# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 23:59:56 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (~{E})-~{N}-oxidanyl-3-[4-[(~{E})-(1,3,5-trimethylpyrazol-4-yl)diazenyl]phenyl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(C)c(N=Nc2ccc(\C=C\C(=O)NO)cc2)c1C
#
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
 9RB  9RB  (~{E})-~{N}-oxidanyl-3-[4-[(~{E})-(1,3,5-trimethylpyrazol-4-yl)diazenyl]phenyl]prop-2-enamide  ligand  39  22  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9RB
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
 9RB  C1   C  CR5   0   0.463  -4.8110  -0.9159   0.0575
 9RB  C2   C  CR5   0   0.046  -3.8136   0.0559  -0.0060
 9RB  C3   C  CR6   0   0.167  -0.3292   0.2860  -0.0825
 9RB  C4   C  CR16  0  -0.226   0.1269  -1.0300  -0.1820
 9RB  C5   C  CR16  0  -0.212   1.4832  -1.2868  -0.2067
 9RB  C6   C  CR6   0   0.142   2.4259  -0.2542  -0.1303
 9RB  C7   C  C1    0  -0.280   3.8417  -0.5995  -0.1598
 9RB  C8   C  C1    0  -0.418   4.8746   0.2410  -0.0476
 9RB  C9   C  C     0   0.453   6.2634  -0.2647  -0.1097
 9RB  C10  C  CR16  0  -0.319   1.9574   1.0596  -0.0359
 9RB  C11  C  CR16  0  -0.279   0.6020   1.3235  -0.0158
 9RB  C12  C  CR5   0   0.179  -4.5022   1.3014  -0.0704
 9RB  C13  C  CH3   0  -0.743  -4.6926  -2.3915   0.1404
 9RB  C14  C  CH3   0  -0.741  -3.9527   2.6790  -0.1618
 9RB  O    O  O     0  -0.257   6.5596  -1.4377  -0.2511
 9RB  N3   N  NH1   0  -0.383   7.1803   0.7157   0.0722
 9RB  O1   O  OH1   0  -0.562   8.4953   0.4541  -0.1660
 9RB  N2   N  N     0  -0.328  -1.6783   0.6730  -0.0588
 9RB  N1   N  N     0  -0.295  -2.4874  -0.2745  -0.0100
 9RB  N4   N  N     0  -0.240  -5.7953   1.0873  -0.0424
 9RB  N    N  NR5   0  -0.413  -5.9644  -0.2455   0.0315
 9RB  C    C  CH3   0  -0.492  -7.3046  -0.7724   0.0983
 9RB  H1   H  HCR6  0   0.262  -0.5794  -1.8461  -0.2437
 9RB  H2   H  HCR6  0   0.259   1.8261  -2.3112  -0.2896
 9RB  H3   H  H     0   0.234   4.0616  -1.6552  -0.2876
 9RB  H4   H  H     0   0.260   4.7264   1.3069   0.0883
 9RB  H5   H  HCR6  0   0.253   2.6527   1.8874   0.0170
 9RB  H6   H  HCR6  0   0.272   0.2430   2.3424   0.0532
 9RB  H7   H  HCH3  0   0.261  -5.1921  -2.7856   1.0262
 9RB  H8   H  HCH3  0   0.221  -5.1307  -2.8788  -0.7322
 9RB  H9   H  HCH3  0   0.248  -3.6433  -2.6720   0.1910
 9RB  H10  H  HCH3  0   0.279  -3.3263   2.7937  -1.0464
 9RB  H11  H  HCH3  0   0.215  -4.7626   3.4049  -0.2083
 9RB  H12  H  HCH3  0   0.259  -3.3222   2.9102   0.6965
 9RB  H13  H  HNH1  0   0.407   6.9351   1.6916  -0.0111
 9RB  H14  H  HOH1  0   0.483   8.8854   0.2425   0.6912
 9RB  H15  H  HCH3  0   0.283  -7.8937  -0.3898  -0.7323
 9RB  H16  H  HCH3  0   0.271  -7.2754  -1.8560   0.0367
 9RB  H17  H  HCH3  0   0.274  -7.7801  -0.4857   1.0349

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
 9RB  C    N    single    1.442  0.020  1.442
 9RB  N4   N    aromatic  1.346  0.020  1.346
 9RB  N4   C12  aromatic  1.311  0.020  1.311
 9RB  N    C1   aromatic  1.334  0.020  1.334
 9RB  C12  C14  single    1.486  0.020  1.486
 9RB  C12  C2   aromatic  1.425  0.020  1.425
 9RB  C1   C13  single    1.483  0.020  1.483
 9RB  C1   C2   aromatic  1.394  0.020  1.394
 9RB  C2   N1   single    1.367  0.020  1.367
 9RB  N1   N2   double    1.247  0.020  1.247
 9RB  N2   C3   single    1.404  0.020  1.404
 9RB  C3   C11  aromatic  1.396  0.020  1.396
 9RB  C3   C4   aromatic  1.396  0.020  1.396
 9RB  C11  C10  aromatic  1.381  0.020  1.381
 9RB  C4   C5   aromatic  1.381  0.020  1.381
 9RB  C10  C6   aromatic  1.398  0.020  1.398
 9RB  C5   C6   aromatic  1.400  0.020  1.400
 9RB  C6   C7   single    1.458  0.020  1.458
 9RB  C7   C8   double    1.336  0.020  1.336
 9RB  C8   C9   single    1.479  0.020  1.479
 9RB  C9   O    double    1.218  0.020  1.218
 9RB  C9   N3   single    1.355  0.020  1.355
 9RB  N3   O1   single    1.362  0.020  1.362
 9RB  C4   H1   single    0.930  0.020  1.080
 9RB  C5   H2   single    0.930  0.020  1.080
 9RB  C7   H3   single    0.930  0.020  1.080
 9RB  C8   H4   single    0.930  0.020  1.080
 9RB  C10  H5   single    0.930  0.020  1.080
 9RB  C11  H6   single    0.930  0.020  1.080
 9RB  C13  H7   single    0.970  0.020  1.090
 9RB  C13  H8   single    0.970  0.020  1.090
 9RB  C13  H9   single    0.970  0.020  1.090
 9RB  C14  H10  single    0.970  0.020  1.090
 9RB  C14  H11  single    0.970  0.020  1.090
 9RB  C14  H12  single    0.970  0.020  1.090
 9RB  N3   H13  single    0.890  0.020  1.040
 9RB  O1   H14  single    0.850  0.020  0.980
 9RB  C    H15  single    0.970  0.020  1.090
 9RB  C    H16  single    0.970  0.020  1.090
 9RB  C    H17  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
 9RB  N    C1   C13  124.76  3.000
 9RB  C13  C1   C2   129.73  3.000
 9RB  N    C1   C2   105.51  3.000
 9RB  N1   C2   C12  132.86  3.000
 9RB  N1   C2   C1   121.73  3.000
 9RB  C12  C2   C1   105.40  3.000
 9RB  N2   C3   C11  115.82  3.000
 9RB  C11  C3   C4   119.08  3.000
 9RB  N2   C3   C4   125.10  3.000
 9RB  H1   C4   C5   120.03  3.000
 9RB  H1   C4   C3   120.14  3.000
 9RB  C5   C4   C3   119.83  3.000
 9RB  H2   C5   C6   119.23  3.000
 9RB  H2   C5   C4   119.22  3.000
 9RB  C6   C5   C4   121.55  3.000
 9RB  C10  C6   C7   123.34  3.000
 9RB  C7   C6   C5   118.56  3.000
 9RB  C10  C6   C5   118.10  3.000
 9RB  H3   C7   C8   117.70  3.000
 9RB  H3   C7   C6   115.43  3.000
 9RB  C8   C7   C6   126.87  3.000
 9RB  H4   C8   C9   118.01  3.000
 9RB  H4   C8   C7   121.53  3.000
 9RB  C9   C8   C7   120.46  3.000
 9RB  N3   C9   O    123.23  3.000
 9RB  N3   C9   C8   112.48  3.000
 9RB  O    C9   C8   124.22  3.000
 9RB  H5   C10  C11  118.93  3.000
 9RB  H5   C10  C6   120.45  3.000
 9RB  C11  C10  C6   120.63  3.000
 9RB  H6   C11  C10  120.41  3.000
 9RB  H6   C11  C3   118.78  3.000
 9RB  C10  C11  C3   120.80  3.000
 9RB  N4   C12  C14  121.16  3.000
 9RB  C14  C12  C2   129.38  3.000
 9RB  N4   C12  C2   109.45  3.000
 9RB  H9   C13  H8   108.03  3.000
 9RB  H9   C13  H7   108.12  3.000
 9RB  H8   C13  H7   107.71  3.000
 9RB  H9   C13  C1   109.66  3.000
 9RB  H8   C13  C1   111.57  3.000
 9RB  H7   C13  C1   111.62  3.000
 9RB  H12  C14  H11  108.81  3.000
 9RB  H12  C14  H10  106.52  3.000
 9RB  H11  C14  H10  108.83  3.000
 9RB  H12  C14  C12  111.24  3.000
 9RB  H11  C14  C12  110.22  3.000
 9RB  H10  C14  C12  111.11  3.000
 9RB  H13  N3   O1   113.94  3.000
 9RB  H13  N3   C9   121.60  3.000
 9RB  O1   N3   C9   119.41  3.000
 9RB  H14  O1   N3   106.08  3.000
 9RB  N1   N2   C3   114.51  3.000
 9RB  N2   N1   C2   116.49  3.000
 9RB  N    N4   C12  106.67  3.000
 9RB  C    N    N4   118.78  3.000
 9RB  N4   N    C1   112.96  3.000
 9RB  C    N    C1   128.25  3.000
 9RB  H17  C    H16  108.86  3.000
 9RB  H17  C    H15  109.13  3.000
 9RB  H16  C    H15  108.80  3.000
 9RB  H17  C    N    110.46  3.000
 9RB  H16  C    N    109.70  3.000
 9RB  H15  C    N    109.85  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
 9RB  CONST_01  C12  N4   N    C1      0.00   0.0  0
 9RB  CONST_02  N4   C12  C2   C1      0.00   0.0  0
 9RB  CONST_03  N    N4   C12  C2      0.00   0.0  0
 9RB  CONST_04  N4   N    C1   C2      0.00   0.0  0
 9RB  CONST_05  C6   C10  C11  C3      0.00   0.0  0
 9RB  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 9RB  CONST_07  C10  C11  C3   C4      0.00   0.0  0
 9RB  CONST_08  C10  C6   C5   C4      0.00   0.0  0
 9RB  CONST_09  C11  C3   C4   C5      0.00   0.0  0
 9RB  CONST_10  C11  C10  C6   C5      0.00   0.0  0
 9RB  CONST_11  N    C1   C2   C12     0.00   0.0  0
 9RB  CONST_12  C14  C12  C2   C1    180.00   0.0  0
 9RB  CONST_13  C    N    C1   C2    180.00   0.0  0
 9RB  CONST_14  C7   C6   C5   C4    180.00   0.0  0
 9RB  CONST_15  N2   C3   C4   C5    180.00   0.0  0
 9RB  CONST_16  C11  C10  C6   C7    180.00   0.0  0
 9RB  CONST_17  N2   C3   C11  C10   180.00   0.0  0
 9RB  CONST_18  C    N    N4   C12   180.00   0.0  0
 9RB  CONST_19  C13  C1   C2   C12   180.00   0.0  0
 9RB  CONST_20  N4   N    C1   C13   180.00   0.0  0
 9RB  CONST_21  N    N4   C12  C14   180.00   0.0  0
 9RB  CONST_22  N4   C12  C2   N1    180.00   0.0  0
 9RB  CONST_23  N    C1   C2   N1    180.00   0.0  0
 9RB  CONST_24  H5   C10  C11  C3    180.00   0.0  0
 9RB  CONST_25  H2   C5   C4   C3    180.00   0.0  0
 9RB  CONST_26  H6   C11  C3   C4    180.00   0.0  0
 9RB  CONST_27  H1   C4   C5   C6    180.00   0.0  0
 9RB  CONST_28  N2   N1   C2   C1    180.00   0.0  0
 9RB  CONST_29  N1   N2   C3   C4      0.00   0.0  0
 9RB  CONST_30  N1   N2   C3   C11   180.00   0.0  0
 9RB  CONST_31  N2   N1   C2   C12     0.00   0.0  0
 9RB  CONST_32  O1   N3   C9   C8    180.00   0.0  0
 9RB  CONST_33  O1   N3   C9   O       0.00   0.0  0
 9RB  Var_01    C8   C7   C6   C5   -177.30  30.0  2
 9RB  Var_02    H15  C    N    C1   -127.48  30.0  2
 9RB  Var_03    H10  C14  C12  C2     58.43  30.0  2
 9RB  Var_04    H7   C13  C1   C2    122.21  30.0  2
 9RB  Var_05    C9   C8   C7   C6   -179.43   0.0  2
 9RB  Var_06    O    C9   C8   C7     -0.60  30.0  2

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
 9RB  plan-1  C1   0.020
 9RB  plan-1  C2   0.020
 9RB  plan-1  C3   0.020
 9RB  plan-1  C12  0.020
 9RB  plan-1  C13  0.020
 9RB  plan-1  C14  0.020
 9RB  plan-1  N2   0.020
 9RB  plan-1  N1   0.020
 9RB  plan-1  N4   0.020
 9RB  plan-1  N    0.020
 9RB  plan-1  C    0.020
 9RB  plan-2  C3   0.020
 9RB  plan-2  C4   0.020
 9RB  plan-2  C5   0.020
 9RB  plan-2  C6   0.020
 9RB  plan-2  C7   0.020
 9RB  plan-2  C10  0.020
 9RB  plan-2  C11  0.020
 9RB  plan-2  N2   0.020
 9RB  plan-2  N1   0.020
 9RB  plan-2  H1   0.020
 9RB  plan-2  H2   0.020
 9RB  plan-2  H5   0.020
 9RB  plan-2  H6   0.020
 9RB  plan-3  C8   0.020
 9RB  plan-3  C9   0.020
 9RB  plan-3  O    0.020
 9RB  plan-3  N3   0.020
 9RB  plan-3  O1   0.020
 9RB  plan-3  H13  0.020
 9RB  plan-4  C6   0.020
 9RB  plan-4  C7   0.020
 9RB  plan-4  C8   0.020
 9RB  plan-4  C9   0.020
 9RB  plan-4  H3   0.020
 9RB  plan-4  H4   0.020

