# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 17:47:07 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: N-(carboxycarbonyl)-D-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](CS)NC(=O)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
 08P  08P  N-(carboxycarbonyl)-D-cysteine  D-peptide  17  12  .  2016-04-22  2022-11-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_08P
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
 08P  OAY  O  OC    -1  -0.586  20.1129  -54.4190  -3.6140
 08P  CAS  C  C      0   0.331  20.1211  -53.9650  -4.7739
 08P  OAX  O  O      0  -0.575  19.1608  -53.6805  -5.4999
 08P  CAR  C  C      0   0.347  21.5334  -53.7219  -5.3972
 08P  OAW  O  O      0  -0.505  21.6865  -53.2229  -6.5049
 08P  N    N  NH1    0  -0.597  22.5368  -54.1115  -4.6026
 08P  CA   C  CH1    0  -0.212  23.9345  -53.9065  -4.8657
 08P  C    C  C      0   0.424  24.6975  -53.5102  -3.5647
 08P  O    O  O      0  -0.597  25.8980  -53.2275  -3.7261
 08P  OXT  O  OC    -1  -0.584  24.0535  -53.5277  -2.5014
 08P  CB   C  CH2    0  -0.532  24.6035  -55.1482  -5.4542
 08P  S    S  S2     0  -0.258  23.7975  -55.6503  -7.0162
 08P  H    H  HNH1   0   0.373  22.2807  -54.4078  -3.6724
 08P  HA   H  HCH1   0   0.241  24.0370  -53.0874  -5.5833
 08P  HB2  H  HCH2   0   0.257  24.5456  -55.9768  -4.7459
 08P  HB3  H  HCH2   0   0.265  25.6513  -54.9322  -5.6495
 08P  H3   H  HSH1   0   0.208  24.5842  -56.7049  -7.2633

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
 08P  S    CB   single  1.828  0.020  1.828
 08P  OAW  CAR  double  1.224  0.020  1.224
 08P  OAX  CAS  deloc   1.237  0.020  1.237
 08P  CB   CA   single  1.521  0.033  1.521
 08P  CAR  CAS  single  1.563  0.020  1.563
 08P  CAR  N    single  1.338  0.020  1.338
 08P  CA   N    single  1.458  0.019  1.458
 08P  CA   C    single  1.525  0.021  1.525
 08P  CAS  OAY  deloc   1.246  0.020  1.246
 08P  O    C    deloc   1.231  0.020  1.231
 08P  C    OXT  deloc   1.243  0.020  1.243
 08P  N    H    single  0.860  0.020  0.860
 08P  CA   HA   single  0.970  0.020  0.970
 08P  CB   HB2  single  0.970  0.020  1.090
 08P  CB   HB3  single  0.970  0.020  1.090
 08P  S    H3   single  1.200  0.020  1.300

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
 08P  CAR  CAS  OAX  115.57  3.000
 08P  CAR  CAS  OAY  115.72  3.000
 08P  OAX  CAS  OAY  128.70  3.000
 08P  N    CAR  OAW  124.21  3.000
 08P  N    CAR  CAS  113.30  3.000
 08P  OAW  CAR  CAS  122.49  3.000
 08P  H    N    CA   114.00  3.000
 08P  H    N    CAR  116.26  3.000
 08P  CA   N    CAR  125.39  3.000
 08P  HA   CA   CB   109.00  3.000
 08P  HA   CA   C    110.00  3.000
 08P  CB   CA   C    110.50  1.500
 08P  HA   CA   N    110.00  3.000
 08P  C    CA   N    111.00  2.800
 08P  CB   CA   N    110.40  1.500
 08P  OXT  C    O    127.89  3.000
 08P  OXT  C    CA   120.80  1.700
 08P  O    C    CA   120.80  1.700
 08P  HB3  CB   HB2  108.57  3.000
 08P  HB3  CB   S    109.02  3.000
 08P  HB2  CB   S    108.82  3.000
 08P  HB3  CB   CA   109.23  3.000
 08P  HB2  CB   CA   110.10  3.000
 08P  S    CB   CA   111.05  3.000
 08P  H3   S    CB    96.60  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
 08P  CONST_01  CA   N    CAR  CAS   180.00   0.0  0
 08P  CONST_02  CA   N    CAR  OAW     0.00   0.0  0
 08P  CONST_03  H    N    CAR  CAS     0.00   0.0  0
 08P  Var_01    OAW  CAR  CAS  OAY  -176.62  30.0  2

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
 08P  chir_01  CA  CB  N  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
 08P  plan-1  CAS  0.020
 08P  plan-1  CAR  0.020
 08P  plan-1  OAW  0.020
 08P  plan-1  N    0.020
 08P  plan-1  CA   0.020
 08P  plan-1  H    0.020
 08P  plan-2  OAY  0.020
 08P  plan-2  CAS  0.020
 08P  plan-2  OAX  0.020
 08P  plan-2  CAR  0.020
 08P  plan-3  CA   0.020
 08P  plan-3  C    0.020
 08P  plan-3  O    0.020
 08P  plan-3  OXT  0.020

