# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:36:37 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: D-homocysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCS)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
 KCY  KCY  'D-homocysteine           '  D-peptide  16  8  .  2016-04-22  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_KCY
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
 KCY  C    C  C      0   0.402   0.6566  18.6947  4.3127
 KCY  N    N  NH2    0  -0.798   2.6283  18.9130  5.7685
 KCY  O    O  O      0  -0.606  -0.3950  18.0376  4.1811
 KCY  CA   C  CH1    0  -0.173   1.8502  17.9719  4.9778
 KCY  CB   C  CH2    0  -0.441   2.6931  17.2648  3.8993
 KCY  SD   S  S2     0  -0.269   3.1296  15.2876  2.0667
 KCY  CG   C  CH2    0  -0.548   1.9543  16.1552  3.1656
 KCY  OXT  O  OC    -1  -0.603   0.8633  19.8622  3.9232
 KCY  HN   H  HNH2   0   0.329   3.5276  18.5098  6.0031
 KCY  HA   H  HCH1   0   0.197   1.4561  17.1997  5.6476
 KCY  HB   H  HCH2   0   0.226   3.5771  16.8410  4.3881
 KCY  HBA  H  HCH2   0   0.222   3.0582  18.0089  3.1836
 KCY  HG   H  HCH2   0   0.255   1.5374  15.4421  3.8775
 KCY  HGA  H  HCH2   0   0.266   1.1377  16.5522  2.5668
 KCY  HNA  H  HNH2   0   0.325   2.8151  19.7242  5.1915
 KCY  HSD  H  HSH1   0   0.216   2.2658  14.4281  1.5147

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
 KCY  OXT  C    deloc   1.248  0.020  1.248
 KCY  O    C    deloc   1.231  0.020  1.231
 KCY  C    CA   single  1.525  0.021  1.525
 KCY  CA   N    single  1.458  0.019  1.458
 KCY  N    HN   single  0.890  0.020  1.040
 KCY  N    HNA  single  0.890  0.020  1.040
 KCY  CB   CA   single  1.521  0.033  1.521
 KCY  CA   HA   single  0.970  0.020  0.970
 KCY  HBA  CB   single  0.970  0.020  1.090
 KCY  CG   CB   single  1.522  0.020  1.522
 KCY  CB   HB   single  0.970  0.020  1.090
 KCY  SD   CG   single  1.828  0.020  1.828
 KCY  SD   HSD  single  1.200  0.020  1.300
 KCY  CG   HG   single  0.970  0.020  1.090
 KCY  CG   HGA  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
 KCY  OXT  C   CA  120.80  1.700
 KCY  CA   C   O   120.80  1.700
 KCY  OXT  C   O   126.84  3.000
 KCY  HNA  N   HN  106.67  3.000
 KCY  HNA  N   CA  107.89  3.000
 KCY  HN   N   CA  110.07  3.000
 KCY  HA   CA  CB  109.00  3.000
 KCY  HA   CA  N   110.00  3.000
 KCY  CB   CA  N   110.40  1.500
 KCY  HA   CA  C   110.00  3.000
 KCY  CB   CA  C   110.50  1.500
 KCY  N    CA  C   111.00  2.800
 KCY  HBA  CB  HB  106.59  3.000
 KCY  HB   CB  CG  108.96  3.000
 KCY  HBA  CB  CG  110.01  3.000
 KCY  HB   CB  CA  107.86  3.000
 KCY  CG   CB  CA  113.99  3.000
 KCY  HBA  CB  CA  109.15  3.000
 KCY  HSD  SD  CG   97.92  3.000
 KCY  HGA  CG  HG  108.12  3.000
 KCY  HGA  CG  SD  108.97  3.000
 KCY  HG   CG  SD  109.14  3.000
 KCY  HGA  CG  CB  111.34  3.000
 KCY  HG   CG  CB  110.35  3.000
 KCY  SD   CG  CB  108.89  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
 KCY  Var_01  SD  CG  CB  CA  -173.45  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
 KCY  chir_01  CA  C  N  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
 KCY  plan-1  C    0.020
 KCY  plan-1  O    0.020
 KCY  plan-1  CA   0.020
 KCY  plan-1  OXT  0.020

