# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 06:19:02 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-{[2-(2-{[2-nitro-4-(triazan-1-yl)phenyl]amino}ethoxy)ethyl]amino}cyclohexane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NNNc1ccc(NCCOCCN[C@H]2C[C@](O)(CO)[C@@H](O)[C@H](O)[C@H]2O)c(c1)[N+]([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
 WAV  WAV  "(1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-{[2-(2-{[2-nitro-4-(triazan-1-yl)phenyl]amino}ethoxy)ethyl]amino}cyclohexane-1,2,3,4-tetrol"
  ligand  61  31  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WAV
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
 WAV  N1   N  NH1    0  -0.653  -13.0132  21.0170  13.6249
 WAV  N3   N  N      1   0.325  -15.1279  26.6174  13.6331
 WAV  C4   C  CH1    0   0.002  -14.9780  19.6289  11.7481
 WAV  C5   C  CH1    0   0.013  -15.1847  19.9250  13.2299
 WAV  C6   C  CH1    0  -0.126  -14.4657  21.2030  13.6754
 WAV  C7   C  CH2    0  -0.164  -15.0576  23.2981  10.4548
 WAV  C8   C  CH2    0  -0.308  -12.2408  21.9061  14.4877
 WAV  C10  C  CH2    0  -0.180  -10.9667  25.2665  14.3270
 WAV  C13  C  CR16   0  -0.323  -12.0251  28.1384  12.2433
 WAV  C15  C  CR6    0   0.333  -13.6892  27.9510  10.4993
 WAV  C17  C  CR6    0   0.203  -14.1161  27.1528  12.7344
 WAV  C1   C  CH2    0  -0.485  -14.9292  22.3522  12.7833
 WAV  C11  C  CH2    0  -0.356  -12.2039  25.9268  14.9383
 WAV  C12  C  CR6    0   0.289  -12.8457  27.5210  13.1947
 WAV  C14  C  CR16   0  -0.304  -12.4297  28.3669  10.9466
 WAV  C16  C  CR16   0  -0.352  -14.5223  27.3224  11.4127
 WAV  C2   C  CT     0   0.152  -14.6389  22.0941  11.2990
 WAV  C3   C  CH1    0   0.075  -15.3951  20.8202  10.8880
 WAV  C9   C  CH2    0  -0.158  -11.6636  23.0926  13.7283
 WAV  N2   N  NH1    0  -0.651  -12.3839  27.3027  14.4924
 WAV  N5   N  NH1    0  -0.356  -15.1670  27.5342   8.7037
 WAV  N6   N  NH2    0  -0.672  -14.8173  26.2638   8.2037
 WAV  O1   O  OH1    0  -0.672  -16.4517  23.4810  10.5351
 WAV  O2   O  OH1    0  -0.709  -13.2536  21.9490  11.0650
 WAV  O3   O  OH1    0  -0.676  -15.1590  20.5667   9.5257
 WAV  O4   O  OH1    0  -0.676  -15.7720  18.5356  11.3340
 WAV  O5   O  OH1    0  -0.667  -14.7537  18.7870  13.9453
 WAV  O6   O  O2     0  -0.489  -10.9177  23.8907  14.6218
 WAV  O7   O  O      0  -0.371  -15.1734  27.0390  14.7640
 WAV  O8   O  O     -1  -0.378  -15.9079  25.8033  13.1905
 WAV  H1   H  HNH1   0   0.369  -12.8119  20.0594  13.8822
 WAV  H3   H  HCH1   0   0.209  -13.9160  19.4114  11.5652
 WAV  H4   H  HCH1   0   0.225  -16.2592  20.0979  13.3890
 WAV  H5   H  HCH1   0   0.237  -14.7864  21.4165  14.7074
 WAV  H6   H  HCH2   0   0.202  -14.7304  23.1447   9.4187
 WAV  H7   H  HCH2   0   0.205  -14.5150  24.1742  10.8333
 WAV  H8   H  HCH2   0   0.244  -11.4159  21.3358  14.9198
 WAV  H9   H  HCH2   0   0.214  -12.8448  22.2732  15.3277
 WAV  H10  H  HCH2   0   0.210  -10.9464  25.4424  13.2433
 WAV  H11  H  HCH2   0   0.233  -10.0644  25.7250  14.7407
 WAV  H12  H  HCR6   0   0.272  -11.0256  28.4327  12.5404
 WAV  H13  H  HCH2   0   0.257  -14.4645  23.2906  13.0940
 WAV  H14  H  HCH2   0   0.249  -16.0030  22.4891  12.9296
 WAV  H15  H  HCH2   0   0.249  -12.1261  25.9223  16.0271
 WAV  H16  H  HCH2   0   0.242  -13.0896  25.3381  14.6948
 WAV  H17  H  HCR6   0   0.272  -11.7495  28.8566  10.2597
 WAV  H18  H  HCR6   0   0.288  -15.5057  26.9996  11.1047
 WAV  H19  H  HCH1   0   0.199  -16.4677  20.9916  11.0687
 WAV  H20  H  HCH2   0   0.207  -12.4702  23.6703  13.2663
 WAV  H21  H  HCH2   0   0.210  -11.0237  22.7345  12.9115
 WAV  H22  H  HNH1   0   0.374  -11.5472  27.8438  14.6672
 WAV  H23  H  HNH1   0   0.367  -13.3003  28.3246   8.5549
 WAV  H24  H  HNH1   0   0.372  -15.5898  28.1162   7.9917
 WAV  H25  H  HNH2   0   0.366  -15.6349  25.6727   8.2662
 WAV  H26  H  HNH2   0   0.348  -14.5564  26.3141   7.2236
 WAV  H27  H  HOH1   0   0.457  -16.6596  24.3709  10.2393
 WAV  H28  H  HOH1   0   0.454  -12.8809  21.5131  11.8608
 WAV  H29  H  HOH1   0   0.444  -15.6010  19.7420   9.2996
 WAV  H30  H  HOH1   0   0.451  -15.4177  17.7337  11.7302
 WAV  H31  H  HOH1   0   0.456  -15.0719  18.8535  14.8515
 WAV  N4   N  NH1    0  -0.549  -14.0786  28.2288   9.1989

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
 WAV  N6   N5   single    1.409  0.020  1.409
 WAV  O1   C7   single    1.408  0.020  1.408
 WAV  N4   N5   single    1.383  0.020  1.383
 WAV  N4   C15  single    1.386  0.020  1.386
 WAV  C7   C2   single    1.529  0.020  1.529
 WAV  C14  C15  aromatic  1.400  0.020  1.400
 WAV  C14  C13  aromatic  1.377  0.020  1.377
 WAV  C15  C16  aromatic  1.387  0.020  1.387
 WAV  C13  C12  aromatic  1.400  0.020  1.400
 WAV  O3   C3   single    1.406  0.020  1.406
 WAV  C2   O2   single    1.412  0.020  1.412
 WAV  C2   C3   single    1.537  0.020  1.537
 WAV  C2   C1   single    1.534  0.020  1.534
 WAV  C3   C4   single    1.527  0.020  1.527
 WAV  C16  C17  aromatic  1.393  0.020  1.393
 WAV  C12  C17  aromatic  1.400  0.020  1.400
 WAV  C12  N2   single    1.395  0.020  1.395
 WAV  C1   C6   single    1.527  0.020  1.527
 WAV  C17  N3   single    1.455  0.020  1.455
 WAV  N2   C11  single    1.457  0.020  1.457
 WAV  C4   O4   single    1.413  0.020  1.413
 WAV  C4   C5   single    1.525  0.020  1.525
 WAV  C9   O6   single    1.411  0.020  1.411
 WAV  C9   C8   single    1.522  0.020  1.522
 WAV  C10  C11  single    1.530  0.020  1.530
 WAV  C10  O6   single    1.408  0.020  1.408
 WAV  C6   C5   single    1.533  0.020  1.533
 WAV  C6   N1   single    1.465  0.020  1.465
 WAV  C5   O5   single    1.412  0.020  1.412
 WAV  N1   C8   single    1.460  0.020  1.460
 WAV  N3   O8   single    1.211  0.020  1.211
 WAV  N3   O7   double    1.208  0.020  1.208
 WAV  N1   H1   single    0.890  0.020  1.040
 WAV  C4   H3   single    0.970  0.020  1.090
 WAV  C5   H4   single    0.970  0.020  1.090
 WAV  C6   H5   single    0.970  0.020  1.090
 WAV  C7   H6   single    0.970  0.020  1.090
 WAV  C7   H7   single    0.970  0.020  1.090
 WAV  C8   H8   single    0.970  0.020  1.090
 WAV  C8   H9   single    0.970  0.020  1.090
 WAV  C10  H10  single    0.970  0.020  1.090
 WAV  C10  H11  single    0.970  0.020  1.090
 WAV  C13  H12  single    0.930  0.020  1.080
 WAV  C1   H13  single    0.970  0.020  1.090
 WAV  C1   H14  single    0.970  0.020  1.090
 WAV  C11  H15  single    0.970  0.020  1.090
 WAV  C11  H16  single    0.970  0.020  1.090
 WAV  C14  H17  single    0.930  0.020  1.080
 WAV  C16  H18  single    0.930  0.020  1.080
 WAV  C3   H19  single    0.970  0.020  1.090
 WAV  C9   H20  single    0.970  0.020  1.090
 WAV  C9   H21  single    0.970  0.020  1.090
 WAV  N2   H22  single    0.890  0.020  1.040
 WAV  N4   H23  single    0.890  0.020  1.040
 WAV  N5   H24  single    0.890  0.020  1.040
 WAV  N6   H25  single    0.890  0.020  1.040
 WAV  N6   H26  single    0.890  0.020  1.040
 WAV  O1   H27  single    0.850  0.020  0.980
 WAV  O2   H28  single    0.850  0.020  0.980
 WAV  O3   H29  single    0.850  0.020  0.980
 WAV  O4   H30  single    0.850  0.020  0.980
 WAV  O5   H31  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
 WAV  H1   N1   C8   108.72  3.000
 WAV  H1   N1   C6   107.98  3.000
 WAV  C8   N1   C6   115.26  3.000
 WAV  O8   N3   O7   123.53  3.000
 WAV  O7   N3   C17  118.42  3.000
 WAV  O8   N3   C17  118.00  3.000
 WAV  H3   C4   O4   109.93  3.000
 WAV  H3   C4   C3   108.93  3.000
 WAV  O4   C4   C3   106.55  3.000
 WAV  H3   C4   C5   109.33  3.000
 WAV  O4   C4   C5   111.03  3.000
 WAV  C3   C4   C5   111.02  3.000
 WAV  H4   C5   O5   110.60  3.000
 WAV  H4   C5   C6   106.57  3.000
 WAV  O5   C5   C6   112.44  3.000
 WAV  H4   C5   C4   107.66  3.000
 WAV  O5   C5   C4   107.13  3.000
 WAV  C6   C5   C4   112.38  3.000
 WAV  H5   C6   C1   108.25  3.000
 WAV  H5   C6   C5   107.30  3.000
 WAV  C1   C6   C5   108.39  3.000
 WAV  H5   C6   N1   110.21  3.000
 WAV  C5   C6   N1   110.44  3.000
 WAV  C1   C6   N1   112.11  3.000
 WAV  H7   C7   H6   106.84  3.000
 WAV  H7   C7   O1   111.46  3.000
 WAV  H6   C7   O1   111.54  3.000
 WAV  H7   C7   C2   107.62  3.000
 WAV  H6   C7   C2   109.25  3.000
 WAV  O1   C7   C2   109.99  3.000
 WAV  H9   C8   H8   106.71  3.000
 WAV  H9   C8   C9   109.25  3.000
 WAV  H8   C8   C9   108.54  3.000
 WAV  H9   C8   N1   111.39  3.000
 WAV  H8   C8   N1   108.39  3.000
 WAV  C9   C8   N1   112.36  3.000
 WAV  H11  C10  H10  106.91  3.000
 WAV  H11  C10  O6   107.57  3.000
 WAV  H10  C10  O6   111.25  3.000
 WAV  H11  C10  C11  109.59  3.000
 WAV  H10  C10  C11  109.89  3.000
 WAV  O6   C10  C11  111.48  3.000
 WAV  H12  C13  C14  118.95  3.000
 WAV  H12  C13  C12  118.31  3.000
 WAV  C14  C13  C12  122.73  3.000
 WAV  N4   C15  C16  122.69  3.000
 WAV  C16  C15  C14  117.69  3.000
 WAV  N4   C15  C14  119.55  3.000
 WAV  C16  C17  C12  122.98  3.000
 WAV  C12  C17  N3   121.63  3.000
 WAV  C16  C17  N3   115.33  3.000
 WAV  H14  C1   H13  105.81  3.000
 WAV  H14  C1   C2   109.67  3.000
 WAV  H13  C1   C2   109.83  3.000
 WAV  H14  C1   C6   108.33  3.000
 WAV  H13  C1   C6   110.57  3.000
 WAV  C2   C1   C6   112.41  3.000
 WAV  H16  C11  H15  106.16  3.000
 WAV  H16  C11  N2   109.93  3.000
 WAV  H15  C11  N2   108.53  3.000
 WAV  H16  C11  C10  109.54  3.000
 WAV  H15  C11  C10  109.82  3.000
 WAV  N2   C11  C10  112.65  3.000
 WAV  N2   C12  C17  124.40  3.000
 WAV  N2   C12  C13  120.49  3.000
 WAV  C17  C12  C13  115.11  3.000
 WAV  H17  C14  C15  119.77  3.000
 WAV  H17  C14  C13  119.16  3.000
 WAV  C15  C14  C13  121.06  3.000
 WAV  H18  C16  C17  119.99  3.000
 WAV  H18  C16  C15  119.65  3.000
 WAV  C17  C16  C15  120.32  3.000
 WAV  O2   C2   C3   110.67  3.000
 WAV  C3   C2   C1   107.76  3.000
 WAV  O2   C2   C1   111.29  3.000
 WAV  C1   C2   C7   110.48  3.000
 WAV  C3   C2   C7   111.73  3.000
 WAV  O2   C2   C7   104.95  3.000
 WAV  H19  C3   O3   110.53  3.000
 WAV  H19  C3   C2   107.83  3.000
 WAV  O3   C3   C2   109.02  3.000
 WAV  H19  C3   C4   107.16  3.000
 WAV  C2   C3   C4   111.19  3.000
 WAV  O3   C3   C4   111.06  3.000
 WAV  H21  C9   H20  106.72  3.000
 WAV  H21  C9   O6   110.33  3.000
 WAV  H20  C9   O6   111.00  3.000
 WAV  H21  C9   C8   109.75  3.000
 WAV  H20  C9   C8   110.03  3.000
 WAV  O6   C9   C8   108.99  3.000
 WAV  H22  N2   C12  110.54  3.000
 WAV  H22  N2   C11  110.48  3.000
 WAV  C12  N2   C11  118.26  3.000
 WAV  H24  N5   N6   111.87  3.000
 WAV  H24  N5   N4   106.97  3.000
 WAV  N6   N5   N4   112.61  3.000
 WAV  H26  N6   H25  107.25  3.000
 WAV  H26  N6   N5   111.19  3.000
 WAV  H25  N6   N5   107.72  3.000
 WAV  H27  O1   C7   108.49  3.000
 WAV  H28  O2   C2   106.49  3.000
 WAV  H29  O3   C3   107.76  3.000
 WAV  H30  O4   C4   108.49  3.000
 WAV  H31  O5   C5   108.69  3.000
 WAV  C9   O6   C10  113.68  3.000
 WAV  H23  N4   N5   115.07  3.000
 WAV  H23  N4   C15  113.52  3.000
 WAV  N5   N4   C15  117.17  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
 WAV  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 WAV  CONST_02  C16  C17  C12  C13     0.00   0.0  0
 WAV  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 WAV  CONST_04  C12  C17  C16  C15     0.00   0.0  0
 WAV  CONST_05  C14  C15  C16  C17     0.00   0.0  0
 WAV  CONST_06  C14  C13  C12  C17     0.00   0.0  0
 WAV  CONST_07  C15  C16  C17  N3    180.00   0.0  0
 WAV  CONST_08  C13  C12  C17  N3    180.00   0.0  0
 WAV  CONST_09  N4   C15  C14  C13   180.00   0.0  0
 WAV  CONST_10  N4   C15  C16  C17   180.00   0.0  0
 WAV  CONST_11  N2   C12  C13  C14   180.00   0.0  0
 WAV  CONST_12  N2   C12  C17  C16   180.00   0.0  0
 WAV  CONST_13  H12  C13  C14  C15   180.00   0.0  0
 WAV  CONST_14  H12  C13  C12  C17   180.00   0.0  0
 WAV  CONST_15  H17  C14  C13  C12   180.00   0.0  0
 WAV  CONST_16  H18  C16  C17  C12   180.00   0.0  0
 WAV  CONST_17  H18  C16  C15  C14   180.00   0.0  0
 WAV  CONST_18  H17  C14  C15  C16   180.00   0.0  0
 WAV  CONST_27  H22  N2   C12  C13     0.00   0.0  0
 WAV  CONST_28  H22  N2   C12  C17   180.00   0.0  0
 WAV  Var_01    C9   C8   N1   C6    -99.06  30.0  3
 WAV  Var_02    C12  N2   C11  C10    74.38  30.0  2
 WAV  Var_03    H8   C8   N1   C6    141.00  30.0  3
 WAV  Var_04    H9   C8   N1   C6     23.90  30.0  3
 WAV  Var_05    H15  C11  N2   C12  -163.78  30.0  3
 WAV  Var_06    H16  C11  N2   C12   -48.07  30.0  3
 WAV  Var_07    O6   C9   C8   N1   -179.14  30.0  1
 WAV  Var_08    C10  O6   C9   C8   -146.51  30.0  3
 WAV  Var_09    C9   O6   C10  C11    84.78  30.0  3
 WAV  Var_10    O6   C10  C11  N2   -171.72  30.0  2
 WAV  Var_11    H20  C9   C8   N1     58.94  30.0  1
 WAV  Var_12    H21  C9   C8   N1    -58.21  30.0  1
 WAV  Var_13    H22  N2   C11  C10   -54.36  30.0  2
 WAV  Var_14    H20  C9   O6   C10   -25.17  30.0  2
 WAV  Var_15    H21  C9   O6   C10    92.92  30.0  2
 WAV  Var_16    H10  C10  O6   C9    -38.27  30.0  2
 WAV  Var_17    H11  C10  O6   C9   -155.05  30.0  2
 WAV  Var_18    H1   N1   C8   C9    139.59  30.0  1
 WAV  Var_19    H10  C10  C11  N2    -47.90  30.0  2
 WAV  Var_20    H11  C10  C11  N2     69.31  30.0  2
 WAV  Var_21    H25  N6   N5   N4    154.12  30.0  2
 WAV  Var_22    H26  N6   N5   N4    -88.64  30.0  2
 WAV  Var_23    H23  N4   N5   N6     53.84  30.0  2
 WAV  Var_24    H8   C8   C9   O6    -59.29  30.0  3
 WAV  Var_25    H9   C8   C9   O6     56.71  30.0  3
 WAV  Var_26    H15  C11  C10  O6     67.18  30.0  3
 WAV  Var_27    H16  C11  C10  O6    -49.05  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
 WAV  chir_01  C4  C3  O4  C5  positiv
 WAV  chir_02  C5  O5  C4  C6  positiv
 WAV  chir_03  C6  N1  C1  C5  negativ
 WAV  chir_04  C2  C7  C3  C1  positiv
 WAV  chir_05  C3  O3  C2  C4  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
 WAV  plan-1  N3   0.020
 WAV  plan-1  C13  0.020
 WAV  plan-1  C15  0.020
 WAV  plan-1  C17  0.020
 WAV  plan-1  C12  0.020
 WAV  plan-1  C14  0.020
 WAV  plan-1  C16  0.020
 WAV  plan-1  N2   0.020
 WAV  plan-1  H12  0.020
 WAV  plan-1  H17  0.020
 WAV  plan-1  H18  0.020
 WAV  plan-1  N4   0.020
 WAV  plan-2  N3   0.020
 WAV  plan-2  C17  0.020
 WAV  plan-2  O7   0.020
 WAV  plan-2  O8   0.020
 WAV  plan-3  C11  0.020
 WAV  plan-3  C12  0.020
 WAV  plan-3  N2   0.020
 WAV  plan-3  H22  0.020
 WAV  plan-4  C15  0.020
 WAV  plan-4  N5   0.020
 WAV  plan-4  H23  0.020
 WAV  plan-4  N4   0.020

