# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:59:30 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: S-(hydroxymethyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCO)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
 M0H  M0H  S-(hydroxymethyl)-L-cysteine  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_M0H
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
 M0H  O    O  O     -1  -0.595  13.7439  7.5311  43.6952
 M0H  OXT  O  OC     0  -0.607  15.4668  6.5475  42.6688
 M0H  C    C  C      0   0.406  14.3119  7.0122  42.7155
 M0H  CA   C  CH1    0  -0.194  13.5217  6.9931  41.3798
 M0H  N    N  NH2    0  -0.793  12.0930  7.0538  41.6106
 M0H  CB   C  CH2    0  -0.576  14.0734  8.1395  40.5206
 M0H  SG   S  S2     0  -0.073  13.2882  8.2988  38.8862
 M0H  CD   C  CH2    0  -0.286  14.0276  6.8832  38.0155
 M0H  OE   O  OH1    0  -0.634  15.4036  6.9842  37.8296
 M0H  HA   H  HCH1   0   0.212  13.7549  6.0502  40.8728
 M0H  HN1  H  HNH2   0   0.325  11.9104  7.7847  42.2874
 M0H  HN2  H  HNH2   0   0.326  11.6187  7.3149  40.7533
 M0H  HB1  H  HCH2   0   0.266  13.8966  9.0966  41.0182
 M0H  HB2  H  HCH2   0   0.262  15.1495  8.0404  40.3757
 M0H  HD1  H  HCH2   0   0.259  13.8445  5.9722  38.5848
 M0H  HD2  H  HCH2   0   0.250  13.4684  6.8122  37.0764
 M0H  HE   H  HOH1   0   0.452  15.5819  7.7498  37.2735

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
 M0H  O    C    deloc   1.231  0.020  1.231
 M0H  OXT  C    deloc   1.246  0.020  1.246
 M0H  C    CA   single  1.525  0.021  1.525
 M0H  CA   N    single  1.458  0.019  1.458
 M0H  CA   CB   single  1.530  0.020  1.530
 M0H  CA   HA   single  0.970  0.020  0.970
 M0H  N    HN1  single  0.890  0.020  1.040
 M0H  N    HN2  single  0.890  0.020  1.040
 M0H  CB   SG   single  1.820  0.020  1.820
 M0H  CB   HB1  single  0.970  0.020  1.090
 M0H  CB   HB2  single  0.970  0.020  1.090
 M0H  SG   CD   single  1.819  0.020  1.819
 M0H  CD   OE   single  1.392  0.020  1.392
 M0H  CD   HD1  single  0.970  0.020  1.090
 M0H  CD   HD2  single  0.970  0.020  1.090
 M0H  OE   HE   single  0.850  0.020  0.980

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
 M0H  CA   C   OXT  115.79  3.000
 M0H  CA   C   O    120.80  1.700
 M0H  OXT  C   O    127.41  3.000
 M0H  HA   CA  CB   109.00  3.000
 M0H  HA   CA  N    110.00  3.000
 M0H  CB   CA  N    110.50  1.700
 M0H  HA   CA  C    109.00  3.000
 M0H  CB   CA  C    110.10  1.900
 M0H  N    CA  C    111.00  2.800
 M0H  HN2  N   HN1  107.15  3.000
 M0H  HN2  N   CA   109.72  3.000
 M0H  HN1  N   CA   108.33  3.000
 M0H  HB2  CB  HB1  107.44  3.000
 M0H  HB2  CB  SG   108.32  3.000
 M0H  HB1  CB  SG   105.21  3.000
 M0H  HB2  CB  CA   111.17  3.000
 M0H  HB1  CB  CA   109.94  3.000
 M0H  SG   CB  CA   114.38  3.000
 M0H  CD   SG  CB   100.74  3.000
 M0H  HD2  CD  HD1  107.94  3.000
 M0H  HD2  CD  OE   113.26  3.000
 M0H  HD1  CD  OE   107.24  3.000
 M0H  HD2  CD  SG   104.68  3.000
 M0H  HD1  CD  SG   109.40  3.000
 M0H  OE   CD  SG   114.15  3.000
 M0H  HE   OE  CD   108.53  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
 M0H  Var_01  OE   CD  SG  CB  -65.17  30.0  3
 M0H  Var_02  HB1  CB  SG  CD  165.09  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
 M0H  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
 M0H  plan-1  O    0.020
 M0H  plan-1  OXT  0.020
 M0H  plan-1  C    0.020
 M0H  plan-1  CA   0.020

