# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 17:05:10 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  29  14  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.504   0.0771  -1.4604   0.5622
 X8Z  C4    C  C     0   0.607   0.2584  -0.2854   0.2626
 X8Z  C2    C  CH1   0  -0.392   1.6221   0.2286  -0.1649
 X8Z  C1    C  CH2   0  -0.534   2.7137  -0.6000   0.5037
 X8Z  S     S  S2    0  -0.259   4.3479   0.1011   0.0851
 X8Z  C3    C  CH3   0  -0.653   1.6905   0.1789  -1.6956
 X8Z  H11C  H  HCH2  0   0.282   2.5965  -0.5723   1.5866
 X8Z  H12C  H  HCH2  0   0.269   2.6694  -1.6383   0.1795
 X8Z  H31C  H  HCH3  0   0.248   0.8871   0.7594  -2.1494
 X8Z  H32C  H  HCH3  0   0.247   2.6323   0.5870  -2.0614
 X8Z  H33C  H  HCH3  0   0.236   1.6060  -0.8488  -2.0508
 X8Z  H     H  HSH1  0   0.227   5.0596  -0.6044   0.9698
 X8Z  H2    H  HCH1  0   0.270   1.7447   1.2662   0.1555
 X8Z  N     N  NT    0  -0.486  -0.7664   0.5840   0.2464
 X8Z  C8    C  CH1   0  -0.150  -2.1070   0.0998   0.5089
 X8Z  C9    C  C     0   0.534  -2.4967  -0.9844  -0.4737
 X8Z  O3    O  O     0  -0.435  -2.1085  -1.0403  -1.6112
 X8Z  O2    O  OH1   0  -0.591  -3.3828  -1.8190   0.0511
 X8Z  C5    C  CH2   0  -0.279  -0.7301   2.0181  -0.0162
 X8Z  C6    C  CH2   0  -0.469  -2.0394   2.5001   0.5903
 X8Z  C7    C  CH2   0  -0.487  -2.9942   1.3435   0.3181
 X8Z  H8    H  HCH1  0   0.289  -2.1907  -0.2788   1.5312
 X8Z  H51C  H  HCH2  0   0.264   0.1357   2.4874   0.4477
 X8Z  H52C  H  HCH2  0   0.246  -0.6925   2.2198  -1.0906
 X8Z  H71C  H  HCH2  0   0.256  -3.3629   1.4013  -0.7082
 X8Z  H72C  H  HCH2  0   0.272  -3.8549   1.3273   0.9838
 X8Z  HA    H  HOH1  0   0.483  -3.6716  -2.4590  -0.6171
 X8Z  H61C  H  HCH2  0   0.248  -1.9200   2.6511   1.6649
 X8Z  H62C  H  HCH2  0   0.261  -2.3766   3.4381   0.1526

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  1.226  0.020  1.226
 X8Z  C4  C2    single  1.519  0.020  1.519
 X8Z  C4  N     single  1.344  0.020  1.344
 X8Z  C2  C1    single  1.525  0.020  1.525
 X8Z  C2  C3    single  1.533  0.020  1.533
 X8Z  C1  S     single  1.827  0.020  1.827
 X8Z  N   C8    single  1.449  0.020  1.449
 X8Z  N   C5    single  1.458  0.020  1.458
 X8Z  C8  C9    single  1.514  0.020  1.514
 X8Z  C8  C7    single  1.540  0.020  1.540
 X8Z  C9  O3    double  1.203  0.020  1.203
 X8Z  C9  O2    single  1.326  0.020  1.326
 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  O2  HA    single  0.850  0.020  0.980
 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    120.67  3.000
 X8Z  C2    C4  O1    121.73  3.000
 X8Z  H2    C2  C3    108.57  3.000
 X8Z  H2    C2  C1    107.88  3.000
 X8Z  C3    C2  C1    112.85  3.000
 X8Z  H2    C2  C4    109.85  3.000
 X8Z  C3    C2  C4    108.07  3.000
 X8Z  C1    C2  C4    109.59  3.000
 X8Z  H12C  C1  H11C  108.42  3.000
 X8Z  H12C  C1  S     109.52  3.000
 X8Z  H11C  C1  S     108.31  3.000
 X8Z  H12C  C1  C2    111.01  3.000
 X8Z  H11C  C1  C2    110.18  3.000
 X8Z  S     C1  C2    109.35  3.000
 X8Z  H     S   C1     97.01  3.000
 X8Z  H33C  C3  H32C  108.09  3.000
 X8Z  H33C  C3  H31C  108.01  3.000
 X8Z  H32C  C3  H31C  107.33  3.000
 X8Z  H33C  C3  C2    110.63  3.000
 X8Z  H32C  C3  C2    111.20  3.000
 X8Z  H31C  C3  C2    111.44  3.000
 X8Z  C5    N   C8    112.59  3.000
 X8Z  C5    N   C4    128.27  3.000
 X8Z  C8    N   C4    119.14  3.000
 X8Z  H8    C8  C7    110.58  3.000
 X8Z  H8    C8  C9    109.82  3.000
 X8Z  C7    C8  C9    110.47  3.000
 X8Z  H8    C8  N     110.85  3.000
 X8Z  C7    C8  N     103.93  3.000
 X8Z  C9    C8  N     111.08  3.000
 X8Z  O2    C9  O3    124.10  3.000
 X8Z  O2    C9  C8    111.47  3.000
 X8Z  O3    C9  C8    124.32  3.000
 X8Z  HA    O2  C9    110.00  3.000
 X8Z  H52C  C5  H51C  108.16  3.000
 X8Z  H52C  C5  C6    111.27  3.000
 X8Z  H51C  C5  C6    112.21  3.000
 X8Z  H52C  C5  N     111.04  3.000
 X8Z  H51C  C5  N     111.53  3.000
 X8Z  C6    C5  N     102.61  3.000
 X8Z  H62C  C6  H61C  108.09  3.000
 X8Z  H62C  C6  C7    112.83  3.000
 X8Z  H61C  C6  C7    110.44  3.000
 X8Z  H62C  C6  C5    112.29  3.000
 X8Z  H61C  C6  C5    110.00  3.000
 X8Z  C7    C6  C5    103.15  3.000
 X8Z  H72C  C7  H71C  107.98  3.000
 X8Z  H72C  C7  C6    113.42  3.000
 X8Z  H71C  C7  C6    109.83  3.000
 X8Z  H72C  C7  C8    111.59  3.000
 X8Z  H71C  C7  C8    110.72  3.000
 X8Z  C6    C7  C8    103.29  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  CONST_05  HA  O2  C9  C8  180.00   0.0  0
 X8Z  Var_01    C7  C6  C5  N   -34.91  30.0  1
 X8Z  Var_02    C6  C5  N   C8   20.06  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
 X8Z  plan-2  HA  0.020

