# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:28:03 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: S-propanoyl-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=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
 6KM  6KM  'S-propanoyl-L-cysteine   '  L-peptide  21  11  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_6KM
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
 6KM  N    N  NH2    0  -0.808   8.8167   0.9677   7.6313
 6KM  CA   C  CH1    0  -0.196   9.6788   0.1945   8.5052
 6KM  CA1  C  C      0   0.267  12.7196   2.0647   9.0345
 6KM  CA2  C  CH2    0  -0.547  13.1905   0.7148   9.5047
 6KM  CA3  C  CH3    0  -0.664  13.4813   0.7515  11.0067
 6KM  C    C  C      0   0.417   8.9845  -1.1127   8.9867
 6KM  O    O  O      0  -0.600   9.5404  -1.7032   9.9323
 6KM  OA1  O  O      0  -0.392  13.4636   2.9032   8.5872
 6KM  CB   C  CH2    0  -0.588  10.0974   1.0348   9.7048
 6KM  SG   S  S2     0  -0.013  11.0225   2.5366   9.2430
 6KM  H1   H  HNH2   0   0.334   9.3686   1.4958   6.9692
 6KM  H2   H  HNH2   0   0.339   8.2509   0.3181   7.1013
 6KM  H4   H  HCH1   0   0.214  10.5974  -0.1387   7.9932
 6KM  H5   H  HCH2   0   0.262  12.4637  -0.0652   9.2809
 6KM  H6   H  HCH2   0   0.275  14.1036   0.4787   8.9565
 6KM  H7   H  HCH3   0   0.251  13.8553  -0.2165  11.3359
 6KM  H8   H  HCH3   0   0.240  14.2361   1.5018  11.2397
 6KM  H9   H  HCH3   0   0.235  12.5880   0.9818  11.5869
 6KM  H11  H  HCH2   0   0.282   9.2113   1.4175  10.2154
 6KM  H12  H  HCH2   0   0.280  10.6663   0.4602  10.4309
 6KM  O1   O  OC    -1  -0.589   7.9663  -1.4696   8.3665

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
 6KM  N    CA   single  1.458  0.019  1.458
 6KM  OA1  CA1  double  1.207  0.020  1.207
 6KM  C    CA   single  1.525  0.021  1.525
 6KM  C    O    deloc   1.231  0.020  1.231
 6KM  CA   CB   single  1.521  0.033  1.521
 6KM  CA1  SG   single  1.774  0.020  1.774
 6KM  CA1  CA2  single  1.505  0.020  1.505
 6KM  CB   SG   single  1.823  0.020  1.823
 6KM  CA2  CA3  single  1.530  0.020  1.530
 6KM  N    H1   single  0.890  0.020  1.040
 6KM  N    H2   single  0.890  0.020  1.040
 6KM  CA   H4   single  0.970  0.020  1.090
 6KM  CA2  H5   single  0.970  0.020  1.090
 6KM  CA2  H6   single  0.970  0.020  1.090
 6KM  CA3  H7   single  0.970  0.020  1.090
 6KM  CA3  H8   single  0.970  0.020  1.090
 6KM  CA3  H9   single  0.970  0.020  1.090
 6KM  CB   H11  single  0.970  0.020  1.090
 6KM  CB   H12  single  0.970  0.020  1.090
 6KM  C    O1   deloc   1.244  0.020  1.244

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
 6KM  H2   N    H1   107.32  3.000
 6KM  H2   N    CA   107.81  3.000
 6KM  H1   N    CA   110.39  3.000
 6KM  H4   CA   CB   107.66  3.000
 6KM  H4   CA   C    105.15  3.000
 6KM  CB   CA   C    110.50  1.500
 6KM  H4   CA   N    112.10  3.000
 6KM  CB   CA   N    110.40  1.500
 6KM  C    CA   N    111.00  2.800
 6KM  SG   CA1  OA1  116.65  3.000
 6KM  SG   CA1  CA2  120.09  3.000
 6KM  OA1  CA1  CA2  123.09  3.000
 6KM  H6   CA2  H5   107.47  3.000
 6KM  H6   CA2  CA3  109.84  3.000
 6KM  H5   CA2  CA3  110.22  3.000
 6KM  H6   CA2  CA1  107.40  3.000
 6KM  H5   CA2  CA1  111.67  3.000
 6KM  CA3  CA2  CA1  110.16  3.000
 6KM  H9   CA3  H8   107.97  3.000
 6KM  H9   CA3  H7   107.96  3.000
 6KM  H8   CA3  H7   108.04  3.000
 6KM  H9   CA3  CA2  111.83  3.000
 6KM  H8   CA3  CA2  110.99  3.000
 6KM  H7   CA3  CA2  109.92  3.000
 6KM  O1   C    O    127.41  3.000
 6KM  O1   C    CA   116.85  3.000
 6KM  O    C    CA   120.80  1.700
 6KM  H12  CB   H11  107.32  3.000
 6KM  H12  CB   SG   109.82  3.000
 6KM  H11  CB   SG   103.97  3.000
 6KM  H12  CB   CA   112.23  3.000
 6KM  H11  CB   CA   109.79  3.000
 6KM  SG   CB   CA   113.22  3.000
 6KM  CB   SG   CA1  107.22  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
 6KM  Var_01  OA1  CA1  CA2  CA3    93.05  30.0  1
 6KM  Var_02  H11  CB   SG   CA1   156.99  30.0  1
 6KM  Var_03  H7   CA3  CA2  CA1  -178.00  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
 6KM  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
 6KM  plan-1  CA   0.020
 6KM  plan-1  C    0.020
 6KM  plan-1  O    0.020
 6KM  plan-1  O1   0.020
 6KM  plan-2  CA1  0.020
 6KM  plan-2  CA2  0.020
 6KM  plan-2  OA1  0.020
 6KM  plan-2  SG   0.020

