY  H3   H   HCH3   0   0.261   3.5507  -0.7824   1.9278
 6KY  H4   H   HCH3   0   0.260   3.4352  -1.8629   0.5208
 6KY  H5   H   HCH3   0   0.267   4.7241  -0.6515   0.6074
 6KY  H6   H   HCH3   0   0.193  -3.9563  -1.5421   0.5342
 6KY  H7   H   HCH3   0   0.213  -2.9212  -2.9593   0.7571
 6KY  H8   H   HCH3   0   0.216  -2.8623  -1.6412   1.9214
 6KY  H9   H   HCH3   0   0.202  -2.7907  -1.3875  -1.8090
 6KY  H10  H   HCH3   0   0.220  -1.0326  -1.2312  -1.7998
 6KY  H11  H   HCH3   0   0.209  -1.7678  -2.7518  -1.3370

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
 6KY  C    CA   single  1.525  0.021  1.525
 6KY  C    O    deloc   1.231  0.020  1.231
 6KY  CN2  N    single  1.445  0.020  1.445
 6KY  CA   N    single  1.458  0.019  1.458
 6KY  CA   CB   single  1.521  0.033  1.521
 6KY  N    CN1  single  1.442  0.020  1.442
 6KY  CG   CB   single  1.520  0.020  1.520
 6KY  CG   SE   single  1.963  0.020  1.963
 6KY  SE   CE   single  1.952  0.020  1.952
 6KY  CA   HA   single  0.970  0.020  0.970
 6KY  CB   HB1  single  0.970  0.020  1.090
 6KY  CG   HG1  single  0.970  0.020  1.090
 6KY  C    OXT  deloc   1.250  0.020  1.250
 6KY  CB   H1   single  0.970  0.020  1.090
 6KY  CG   H2   single  0.970  0.020  1.090
 6KY  CE   H3   single  0.970  0.020  1.090
 6KY  CE   H4   single  0.970  0.020  1.090
 6KY  CE   H5   single  0.970  0.020  1.090
 6KY  CN1  H6   single  0.970  0.020  1.090
 6KY  CN1  H7   single  0.970  0.020  1.090
 6KY  CN1  H8   single  0.970  0.020  1.090
 6KY  CN2  H9   single  0.970  0.020  1.090
 6KY  CN2  H10  single  0.970  0.020  1.090
 6KY  CN2  H11  single  0.970  0.020  1.090

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
 6KY  CN2  N    CN1  112.00  3.000
 6KY  CN1  N    CA   113.77  3.000
 6KY  CN2  N    CA   117.12  3.000
 6KY  HA   CA   CB   109.00  3.000
 6KY  HA   CA   C    110.00  3.000
 6KY  CB   CA   C    110.50  1.500
 6KY  HA   CA   N    110.00  3.000
 6KY  CB   CA   N    110.40  1.500
 6KY  C    CA   N    111.00  2.800
 6KY  OXT  C    O    126.19  3.000
 6KY  OXT  C    CA   120.80  1.700
 6KY  O    C    CA   120.80  1.700
 6KY  H1   CB   HB1  106.12  3.000
 6KY  H1   CB   CG   110.03  3.000
 6KY  HB1  CB   CG   110.28  3.000
 6KY  H1   CB   CA   107.42  3.000
 6KY  HB1  CB   CA   110.61  3.000
 6KY  CG   CB   CA   112.16  3.000
 6KY  H2   CG   HG1  107.73  3.000
 6KY  H2   CG   SE   108.64  3.000
 6KY  HG1  CG   SE   108.53  3.000
 6KY  H2   CG   CB   111.17  3.000
 6KY  HG1  CG   CB   110.18  3.000
 6KY  SE   CG   CB   110.49  3.000
 6KY  CE   SE   CG    97.31  3.000
 6KY  H5   CE   H4   108.77  3.000
 6KY  H5   CE   H3   108.77  3.000
 6KY  H4   CE   H3   109.38  3.000
 6KY  H5   CE   SE   108.35  3.000
 6KY  H4   CE   SE   110.72  3.000
 6KY  H3   CE   SE   110.79  3.000
 6KY  H8   CN1  H7   107.22  3.000
 6KY  H8   CN1  H6   107.80  3.000
 6KY  H7   CN1  H6   107.72  3.000
 6KY  H8   CN1  N    109.95  3.000
 6KY  H7   CN1  N    109.77  3.000
 6KY  H6   CN1  N    114.14  3.000
 6KY  H11  CN2  H10  106.58  3.000
 6KY  H11  CN2  H9   107.91  3.000
 6KY  H10  CN2  H9   107.70  3.000
 6KY  H11  CN2  N    109.26  3.000
 6KY  H10  CN2  N    110.90  3.000
 6KY  H9   CN2  N    114.18  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
 6KY  Var_01  SE  CG   CB  CA  -178.20  30.0  1
 6KY  Var_02  H9  CN2  N   CA   -74.03  30.0  3
 6KY  Var_03  H6  CN1  N   CA    70.79  30.0  3
 6KY  Var_04  H3  CE   SE  CG   -63.05  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
 6KY  chir_01  CA  C  N  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
 6KY  plan-1  CA   0.020
 6KY  plan-1  C    0.020
 6KY  plan-1  O    0.020
 6KY  plan-1  OXT  0.020

