# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 20:28:36 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: S-cyano-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC#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
 XCN  XCN  'S-cyano-L-cysteine       '  L-peptide  14  9  .  2012-08-28  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_XCN
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
 XCN  C    C  C      0   0.391  -12.1503  -41.3836  -3.0146
 XCN  N    N  NH2    0  -0.802  -10.2526  -42.8528  -2.3944
 XCN  O    O  O      0  -0.596  -11.4370  -40.6554  -3.7289
 XCN  CA   C  CH1    0  -0.148  -11.4200  -42.1480  -1.8789
 XCN  CB   C  CH2    0  -0.576  -10.8895  -41.1655  -0.8426
 XCN  NC   N  NS     0  -0.268  -12.7786  -38.0381  -1.5407
 XCN  SG   S  S2     0   0.121  -12.2140  -40.2930   0.0792
 XCN  CS   C  CSP    0  -0.013  -12.5261  -38.9788  -0.9191
 XCN  OXT  O  OC    -1  -0.595  -13.3811  -41.5533  -3.0910
 XCN  HN   H  HNH2   0   0.342   -9.9367  -43.5255  -1.7062
 XCN  HNX  H  HNH2   0   0.347  -10.5073  -43.3924  -3.2120
 XCN  HA   H  HCH1   0   0.201  -12.1402  -42.8139  -1.3848
 XCN  HB   H  HCH2   0   0.301  -10.3434  -41.6807  -0.0497
 XCN  HBA  H  HCH2   0   0.296  -10.2249  -40.4300  -1.2929

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
 XCN  C   CA   single  1.525  0.021  1.525
 XCN  C   OXT  deloc   1.245  0.020  1.245
 XCN  N   CA   single  1.458  0.019  1.458
 XCN  N   HN   single  0.890  0.020  1.040
 XCN  N   HNX  single  0.890  0.020  1.040
 XCN  O   C    deloc   1.231  0.020  1.231
 XCN  CA  CB   single  1.530  0.020  1.530
 XCN  CA  HA   single  0.970  0.020  0.970
 XCN  CB  SG   single  1.835  0.020  1.835
 XCN  CB  HB   single  0.970  0.020  1.090
 XCN  CB  HBA  single  0.970  0.020  1.090
 XCN  NC  CS   triple  1.155  0.020  1.155
 XCN  CS  SG   single  1.680  0.020  1.680

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
 XCN  OXT  C   CA  116.31  3.000
 XCN  OXT  C   O   127.67  3.000
 XCN  CA   C   O   120.80  1.700
 XCN  HNX  N   HN  105.86  3.000
 XCN  HNX  N   CA  109.99  3.000
 XCN  HN   N   CA  109.30  3.000
 XCN  HA   CA  CB  109.00  3.000
 XCN  HA   CA  N   110.00  3.000
 XCN  CB   CA  N   110.50  1.700
 XCN  HA   CA  C   109.00  3.000
 XCN  CB   CA  C   110.10  1.900
 XCN  N    CA  C   111.00  2.800
 XCN  HBA  CB  HB  108.29  3.000
 XCN  HBA  CB  SG  109.10  3.000
 XCN  HB   CB  SG  102.74  3.000
 XCN  HBA  CB  CA  111.53  3.000
 XCN  HB   CB  CA  111.33  3.000
 XCN  SG   CB  CA  113.40  3.000
 XCN  CS   SG  CB  101.98  3.000
 XCN  SG   CS  NC  180.00  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
 XCN  Var_01  HB  CB  SG  CS  152.71  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
 XCN  chir_01  CA  C  N  CB  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
 XCN  plan-1  C    0.020
 XCN  plan-1  O    0.020
 XCN  plan-1  CA   0.020
 XCN  plan-1  OXT  0.020

