# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:48:58 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-(cyclohexyldisulfanyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSSC1CCCCC1)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
 C6C  C6C  3-(cyclohexyldisulfanyl)-L-alanine  L-peptide  30  14  .  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_C6C
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
 C6C  N    N  NH2    0  -0.778  12.6804  21.1748  16.6260
 C6C  CA   C  CH1    0  -0.245  13.9960  21.5006  16.0925
 C6C  C    C  C      0   0.398  14.9374  22.2609  17.0719
 C6C  O    O  O      0  -0.598  14.7287  22.0860  18.2870
 C6C  CB   C  CH2    0  -0.531  13.8652  22.1994  14.7481
 C6C  SG   S  S2     0  -0.077  13.2207  23.9013  14.9840
 C6C  SD   S  S2     0  -0.073  12.1076  24.2623  13.3038
 C6C  C1   C  CH1    0  -0.359  10.3901  23.8117  13.7900
 C6C  C2   C  CH2    0  -0.440   9.4645  24.3392  12.6932
 C6C  C3   C  CH2    0  -0.436   9.5872  23.5502  11.3919
 C6C  C4   C  CH2    0  -0.426   9.3813  22.0573  11.6297
 C6C  C5   C  CH2    0  -0.432  10.3299  21.5238  12.6991
 C6C  C6   C  CH2    0  -0.434  10.1994  22.3149  13.9947
 C6C  OXT  O  OC    -1  -0.598  15.8419  22.9443  16.5521
 C6C  H    H  HNH2   0   0.337  12.8136  20.7939  17.5554
 C6C  H2   H  HNH2   0   0.329  12.1771  22.0424  16.7795
 C6C  HA   H  HCH1   0   0.245  14.4989  20.5478  15.8734
 C6C  HB2  H  HCH2   0   0.269  14.8278  22.2629  14.2473
 C6C  HB3  H  HCH2   0   0.275  13.1702  21.6644  14.1024
 C6C  H1   H  HCH1   0   0.281  10.1917  24.3451  14.7218
 C6C  H21  H  HCH2   0   0.241   8.4396  24.2541  13.0691
 C6C  H22  H  HCH2   0   0.244   9.6421  25.4038  12.5220
 C6C  H31  H  HCH2   0   0.234   8.8556  23.9232  10.6718
 C6C  H32  H  HCH2   0   0.218  10.5709  23.7187  10.9422
 C6C  H41  H  HCH2   0   0.209   8.3477  21.8864  11.9501
 C6C  H42  H  HCH2   0   0.227   9.5127  21.5055  10.6961
 C6C  H51  H  HCH2   0   0.230  10.1252  20.4688  12.8934
 C6C  H52  H  HCH2   0   0.215  11.3615  21.5760  12.3375
 C6C  H61  H  HCH2   0   0.245  10.8884  21.9395  14.7540
 C6C  H62  H  HCH2   0   0.230   9.1919  22.1720  14.4025

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
 C6C  N   CA   single  1.458  0.019  1.458
 C6C  N   H    single  0.860  0.020  0.860
 C6C  N   H2   single  0.890  0.020  1.040
 C6C  CA  C    single  1.525  0.021  1.525
 C6C  CA  CB   single  1.530  0.020  1.530
 C6C  CA  HA   single  0.970  0.020  0.970
 C6C  C   O    deloc   1.231  0.020  1.231
 C6C  C   OXT  deloc   1.247  0.020  1.247
 C6C  CB  SG   single  1.835  0.020  1.835
 C6C  CB  HB2  single  0.970  0.020  1.090
 C6C  CB  HB3  single  0.970  0.020  1.090
 C6C  SG  SD   single  2.048  0.020  2.048
 C6C  SD  C1   single  1.841  0.020  1.841
 C6C  C1  C2   single  1.529  0.020  1.529
 C6C  C1  C6   single  1.523  0.020  1.523
 C6C  C1  H1   single  0.970  0.020  1.090
 C6C  C2  C3   single  1.527  0.020  1.527
 C6C  C2  H21  single  0.970  0.020  1.090
 C6C  C2  H22  single  0.970  0.020  1.090
 C6C  C3  C4   single  1.526  0.020  1.526
 C6C  C3  H31  single  0.970  0.020  1.090
 C6C  C3  H32  single  0.970  0.020  1.090
 C6C  C4  C5   single  1.526  0.020  1.526
 C6C  C4  H41  single  0.970  0.020  1.090
 C6C  C4  H42  single  0.970  0.020  1.090
 C6C  C5  C6   single  1.524  0.020  1.524
 C6C  C5  H51  single  0.970  0.020  1.090
 C6C  C5  H52  single  0.970  0.020  1.090
 C6C  C6  H61  single  0.970  0.020  1.090
 C6C  C6  H62  single  0.970  0.020  1.090

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
 C6C  H2   N   H    104.35  3.000
 C6C  H2   N   CA   108.19  3.000
 C6C  H    N   CA   114.00  3.000
 C6C  HA   CA  CB   109.00  3.000
 C6C  HA   CA  C    109.00  3.000
 C6C  CB   CA  C    110.10  1.900
 C6C  HA   CA  N    110.00  3.000
 C6C  CB   CA  N    110.50  1.700
 C6C  C    CA  N    111.00  2.800
 C6C  OXT  C   O    127.25  3.000
 C6C  OXT  C   CA   116.36  3.000
 C6C  O    C   CA   120.80  1.700
 C6C  HB3  CB  HB2  108.70  3.000
 C6C  HB3  CB  SG   107.92  3.000
 C6C  HB2  CB  SG   108.42  3.000
 C6C  HB3  CB  CA   110.69  3.000
 C6C  HB2  CB  CA   110.98  3.000
 C6C  SG   CB  CA   110.04  3.000
 C6C  SD   SG  CB   104.42  3.000
 C6C  C1   SD  SG   104.32  3.000
 C6C  H1   C1  C6   110.04  3.000
 C6C  H1   C1  C2   109.49  3.000
 C6C  C6   C1  C2   111.08  3.000
 C6C  H1   C1  SD   105.98  3.000
 C6C  C6   C1  SD   113.14  3.000
 C6C  C2   C1  SD   106.91  3.000
 C6C  H22  C2  H21  106.36  3.000
 C6C  H22  C2  C3   110.91  3.000
 C6C  H21  C2  C3   109.13  3.000
 C6C  H22  C2  C1   110.49  3.000
 C6C  H21  C2  C1   107.07  3.000
 C6C  C3   C2  C1   112.61  3.000
 C6C  H32  C3  H31  106.17  3.000
 C6C  H32  C3  C4   109.62  3.000
 C6C  H31  C3  C4   110.27  3.000
 C6C  H32  C3  C2   110.05  3.000
 C6C  H31  C3  C2   109.37  3.000
 C6C  C4   C3  C2   111.22  3.000
 C6C  H42  C4  H41  106.53  3.000
 C6C  H42  C4  C5   110.34  3.000
 C6C  H41  C4  C5   109.09  3.000
 C6C  H42  C4  C3   110.18  3.000
 C6C  H41  C4  C3   109.00  3.000
 C6C  C5   C4  C3   111.56  3.000
 C6C  H52  C5  H51  106.35  3.000
 C6C  H52  C5  C6   109.69  3.000
 C6C  H51  C5  C6   109.52  3.000
 C6C  H52  C5  C4   109.74  3.000
 C6C  H51  C5  C4   110.24  3.000
 C6C  C6   C5  C4   111.17  3.000
 C6C  H62  C6  H61  106.04  3.000
 C6C  H62  C6  C5   109.11  3.000
 C6C  H61  C6  C5   111.02  3.000
 C6C  H62  C6  C1   107.06  3.000
 C6C  H61  C6  C1   110.63  3.000
 C6C  C5   C6  C1   112.66  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
 C6C  Var_01  C4   C3  C2  C1   53.91  30.0  1
 C6C  Var_02  C4   C5  C6  C1  -54.54  30.0  1
 C6C  Var_03  C5   C4  C3  C2  -54.80  30.0  1
 C6C  Var_04  C6   C5  C4  C3   55.06  30.0  1
 C6C  Var_05  HB2  CB  SG  SD   90.89  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
 C6C  chir_01  CA  N   C   CB  positiv
 C6C  chir_02  C1  SD  C2  C6  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
 C6C  plan-1  CA   0.020
 C6C  plan-1  C    0.020
 C6C  plan-1  O    0.020
 C6C  plan-1  OXT  0.020

