# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 07:05:38 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: N-acetyl-S-[(1S)-1,2-dichloroethyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](CS[C@@H](Cl)CCl)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
 DC2  DC2  N-acetyl-S-[(1S)-1,2-dichloroethyl]-L-cysteine  L-peptide  25  14  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DC2
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
 DC2  O1    O   O     0  -0.420  -3.5012   1.7389  -0.6910
 DC2  CL1   CL  CL    0  -0.126   3.0145   0.9837   0.7696
 DC2  C2    C   C     0   0.563  -2.4643   1.7549  -0.0856
 DC2  CL2   CL  CL    0  -0.140   3.4739  -2.3318   0.7820
 DC2  C4    C   CH1   0  -0.210  -1.5961   0.5247   0.1653
 DC2  N     N   NH1   0  -0.623  -2.1999  -0.6520  -0.3865
 DC2  C6    C   C     0   0.533  -3.1605  -1.3437   0.2670
 DC2  O7    O   O     0  -0.491  -3.5103  -1.0596   1.4012
 DC2  C8    C   CH3   0  -0.778  -3.7288  -2.5191  -0.4828
 DC2  C9    C   CH2   0  -0.574  -0.1918   0.7263  -0.3986
 DC2  S10   S   S2    0   0.079   0.7680  -0.7846  -0.0890
 DC2  C11   C   CH1   0  -0.382   2.4033  -0.1607  -0.4864
 DC2  C12   C   CH2   0  -0.437   3.3786  -1.2965  -0.6707
 DC2  OXT   O   OH1   0  -0.588  -1.9302   2.8361   0.4597
 DC2  H4    H   HCH1  0   0.313  -1.5162   0.3992   1.2488
 DC2  H2    H   HNH1  0   0.408  -2.0478  -0.8454  -1.3642
 DC2  H8    H   HCH3  0   0.274  -3.3350  -3.4401  -0.0509
 DC2  H8A   H   HCH3  0   0.267  -4.8109  -2.5394  -0.3665
 DC2  H8B   H   HCH3  0   0.252  -3.4885  -2.5143  -1.5440
 DC2  H9    H   HCH2  0   0.297  -0.2183   0.9364  -1.4697
 DC2  H9A   H   HCH2  0   0.302   0.2943   1.5601   0.1061
 DC2  H11   H   HCH1  0   0.354   2.3690   0.4073  -1.4171
 DC2  H12   H   HCH2  0   0.321   4.3749  -0.9122  -0.8756
 DC2  H12A  H   HCH2  0   0.317   3.0586  -1.9180  -1.5048
 DC2  HOXT  H   HOH1  0   0.489  -2.4887   3.6108   0.2928

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
 DC2  O1   C2    double  1.201  0.020  1.201
 DC2  CL1  C11   single  1.806  0.020  1.806
 DC2  C2   OXT   single  1.323  0.020  1.323
 DC2  C2   C4    single  1.526  0.020  1.526
 DC2  C12  CL2   single  1.786  0.020  1.786
 DC2  C4   C9    single  1.527  0.020  1.527
 DC2  C4   N     single  1.433  0.020  1.433
 DC2  C4   H4    single  0.970  0.020  1.090
 DC2  C6   N     single  1.352  0.020  1.352
 DC2  N    H2    single  0.860  0.020  1.020
 DC2  O7   C6    double  1.221  0.020  1.221
 DC2  C6   C8    single  1.505  0.020  1.505
 DC2  C8   H8    single  0.970  0.020  1.090
 DC2  C8   H8A   single  0.970  0.020  1.090
 DC2  C8   H8B   single  0.970  0.020  1.090
 DC2  S10  C9    single  1.817  0.020  1.817
 DC2  C9   H9    single  0.970  0.020  1.090
 DC2  C9   H9A   single  0.970  0.020  1.090
 DC2  C11  S10   single  1.795  0.020  1.795
 DC2  C11  C12   single  1.508  0.020  1.508
 DC2  C11  H11   single  0.970  0.020  1.090
 DC2  C12  H12   single  0.970  0.020  1.090
 DC2  C12  H12A  single  0.970  0.020  1.090
 DC2  OXT  HOXT  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
 DC2  OXT   C2   C4   111.17  3.000
 DC2  C4    C2   O1   124.28  3.000
 DC2  OXT   C2   O1   124.55  3.000
 DC2  H4    C4   C9   108.30  3.000
 DC2  H4    C4   N    108.54  3.000
 DC2  C9    C4   N    110.72  3.000
 DC2  H4    C4   C2   107.27  3.000
 DC2  N     C4   C2   111.03  3.000
 DC2  C9    C4   C2   110.86  3.000
 DC2  H2    N    C6   118.54  3.000
 DC2  H2    N    C4   117.86  3.000
 DC2  C6    N    C4   122.23  3.000
 DC2  C8    C6   O7   122.44  3.000
 DC2  C8    C6   N    115.27  3.000
 DC2  O7    C6   N    122.26  3.000
 DC2  H8B   C8   H8A  108.89  3.000
 DC2  H8B   C8   H8   108.06  3.000
 DC2  H8A   C8   H8   107.51  3.000
 DC2  H8B   C8   C6   113.51  3.000
 DC2  H8A   C8   C6   109.67  3.000
 DC2  H8    C8   C6   109.01  3.000
 DC2  H9A   C9   H9   108.55  3.000
 DC2  H9A   C9   S10  108.78  3.000
 DC2  H9    C9   S10  109.88  3.000
 DC2  H9A   C9   C4   109.91  3.000
 DC2  H9    C9   C4   111.44  3.000
 DC2  S10   C9   C4   108.25  3.000
 DC2  C11   S10  C9    98.89  3.000
 DC2  H11   C11  C12  107.95  3.000
 DC2  H11   C11  S10  109.96  3.000
 DC2  C12   C11  S10  110.76  3.000
 DC2  H11   C11  CL1  105.90  3.000
 DC2  C12   C11  CL1  110.08  3.000
 DC2  S10   C11  CL1  112.00  3.000
 DC2  H12A  C12  H12  109.08  3.000
 DC2  H12A  C12  C11  109.48  3.000
 DC2  H12   C12  C11  110.45  3.000
 DC2  H12A  C12  CL2  107.93  3.000
 DC2  H12   C12  CL2  108.01  3.000
 DC2  C11   C12  CL2  111.81  3.000
 DC2  HOXT  OXT  C2   110.45  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
 DC2  CONST_01  O7    C6   N    C4     0.00   0.0  0
 DC2  CONST_02  C8    C6   N    C4   180.00   0.0  0
 DC2  CONST_03  H2    N    C6   O7   180.00   0.0  0
 DC2  CONST_04  HOXT  OXT  C2   O1     0.00   0.0  0
 DC2  Var_01    H8    C8   C6   N    105.45  30.0  3
 DC2  Var_02    H9    C9   S10  C11   70.21  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
 DC2  chir_01  C4   C2   C9   N    positiv
 DC2  chir_02  C11  CL1  S10  C12  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
 DC2  plan-1  C4    0.020
 DC2  plan-1  N     0.020
 DC2  plan-1  C6    0.020
 DC2  plan-1  O7    0.020
 DC2  plan-1  C8    0.020
 DC2  plan-1  H2    0.020
 DC2  plan-2  O1    0.020
 DC2  plan-2  C2    0.020
 DC2  plan-2  C4    0.020
 DC2  plan-2  OXT   0.020
 DC2  plan-2  HOXT  0.020

