# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 03:19:55 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  15  10  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.553  -0.4724  -1.4790   0.4943
 J3D  S02   S  S2     0  -0.284   1.2250  -2.1307   0.3083
 J3D  C03   C  CH1    0  -0.207  -0.6029  -0.0928  -0.1399
 J3D  N04   N  NH1    0  -0.678   0.3051   0.8579   0.4369
 J3D  C05   C  C      0   0.432   1.4814   1.2692  -0.1987
 J3D  O06   O  O      0  -0.306   1.9156   0.5612  -1.1374
 J3D  O07   O  OC    -1  -0.901   2.0203   2.3032   0.2599
 J3D  C08   C  C      0   0.383  -2.0821   0.3648  -0.0045
 J3D  O09   O  O      0  -0.675  -2.3027   1.4404   0.5830
 J3D  O10   O  OC    -1  -0.588  -2.9335  -0.4092  -0.4851
 J3D  H011  H  HCH2   0   0.296  -1.1665  -2.1712   0.0225
 J3D  H012  H  HCH2   0   0.257  -0.7097  -1.4237   1.5590
 J3D  H021  H  HSH1   0   0.182   0.9776  -3.3212   0.8730
 J3D  H031  H  HCH1   0   0.291  -0.3937  -0.1977  -1.2099
 J3D  H041  H  HNH1   0   0.350  -0.1675   1.5753   0.9638

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   deloc   1.253  0.020  1.253
 J3D  O07  C05   deloc   1.253  0.020  1.253
 J3D  C05  N04   single  1.399  0.020  1.399
 J3D  N04  C03   single  1.436  0.020  1.436
 J3D  C03  C08   single  1.554  0.020  1.554
 J3D  C03  C01   single  1.530  0.020  1.530
 J3D  O09  C08   deloc   1.245  0.020  1.245
 J3D  C08  O10   deloc   1.247  0.020  1.247
 J3D  S02  C01   single  1.828  0.020  1.828
 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

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  108.44  3.000
 J3D  H012  C01  C03   109.86  3.000
 J3D  H011  C01  C03   110.02  3.000
 J3D  H012  C01  S02   108.61  3.000
 J3D  H011  C01  S02   108.75  3.000
 J3D  C03   C01  S02   111.11  3.000
 J3D  H021  S02  C01    95.88  3.000
 J3D  H031  C03  C08   107.16  3.000
 J3D  H031  C03  N04   109.58  3.000
 J3D  C08   C03  N04   111.84  3.000
 J3D  H031  C03  C01   107.57  3.000
 J3D  C08   C03  C01   108.17  3.000
 J3D  N04   C03  C01   112.30  3.000
 J3D  H041  N04  C05   115.00  3.000
 J3D  H041  N04  C03   112.63  3.000
 J3D  C05   N04  C03   122.96  3.000
 J3D  O07   C05  O06   126.25  3.000
 J3D  O07   C05  N04   115.98  3.000
 J3D  O06   C05  N04   117.74  3.000
 J3D  O10   C08  O09   126.66  3.000
 J3D  O10   C08  C03   115.69  3.000
 J3D  O09   C08  C03   117.64  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  Var_01  O06  C05  N04  C03  -17.27  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
 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-2  C03  0.020
 J3D  plan-2  C08  0.020
 J3D  plan-2  O09  0.020
 J3D  plan-2  O10  0.020

