# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 12:09:27 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (2~{S})-2-(dimethylamino)-3-(2-sulfo-1~{H}-imidazol-4-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)[C@@H](Cc1c[nH]c(n1)[S](O)(=O)=O)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
 KZ5  KZ5  '(2~{S})-2-(dimethylamino)-3-(2-sulfo-1~{H}-imidazol-4-yl)propanoic acid'  ligand  28  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KZ5
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
 KZ5  C6    C  CH2    0  -0.561   1.5797  -0.0200  -1.2782
 KZ5  C7    C  CH1    0  -0.184   2.3948  -0.3898  -0.0272
 KZ5  C13   C  CH3    0  -0.505   2.7470   0.2583   2.2854
 KZ5  C9    C  C      0   0.398   3.7873  -0.9347  -0.4470
 KZ5  C5    C  CR5    0   0.139  -1.8341   0.2309  -0.3035
 KZ5  C3    C  CR15   0  -0.134  -0.3758   1.6451  -1.0946
 KZ5  C2    C  CR5    0   0.188   0.1872   0.4030  -0.9657
 KZ5  N1    N  N      0  -0.449  -0.7429  -0.4691  -0.4730
 KZ5  O16   O  OS     0  -0.742  -3.1083  -1.1104   1.5112
 KZ5  O15   O  OS     0  -0.750  -4.2105   0.8194   0.4363
 KZ5  C12   C  CH3    0  -0.509   2.9272   1.9382   0.5872
 KZ5  N4    N  NR15   0  -0.577  -1.6643   1.5148  -0.6666
 KZ5  N8    N  NT     0  -0.396   2.3546   0.6681   0.9609
 KZ5  O10   O  O      0  -0.587   4.8058  -0.4144   0.0463
 KZ5  O11   O  OC    -1  -0.624   3.7670  -1.8872  -1.2568
 KZ5  O17   O  OS    -1  -0.744  -3.8767  -1.2788  -0.8139
 KZ5  HC6B  H  HCH2   0   0.230   2.0761   0.7715  -1.8465
 KZ5  HC6A  H  HCH2   0   0.245   1.5630  -0.8939  -1.9301
 KZ5  HC7   H  HCH1   0   0.221   1.8658  -1.2384   0.4280
 KZ5  H13C  H  HCH3   0   0.209   2.4638   1.0276   3.0096
 KZ5  H13A  H  HCH3   0   0.214   2.2173  -0.6560   2.5633
 KZ5  H13B  H  HCH3   0   0.190   3.8220   0.0718   2.4037
 KZ5  HC3   H  HCR5   0   0.279   0.0258   2.5843  -1.4356
 KZ5  H12A  H  HCH3   0   0.195   4.0213   1.9412   0.5234
 KZ5  H12C  H  HCH3   0   0.218   2.5354   2.2722  -0.3743
 KZ5  H12B  H  HCH3   0   0.208   2.6354   2.6935   1.3219
 KZ5  HN4   H  HNR5   0   0.416  -2.3617   2.2408  -0.6231
 KZ5  S14   S  S      0   1.410  -3.4010  -0.3976   0.2614

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
 KZ5  C13  N8    single    1.441  0.020  1.441
 KZ5  N8   C12   single    1.442  0.020  1.442
 KZ5  N8   C7    single    1.448  0.020  1.448
 KZ5  C7   C9    single    1.553  0.020  1.553
 KZ5  C7   C6    single    1.538  0.020  1.538
 KZ5  O16  S14   deloc     1.468  0.020  1.468
 KZ5  C9   O10   deloc     1.246  0.020  1.246
 KZ5  C9   O11   deloc     1.250  0.020  1.250
 KZ5  N1   C2    aromatic  1.367  0.020  1.367
 KZ5  N1   C5    aromatic  1.307  0.020  1.307
 KZ5  C6   C2    single    1.488  0.020  1.488
 KZ5  S14  C5    single    1.780  0.020  1.780
 KZ5  S14  O15   deloc     1.472  0.020  1.472
 KZ5  S14  O17   deloc     1.469  0.020  1.469
 KZ5  C2   C3    aromatic  1.370  0.020  1.370
 KZ5  C5   N4    aromatic  1.345  0.020  1.345
 KZ5  C3   N4    aromatic  1.364  0.020  1.364
 KZ5  C6   HC6B  single    0.970  0.020  1.090
 KZ5  C6   HC6A  single    0.970  0.020  1.090
 KZ5  C7   HC7   single    0.970  0.020  1.090
 KZ5  C13  H13C  single    0.970  0.020  1.090
 KZ5  C13  H13A  single    0.970  0.020  1.090
 KZ5  C13  H13B  single    0.970  0.020  1.090
 KZ5  C3   HC3   single    0.930  0.020  1.080
 KZ5  C12  H12A  single    0.970  0.020  1.090
 KZ5  C12  H12C  single    0.970  0.020  1.090
 KZ5  C12  H12B  single    0.970  0.020  1.090
 KZ5  N4   HN4   single    0.860  0.020  1.020

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
 KZ5  HC6A  C6   HC6B  106.04  3.000
 KZ5  HC6A  C6   C2    109.81  3.000
 KZ5  HC6B  C6   C2    109.15  3.000
 KZ5  HC6A  C6   C7    107.56  3.000
 KZ5  HC6B  C6   C7    110.86  3.000
 KZ5  C2    C6   C7    113.16  3.000
 KZ5  HC7   C7   N8    105.55  3.000
 KZ5  HC7   C7   C9    105.82  3.000
 KZ5  N8    C7   C9    117.75  3.000
 KZ5  HC7   C7   C6    105.51  3.000
 KZ5  C9    C7   C6    109.85  3.000
 KZ5  N8    C7   C6    111.38  3.000
 KZ5  H13B  C13  H13A  107.77  3.000
 KZ5  H13B  C13  H13C  107.57  3.000
 KZ5  H13A  C13  H13C  107.14  3.000
 KZ5  H13B  C13  N8    114.47  3.000
 KZ5  H13A  C13  N8    109.86  3.000
 KZ5  H13C  C13  N8    109.76  3.000
 KZ5  O11   C9   O10   126.01  3.000
 KZ5  O11   C9   C7    115.33  3.000
 KZ5  O10   C9   C7    118.65  3.000
 KZ5  S14   C5   N4    122.26  3.000
 KZ5  N4    C5   N1    111.76  3.000
 KZ5  S14   C5   N1    125.93  3.000
 KZ5  HC3   C3   N4    122.34  3.000
 KZ5  HC3   C3   C2    131.86  3.000
 KZ5  N4    C3   C2    105.79  3.000
 KZ5  N1    C2   C3    109.43  3.000
 KZ5  C3    C2   C6    128.49  3.000
 KZ5  N1    C2   C6    122.07  3.000
 KZ5  C2    N1   C5    105.85  3.000
 KZ5  H12B  C12  H12C  106.55  3.000
 KZ5  H12B  C12  H12A  107.68  3.000
 KZ5  H12C  C12  H12A  107.85  3.000
 KZ5  H12B  C12  N8    109.16  3.000
 KZ5  H12C  C12  N8    110.83  3.000
 KZ5  H12A  C12  N8    114.44  3.000
 KZ5  HN4   N4   C3    126.76  3.000
 KZ5  HN4   N4   C5    126.07  3.000
 KZ5  C3    N4   C5    107.17  3.000
 KZ5  C12   N8   C13   112.36  3.000
 KZ5  C12   N8   C7    117.09  3.000
 KZ5  C13   N8   C7    114.33  3.000
 KZ5  O17   S14  O15   113.88  3.000
 KZ5  O17   S14  O16   113.35  3.000
 KZ5  O15   S14  O16   114.19  3.000
 KZ5  O17   S14  C5    105.34  3.000
 KZ5  O15   S14  C5    103.29  3.000
 KZ5  O16   S14  C5    105.42  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
 KZ5  CONST_01  C3    C2   N1  C5     0.00   0.0  0
 KZ5  CONST_02  C2    C3   N4  C5     0.00   0.0  0
 KZ5  CONST_03  N1    C5   N4  C3     0.00   0.0  0
 KZ5  CONST_04  N4    C5   N1  C2     0.00   0.0  0
 KZ5  CONST_05  N4    C3   C2  N1     0.00   0.0  0
 KZ5  CONST_06  C5    N1   C2  C6   180.00   0.0  0
 KZ5  CONST_07  N4    C3   C2  C6   180.00   0.0  0
 KZ5  CONST_08  S14   C5   N4  C3   180.00   0.0  0
 KZ5  CONST_09  S14   C5   N1  C2   180.00   0.0  0
 KZ5  CONST_10  HC3   C3   N4  C5   180.00   0.0  0
 KZ5  CONST_11  HN4   N4   C3  C2   180.00   0.0  0
 KZ5  Var_01    N1    C2   C6  C7   -67.77  30.0  2
 KZ5  Var_02    O16   S14  C5  N1    52.80  30.0  2
 KZ5  Var_03    H13C  C13  N8  C7  -166.38  30.0  3
 KZ5  Var_04    H12A  C12  N8  C7   -71.75  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
 KZ5  chir_01  C7  N8  C9  C6  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
 KZ5  plan-1  C6   0.020
 KZ5  plan-1  C5   0.020
 KZ5  plan-1  C3   0.020
 KZ5  plan-1  C2   0.020
 KZ5  plan-1  N1   0.020
 KZ5  plan-1  N4   0.020
 KZ5  plan-1  HC3  0.020
 KZ5  plan-1  HN4  0.020
 KZ5  plan-1  S14  0.020
 KZ5  plan-2  C7   0.020
 KZ5  plan-2  C9   0.020
 KZ5  plan-2  O10  0.020
 KZ5  plan-2  O11  0.020

