# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 01:18:43 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: N-carboxy-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)N[C@@H](CS)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
 J3D  J3D  'N-carboxy-L-cysteine     '  L-peptide  17  10  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_J3D
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
 J3D  C01   C  CH2   0  -0.578  -0.5528  -1.5898   0.7049
 J3D  S02   S  S2    0  -0.227   1.0462  -2.4678   0.7232
 J3D  C03   C  CH1   0  -0.192  -0.3986  -0.3185  -0.1255
 J3D  N04   N  NH1   0  -0.633   0.6748   0.4810   0.3862
 J3D  C05   C  C     0   0.687   1.2348   1.4490  -0.3728
 J3D  O06   O  O     0  -0.507   1.0082   1.6155  -1.5526
 J3D  O07   O  OH1   0  -0.615   2.0929   2.1831   0.3352
 J3D  C08   C  C     0   0.557  -1.7072   0.4672  -0.1467
 J3D  O09   O  O     0  -0.422  -1.8427   1.5667   0.3181
 J3D  O10   O  OH1   0  -0.588  -2.6686  -0.2195  -0.7427
 J3D  H011  H  HCH2  0   0.306  -1.3081  -2.2322   0.2589
 J3D  H012  H  HCH2  0   0.286  -0.8607  -1.3532   1.7247
 J3D  H021  H  HSH1  0   0.230   0.5635  -3.6523   1.1133
 J3D  H031  H  HCH1  0   0.311  -0.1668  -0.6071  -1.1541
 J3D  H041  H  HNH1  0   0.409   0.7944   0.5291   1.3871
 J3D  H1    H  HOH1  0   0.487   2.4931   2.8504  -0.2380
 J3D  H2    H  HOH1  0   0.489  -3.4979   0.2826  -0.7373

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
 J3D  O06  C05   double  1.213  0.020  1.213
 J3D  O07  C05   single  1.333  0.020  1.333
 J3D  C05  N04   single  1.352  0.020  1.352
 J3D  N04  C03   single  1.433  0.020  1.433
 J3D  C03  C08   single  1.526  0.020  1.526
 J3D  C03  C01   single  1.526  0.020  1.526
 J3D  O09  C08   double  1.201  0.020  1.201
 J3D  C08  O10   single  1.323  0.020  1.323
 J3D  S02  C01   single  1.824  0.020  1.824
 J3D  C01  H011  single  0.970  0.020  1.090
 J3D  C01  H012  single  0.970  0.020  1.090
 J3D  S02  H021  single  1.200  0.020  1.300
 J3D  C03  H031  single  0.970  0.020  1.090
 J3D  N04  H041  single  0.890  0.020  1.040
 J3D  O07  H1    single  0.850  0.020  0.980
 J3D  O10  H2    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
 J3D  H012  C01  H011  108.39  3.000
 J3D  H012  C01  C03   110.87  3.000
 J3D  H011  C01  C03   109.82  3.000
 J3D  H012  C01  S02   110.02  3.000
 J3D  H011  C01  S02   109.18  3.000
 J3D  C03   C01  S02   108.53  3.000
 J3D  H021  S02  C01    96.48  3.000
 J3D  H031  C03  C08   107.74  3.000
 J3D  H031  C03  N04   108.93  3.000
 J3D  C08   C03  N04   111.09  3.000
 J3D  H031  C03  C01   108.27  3.000
 J3D  C08   C03  C01   110.47  3.000
 J3D  N04   C03  C01   110.25  3.000
 J3D  H041  N04  C05   118.28  3.000
 J3D  H041  N04  C03   118.01  3.000
 J3D  C05   N04  C03   120.63  3.000
 J3D  O07   C05  O06   124.15  3.000
 J3D  O07   C05  N04   111.28  3.000
 J3D  O06   C05  N04   124.56  3.000
 J3D  H1    O07  C05   109.38  3.000
 J3D  O10   C08  O09   124.56  3.000
 J3D  O10   C08  C03   111.22  3.000
 J3D  O09   C08  C03   124.22  3.000
 J3D  H2    O10  C08   110.50  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
 J3D  CONST_01  H2   O10  C08  C03  180.00   0.0  0
 J3D  CONST_02  H1   O07  C05  N04  180.00   0.0  0
 J3D  Var_01    O06  C05  N04  C03   -9.14  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
 J3D  chir_01  C03  N04  C08  C01  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
 J3D  plan-1  N04  0.020
 J3D  plan-1  C05  0.020
 J3D  plan-1  O06  0.020
 J3D  plan-1  O07  0.020
 J3D  plan-1  H1   0.020
 J3D  plan-2  C03  0.020
 J3D  plan-2  C08  0.020
 J3D  plan-2  O09  0.020
 J3D  plan-2  O10  0.020
 J3D  plan-2  H2   0.020

