# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 20:14:46 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: S-[(2-phenylethyl)carbamothioyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC(=S)NCCc1ccccc1)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
 6M6  6M6  S-[(2-phenylethyl)carbamothioyl]-L-cysteine  L-peptide  33  18  .  2017-07-04  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_6M6
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
 6M6  SG   S  S2     0   0.020  88.7810  17.3243  25.0976
 6M6  CB   C  CH2    0  -0.559  90.1898  18.4526  25.4655
 6M6  CA   C  CH1    0  -0.228  90.1000  19.9240  25.0837
 6M6  C    C  C      0   0.423  91.5001  20.5954  25.2153
 6M6  O    O  O      0  -0.588  91.8195  21.3955  24.3192
 6M6  N    N  NH2    0  -0.810  89.4495  20.0953  23.7930
 6M6  C01  C  CH2    0  -0.283  85.9220  20.1843  25.1805
 6M6  C03  C  CH2    0  -0.536  85.3086  20.4945  23.8107
 6M6  C07  C  CR6    0   0.138  84.8641  19.2578  23.0838
 6M6  N01  N  NH1    0  -0.542  87.1098  19.3717  25.0536
 6M6  S01  S  S1     0  -0.372  86.0578  17.1658  26.1435
 6M6  C02  C  C      0   0.034  87.2357  18.1259  25.4504
 6M6  C08  C  CR16   0  -0.303  83.5720  18.7631  23.2478
 6M6  C09  C  CR16   0  -0.240  83.1733  17.5890  22.6239
 6M6  C04  C  CR16   0  -0.270  84.0665  16.8871  21.8248
 6M6  C05  C  CR16   0  -0.241  85.3551  17.3743  21.6481
 6M6  C06  C  CR16   0  -0.299  85.7472  18.5529  22.2689
 6M6  HB2  H  HCH2   0   0.287  90.4108  18.3626  26.5250
 6M6  HB3  H  HCH2   0   0.278  90.9991  17.9618  24.9184
 6M6  HA   H  HCH1   0   0.242  89.4654  20.4183  25.8301
 6M6  OXT  O  OC    -1  -0.596  92.1488  20.2927  26.2340
 6M6  H    H  HNH2   0   0.363  89.6495  21.0279  23.4505
 6M6  H2   H  HNH2   0   0.359  89.8436  19.4587  23.1093
 6M6  H8   H  HCH2   0   0.260  86.1968  21.1210  25.6702
 6M6  H9   H  HCH2   0   0.252  85.2040  19.6685  25.8151
 6M6  H10  H  HCH2   0   0.254  86.0372  21.0455  23.2103
 6M6  H11  H  HCH2   0   0.259  84.4643  21.1678  23.9736
 6M6  H12  H  HNH1   0   0.462  87.8841  19.7561  24.4602
 6M6  H13  H  HCR6   0   0.245  82.8705  19.3024  23.8742
 6M6  H14  H  HCR6   0   0.250  82.1641  17.2218  22.7617
 6M6  H15  H  HCR6   0   0.250  83.7589  15.9699  21.3391
 6M6  H16  H  HCR6   0   0.250  86.0561  16.8379  21.0212
 6M6  H17  H  HCR6   0   0.243  86.7537  18.9272  22.1194

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
 6M6  C05  C06  aromatic  1.389  0.020  1.389
 6M6  C05  C04  aromatic  1.389  0.020  1.389
 6M6  C06  C07  aromatic  1.393  0.020  1.393
 6M6  C04  C09  aromatic  1.389  0.020  1.389
 6M6  C07  C03  single    1.502  0.020  1.502
 6M6  C07  C08  aromatic  1.393  0.020  1.393
 6M6  C09  C08  aromatic  1.388  0.020  1.388
 6M6  C03  C01  single    1.533  0.020  1.533
 6M6  SG   C02  single    1.776  0.020  1.776
 6M6  SG   CB   single    1.842  0.020  1.842
 6M6  N    CA   single    1.458  0.019  1.458
 6M6  N01  C02  single    1.314  0.020  1.314
 6M6  N01  C01  single    1.445  0.020  1.445
 6M6  C02  S01  double    1.670  0.020  1.670
 6M6  CB   CA   single    1.530  0.020  1.530
 6M6  CA   C    single    1.525  0.021  1.525
 6M6  O    C    deloc     1.231  0.020  1.231
 6M6  CB   HB2  single    0.970  0.020  1.090
 6M6  CB   HB3  single    0.970  0.020  1.090
 6M6  CA   HA   single    0.970  0.020  0.970
 6M6  C    OXT  deloc     1.245  0.020  1.245
 6M6  N    H    single    0.860  0.020  0.860
 6M6  N    H2   single    0.890  0.020  1.040
 6M6  C01  H8   single    0.970  0.020  1.090
 6M6  C01  H9   single    0.970  0.020  1.090
 6M6  C03  H10  single    0.970  0.020  1.090
 6M6  C03  H11  single    0.970  0.020  1.090
 6M6  N01  H12  single    0.860  0.020  1.020
 6M6  C08  H13  single    0.930  0.020  1.080
 6M6  C09  H14  single    0.930  0.020  1.080
 6M6  C04  H15  single    0.930  0.020  1.080
 6M6  C05  H16  single    0.930  0.020  1.080
 6M6  C06  H17  single    0.930  0.020  1.080

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
 6M6  C02  SG   CB   110.44  3.000
 6M6  HB3  CB   HB2  107.48  3.000
 6M6  HB3  CB   CA   110.61  3.000
 6M6  HB2  CB   CA   109.68  3.000
 6M6  HB3  CB   SG   101.02  3.000
 6M6  HB2  CB   SG   107.44  3.000
 6M6  CA   CB   SG   119.78  3.000
 6M6  HA   CA   N    110.00  3.000
 6M6  HA   CA   C    109.00  3.000
 6M6  N    CA   C    111.00  2.800
 6M6  HA   CA   CB   109.00  3.000
 6M6  C    CA   CB   110.10  1.900
 6M6  N    CA   CB   110.50  1.700
 6M6  OXT  C    O    127.77  3.000
 6M6  OXT  C    CA   115.63  3.000
 6M6  O    C    CA   120.80  1.700
 6M6  H2   N    H    105.85  3.000
 6M6  H2   N    CA   110.51  3.000
 6M6  H    N    CA   114.00  3.000
 6M6  H9   C01  H8   108.12  3.000
 6M6  H9   C01  N01  109.10  3.000
 6M6  H8   C01  N01  108.36  3.000
 6M6  H9   C01  C03  110.68  3.000
 6M6  H8   C01  C03  109.14  3.000
 6M6  N01  C01  C03  111.37  3.000
 6M6  H11  C03  H10  106.64  3.000
 6M6  H11  C03  C07  110.55  3.000
 6M6  H10  C03  C07  110.28  3.000
 6M6  H11  C03  C01  107.51  3.000
 6M6  H10  C03  C01  109.04  3.000
 6M6  C07  C03  C01  112.61  3.000
 6M6  C06  C07  C08  118.50  3.000
 6M6  C08  C07  C03  120.66  3.000
 6M6  C06  C07  C03  120.81  3.000
 6M6  H12  N01  C02  116.61  3.000
 6M6  H12  N01  C01  116.79  3.000
 6M6  C02  N01  C01  125.85  3.000
 6M6  S01  C02  N01  127.08  3.000
 6M6  S01  C02  SG   115.89  3.000
 6M6  N01  C02  SG   116.83  3.000
 6M6  H13  C08  C09  119.64  3.000
 6M6  H13  C08  C07  119.44  3.000
 6M6  C09  C08  C07  120.92  3.000
 6M6  H14  C09  C04  120.08  3.000
 6M6  H14  C09  C08  119.83  3.000
 6M6  C04  C09  C08  120.09  3.000
 6M6  H15  C04  C05  120.25  3.000
 6M6  H15  C04  C09  120.24  3.000
 6M6  C05  C04  C09  119.51  3.000
 6M6  H16  C05  C06  119.77  3.000
 6M6  H16  C05  C04  120.04  3.000
 6M6  C06  C05  C04  120.19  3.000
 6M6  H17  C06  C05  119.58  3.000
 6M6  H17  C06  C07  119.63  3.000
 6M6  C05  C06  C07  120.79  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
 6M6  CONST_01  C04  C05  C06  C07     0.00   0.0  0
 6M6  CONST_02  C04  C09  C08  C07     0.00   0.0  0
 6M6  CONST_03  C05  C06  C07  C08     0.00   0.0  0
 6M6  CONST_04  C05  C04  C09  C08     0.00   0.0  0
 6M6  CONST_05  C06  C05  C04  C09     0.00   0.0  0
 6M6  CONST_06  C06  C07  C08  C09     0.00   0.0  0
 6M6  CONST_07  C05  C06  C07  C03   180.00   0.0  0
 6M6  CONST_08  C09  C08  C07  C03   180.00   0.0  0
 6M6  CONST_09  H16  C05  C06  C07   180.00   0.0  0
 6M6  CONST_10  H14  C09  C08  C07   180.00   0.0  0
 6M6  CONST_11  H17  C06  C07  C08   180.00   0.0  0
 6M6  CONST_12  H15  C04  C09  C08   180.00   0.0  0
 6M6  CONST_13  H13  C08  C09  C04   180.00   0.0  0
 6M6  Var_01    C06  C07  C03  C01   -87.82  30.0  2
 6M6  Var_02    N01  C01  C03  C07    62.09  30.0  3
 6M6  Var_03    C01  N01  C02  SG    176.85  30.0  1
 6M6  Var_04    N01  C02  SG   CB     43.65  30.0  3
 6M6  Var_05    C02  N01  C01  C03  -112.34  30.0  1
 6M6  Var_06    HB2  CB   SG   C02    84.61  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
 6M6  chir_01  CA  N  CB  C  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
 6M6  plan-1  C03  0.020
 6M6  plan-1  C07  0.020
 6M6  plan-1  C08  0.020
 6M6  plan-1  C09  0.020
 6M6  plan-1  C04  0.020
 6M6  plan-1  C05  0.020
 6M6  plan-1  C06  0.020
 6M6  plan-1  H13  0.020
 6M6  plan-1  H14  0.020
 6M6  plan-1  H15  0.020
 6M6  plan-1  H16  0.020
 6M6  plan-1  H17  0.020
 6M6  plan-2  CA   0.020
 6M6  plan-2  C    0.020
 6M6  plan-2  O    0.020
 6M6  plan-2  OXT  0.020
 6M6  plan-3  SG   0.020
 6M6  plan-3  N01  0.020
 6M6  plan-3  S01  0.020
 6M6  plan-3  C02  0.020

