# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 19:53:36 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: S-(dimethylarsoryl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[As](C)(=O)SC[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
 CAF  CAF  S-(dimethylarsoryl)-L-cysteine  L-peptide  22  11  .  2022-07-24  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_CAF
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
 CAF  N     N   NH2    0  -0.787   2.2821   1.0938   1.3174
 CAF  CA    C   CH1    0  -0.209   1.9749   0.1657   0.2526
 CAF  CB    C   CH2    0  -0.581   1.0755   0.7249  -0.8578
 CAF  C     C   C      0   0.412   3.2616  -0.3548  -0.4408
 CAF  O     O   O      0  -0.597   4.2999   0.3146  -0.2913
 CAF  OXT   O   OC    -1  -0.610   3.1226  -1.3861  -1.1256
 CAF  SG    S   S2     0  -0.221  -0.4928   1.4642  -0.2656
 CAF  AS    AS  AS     0   1.049  -1.6709  -0.3622   0.1695
 CAF  CE1   C   CH3    0  -0.922  -1.3093  -0.8317   2.0022
 CAF  CE2   C   CH3    0  -0.911  -3.4665   0.3256   0.1251
 CAF  O1    O   O      0  -0.765  -1.3593  -1.5633  -0.8847
 CAF  H     H   HNH2   0   0.330   2.9124   1.8025   0.9636
 CAF  H2    H   HNH2   0   0.331   1.4389   1.5711   1.6151
 CAF  HA    H   HCH1   0   0.225   1.4664  -0.7035   0.6839
 CAF  HB2   H   HCH2   0   0.284   1.5727   1.5515  -1.3719
 CAF  HB3   H   HCH2   0   0.281   0.8454  -0.0403  -1.5975
 CAF  HE11  H   HCH3   0   0.277  -1.4750   0.0300   2.6475
 CAF  HE12  H   HCH3   0   0.281  -1.9711  -1.6429   2.3080
 CAF  HE13  H   HCH3   0   0.284  -0.2756  -1.1596   2.1044
 CAF  HE21  H   HCH3   0   0.284  -3.7112   0.6496  -0.8854
 CAF  HE22  H   HCH3   0   0.283  -4.1587  -0.4604   0.4279
 CAF  HE23  H   HCH3   0   0.279  -3.5671   1.1681   0.8090

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
 CAF  N    CA    single  1.458  0.019  1.458
 CAF  N    H     single  0.860  0.020  0.860
 CAF  N    H2    single  0.890  0.020  1.040
 CAF  CA   CB    single  1.530  0.020  1.530
 CAF  CA   C     single  1.525  0.021  1.525
 CAF  CA   HA    single  0.970  0.020  0.970
 CAF  CB   SG    single  1.832  0.020  1.832
 CAF  CB   HB2   single  0.970  0.020  1.090
 CAF  CB   HB3   single  0.970  0.020  1.090
 CAF  C    O     deloc   1.231  0.020  1.231
 CAF  C    OXT   deloc   1.246  0.020  1.246
 CAF  SG   AS    single  2.217  0.020  2.217
 CAF  AS   CE1   single  1.926  0.020  1.926
 CAF  AS   CE2   single  1.923  0.020  1.923
 CAF  AS   O1    double  1.628  0.020  1.628
 CAF  CE1  HE11  single  0.970  0.020  1.090
 CAF  CE1  HE12  single  0.970  0.020  1.090
 CAF  CE1  HE13  single  0.970  0.020  1.090
 CAF  CE2  HE21  single  0.970  0.020  1.090
 CAF  CE2  HE22  single  0.970  0.020  1.090
 CAF  CE2  HE23  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
 CAF  H2    N    H     106.91  3.000
 CAF  H2    N    CA    110.00  3.000
 CAF  H     N    CA    114.00  3.000
 CAF  HA    CA   C     109.00  3.000
 CAF  HA    CA   CB    109.00  3.000
 CAF  C     CA   CB    110.10  1.900
 CAF  HA    CA   N     110.00  3.000
 CAF  C     CA   N     111.00  2.800
 CAF  CB    CA   N     110.50  1.700
 CAF  HB3   CB   HB2   107.94  3.000
 CAF  HB3   CB   SG    108.81  3.000
 CAF  HB2   CB   SG    103.67  3.000
 CAF  HB3   CB   CA    111.06  3.000
 CAF  HB2   CB   CA    110.44  3.000
 CAF  SG    CB   CA    114.51  3.000
 CAF  OXT   C    O     127.19  3.000
 CAF  OXT   C    CA    115.52  3.000
 CAF  O     C    CA    120.80  1.700
 CAF  AS    SG   CB    100.71  3.000
 CAF  O1    AS   CE2   115.31  3.000
 CAF  O1    AS   CE1   113.60  3.000
 CAF  CE2   AS   CE1   106.53  3.000
 CAF  O1    AS   SG    112.27  3.000
 CAF  CE2   AS   SG    101.36  3.000
 CAF  CE1   AS   SG    106.73  3.000
 CAF  HE13  CE1  HE12  109.01  3.000
 CAF  HE13  CE1  HE11  109.08  3.000
 CAF  HE12  CE1  HE11  109.27  3.000
 CAF  HE13  CE1  AS    109.93  3.000
 CAF  HE12  CE1  AS    109.52  3.000
 CAF  HE11  CE1  AS    110.02  3.000
 CAF  HE23  CE2  HE22  108.93  3.000
 CAF  HE23  CE2  HE21  109.36  3.000
 CAF  HE22  CE2  HE21  109.24  3.000
 CAF  HE23  CE2  AS    110.37  3.000
 CAF  HE22  CE2  AS    109.18  3.000
 CAF  HE21  CE2  AS    109.73  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
 CAF  Var_01  CE1   AS   SG  CB   89.69  30.0  3
 CAF  Var_02  HE11  CE1  AS  SG   52.06  30.0  3
 CAF  Var_03  HE21  CE2  AS  SG   66.06  30.0  3
 CAF  Var_04  HB2   CB   SG  AS  163.06  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
 CAF  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
 CAF  plan-1  CA   0.020
 CAF  plan-1  C    0.020
 CAF  plan-1  O    0.020
 CAF  plan-1  OXT  0.020

