# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 15:40:11 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  23  11  .  2022-07-24  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.774   2.4276   1.1588   1.2996
 CAF  CA    C   CH1   0  -0.214   2.0558   0.1776   0.3130
 CAF  CB    C   CH2   0  -0.594   1.1374   0.6813  -0.8175
 CAF  C     C   C     0   0.554   3.3083  -0.3976  -0.3252
 CAF  O     O   O     0  -0.430   4.3923   0.1237  -0.2899
 CAF  OXT   O   OH1   0  -0.588   3.0551  -1.5339  -0.9592
 CAF  SG    S   S2    0  -0.197  -0.3991   1.4391  -0.1962
 CAF  AS    AS  AS    0   1.052  -1.6168  -0.3863   0.1816
 CAF  CE1   C   CH3   0  -0.919  -1.3634  -0.8239   2.0388
 CAF  CE2   C   CH3   0  -0.910  -3.4034   0.2992   0.0081
 CAF  O1    O   O     0  -0.757  -1.2169  -1.5892  -0.8385
 CAF  H     H   HNH2  0   0.349   2.8772   1.9519   0.8576
 CAF  H2    H   HNH2  0   0.356   1.5916   1.5163   1.7450
 CAF  HA    H   HCH1  0   0.281   1.5486  -0.6473   0.8229
 CAF  HB2   H   HCH2  0   0.305   1.6322   1.4792  -1.3759
 CAF  HB3   H   HCH2  0   0.298   0.8850  -0.1109  -1.5213
 CAF  HXT   H   HOH1  0   0.485   3.8572  -1.8610  -1.3940
 CAF  HE11  H   HCH3  0   0.281  -1.5793   0.0451   2.6590
 CAF  HE12  H   HCH3  0   0.285  -2.0340  -1.6383   2.3148
 CAF  HE13  H   HCH3  0   0.282  -0.3351  -1.1392   2.2119
 CAF  HE21  H   HCH3  0   0.287  -3.5755   0.6197  -1.0182
 CAF  HE22  H   HCH3  0   0.287  -4.1138  -0.4871   0.2643
 CAF  HE23  H   HCH3  0   0.282  -3.5523   1.1431   0.6814

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  1.822  0.020  1.822
 CAF  CB   HB2   single  0.970  0.020  1.090
 CAF  CB   HB3   single  0.970  0.020  1.090
 CAF  C    O     double  1.231  0.020  1.231
 CAF  C    OXT   single  1.326  0.020  1.326
 CAF  OXT  HXT   single  0.850  0.020  0.980
 CAF  SG   AS    single  2.227  0.020  2.227
 CAF  AS   CE1   single  1.925  0.020  1.925
 CAF  AS   CE2   single  1.922  0.020  1.922
 CAF  AS   O1    double  1.627  0.020  1.627
 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     106.38  3.000
 CAF  H2    N    CA    109.20  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   107.81  3.000
 CAF  HB3   CB   SG    109.10  3.000
 CAF  HB2   CB   SG    104.62  3.000
 CAF  HB3   CB   CA    111.98  3.000
 CAF  HB2   CB   CA    110.11  3.000
 CAF  SG    CB   CA    112.85  3.000
 CAF  OXT   C    O     123.88  3.000
 CAF  OXT   C    CA    111.60  3.000
 CAF  O     C    CA    120.80  1.700
 CAF  HXT   OXT  C     110.23  3.000
 CAF  AS    SG   CB    100.26  3.000
 CAF  O1    AS   CE2   115.83  3.000
 CAF  O1    AS   CE1   113.86  3.000
 CAF  CE2   AS   CE1   106.89  3.000
 CAF  O1    AS   SG    111.42  3.000
 CAF  CE2   AS   SG    101.58  3.000
 CAF  CE1   AS   SG    106.15  3.000
 CAF  HE13  CE1  HE12  108.91  3.000
 CAF  HE13  CE1  HE11  109.12  3.000
 CAF  HE12  CE1  HE11  109.25  3.000
 CAF  HE13  CE1  AS    110.09  3.000
 CAF  HE12  CE1  AS    109.45  3.000
 CAF  HE11  CE1  AS    110.00  3.000
 CAF  HE23  CE2  HE22  108.92  3.000
 CAF  HE23  CE2  HE21  109.44  3.000
 CAF  HE22  CE2  HE21  109.32  3.000
 CAF  HE23  CE2  AS    110.34  3.000
 CAF  HE22  CE2  AS    109.11  3.000
 CAF  HE21  CE2  AS    109.69  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  CONST_01  HXT   OXT  C   CA  180.00   0.0  0
 CAF  Var_01    CE1   AS   SG  CB   94.48  30.0  3
 CAF  Var_02    HE11  CE1  AS  SG   52.93  30.0  3
 CAF  Var_03    HE21  CE2  AS  SG   65.50  30.0  3
 CAF  Var_04    HB2   CB   SG  AS  158.90  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
 CAF  plan-1  HXT  0.020

