# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 03:34:55 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (2S)-2-amino-4-(methyldisulfanyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSSCC[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
 HCM  HCM  '(2S)-2-amino-4-(methyldisulfanyl)butanoic acid'  L-peptide  20  10  .  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_HCM
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
 HCM  C1   C  CH3    0  -0.760  38.0768  -15.6918   4.4607
 HCM  S2   S  S2     0  -0.081  39.1154  -14.2382   4.7632
 HCM  SD   S  S2     0  -0.052  40.3986  -14.8913   6.2299
 HCM  CG   C  CH2    0  -0.569  39.4168  -14.6289   7.7491
 HCM  CB   C  CH2    0  -0.402  39.5591  -13.2439   8.3594
 HCM  CA   C  CH1    0  -0.195  40.7918  -13.0497   9.2495
 HCM  C    C  C      0   0.396  42.0883  -13.4501   8.5042
 HCM  OXT  O  OC    -1  -0.613  42.3854  -14.6645   8.5262
 HCM  O    O  O      0  -0.599  42.7115  -12.5365   7.9283
 HCM  N    N  NH2    0  -0.792  40.7707  -11.6832   9.7579
 HCM  H11  H  HCH3   0   0.272  37.3692  -15.4196   3.6776
 HCM  H12  H  HCH3   0   0.268  38.6758  -16.5337   4.1219
 HCM  H13  H  HCH3   0   0.268  37.5201  -15.9666   5.3544
 HCM  HG1  H  HCH2   0   0.276  38.3784  -14.8441   7.4974
 HCM  HG2  H  HCH2   0   0.271  39.7424  -15.4035   8.4444
 HCM  HB2  H  HCH2   0   0.220  39.5491  -12.4923   7.5627
 HCM  HB1  H  HCH2   0   0.232  38.6753  -13.0469   8.9730
 HCM  HA   H  HCH1   0   0.205  40.6785  -13.7237  10.1053
 HCM  H    H  HNH2   0   0.333  41.4633  -11.5988  10.4930
 HCM  H2   H  HNH2   0   0.322  41.1158  -11.0822   9.0169

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
 HCM  C1  S2   single  1.812  0.020  1.812
 HCM  S2  SD   single  2.055  0.020  2.055
 HCM  SD  CG   single  1.828  0.020  1.828
 HCM  CG  CB   single  1.520  0.020  1.520
 HCM  CB  CA   single  1.530  0.020  1.530
 HCM  O   C    deloc   1.231  0.020  1.231
 HCM  N   CA   single  1.458  0.019  1.458
 HCM  CA  C    single  1.525  0.021  1.525
 HCM  C   OXT  deloc   1.250  0.020  1.250
 HCM  C1  H11  single  0.970  0.020  1.090
 HCM  C1  H12  single  0.970  0.020  1.090
 HCM  C1  H13  single  0.970  0.020  1.090
 HCM  CG  HG1  single  0.970  0.020  1.090
 HCM  CG  HG2  single  0.970  0.020  1.090
 HCM  CB  HB2  single  0.970  0.020  1.090
 HCM  CB  HB1  single  0.970  0.020  1.090
 HCM  CA  HA   single  0.970  0.020  0.970
 HCM  N   H    single  0.860  0.020  0.860
 HCM  N   H2   single  0.890  0.020  1.040

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
 HCM  H13  C1  H12  110.01  3.000
 HCM  H13  C1  H11  108.72  3.000
 HCM  H12  C1  H11  109.09  3.000
 HCM  H13  C1  S2   111.02  3.000
 HCM  H12  C1  S2   110.94  3.000
 HCM  H11  C1  S2   106.96  3.000
 HCM  SD   S2  C1   102.83  3.000
 HCM  CG   SD  S2   102.25  3.000
 HCM  HG2  CG  HG1  106.94  3.000
 HCM  HG2  CG  CB   111.30  3.000
 HCM  HG1  CG  CB   111.21  3.000
 HCM  HG2  CG  SD   105.52  3.000
 HCM  HG1  CG  SD   106.95  3.000
 HCM  CB   CG  SD   114.47  3.000
 HCM  HB1  CB  HB2  106.09  3.000
 HCM  HB1  CB  CA   107.53  3.000
 HCM  HB2  CB  CA   110.05  3.000
 HCM  HB1  CB  CG   108.28  3.000
 HCM  HB2  CB  CG   109.41  3.000
 HCM  CA   CB  CG   115.08  3.000
 HCM  HA   CA  N    110.00  3.000
 HCM  HA   CA  C    109.00  3.000
 HCM  N    CA  C    111.00  2.800
 HCM  HA   CA  CB   109.00  3.000
 HCM  C    CA  CB   110.10  1.900
 HCM  N    CA  CB   110.50  1.700
 HCM  O    C   OXT  126.94  3.000
 HCM  OXT  C   CA   116.21  3.000
 HCM  O    C   CA   120.80  1.700
 HCM  H2   N   H    104.35  3.000
 HCM  H2   N   CA   107.19  3.000
 HCM  H    N   CA   114.00  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
 HCM  Var_01  CB   CG  SD  S2   -87.91  30.0  3
 HCM  Var_02  CA   CB  CG  SD   -82.57  30.0  3
 HCM  Var_03  H11  C1  S2  SD  -179.48  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
 HCM  chir_01  CA  CB  N  C  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
 HCM  plan-1  CA   0.020
 HCM  plan-1  C    0.020
 HCM  plan-1  OXT  0.020
 HCM  plan-1  O    0.020

