# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:42:48 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-[(2S)-2-methyl-3-sulfanylpropanoyl]-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CS)C(=O)N1CCC[C@H]1C(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
 X8Z  X8Z  1-[(2S)-2-methyl-3-sulfanylpropanoyl]-L-proline  ligand  28  14  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_X8Z
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
 X8Z  O1    O  O      0  -0.518   0.1606  -1.4536   0.6614
 X8Z  C4    C  C      0   0.598   0.2921  -0.2893   0.2944
 X8Z  C2    C  CH1    0  -0.389   1.6339   0.2240  -0.2096
 X8Z  C1    C  CH2    0  -0.533   2.7635  -0.5443   0.4672
 X8Z  S     S  S2     0  -0.264   4.3715   0.1551  -0.0480
 X8Z  C3    C  CH3    0  -0.648   1.6529   0.0891  -1.7356
 X8Z  H11C  H  HCH2   0   0.278   2.6834  -0.4539   1.5500
 X8Z  H12C  H  HCH2   0   0.266   2.7277  -1.6006   0.2070
 X8Z  H31C  H  HCH3   0   0.246   0.8154   0.6188  -2.1892
 X8Z  H32C  H  HCH3   0   0.239   2.5698   0.4997  -2.1586
 X8Z  H33C  H  HCH3   0   0.231   1.5840  -0.9588  -2.0308
 X8Z  H     H  HSH1   0   0.225   5.1258  -0.4873   0.8495
 X8Z  H2    H  HCH1   0   0.262   1.7497   1.2801   0.0461
 X8Z  N     N  NR5    0  -0.473  -0.7397   0.5639   0.2859
 X8Z  C8    C  CR15   0  -0.144  -2.0904   0.0662   0.5121
 X8Z  C9    C  C      0   0.400  -2.5020  -1.0376  -0.4840
 X8Z  O3    O  O      0  -0.598  -1.9868  -0.9985  -1.6142
 X8Z  O2    O  OC    -1  -0.619  -3.3769  -1.8277  -0.0755
 X8Z  C5    C  CH2    0  -0.281  -0.7174   1.9756  -0.0652
 X8Z  C6    C  CH2    0  -0.460  -2.0185   2.4838   0.5368
 X8Z  C7    C  CH2    0  -0.492  -2.9685   1.3133   0.3133
 X8Z  H8    H  HCR5   0   0.228  -2.1839  -0.3032   1.5376
 X8Z  H51C  H  HCH2   0   0.252   0.1543   2.4830   0.3463
 X8Z  H52C  H  HCH2   0   0.232  -0.7098   2.1143  -1.1512
 X8Z  H71C  H  HCH2   0   0.234  -3.3511   1.3475  -0.7101
 X8Z  H72C  H  HCH2   0   0.248  -3.8251   1.3203   0.9859
 X8Z  H61C  H  HCH2   0   0.235  -1.8850   2.6731   1.6043
 X8Z  H62C  H  HCH2   0   0.246  -2.3564   3.4089   0.0709

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
 X8Z  O1  C4    double  1.228  0.020  1.228
 X8Z  C4  C2    single  1.523  0.020  1.523
 X8Z  C4  N     single  1.339  0.020  1.339
 X8Z  C2  C1    single  1.524  0.020  1.524
 X8Z  C2  C3    single  1.532  0.020  1.532
 X8Z  C1  S     single  1.828  0.020  1.828
 X8Z  N   C8    single  1.457  0.020  1.457
 X8Z  N   C5    single  1.455  0.020  1.455
 X8Z  C8  C9    single  1.543  0.020  1.543
 X8Z  C8  C7    single  1.538  0.020  1.538
 X8Z  C9  O3    deloc   1.243  0.020  1.243
 X8Z  C9  O2    deloc   1.248  0.020  1.248
 X8Z  C5  C6    single  1.521  0.020  1.521
 X8Z  C6  C7    single  1.524  0.020  1.524
 X8Z  C2  H2    single  0.970  0.020  1.090
 X8Z  C1  H11C  single  0.970  0.020  1.090
 X8Z  C1  H12C  single  0.970  0.020  1.090
 X8Z  C3  H31C  single  0.970  0.020  1.090
 X8Z  C3  H32C  single  0.970  0.020  1.090
 X8Z  C3  H33C  single  0.970  0.020  1.090
 X8Z  S   H     single  1.200  0.020  1.300
 X8Z  C8  H8    single  0.970  0.020  1.090
 X8Z  C5  H51C  single  0.970  0.020  1.090
 X8Z  C5  H52C  single  0.970  0.020  1.090
 X8Z  C7  H71C  single  0.970  0.020  1.090
 X8Z  C7  H72C  single  0.970  0.020  1.090
 X8Z  C6  H61C  single  0.970  0.020  1.090
 X8Z  C6  H62C  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
 X8Z  N     C4  C2    117.53  3.000
 X8Z  N     C4  O1    121.58  3.000
 X8Z  C2    C4  O1    120.87  3.000
 X8Z  H2    C2  C3    108.47  3.000
 X8Z  H2    C2  C1    107.74  3.000
 X8Z  C3    C2  C1    112.87  3.000
 X8Z  H2    C2  C4    109.98  3.000
 X8Z  C3    C2  C4    108.12  3.000
 X8Z  C1    C2  C4    109.64  3.000
 X8Z  H12C  C1  H11C  108.40  3.000
 X8Z  H12C  C1  S     109.45  3.000
 X8Z  H11C  C1  S     108.24  3.000
 X8Z  H12C  C1  C2    111.02  3.000
 X8Z  H11C  C1  C2    110.18  3.000
 X8Z  S     C1  C2    109.51  3.000
 X8Z  H     S   C1     97.08  3.000
 X8Z  H33C  C3  H32C  108.06  3.000
 X8Z  H33C  C3  H31C  107.80  3.000
 X8Z  H32C  C3  H31C  107.57  3.000
 X8Z  H33C  C3  C2    110.69  3.000
 X8Z  H32C  C3  C2    111.33  3.000
 X8Z  H31C  C3  C2    111.24  3.000
 X8Z  C5    N   C8    112.52  3.000
 X8Z  C5    N   C4    127.45  3.000
 X8Z  C8    N   C4    119.72  3.000
 X8Z  H8    C8  C7    110.25  3.000
 X8Z  H8    C8  C9    109.92  3.000
 X8Z  C7    C8  C9    110.14  3.000
 X8Z  H8    C8  N     109.88  3.000
 X8Z  C7    C8  N     103.43  3.000
 X8Z  C9    C8  N     113.05  3.000
 X8Z  O2    C9  O3    127.48  3.000
 X8Z  O2    C9  C8    115.40  3.000
 X8Z  O3    C9  C8    117.00  3.000
 X8Z  H52C  C5  H51C  108.07  3.000
 X8Z  H52C  C5  C6    110.87  3.000
 X8Z  H51C  C5  C6    112.30  3.000
 X8Z  H52C  C5  N     111.24  3.000
 X8Z  H51C  C5  N     111.91  3.000
 X8Z  C6    C5  N     102.45  3.000
 X8Z  H62C  C6  H61C  107.98  3.000
 X8Z  H62C  C6  C7    113.33  3.000
 X8Z  H61C  C6  C7    110.65  3.000
 X8Z  H62C  C6  C5    112.31  3.000
 X8Z  H61C  C6  C5    109.88  3.000
 X8Z  C7    C6  C5    102.63  3.000
 X8Z  H72C  C7  H71C  107.62  3.000
 X8Z  H72C  C7  C6    113.25  3.000
 X8Z  H71C  C7  C6    109.36  3.000
 X8Z  H72C  C7  C8    111.98  3.000
 X8Z  H71C  C7  C8    110.25  3.000
 X8Z  C6    C7  C8    104.35  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
 X8Z  CONST_01  C8  N   C4  O1    0.00   0.0  0
 X8Z  CONST_02  C5  N   C4  O1  180.00   0.0  0
 X8Z  CONST_03  C8  N   C4  C2  180.00   0.0  0
 X8Z  CONST_04  C5  N   C4  C2    0.00   0.0  0
 X8Z  Var_01    C7  C6  C5  N   -36.44  30.0  1
 X8Z  Var_02    C6  C5  N   C8   24.18  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
 X8Z  chir_01  C2  C4  C1  C3  negativ
 X8Z  chir_02  C8  N   C9  C7  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
 X8Z  plan-1  O1  0.020
 X8Z  plan-1  C4  0.020
 X8Z  plan-1  C2  0.020
 X8Z  plan-1  N   0.020
 X8Z  plan-1  C8  0.020
 X8Z  plan-1  C5  0.020
 X8Z  plan-2  C8  0.020
 X8Z  plan-2  C9  0.020
 X8Z  plan-2  O3  0.020
 X8Z  plan-2  O2  0.020

