# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:06:03 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (2R)-7-amino-2-(selanylmethyl)heptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCC[C@@H](C[SeH])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
 DDK  DDK  '(2R)-7-amino-2-(selanylmethyl)heptanoic acid'  ligand  28  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DDK
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
 DDK  OAB  O   O      0  -0.609   1.2827  -2.9799  -0.5887
 DDK  CAK  C   C      0   0.449   1.6337  -1.9072  -0.0624
 DDK  OAC  O   OC    -1  -0.592   2.6932  -1.7123   0.5729
 DDK  CAL  C   CH1    0  -0.372   0.6765  -0.7046  -0.2196
 DDK  CAF  C   CH2    0  -0.558   1.1326   0.5049   0.5796
 DDK  SED  SE  SE     0  -0.209   2.9677   1.0537   0.1250
 DDK  CAJ  C   CH2    0  -0.408  -0.7568  -1.1006   0.1557
 DDK  CAI  C   CH2    0  -0.417  -1.8040  -0.0214  -0.0993
 DDK  CAH  C   CH2    0  -0.414  -3.2265  -0.5276   0.1081
 DDK  CAG  C   CH2    0  -0.424  -4.2845   0.5515  -0.0832
 DDK  CAE  C   CH2    0  -0.270  -5.7009   0.0262   0.0932
 DDK  NAA  N   NH2    0  -0.801  -6.6813   1.0903  -0.0756
 DDK  H2   H   HCH1   0   0.226   0.6710  -0.4316  -1.2839
 DDK  H3   H   HCH2   0   0.263   0.4905   1.3652   0.3907
 DDK  H4   H   HCH2   0   0.246   1.0927   0.2941   1.6503
 DDK  H5   H   H      0   0.140   2.6413   2.4671  -0.0633
 DDK  H6   H   HCH2   0   0.221  -1.0210  -1.9921  -0.4171
 DDK  H7   H   HCH2   0   0.206  -0.7919  -1.3944   1.2115
 DDK  H8   H   HCH2   0   0.211  -1.6330   0.8377   0.5574
 DDK  H9   H   HCH2   0   0.206  -1.6967   0.3530  -1.1240
 DDK  H10  H   HCH2   0   0.208  -3.4196  -1.3545  -0.5837
 DDK  H11  H   HCH2   0   0.207  -3.3177  -0.9485   1.1157
 DDK  H12  H   HCH2   0   0.210  -4.1140   1.3668   0.6266
 DDK  H13  H   HCH2   0   0.208  -4.1832   0.9866  -1.0843
 DDK  H14  H   HCH2   0   0.185  -5.8525  -0.8207  -0.5922
 DDK  H15  H   HCH2   0   0.209  -5.8081  -0.3782   1.1040
 DDK  H16  H   HNH2   0   0.336  -6.6592   1.4136  -1.0354
 DDK  H17  H   HNH2   0   0.344  -7.6116   0.7159   0.0608

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
 DDK  CAG  CAH  single  1.523  0.020  1.523
 DDK  CAG  CAE  single  1.521  0.020  1.521
 DDK  CAH  CAI  single  1.524  0.020  1.524
 DDK  NAA  CAE  single  1.457  0.020  1.457
 DDK  CAI  CAJ  single  1.525  0.020  1.525
 DDK  CAJ  CAL  single  1.534  0.020  1.534
 DDK  CAL  CAF  single  1.520  0.020  1.520
 DDK  CAL  CAK  single  1.545  0.020  1.545
 DDK  CAF  SED  single  1.969  0.020  1.969
 DDK  CAK  OAB  deloc   1.245  0.020  1.245
 DDK  CAK  OAC  deloc   1.251  0.020  1.251
 DDK  CAL  H2   single  0.939  0.020  1.096
 DDK  CAF  H3   single  0.939  0.020  1.096
 DDK  CAF  H4   single  0.939  0.020  1.096
 DDK  SED  H5   single  1.444  0.020  1.000
 DDK  CAJ  H6   single  0.939  0.020  1.096
 DDK  CAJ  H7   single  0.939  0.020  1.096
 DDK  CAI  H8   single  0.939  0.020  1.096
 DDK  CAI  H9   single  0.939  0.020  1.096
 DDK  CAH  H10  single  0.939  0.020  1.096
 DDK  CAH  H11  single  0.939  0.020  1.096
 DDK  CAG  H12  single  0.939  0.020  1.096
 DDK  CAG  H13  single  0.939  0.020  1.096
 DDK  CAE  H14  single  0.939  0.020  1.096
 DDK  CAE  H15  single  0.939  0.020  1.096
 DDK  NAA  H16  single  0.868  0.020  1.013
 DDK  NAA  H17  single  0.868  0.020  1.013

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
 DDK  CAL  CAK  OAC  117.08  3.000
 DDK  OAC  CAK  OAB  125.99  3.000
 DDK  CAL  CAK  OAB  116.93  3.000
 DDK  H2   CAL  CAJ  107.25  3.000
 DDK  H2   CAL  CAF  108.25  3.000
 DDK  CAJ  CAL  CAF  110.93  3.000
 DDK  H2   CAL  CAK  107.16  3.000
 DDK  CAF  CAL  CAK  112.34  3.000
 DDK  CAJ  CAL  CAK  110.68  3.000
 DDK  H4   CAF  H3   107.50  3.000
 DDK  H4   CAF  SED  108.32  3.000
 DDK  H3   CAF  SED  106.80  3.000
 DDK  H4   CAF  CAL  110.55  3.000
 DDK  H3   CAF  CAL  111.12  3.000
 DDK  SED  CAF  CAL  112.35  3.000
 DDK  H5   SED  CAF   95.23  3.000
 DDK  H7   CAJ  H6   106.17  3.000
 DDK  H7   CAJ  CAI  109.18  3.000
 DDK  H6   CAJ  CAI  108.90  3.000
 DDK  H7   CAJ  CAL  109.56  3.000
 DDK  H6   CAJ  CAL  107.97  3.000
 DDK  CAI  CAJ  CAL  114.71  3.000
 DDK  H9   CAI  H8   106.11  3.000
 DDK  H9   CAI  CAH  109.38  3.000
 DDK  H8   CAI  CAH  108.95  3.000
 DDK  H9   CAI  CAJ  109.31  3.000
 DDK  H8   CAI  CAJ  110.35  3.000
 DDK  CAH  CAI  CAJ  112.52  3.000
 DDK  H11  CAH  H10  106.03  3.000
 DDK  H11  CAH  CAG  109.26  3.000
 DDK  H10  CAH  CAG  109.46  3.000
 DDK  H11  CAH  CAI  109.29  3.000
 DDK  H10  CAH  CAI  109.23  3.000
 DDK  CAG  CAH  CAI  113.32  3.000
 DDK  H13  CAG  H12  106.39  3.000
 DDK  H13  CAG  CAE  109.21  3.000
 DDK  H12  CAG  CAE  109.10  3.000
 DDK  H13  CAG  CAH  109.37  3.000
 DDK  H12  CAG  CAH  109.76  3.000
 DDK  CAE  CAG  CAH  112.80  3.000
 DDK  H15  CAE  H14  106.12  3.000
 DDK  H15  CAE  NAA  108.13  3.000
 DDK  H14  CAE  NAA  113.42  3.000
 DDK  H15  CAE  CAG  109.03  3.000
 DDK  H14  CAE  CAG  108.79  3.000
 DDK  NAA  CAE  CAG  111.16  3.000
 DDK  H17  NAA  H16  105.41  3.000
 DDK  H17  NAA  CAE  109.44  3.000
 DDK  H16  NAA  CAE  109.17  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
 DDK  Var_01  CAH  CAI  CAJ  CAL  172.13  30.0  1
 DDK  Var_02  CAG  CAH  CAI  CAJ  177.51  30.0  1
 DDK  Var_03  CAE  CAG  CAH  CAI  178.60  30.0  1
 DDK  Var_04  NAA  CAE  CAG  CAH  179.07  30.0  3
 DDK  Var_05  H16  NAA  CAE  CAG   65.96  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
 DDK  chir_01  CAL  CAJ  CAF  CAK  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
 DDK  plan-1  OAB  0.020
 DDK  plan-1  CAK  0.020
 DDK  plan-1  OAC  0.020
 DDK  plan-1  CAL  0.020

