# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 06:34:53 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: ~{N}-[(1~{R},2~{R},3~{R},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC(=O)N[C@H]1[C@H](O)[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO
#
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
 K35  K35  ~{N}-[(1~{R},2~{R},3~{R},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]pentanamide  ligand  42  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_K35
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
 K35  N1   N  NH1   0  -0.657   0.6736   0.4286  -0.1408
 K35  C6   C  CH1   0  -0.150  -0.5061   0.2472  -0.9628
 K35  C7   C  CH1   0   0.034  -0.8429  -1.2431  -1.0939
 K35  C8   C  CH1   0   0.007  -1.3638  -1.7910   0.2293
 K35  O2   O  OH1   0  -0.677  -1.6792  -3.1489   0.0346
 K35  C11  C  CH1   0  -0.307  -1.6916   1.0655  -0.4332
 K35  C12  C  CH2   0  -0.126  -1.3180   2.5446  -0.3544
 K35  O5   O  OH1   0  -0.667  -2.4676   3.3395  -0.5330
 K35  C10  C  CH1   0   0.052  -2.2010   0.4831   0.8839
 K35  O4   O  OH1   0  -0.663  -3.3052   1.2340   1.3222
 K35  C9   C  CH1   0  -0.006  -2.5691  -0.9911   0.7108
 K35  O3   O  OH1   0  -0.684  -2.9965  -1.5396   1.9462
 K35  O1   O  OH1   0  -0.671  -1.7940  -1.3687  -2.1243
 K35  H1   H  HNH1  0   0.401   0.5643   0.5223   0.8564
 K35  H4   H  HCH1  0   0.280  -0.2628   0.6179  -1.9611
 K35  H5   H  HCH1  0   0.236   0.0814  -1.7786  -1.3545
 K35  H6   H  HCH1  0   0.208  -0.5601  -1.6866   0.9751
 K35  H7   H  HOH1  0   0.451  -2.1175  -3.4701   0.8305
 K35  H8   H  HCH1  0   0.259  -2.4856   0.9670  -1.1816
 K35  H9   H  HCH2  0   0.192  -0.8282   2.7589   0.6048
 K35  H10  H  HCH2  0   0.204  -0.5756   2.7575  -1.1364
 K35  H11  H  HOH1  0   0.451  -2.1941   4.2603  -0.4938
 K35  H12  H  HCH1  0   0.193  -1.3950   0.5434   1.6367
 K35  H13  H  HOH1  0   0.444  -3.5680   0.8914   2.1830
 K35  H14  H  HCH1  0   0.226  -3.3710  -1.0653  -0.0350
 K35  H15  H  HOH1  0   0.463  -3.9511  -1.6434   1.9299
 K35  H16  H  HOH1  0   0.452  -2.1257  -2.2732  -2.1203
 K35  C1   C  C     0   0.576   1.9322   0.3978  -0.6284
 K35  C2   C  CH2   0  -0.588   3.0164   0.5832   0.4122
 K35  C3   C  CH2   0  -0.406   4.3688   0.0325  -0.0162
 K35  C4   C  CH2   0  -0.422   5.4221   0.1811   1.0747
 K35  C5   C  CH3   0  -0.663   6.7824  -0.3529   0.6483
 K35  O6   O  O     0  -0.496   2.1746   0.2488  -1.8165
 K35  H2   H  HCH2  0   0.271   3.1004   1.6554   0.6209
 K35  H3   H  HCH2  0   0.251   2.7037   0.1210   1.3529
 K35  H17  H  HCH2  0   0.220   4.2694  -1.0248  -0.2788
 K35  H18  H  HCH2  0   0.222   4.7073   0.5435  -0.9208
 K35  H19  H  HCH2  0   0.214   5.5138   1.2358   1.3515
 K35  H20  H  HCH2  0   0.214   5.0879  -0.3406   1.9767
 K35  H21  H  HCH3  0   0.217   6.7286  -1.4124   0.3910
 K35  H22  H  HCH3  0   0.217   7.1554   0.1796  -0.2284
 K35  H23  H  HCH3  0   0.228   7.5221  -0.2425   1.4416

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
 K35  O5   C12  single  1.409  0.020  1.409
 K35  C12  C11  single  1.528  0.020  1.528
 K35  O4   C10  single  1.405  0.020  1.405
 K35  C11  C10  single  1.528  0.020  1.528
 K35  C11  C6   single  1.535  0.020  1.535
 K35  C10  C9   single  1.529  0.020  1.529
 K35  C6   N1   single  1.449  0.020  1.449
 K35  C6   C7   single  1.533  0.020  1.533
 K35  C9   O3   single  1.418  0.020  1.418
 K35  C9   C8   single  1.524  0.020  1.524
 K35  C7   C8   single  1.524  0.020  1.524
 K35  C8   O2   single  1.408  0.020  1.408
 K35  C7   O1   single  1.408  0.020  1.408
 K35  N1   H1   single  0.860  0.020  1.020
 K35  C6   H4   single  0.970  0.020  1.090
 K35  C7   H5   single  0.970  0.020  1.090
 K35  C8   H6   single  0.970  0.020  1.090
 K35  O2   H7   single  0.850  0.020  0.980
 K35  C11  H8   single  0.970  0.020  1.090
 K35  C12  H9   single  0.970  0.020  1.090
 K35  C12  H10  single  0.970  0.020  1.090
 K35  O5   H11  single  0.850  0.020  0.980
 K35  C10  H12  single  0.970  0.020  1.090
 K35  O4   H13  single  0.850  0.020  0.980
 K35  C9   H14  single  0.970  0.020  1.090
 K35  O3   H15  single  0.850  0.020  0.980
 K35  O1   H16  single  0.850  0.020  0.980
 K35  N1   C1   single  1.350  0.020  1.350
 K35  C1   C2   single  1.514  0.020  1.514
 K35  C2   C3   single  1.522  0.020  1.522
 K35  C3   C4   single  1.524  0.020  1.524
 K35  C4   C5   single  1.522  0.020  1.522
 K35  C1   O6   double  1.222  0.020  1.222
 K35  C2   H2   single  0.970  0.020  1.090
 K35  C2   H3   single  0.970  0.020  1.090
 K35  C3   H17  single  0.970  0.020  1.090
 K35  C3   H18  single  0.970  0.020  1.090
 K35  C4   H19  single  0.970  0.020  1.090
 K35  C4   H20  single  0.970  0.020  1.090
 K35  C5   H21  single  0.970  0.020  1.090
 K35  C5   H22  single  0.970  0.020  1.090
 K35  C5   H23  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
 K35  C1   N1   H1   117.44  3.000
 K35  C1   N1   C6   123.45  3.000
 K35  H1   N1   C6   118.99  3.000
 K35  H4   C6   C11  107.84  3.000
 K35  H4   C6   C7   107.49  3.000
 K35  C11  C6   C7   112.21  3.000
 K35  H4   C6   N1   107.13  3.000
 K35  C7   C6   N1   110.42  3.000
 K35  C11  C6   N1   111.49  3.000
 K35  H5   C7   O1   110.55  3.000
 K35  H5   C7   C8   108.54  3.000
 K35  O1   C7   C8   111.87  3.000
 K35  H5   C7   C6   108.00  3.000
 K35  O1   C7   C6   107.32  3.000
 K35  C8   C7   C6   110.50  3.000
 K35  H6   C8   C9   108.26  3.000
 K35  H6   C8   O2   110.40  3.000
 K35  C9   C8   O2   111.88  3.000
 K35  H6   C8   C7   107.72  3.000
 K35  O2   C8   C7   107.65  3.000
 K35  C9   C8   C7   110.84  3.000
 K35  H7   O2   C8   108.01  3.000
 K35  H8   C11  C10  108.24  3.000
 K35  H8   C11  C12  107.44  3.000
 K35  C10  C11  C12  113.97  3.000
 K35  H8   C11  C6   106.03  3.000
 K35  C10  C11  C6   110.59  3.000
 K35  C12  C11  C6   110.19  3.000
 K35  H10  C12  H9   106.40  3.000
 K35  H10  C12  O5   110.59  3.000
 K35  H9   C12  O5   111.38  3.000
 K35  H10  C12  C11  108.43  3.000
 K35  H9   C12  C11  110.07  3.000
 K35  O5   C12  C11  109.89  3.000
 K35  H11  O5   C12  107.64  3.000
 K35  H12  C10  C9   107.78  3.000
 K35  H12  C10  O4   109.36  3.000
 K35  C9   C10  O4   111.18  3.000
 K35  H12  C10  C11  108.87  3.000
 K35  C9   C10  C11  110.50  3.000
 K35  O4   C10  C11  109.10  3.000
 K35  H13  O4   C10  107.64  3.000
 K35  H14  C9   O3   110.22  3.000
 K35  H14  C9   C10  108.53  3.000
 K35  O3   C9   C10  110.29  3.000
 K35  H14  C9   C8   109.13  3.000
 K35  O3   C9   C8   108.10  3.000
 K35  C10  C9   C8   110.56  3.000
 K35  H15  O3   C9   109.07  3.000
 K35  H16  O1   C7   108.26  3.000
 K35  O6   C1   C2   122.76  3.000
 K35  O6   C1   N1   122.62  3.000
 K35  C2   C1   N1   114.61  3.000
 K35  H3   C2   H2   105.76  3.000
 K35  H3   C2   C3   110.07  3.000
 K35  H2   C2   C3   109.86  3.000
 K35  H3   C2   C1   109.55  3.000
 K35  H2   C2   C1   107.80  3.000
 K35  C3   C2   C1   113.48  3.000
 K35  H18  C3   H17  106.35  3.000
 K35  H18  C3   C4   109.44  3.000
 K35  H17  C3   C4   109.20  3.000
 K35  H18  C3   C2   109.82  3.000
 K35  H17  C3   C2   109.67  3.000
 K35  C4   C3   C2   112.18  3.000
 K35  H20  C4   H19  106.06  3.000
 K35  H20  C4   C5   109.67  3.000
 K35  H19  C4   C5   109.51  3.000
 K35  H20  C4   C3   109.42  3.000
 K35  H19  C4   C3   109.46  3.000
 K35  C5   C4   C3   112.52  3.000
 K35  H23  C5   H22  107.65  3.000
 K35  H23  C5   H21  107.65  3.000
 K35  H22  C5   H21  107.52  3.000
 K35  H23  C5   C4   111.53  3.000
 K35  H22  C5   C4   111.05  3.000
 K35  H21  C5   C4   111.25  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
 K35  CONST_01  C2   C1  N1  C6   180.00   0.0  0
 K35  CONST_02  O6   C1  N1  C6     0.00   0.0  0
 K35  CONST_03  C2   C1  N1  H1     0.00   0.0  0
 K35  Var_01    C3   C2  C1  N1   157.88  30.0  3
 K35  Var_02    C4   C3  C2  C1  -177.56  30.0  3
 K35  Var_03    C5   C4  C3  C2  -179.34  30.0  3
 K35  Var_04    H21  C5  C4  C3   -59.55  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
 K35  chir_01  C6   C11  N1   C7  negativ
 K35  chir_02  C7   O1   C6   C8  negativ
 K35  chir_03  C8   O2   C7   C9  negativ
 K35  chir_04  C11  C12  C10  C6  positiv
 K35  chir_05  C10  O4   C11  C9  positiv
 K35  chir_06  C9   O3   C10  C8  negativ

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
 K35  plan-1  N1  0.020
 K35  plan-1  C6  0.020
 K35  plan-1  H1  0.020
 K35  plan-1  C1  0.020
 K35  plan-1  C2  0.020
 K35  plan-1  O6  0.020

