# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:30:27 2021
#   Inital geometry file: a 111 line input string
#   Ligand name: (2~{S})-2-azanyl-5-oxidanylidene-5-[[(2~{S})-1-oxidanylidene-1-[(2-oxidanylidene-2-propan-2-yloxy-ethyl)amino]-3-sulfanyl-propan-2-yl]amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)OC(=O)CNC(=O)[C@@H](CS)NC(=O)CC[C@H](N)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
 S8H  S8H  '(2~{S})-2-azanyl-5-oxidanylidene-5-[[(2~{S})-1-oxidanylidene-1-[(2-oxidanylidene-2-propan-2-yloxy-ethyl)amino]-3-sulfanyl-propan-2-yl]amino]pentanoic acid'  ligand  46  23  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S8H
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
 S8H  N1   N  NH1   0  -0.609  16.7297  -17.2757  -2.9412
 S8H  N3   N  NH2   0  -0.795  19.3195  -11.3221  -5.8993
 S8H  C4   C  C     0   0.581  17.9899  -18.0993  -0.9756
 S8H  C5   C  CH2   0  -0.411  16.6577  -17.9870  -1.6978
 S8H  C6   C  C     0   0.553  17.4127  -17.7757  -3.9795
 S8H  C7   C  CH1   0  -0.169  17.4908  -16.8964  -5.2293
 S8H  C8   C  CH2   0  -0.594  16.3433  -17.2167  -6.1848
 S8H  C10  C  CH2   0  -0.583  18.4773  -13.4722  -4.0046
 S8H  C13  C  C     0   0.537  20.7323  -13.3145  -6.1399
 S8H  C11  C  CH2   0  -0.464  19.7712  -12.6778  -3.9171
 S8H  C12  C  CH1   0  -0.184  20.3148  -12.1564  -5.2567
 S8H  C2   C  CH1   0   0.016  20.1085  -17.0295  -0.6905
 S8H  C3   C  CH3   0  -0.685  20.5166  -15.5709  -0.7063
 S8H  N2   N  NH1   0  -0.651  17.5411  -15.4923  -4.9318
 S8H  O1   O  O2    0  -0.441  18.7757  -17.0790  -1.2449
 S8H  O2   O  O     0  -0.460  18.2493  -18.9996  -0.2161
 S8H  O3   O  O     0  -0.487  17.9131  -18.8895  -3.9627
 S8H  O4   O  O     0  -0.477  19.6909  -15.5339  -4.2724
 S8H  O6   O  O     0  -0.449  21.8323  -13.8091  -6.1046
 S8H  S1   S  S2    0  -0.243  14.7029  -16.6770  -5.5962
 S8H  H10  H  HNH1  0   0.402  16.3969  -16.3269  -2.9727
 S8H  H21  H  HNH2  0   0.354  19.0803  -10.5675  -5.2685
 S8H  H22  H  HNH2  0   0.355  19.7092  -10.8783  -6.7216
 S8H  H9   H  HCH2  0   0.303  15.9629  -17.4585  -1.0426
 S8H  H8   H  HCH2  0   0.280  16.2626  -18.9931  -1.8384
 S8H  H11  H  HCH1  0   0.295  18.4109  -17.1912  -5.7390
 S8H  H12  H  HCH2  0   0.314  16.5303  -16.7536  -7.1512
 S8H  H13  H  HCH2  0   0.305  16.3004  -18.2931  -6.3428
 S8H  H17  H  HCH2  0   0.284  18.0157  -13.5022  -3.0123
 S8H  H16  H  HCH2  0   0.267  17.7597  -12.9681  -4.6543
 S8H  H2   H  HCH3  0   0.235  22.0546  -17.8070  -1.1495
 S8H  H3   H  HCH3  0   0.238  20.7591  -18.9543  -1.4649
 S8H  H1   H  HCH3  0   0.237  21.0162  -17.5870  -2.5628
 S8H  H18  H  HCH2  0   0.257  20.5456  -13.2593  -3.4155
 S8H  H19  H  HCH2  0   0.259  19.5959  -11.8013  -3.2889
 S8H  H20  H  HCH1  0   0.256  21.2473  -11.6250  -5.0253
 S8H  H4   H  HCH1  0   0.237  20.0758  -17.3892   0.3403
 S8H  H6   H  HCH3  0   0.232  21.5100  -15.4652  -0.2705
 S8H  H7   H  HCH3  0   0.245  20.5483  -15.1862  -1.7262
 S8H  H5   H  HCH3  0   0.237  19.8307  -14.9583  -0.1212
 S8H  H15  H  HNH1  0   0.397  16.7036  -14.9402  -5.0451
 S8H  H14  H  HOH1  0   0.477  20.0908  -14.4973  -7.4577
 S8H  H24  H  HSH1  0   0.237  14.5923  -15.5819  -6.3531
 S8H  C9   C  C     0   0.576  18.6511  -14.9143  -4.4229
 S8H  O5   O  OH1   0  -0.583  19.7684  -13.7419  -6.9434
 S8H  C1   C  CH3   0  -0.677  21.0333  -17.9009  -1.5191

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
 S8H  O6   C13  double  1.207  0.020  1.207
 S8H  C13  O5   single  1.326  0.020  1.326
 S8H  C13  C12  single  1.515  0.020  1.515
 S8H  C12  C11  single  1.537  0.020  1.537
 S8H  C12  N3   single  1.449  0.020  1.449
 S8H  C11  C10  single  1.521  0.020  1.521
 S8H  O4   C9   double  1.220  0.020  1.220
 S8H  C10  C9   single  1.512  0.020  1.512
 S8H  C9   N2   single  1.351  0.020  1.351
 S8H  O3   C6   double  1.221  0.020  1.221
 S8H  C8   C7   single  1.527  0.020  1.527
 S8H  C8   S1   single  1.825  0.020  1.825
 S8H  C7   N2   single  1.436  0.020  1.436
 S8H  C7   C6   single  1.530  0.020  1.530
 S8H  C6   N1   single  1.340  0.020  1.340
 S8H  N1   C5   single  1.434  0.020  1.434
 S8H  C5   C4   single  1.519  0.020  1.519
 S8H  C4   O1   single  1.316  0.020  1.316
 S8H  C4   O2   double  1.206  0.020  1.206
 S8H  O1   C2   single  1.444  0.020  1.444
 S8H  C2   C3   single  1.515  0.020  1.515
 S8H  C2   C1   single  1.517  0.020  1.517
 S8H  N1   H10  single  0.860  0.020  1.020
 S8H  N3   H21  single  0.890  0.020  1.040
 S8H  N3   H22  single  0.890  0.020  1.040
 S8H  C5   H9   single  0.970  0.020  1.090
 S8H  C5   H8   single  0.970  0.020  1.090
 S8H  C7   H11  single  0.970  0.020  1.090
 S8H  C8   H12  single  0.970  0.020  1.090
 S8H  C8   H13  single  0.970  0.020  1.090
 S8H  C10  H17  single  0.970  0.020  1.090
 S8H  C10  H16  single  0.970  0.020  1.090
 S8H  C1   H2   single  0.970  0.020  1.090
 S8H  C1   H3   single  0.970  0.020  1.090
 S8H  C1   H1   single  0.970  0.020  1.090
 S8H  C11  H18  single  0.970  0.020  1.090
 S8H  C11  H19  single  0.970  0.020  1.090
 S8H  C12  H20  single  0.970  0.020  1.090
 S8H  C2   H4   single  0.970  0.020  1.090
 S8H  C3   H6   single  0.970  0.020  1.090
 S8H  C3   H7   single  0.970  0.020  1.090
 S8H  C3   H5   single  0.970  0.020  1.090
 S8H  N2   H15  single  0.860  0.020  1.020
 S8H  O5   H14  single  0.850  0.020  0.980
 S8H  S1   H24  single  1.200  0.020  1.300

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
 S8H  H10  N1   C6   119.76  3.000
 S8H  H10  N1   C5   118.58  3.000
 S8H  C6   N1   C5   120.83  3.000
 S8H  H22  N3   H21  105.68  3.000
 S8H  H22  N3   C12  110.38  3.000
 S8H  H21  N3   C12  108.37  3.000
 S8H  O2   C4   O1   125.40  3.000
 S8H  O2   C4   C5   122.89  3.000
 S8H  O1   C4   C5   111.66  3.000
 S8H  H8   C5   H9   107.07  3.000
 S8H  H8   C5   C4   108.11  3.000
 S8H  H9   C5   C4   107.97  3.000
 S8H  H8   C5   N1   111.35  3.000
 S8H  H9   C5   N1   108.19  3.000
 S8H  C4   C5   N1   113.87  3.000
 S8H  O3   C6   C7   120.96  3.000
 S8H  C7   C6   N1   116.40  3.000
 S8H  O3   C6   N1   122.59  3.000
 S8H  H11  C7   N2   109.33  3.000
 S8H  H11  C7   C8   106.52  3.000
 S8H  N2   C7   C8   111.16  3.000
 S8H  H11  C7   C6   105.60  3.000
 S8H  N2   C7   C6   113.23  3.000
 S8H  C8   C7   C6   110.62  3.000
 S8H  H13  C8   H12  107.38  3.000
 S8H  H13  C8   S1   107.69  3.000
 S8H  H12  C8   S1   108.37  3.000
 S8H  H13  C8   C7   109.13  3.000
 S8H  H12  C8   C7   109.72  3.000
 S8H  S1   C8   C7   114.31  3.000
 S8H  H16  C10  H17  105.96  3.000
 S8H  H16  C10  C9   110.58  3.000
 S8H  H17  C10  C9   105.85  3.000
 S8H  H16  C10  C11  110.63  3.000
 S8H  H17  C10  C11  108.72  3.000
 S8H  C9   C10  C11  114.61  3.000
 S8H  O6   C13  O5   123.26  3.000
 S8H  O5   C13  C12  113.54  3.000
 S8H  O6   C13  C12  123.19  3.000
 S8H  H19  C11  H18  106.09  3.000
 S8H  H19  C11  C12  106.60  3.000
 S8H  H18  C11  C12  109.31  3.000
 S8H  H19  C11  C10  108.40  3.000
 S8H  H18  C11  C10  110.61  3.000
 S8H  C12  C11  C10  115.34  3.000
 S8H  H20  C12  C11  106.32  3.000
 S8H  H20  C12  C13  104.99  3.000
 S8H  C11  C12  C13  110.26  3.000
 S8H  H20  C12  N3   113.47  3.000
 S8H  C11  C12  N3   109.81  3.000
 S8H  C13  C12  N3   111.76  3.000
 S8H  H4   C2   O1   108.87  3.000
 S8H  H4   C2   C3   109.57  3.000
 S8H  O1   C2   C3   106.12  3.000
 S8H  H4   C2   C1   110.15  3.000
 S8H  C3   C2   C1   112.53  3.000
 S8H  O1   C2   C1   109.46  3.000
 S8H  H5   C3   H7   108.79  3.000
 S8H  H5   C3   H6   107.72  3.000
 S8H  H7   C3   H6   108.26  3.000
 S8H  H5   C3   C2   111.47  3.000
 S8H  H7   C3   C2   110.93  3.000
 S8H  H6   C3   C2   109.56  3.000
 S8H  H15  N2   C9   119.34  3.000
 S8H  H15  N2   C7   118.84  3.000
 S8H  C9   N2   C7   121.67  3.000
 S8H  C2   O1   C4   119.95  3.000
 S8H  H24  S1   C8    97.70  3.000
 S8H  O4   C9   N2   121.98  3.000
 S8H  N2   C9   C10  114.71  3.000
 S8H  O4   C9   C10  123.26  3.000
 S8H  H14  O5   C13  109.34  3.000
 S8H  H1   C1   H3   108.79  3.000
 S8H  H1   C1   H2   108.33  3.000
 S8H  H3   C1   H2   107.58  3.000
 S8H  H1   C1   C2   110.37  3.000
 S8H  H3   C1   C2   112.00  3.000
 S8H  H2   C1   C2   109.66  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
 S8H  CONST_01  O3   C6   N1   C5      0.00   0.0  0
 S8H  CONST_02  C7   C6   N1   C5    180.00   0.0  0
 S8H  CONST_03  O4   C9   N2   C7      0.00   0.0  0
 S8H  CONST_04  C10  C9   N2   C7    180.00   0.0  0
 S8H  CONST_05  H10  N1   C6   C7      0.00   0.0  0
 S8H  CONST_06  H15  N2   C9   C10     0.00   0.0  0
 S8H  CONST_07  H14  O5   C13  C12   180.00   0.0  0
 S8H  Var_01    O1   C4   C5   N1     29.28  30.0  3
 S8H  Var_02    C6   N1   C5   C4     66.47  30.0  1
 S8H  Var_03    C3   C2   O1   C4   -157.89  30.0  3
 S8H  Var_04    O4   C9   C10  C11    23.82  30.0  3
 S8H  Var_05    C9   C10  C11  C12    80.44  30.0  3
 S8H  Var_06    H6   C3   C2   C1    -61.91  30.0  3
 S8H  Var_07    H2   C1   C2   C3     58.01  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
 S8H  chir_01  C7   C8  N2   C6   negativ
 S8H  chir_02  C12  N3  C13  C11  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
 S8H  plan-1  N1   0.020
 S8H  plan-1  C5   0.020
 S8H  plan-1  C6   0.020
 S8H  plan-1  C7   0.020
 S8H  plan-1  O3   0.020
 S8H  plan-1  H10  0.020
 S8H  plan-2  C7   0.020
 S8H  plan-2  C10  0.020
 S8H  plan-2  N2   0.020
 S8H  plan-2  O4   0.020
 S8H  plan-2  H15  0.020
 S8H  plan-2  C9   0.020
 S8H  plan-3  C13  0.020
 S8H  plan-3  C12  0.020
 S8H  plan-3  O6   0.020
 S8H  plan-3  H14  0.020
 S8H  plan-3  O5   0.020
 S8H  plan-4  C4   0.020
 S8H  plan-4  C5   0.020
 S8H  plan-4  O1   0.020
 S8H  plan-4  O2   0.020

