# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 14:02:20 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: 3-(methyldisulfanyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSSC[C@H](N)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
 SCH  SCH  3-(methyldisulfanyl)-L-alanine  L-peptide  17  9  .  2012-08-28  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_SCH
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
 SCH  N    N  NH2    0  -0.786  12.7861  20.9935  16.1210
 SCH  CA   C  CH1    0  -0.227  14.0393  21.5610  15.6289
 SCH  CB   C  CH2    0  -0.534  13.7902  22.4292  14.4123
 SCH  SG   S  S2     0  -0.059  12.9219  23.9770  14.8744
 SCH  SD   S  S2     0  -0.101  11.2719  23.9645  13.6300
 SCH  CE   C  CH3    0  -0.760  10.1046  22.9184  14.5385
 SCH  C    C  C      0   0.420  14.8418  22.3145  16.7183
 SCH  O    O  O      0  -0.603  15.1034  21.6702  17.7508
 SCH  OXT  O  OC    -1  -0.589  15.1453  23.5025  16.4741
 SCH  H    H  HNH2   0   0.339  12.9964  20.4286  16.9352
 SCH  H2   H  HNH2   0   0.334  12.2034  21.7488  16.4670
 SCH  HA   H  HCH1   0   0.236  14.6550  20.7178  15.2891
 SCH  HB2  H  HCH2   0   0.266  14.7280  22.7027  13.9315
 SCH  HB3  H  HCH2   0   0.268  13.1710  21.9095  13.6821
 SCH  HE1  H  HCH3   0   0.270   9.1949  22.8557  13.9413
 SCH  HE2  H  HCH3   0   0.262  10.5087  21.9171  14.6755
 SCH  HE3  H  HCH3   0   0.264   9.8652  23.3545  15.5060

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
 SCH  N   CA   single  1.458  0.019  1.458
 SCH  N   H    single  0.860  0.020  0.860
 SCH  N   H2   single  0.890  0.020  1.040
 SCH  CA  CB   single  1.530  0.020  1.530
 SCH  CA  C    single  1.525  0.021  1.525
 SCH  CA  HA   single  0.970  0.020  0.970
 SCH  CB  SG   single  1.834  0.020  1.834
 SCH  CB  HB2  single  0.970  0.020  1.090
 SCH  CB  HB3  single  0.970  0.020  1.090
 SCH  SG  SD   single  2.067  0.020  2.067
 SCH  SD  CE   single  1.812  0.020  1.812
 SCH  CE  HE1  single  0.970  0.020  1.090
 SCH  CE  HE2  single  0.970  0.020  1.090
 SCH  CE  HE3  single  0.970  0.020  1.090
 SCH  C   O    deloc   1.231  0.020  1.231
 SCH  C   OXT  deloc   1.250  0.020  1.250

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
 SCH  H2   N   H    105.08  3.000
 SCH  H2   N   CA   108.56  3.000
 SCH  H    N   CA   114.00  3.000
 SCH  HA   CA  C    109.00  3.000
 SCH  HA   CA  CB   109.00  3.000
 SCH  C    CA  CB   110.10  1.900
 SCH  HA   CA  N    110.00  3.000
 SCH  C    CA  N    111.00  2.800
 SCH  CB   CA  N    110.50  1.700
 SCH  HB3  CB  HB2  108.26  3.000
 SCH  HB3  CB  SG   107.60  3.000
 SCH  HB2  CB  SG   107.88  3.000
 SCH  HB3  CB  CA   111.00  3.000
 SCH  HB2  CB  CA   110.91  3.000
 SCH  SG   CB  CA   111.05  3.000
 SCH  SD   SG  CB   102.78  3.000
 SCH  CE   SD  SG   102.47  3.000
 SCH  HE3  CE  HE2  109.79  3.000
 SCH  HE3  CE  HE1  109.07  3.000
 SCH  HE2  CE  HE1  109.02  3.000
 SCH  HE3  CE  SD   110.87  3.000
 SCH  HE2  CE  SD   110.80  3.000
 SCH  HE1  CE  SD   107.23  3.000
 SCH  OXT  C   O    127.07  3.000
 SCH  OXT  C   CA   116.79  3.000
 SCH  O    C   CA   120.80  1.700

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
 SCH  Var_01  HE1  CE  SD  SG  -179.81  30.0  3
 SCH  Var_02  HB2  CB  SG  SD   112.51  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
 SCH  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
 SCH  plan-1  CA   0.020
 SCH  plan-1  C    0.020
 SCH  plan-1  O    0.020
 SCH  plan-1  OXT  0.020

