# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:07:41 2022
#   Inital geometry file: a 40 line input string
#   Ligand name: L-cysteinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CS)C(N)=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
 CY3  CY3  'L-cysteinamide           '  L-peptide  15  7  .  2019-03-22  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CY3
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
 CY3  N     N  NH2   0  -0.777  26.0719  19.2339  17.7984
 CY3  CA    C  CH1   0  -0.194  25.2028  18.3996  17.0033
 CY3  C     C  C     0   0.513  25.4494  18.6913  15.5230
 CY3  O     O  O     0  -0.478  25.7250  19.8144  15.1320
 CY3  CB    C  CH2   0  -0.576  23.6959  18.5726  17.2570
 CY3  SG    S  S2    0  -0.237  23.2088  18.2077  18.9713
 CY3  N1    N  NH2   0  -0.797  25.2901  17.6422  14.7042
 CY3  H     H  HNH2  0   0.347  25.9449  19.0197  18.7793
 CY3  H2    H  HNH2  0   0.343  25.8283  20.2097  17.6781
 CY3  HA    H  HCH1  0   0.261  25.4558  17.3560  17.2103
 CY3  HB2   H  HCH2  0   0.284  23.1207  17.8811  16.6393
 CY3  HB3   H  HCH2  0   0.282  23.3716  19.5838  17.0046
 CY3  HG    H  HSH1  0   0.222  23.6422  19.3445  19.5277
 CY3  HN11  H  HNH2  0   0.408  25.0729  16.7223  15.0479
 CY3  HN12  H  HNH2  0   0.399  25.3595  17.7583  13.7059

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
 CY3  N   CA    single  1.458  0.019  1.458
 CY3  N   H     single  0.860  0.020  0.860
 CY3  N   H2    single  0.890  0.020  1.040
 CY3  CA  C     single  1.525  0.021  1.525
 CY3  CA  CB    single  1.530  0.020  1.530
 CY3  CA  HA    single  0.970  0.020  0.970
 CY3  C   O     double  1.231  0.020  1.231
 CY3  C   N1    single  1.340  0.020  1.340
 CY3  CB  SG    single  1.819  0.020  1.819
 CY3  CB  HB2   single  0.970  0.020  1.090
 CY3  CB  HB3   single  0.970  0.020  1.090
 CY3  SG  HG    single  1.200  0.020  1.300
 CY3  N1  HN11  single  0.860  0.020  1.020
 CY3  N1  HN12  single  0.860  0.020  1.020

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
 CY3  H2    N   H     106.79  3.000
 CY3  H2    N   CA    110.28  3.000
 CY3  H     N   CA    114.00  3.000
 CY3  HA    CA  CB    109.00  3.000
 CY3  HA    CA  C     109.00  3.000
 CY3  CB    CA  C     110.10  1.900
 CY3  HA    CA  N     110.00  3.000
 CY3  CB    CA  N     110.50  1.700
 CY3  C     CA  N     111.00  2.800
 CY3  N1    C   O     123.45  3.000
 CY3  N1    C   CA    115.03  3.000
 CY3  O     C   CA    120.80  1.700
 CY3  HB3   CB  HB2   107.43  3.000
 CY3  HB3   CB  SG    108.91  3.000
 CY3  HB2   CB  SG    105.38  3.000
 CY3  HB3   CB  CA    110.92  3.000
 CY3  HB2   CB  CA    110.61  3.000
 CY3  SG    CB  CA    113.28  3.000
 CY3  HG    SG  CB     97.74  3.000
 CY3  HN12  N1  HN11  117.32  3.000
 CY3  HN12  N1  C     120.46  3.000
 CY3  HN11  N1  C     122.19  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
 CY3  CONST_01  HN11  N1  C  CA    0.00  0.0  0
 CY3  CONST_02  HN12  N1  C  CA  180.00  0.0  0

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
 CY3  chir_01  CA  N  C  CB  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
 CY3  plan-1  CA    0.020
 CY3  plan-1  C     0.020
 CY3  plan-1  O     0.020
 CY3  plan-1  N1    0.020
 CY3  plan-1  HN11  0.020
 CY3  plan-1  HN12  0.020

