# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 08:18:03 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] 1H-imidazole-4-carbothioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)c1c[nH]cn1
#
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
 KH4  KH4  'S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] 1H-imidazole-4-carbothioate'  ligand  54  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KH4
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
 KH4  C16  C  C     0   0.519  -2.9888  -1.9205  -0.1326
 KH4  O3   O  O     0  -0.493  -3.0591  -2.7631   0.7529
 KH4  C17  C  CH1   0  -0.033  -4.2440  -1.2798  -0.7417
 KH4  O4   O  OH1   0  -0.660  -3.9321  -0.5147  -1.8849
 KH4  C18  C  CT    0  -0.203  -5.0747  -0.4808   0.3018
 KH4  C19  C  CH2   0  -0.127  -6.1692   0.2474  -0.4927
 KH4  C20  C  CH3   0  -0.651  -5.7440  -1.4309   1.2973
 KH4  C21  C  CH3   0  -0.669  -4.1926   0.5251   1.0459
 KH4  P    P  P     0   1.456  -8.3586   1.6328  -0.1095
 KH4  O1P  O  O     0  -0.712  -9.2537   0.8205  -0.9541
 KH4  O2P  O  O2    0  -0.588  -7.0380   0.9197   0.4255
 KH4  O3P  O  OH1   0  -0.744  -7.8982   2.9328  -0.9190
 KH4  OXT  O  OH1   0  -0.731  -8.9029   2.1087   1.3108
 KH4  N2   N  NH1   0  -0.638  -1.8244  -1.5011  -0.6377
 KH4  C15  C  CH2   0  -0.231  -0.5498  -2.0071  -0.1764
 KH4  C14  C  CH2   0  -0.630   0.5729  -1.2341  -0.8497
 KH4  C13  C  C     0   0.570   1.9365  -1.7305  -0.4195
 KH4  O2   O  O     0  -0.499   2.1650  -2.9142  -0.2135
 KH4  C4   C  CR15  0  -0.031   9.9725   2.2064  -0.2128
 KH4  N3   N  NR15  0  -0.556  11.1596   1.7100   0.1961
 KH4  C2   C  CR15  0   0.106  10.9544   0.4512   0.6544
 KH4  N4   N  N     0  -0.436   9.7007   0.1114   0.5627
 KH4  C5   C  CR5   0   0.078   9.0709   1.1967   0.0225
 KH4  O6   O  O     0  -0.399   7.0628   2.1710  -0.7292
 KH4  C22  C  C     0   0.155   7.6421   1.2229  -0.2521
 KH4  S1   S  S2    0   0.018   6.8281  -0.2910   0.1827
 KH4  C11  C  CH2   0  -0.599   5.1289   0.1128  -0.3013
 KH4  C12  C  CH2   0  -0.245   4.2450  -1.0722   0.0589
 KH4  N1   N  NH1   0  -0.645   2.8784  -0.7806  -0.3129
 KH4  H15  H  HCH1  0   0.274  -4.8633  -2.1094  -1.1004
 KH4  H16  H  HOH1  0   0.454  -3.6457   0.3677  -1.6228
 KH4  H17  H  HCH2  0   0.240  -5.7451   0.9851  -1.1760
 KH4  H18  H  HCH2  0   0.246  -6.7402  -0.4766  -1.0823
 KH4  H19  H  HCH3  0   0.252  -5.0118  -1.9861   1.8757
 KH4  H20  H  HCH3  0   0.236  -6.3651  -0.8764   1.9997
 KH4  H21  H  HCH3  0   0.226  -6.3838  -2.1525   0.7837
 KH4  H22  H  HCH3  0   0.224  -3.6288   1.1753   0.3722
 KH4  H23  H  HCH3  0   0.253  -4.7937   1.1724   1.6838
 KH4  H24  H  HCH3  0   0.246  -3.4753   0.0162   1.6909
 KH4  H27  H  HOH1  0   0.504  -9.7771   2.5206   1.2801
 KH4  H4   H  HOH1  0   0.495  -7.3404   3.5555  -0.4339
 KH4  H14  H  HNH1  0   0.401  -1.8394  -0.8981  -1.4439
 KH4  H13  H  HCH2  0   0.246  -0.4851  -1.8929   0.9079
 KH4  H12  H  HCH2  0   0.244  -0.4568  -3.0728  -0.3942
 KH4  H10  H  HCH2  0   0.269   0.4666  -0.1659  -0.6483
 KH4  H11  H  HCH2  0   0.285   0.5076  -1.3565  -1.9361
 KH4  H2   H  HNR5  0   0.435  12.0459   2.1910   0.1605
 KH4  H3   H  HCR5  0   0.292  11.7559  -0.1609   1.0366
 KH4  H5   H  HCH2  0   0.288   4.8074   1.0099   0.2293
 KH4  H6   H  HCH2  0   0.290   5.0888   0.3077  -1.3730
 KH4  H7   H  HCH2  0   0.255   4.5787  -1.9649  -0.4719
 KH4  H8   H  HCH2  0   0.250   4.3182  -1.2841   1.1298
 KH4  H9   H  HNH1  0   0.407   2.6080   0.1840  -0.4195
 KH4  H1   H  HCR5  0   0.309   9.8620   3.1950  -0.6243

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
 KH4  N3   C2   aromatic  1.355  0.020  1.355
 KH4  N3   C4   aromatic  1.350  0.020  1.350
 KH4  C2   N4   aromatic  1.302  0.020  1.302
 KH4  C4   C5   aromatic  1.374  0.020  1.374
 KH4  N4   C5   aromatic  1.366  0.020  1.366
 KH4  C5   C22  single    1.455  0.020  1.455
 KH4  C22  O6   double    1.209  0.020  1.209
 KH4  C22  S1   single    1.773  0.020  1.773
 KH4  S1   C11  single    1.812  0.020  1.812
 KH4  C11  C12  single    1.522  0.020  1.522
 KH4  O2   C13  double    1.223  0.020  1.223
 KH4  C13  C14  single    1.514  0.020  1.514
 KH4  C13  N1   single    1.342  0.020  1.342
 KH4  C15  C14  single    1.520  0.020  1.520
 KH4  C15  N2   single    1.447  0.020  1.447
 KH4  C12  N1   single    1.446  0.020  1.446
 KH4  N2   C16  single    1.337  0.020  1.337
 KH4  O3   C16  double    1.224  0.020  1.224
 KH4  C16  C17  single    1.535  0.020  1.535
 KH4  O4   C17  single    1.410  0.020  1.410
 KH4  C17  C18  single    1.555  0.020  1.555
 KH4  O3P  P    single    1.599  0.020  1.599
 KH4  O2P  C19  single    1.432  0.020  1.432
 KH4  O2P  P    single    1.593  0.020  1.593
 KH4  C20  C18  single    1.530  0.020  1.530
 KH4  C18  C19  single    1.536  0.020  1.536
 KH4  C18  C21  single    1.531  0.020  1.531
 KH4  P    O1P  double    1.475  0.020  1.475
 KH4  C4   H1   single    0.930  0.020  1.080
 KH4  N3   H2   single    0.860  0.020  1.020
 KH4  C2   H3   single    0.930  0.020  1.080
 KH4  C11  H5   single    0.970  0.020  1.090
 KH4  C11  H6   single    0.970  0.020  1.090
 KH4  C12  H7   single    0.970  0.020  1.090
 KH4  C12  H8   single    0.970  0.020  1.090
 KH4  N1   H9   single    0.860  0.020  1.020
 KH4  C14  H10  single    0.970  0.020  1.090
 KH4  C14  H11  single    0.970  0.020  1.090
 KH4  C15  H12  single    0.970  0.020  1.090
 KH4  C15  H13  single    0.970  0.020  1.090
 KH4  N2   H14  single    0.860  0.020  1.020
 KH4  C17  H15  single    0.970  0.020  1.090
 KH4  O4   H16  single    0.850  0.020  0.980
 KH4  C19  H17  single    0.970  0.020  1.090
 KH4  C19  H18  single    0.970  0.020  1.090
 KH4  C20  H19  single    0.970  0.020  1.090
 KH4  C20  H20  single    0.970  0.020  1.090
 KH4  C20  H21  single    0.970  0.020  1.090
 KH4  C21  H22  single    0.970  0.020  1.090
 KH4  C21  H23  single    0.970  0.020  1.090
 KH4  C21  H24  single    0.970  0.020  1.090
 KH4  P    OXT  single    1.594  0.020  1.594
 KH4  OXT  H27  single    0.850  0.020  0.980
 KH4  O3P  H4   single    0.850  0.020  0.980

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
 KH4  N2   C16  C17  115.55  3.000
 KH4  C17  C16  O3   121.81  3.000
 KH4  N2   C16  O3   122.63  3.000
 KH4  H15  C17  C18  107.87  3.000
 KH4  H15  C17  O4   105.69  3.000
 KH4  C18  C17  O4   112.54  3.000
 KH4  H15  C17  C16  106.02  3.000
 KH4  C18  C17  C16  112.64  3.000
 KH4  O4   C17  C16  111.54  3.000
 KH4  H16  O4   C17  109.99  3.000
 KH4  C21  C18  C20  110.11  3.000
 KH4  C21  C18  C19  110.52  3.000
 KH4  C20  C18  C19  108.61  3.000
 KH4  C21  C18  C17  110.86  3.000
 KH4  C19  C18  C17  106.09  3.000
 KH4  C20  C18  C17  110.56  3.000
 KH4  H18  C19  H17  108.21  3.000
 KH4  H18  C19  O2P  109.85  3.000
 KH4  H17  C19  O2P  108.66  3.000
 KH4  H18  C19  C18  109.69  3.000
 KH4  H17  C19  C18  111.56  3.000
 KH4  O2P  C19  C18  108.86  3.000
 KH4  H21  C20  H20  107.78  3.000
 KH4  H21  C20  H19  107.92  3.000
 KH4  H20  C20  H19  107.54  3.000
 KH4  H21  C20  C18  111.12  3.000
 KH4  H20  C20  C18  110.66  3.000
 KH4  H19  C20  C18  111.66  3.000
 KH4  H24  C21  H23  107.08  3.000
 KH4  H24  C21  H22  107.63  3.000
 KH4  H23  C21  H22  106.98  3.000
 KH4  H24  C21  C18  111.09  3.000
 KH4  H23  C21  C18  110.92  3.000
 KH4  H22  C21  C18  112.87  3.000
 KH4  OXT  P    O3P  107.86  3.000
 KH4  OXT  P    O2P   96.75  3.000
 KH4  O3P  P    O2P  107.17  3.000
 KH4  OXT  P    O1P  117.88  3.000
 KH4  O2P  P    O1P  116.67  3.000
 KH4  O3P  P    O1P  109.43  3.000
 KH4  P    O2P  C19  119.85  3.000
 KH4  H4   O3P  P    115.84  3.000
 KH4  H27  OXT  P    114.06  3.000
 KH4  H14  N2   C15  118.55  3.000
 KH4  H14  N2   C16  118.51  3.000
 KH4  C15  N2   C16  122.49  3.000
 KH4  H12  C15  H13  107.17  3.000
 KH4  H13  C15  C14  110.05  3.000
 KH4  H12  C15  C14  110.19  3.000
 KH4  H13  C15  N2   109.40  3.000
 KH4  H12  C15  N2   110.66  3.000
 KH4  C14  C15  N2   109.36  3.000
 KH4  H11  C14  H10  106.64  3.000
 KH4  H11  C14  C13  107.40  3.000
 KH4  H10  C14  C13  110.86  3.000
 KH4  H11  C14  C15  109.78  3.000
 KH4  H10  C14  C15  110.11  3.000
 KH4  C13  C14  C15  111.88  3.000
 KH4  N1   C13  O2   122.72  3.000
 KH4  N1   C13  C14  115.01  3.000
 KH4  O2   C13  C14  122.25  3.000
 KH4  H1   C4   C5   132.29  3.000
 KH4  H1   C4   N3   122.93  3.000
 KH4  C5   C4   N3   104.77  3.000
 KH4  H2   N3   C2   125.99  3.000
 KH4  H2   N3   C4   125.91  3.000
 KH4  C2   N3   C4   108.10  3.000
 KH4  H3   C2   N4   126.33  3.000
 KH4  H3   C2   N3   122.30  3.000
 KH4  N4   C2   N3   111.37  3.000
 KH4  C5   N4   C2   105.33  3.000
 KH4  C22  C5   N4   122.79  3.000
 KH4  C22  C5   C4   126.78  3.000
 KH4  N4   C5   C4   110.42  3.000
 KH4  S1   C22  O6   123.12  3.000
 KH4  S1   C22  C5   112.90  3.000
 KH4  O6   C22  C5   123.99  3.000
 KH4  C11  S1   C22  100.06  3.000
 KH4  H6   C11  H5   108.68  3.000
 KH4  H6   C11  C12  110.53  3.000
 KH4  H5   C11  C12  110.74  3.000
 KH4  H6   C11  S1   109.69  3.000
 KH4  H5   C11  S1   109.25  3.000
 KH4  C12  C11  S1   107.93  3.000
 KH4  H8   C12  H7   107.29  3.000
 KH4  H8   C12  N1   110.73  3.000
 KH4  H7   C12  N1   109.21  3.000
 KH4  H8   C12  C11  110.10  3.000
 KH4  H7   C12  C11  110.15  3.000
 KH4  N1   C12  C11  109.34  3.000
 KH4  H9   N1   C12  118.29  3.000
 KH4  H9   N1   C13  118.75  3.000
 KH4  C12  N1   C13  122.76  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
 KH4  CONST_01  N4   C2   N3   C4      0.00   0.0  0
 KH4  CONST_02  C2   N4   C5   C4      0.00   0.0  0
 KH4  CONST_03  C5   N4   C2   N3      0.00   0.0  0
 KH4  CONST_04  N4   C5   C4   N3      0.00   0.0  0
 KH4  CONST_05  C5   C4   N3   C2      0.00   0.0  0
 KH4  CONST_06  C22  C5   C4   N3    180.00   0.0  0
 KH4  CONST_07  C22  C5   N4   C2    180.00   0.0  0
 KH4  CONST_08  H3   C2   N3   C4    180.00   0.0  0
 KH4  CONST_09  H1   C4   N3   C2    180.00   0.0  0
 KH4  CONST_10  H2   N3   C2   N4    180.00   0.0  0
 KH4  CONST_11  C15  N2   C16  O3      0.00   0.0  0
 KH4  CONST_12  C15  N2   C16  C17   180.00   0.0  0
 KH4  CONST_13  C12  N1   C13  C14   180.00   0.0  0
 KH4  CONST_14  C12  N1   C13  O2      0.00   0.0  0
 KH4  CONST_15  H14  N2   C16  O3    180.00   0.0  0
 KH4  CONST_16  H9   N1   C13  C14     0.00   0.0  0
 KH4  Var_01    O6   C22  C5   C4     -0.39  30.0  2
 KH4  Var_02    C14  C15  N2   C16  -174.46  30.0  2
 KH4  Var_03    O2P  C19  C18  C17   175.43  30.0  3
 KH4  Var_04    O3P  P    O2P  C19   -71.38  30.0  3
 KH4  Var_05    C13  C14  C15  N2   -179.28  30.0  3
 KH4  Var_06    O2   C13  C14  C15    36.90  30.0  2
 KH4  Var_07    C11  C12  N1   C13   163.55  30.0  2
 KH4  Var_08    C12  C11  S1   C22  -177.56  30.0  3
 KH4  Var_09    N1   C12  C11  S1    179.89  30.0  3
 KH4  Var_10    H19  C20  C18  C17    62.99  30.0  3
 KH4  Var_11    H22  C21  C18  C17    52.69  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
 KH4  chir_01  C17  C16  O4  C18  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
 KH4  plan-1  C4   0.020
 KH4  plan-1  N3   0.020
 KH4  plan-1  C2   0.020
 KH4  plan-1  N4   0.020
 KH4  plan-1  C5   0.020
 KH4  plan-1  C22  0.020
 KH4  plan-1  H2   0.020
 KH4  plan-1  H3   0.020
 KH4  plan-1  H1   0.020
 KH4  plan-2  C16  0.020
 KH4  plan-2  O3   0.020
 KH4  plan-2  C17  0.020
 KH4  plan-2  N2   0.020
 KH4  plan-2  C15  0.020
 KH4  plan-2  H14  0.020
 KH4  plan-3  C14  0.020
 KH4  plan-3  C13  0.020
 KH4  plan-3  O2   0.020
 KH4  plan-3  C12  0.020
 KH4  plan-3  N1   0.020
 KH4  plan-3  H9   0.020
 KH4  plan-4  C5   0.020
 KH4  plan-4  O6   0.020
 KH4  plan-4  C22  0.020
 KH4  plan-4  S1   0.020

