# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:56:38 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2E,4E,6S)-7-[4-(dimethylamino)phenyl]-4,6-dimethyl-N-oxidanyl-7-oxidanylidene-hepta-2,4-dienamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](\C=C(C)\C=C\C(=O)NO)C(=O)c1ccc(cc1)N(C)C
#
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
 E1Z  E1Z  (2E,4E,6S)-7-[4-(dimethylamino)phenyl]-4,6-dimethyl-N-oxidanyl-7-oxidanylidene-hepta-2,4-dienamide  ligand  44  22  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E1Z
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
 E1Z  O1    O  OH1   0  -0.542   8.2266   0.9493  -0.7941
 E1Z  O2    O  O     0  -0.479   6.3385  -0.9792  -0.6126
 E1Z  N1    N  NH1   0  -0.393   6.9858   1.1639  -0.2760
 E1Z  N2    N  NT    0  -0.496  -6.2659   0.8915  -0.1479
 E1Z  C1    C  CR6   0  -0.054  -2.2952  -0.4762  -0.2070
 E1Z  C2    C  CR16  0  -0.250  -3.1523  -0.6646  -1.2994
 E1Z  C3    C  CR16  0  -0.343  -4.4533  -0.2208  -1.2911
 E1Z  C4    C  CR6   0   0.406  -4.9871   0.4490  -0.1647
 E1Z  C5    C  CR16  0  -0.344  -4.1256   0.6353   0.9389
 E1Z  C6    C  CR16  0  -0.281  -2.8237   0.1860   0.9068
 E1Z  C7    C  C     0   0.398  -0.9125  -0.9720  -0.2812
 E1Z  C8    C  CH1   0  -0.499  -0.0075  -0.8106   0.9374
 E1Z  C9    C  C1    0  -0.192   1.4326  -0.8828   0.5421
 E1Z  C10   C  C     0   0.118   2.3264   0.1194   0.5190
 E1Z  C11   C  C1    0  -0.214   3.6918  -0.2188   0.1406
 E1Z  C12   C  C1    0  -0.437   4.7172   0.6384   0.0682
 E1Z  C13   C  C     0   0.534   6.0644   0.1739  -0.3197
 E1Z  C14   C  CH3   0  -0.647  -0.3276  -1.9251   1.9481
 E1Z  C15   C  CH3   0  -0.758   2.0239   1.5503   0.8454
 E1Z  C17   C  CH3   0  -0.541  -7.1219   0.6841  -1.2948
 E1Z  C16   C  CH3   0  -0.541  -6.7924   1.5536   1.0248
 E1Z  H1    H  HNH1  0   0.413   6.7159   2.1364  -0.2308
 E1Z  H171  H  HCH3  0   0.241  -7.2505  -0.3762  -1.5259
 E1Z  H172  H  HCH3  0   0.261  -8.1043   1.0981  -1.0887
 E1Z  H173  H  HCH3  0   0.241  -6.7346   1.1796  -2.1886
 E1Z  H161  H  HCH3  0   0.241  -6.7791   0.9037   1.9037
 E1Z  H162  H  HCH3  0   0.241  -6.2353   2.4615   1.2683
 E1Z  H163  H  HCH3  0   0.262  -7.8231   1.8412   0.8411
 E1Z  H2    H  HCR6  0   0.255  -2.7864  -1.1734  -2.1819
 E1Z  H6    H  HCR6  0   0.257  -2.2161   0.3641   1.7848
 E1Z  H3    H  HCR6  0   0.273  -5.0638  -0.3955  -2.1656
 E1Z  H5    H  HCR6  0   0.273  -4.4726   1.1367   1.8308
 E1Z  H8    H  HCH1  0   0.271  -0.2177   0.1465   1.4152
 E1Z  H9    H  H     0   0.251   1.7872  -1.8733   0.2709
 E1Z  H141  H  HCH3  0   0.251   0.2870  -1.8076   2.8402
 E1Z  H142  H  HCH3  0   0.245  -1.3727  -1.9019   2.2551
 E1Z  H143  H  HCH3  0   0.236  -0.1210  -2.9080   1.5225
 E1Z  H11   H  H     0   0.257   3.8779  -1.2626  -0.0945
 E1Z  H151  H  HCH3  0   0.247   2.6303   1.8985   1.6838
 E1Z  H152  H  HCH3  0   0.249   2.2538   2.1970  -0.0036
 E1Z  H153  H  HCH3  0   0.255   0.9811   1.7152   1.1031
 E1Z  H12   H  H     0   0.271   4.5877   1.6912   0.2931
 E1Z  HO1   H  HOH1  0   0.478   8.8038   0.7703  -0.0409
 E1Z  O3    O  O     0  -0.415  -0.4918  -1.5285  -1.2799

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
 E1Z  O1   N1    single    1.362  0.020  1.362
 E1Z  O1   HO1   single    0.850  0.020  0.980
 E1Z  O2   C13   double    1.221  0.020  1.221
 E1Z  O3   C7    double    1.218  0.020  1.218
 E1Z  N1   C13   single    1.353  0.020  1.353
 E1Z  N2   C4    single    1.353  0.020  1.353
 E1Z  N2   C17   single    1.446  0.020  1.446
 E1Z  N2   C16   single    1.446  0.020  1.446
 E1Z  C1   C2    aromatic  1.401  0.020  1.401
 E1Z  C1   C6    aromatic  1.399  0.020  1.399
 E1Z  C1   C7    single    1.471  0.020  1.471
 E1Z  C2   C3    aromatic  1.375  0.020  1.375
 E1Z  C3   C4    aromatic  1.415  0.020  1.415
 E1Z  C4   C5    aromatic  1.412  0.020  1.412
 E1Z  C5   C6    aromatic  1.378  0.020  1.378
 E1Z  C7   C8    single    1.526  0.020  1.526
 E1Z  C8   C9    single    1.495  0.020  1.495
 E1Z  C8   C14   single    1.538  0.020  1.538
 E1Z  C9   C10   double    1.343  0.020  1.343
 E1Z  C10  C11   single    1.457  0.020  1.457
 E1Z  C10  C15   single    1.499  0.020  1.499
 E1Z  C11  C12   double    1.338  0.020  1.338
 E1Z  C12  C13   single    1.477  0.020  1.477
 E1Z  N1   H1    single    0.890  0.020  1.040
 E1Z  C17  H171  single    0.970  0.020  1.090
 E1Z  C17  H172  single    0.970  0.020  1.090
 E1Z  C17  H173  single    0.970  0.020  1.090
 E1Z  C16  H161  single    0.970  0.020  1.090
 E1Z  C16  H162  single    0.970  0.020  1.090
 E1Z  C16  H163  single    0.970  0.020  1.090
 E1Z  C2   H2    single    0.930  0.020  1.080
 E1Z  C6   H6    single    0.930  0.020  1.080
 E1Z  C3   H3    single    0.930  0.020  1.080
 E1Z  C5   H5    single    0.930  0.020  1.080
 E1Z  C8   H8    single    0.970  0.020  1.090
 E1Z  C9   H9    single    0.930  0.020  1.080
 E1Z  C14  H141  single    0.970  0.020  1.090
 E1Z  C14  H142  single    0.970  0.020  1.090
 E1Z  C14  H143  single    0.970  0.020  1.090
 E1Z  C11  H11   single    0.930  0.020  1.080
 E1Z  C15  H151  single    0.970  0.020  1.090
 E1Z  C15  H152  single    0.970  0.020  1.090
 E1Z  C15  H153  single    0.970  0.020  1.090
 E1Z  C12  H12   single    0.930  0.020  1.080

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
 E1Z  HO1   O1   N1    106.09  3.000
 E1Z  H1    N1   C13   121.59  3.000
 E1Z  H1    N1   O1    114.34  3.000
 E1Z  C13   N1   O1    119.53  3.000
 E1Z  C16   N2   C17   119.56  3.000
 E1Z  C16   N2   C4    120.26  3.000
 E1Z  C17   N2   C4    120.17  3.000
 E1Z  C7    C1   C6    123.69  3.000
 E1Z  C7    C1   C2    119.36  3.000
 E1Z  C6    C1   C2    116.95  3.000
 E1Z  H2    C2   C3    118.47  3.000
 E1Z  H2    C2   C1    119.47  3.000
 E1Z  C3    C2   C1    122.05  3.000
 E1Z  H3    C3   C4    120.50  3.000
 E1Z  H3    C3   C2    118.52  3.000
 E1Z  C4    C3   C2    120.98  3.000
 E1Z  C5    C4   C3    117.02  3.000
 E1Z  C5    C4   N2    121.57  3.000
 E1Z  C3    C4   N2    121.41  3.000
 E1Z  H5    C5   C6    118.30  3.000
 E1Z  H5    C5   C4    120.69  3.000
 E1Z  C6    C5   C4    121.01  3.000
 E1Z  H6    C6   C5    117.25  3.000
 E1Z  H6    C6   C1    120.76  3.000
 E1Z  C5    C6   C1    121.99  3.000
 E1Z  C8    C7   C1    118.78  3.000
 E1Z  C8    C7   O3    119.87  3.000
 E1Z  C1    C7   O3    121.33  3.000
 E1Z  H8    C8   C14   107.95  3.000
 E1Z  H8    C8   C9    110.11  3.000
 E1Z  C14   C8   C9    109.82  3.000
 E1Z  H8    C8   C7    109.17  3.000
 E1Z  C14   C8   C7    108.94  3.000
 E1Z  C9    C8   C7    110.78  3.000
 E1Z  H9    C9   C10   117.32  3.000
 E1Z  H9    C9   C8    115.11  3.000
 E1Z  C10   C9   C8    127.55  3.000
 E1Z  C15   C10  C11   117.87  3.000
 E1Z  C15   C10  C9    125.06  3.000
 E1Z  C11   C10  C9    117.06  3.000
 E1Z  H11   C11  C12   118.20  3.000
 E1Z  H11   C11  C10   116.10  3.000
 E1Z  C12   C11  C10   125.69  3.000
 E1Z  H12   C12  C13   117.96  3.000
 E1Z  H12   C12  C11   121.27  3.000
 E1Z  C13   C12  C11   120.77  3.000
 E1Z  C12   C13  N1    112.49  3.000
 E1Z  C12   C13  O2    124.39  3.000
 E1Z  N1    C13  O2    123.09  3.000
 E1Z  H143  C14  H142  108.11  3.000
 E1Z  H143  C14  H141  108.05  3.000
 E1Z  H142  C14  H141  107.94  3.000
 E1Z  H143  C14  C8    110.92  3.000
 E1Z  H142  C14  C8    111.67  3.000
 E1Z  H141  C14  C8    110.02  3.000
 E1Z  H153  C15  H152  107.25  3.000
 E1Z  H153  C15  H151  107.61  3.000
 E1Z  H152  C15  H151  106.94  3.000
 E1Z  H153  C15  C10   112.97  3.000
 E1Z  H152  C15  C10   110.71  3.000
 E1Z  H151  C15  C10   111.08  3.000
 E1Z  H173  C17  H172  107.64  3.000
 E1Z  H173  C17  H171  107.98  3.000
 E1Z  H172  C17  H171  107.68  3.000
 E1Z  H173  C17  N2    111.95  3.000
 E1Z  H172  C17  N2    109.29  3.000
 E1Z  H171  C17  N2    112.11  3.000
 E1Z  H163  C16  H162  107.56  3.000
 E1Z  H163  C16  H161  107.76  3.000
 E1Z  H162  C16  H161  107.97  3.000
 E1Z  H163  C16  N2    109.26  3.000
 E1Z  H162  C16  N2    112.06  3.000
 E1Z  H161  C16  N2    112.05  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
 E1Z  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 E1Z  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 E1Z  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 E1Z  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 E1Z  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 E1Z  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 E1Z  CONST_07  C2    C3   C4   N2    180.00   0.0  0
 E1Z  CONST_08  C6    C5   C4   N2    180.00   0.0  0
 E1Z  CONST_09  C7    C1   C2   C3    180.00   0.0  0
 E1Z  CONST_10  C7    C1   C6   C5    180.00   0.0  0
 E1Z  CONST_11  H3    C3   C2   C1    180.00   0.0  0
 E1Z  CONST_12  H5    C5   C6   C1    180.00   0.0  0
 E1Z  CONST_13  H6    C6   C1   C2    180.00   0.0  0
 E1Z  CONST_14  H2    C2   C3   C4    180.00   0.0  0
 E1Z  CONST_15  C17   N2   C4   C3      0.00   0.0  0
 E1Z  CONST_16  C16   N2   C4   C3    180.00   0.0  0
 E1Z  CONST_17  C17   N2   C4   C5    180.00   0.0  0
 E1Z  CONST_18  C16   N2   C4   C5      0.00   0.0  0
 E1Z  CONST_19  O2    C13  N1   O1      0.00   0.0  0
 E1Z  CONST_20  C12   C13  N1   O1    180.00   0.0  0
 E1Z  CONST_21  H1    N1   C13  O2    180.00   0.0  0
 E1Z  Var_01    C2    C1   C7   O3      0.93  30.0  2
 E1Z  Var_02    H171  C17  N2   C4     60.21  30.0  3
 E1Z  Var_03    H161  C16  N2   C4    -61.25  30.0  3
 E1Z  Var_04    C11   C10  C9   C8    177.75   0.0  2
 E1Z  Var_05    C13   C12  C11  C10   179.55   0.0  2
 E1Z  Var_06    C11   C12  C13  O2      1.05  30.0  1
 E1Z  Var_07    C12   C11  C10  C9   -179.61  30.0  2
 E1Z  Var_08    H151  C15  C10  C9    120.52  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
 E1Z  chir_01  C8  C7  C9  C14  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
 E1Z  plan-1  N2   0.020
 E1Z  plan-1  C1   0.020
 E1Z  plan-1  C2   0.020
 E1Z  plan-1  C3   0.020
 E1Z  plan-1  C4   0.020
 E1Z  plan-1  C5   0.020
 E1Z  plan-1  C6   0.020
 E1Z  plan-1  C7   0.020
 E1Z  plan-1  H2   0.020
 E1Z  plan-1  H6   0.020
 E1Z  plan-1  H3   0.020
 E1Z  plan-1  H5   0.020
 E1Z  plan-2  O1   0.020
 E1Z  plan-2  O2   0.020
 E1Z  plan-2  N1   0.020
 E1Z  plan-2  C12  0.020
 E1Z  plan-2  C13  0.020
 E1Z  plan-2  H1   0.020
 E1Z  plan-3  N2   0.020
 E1Z  plan-3  C4   0.020
 E1Z  plan-3  C17  0.020
 E1Z  plan-3  C16  0.020
 E1Z  plan-4  C1   0.020
 E1Z  plan-4  C7   0.020
 E1Z  plan-4  C8   0.020
 E1Z  plan-4  O3   0.020
 E1Z  plan-5  C8   0.020
 E1Z  plan-5  C9   0.020
 E1Z  plan-5  C10  0.020
 E1Z  plan-5  C11  0.020
 E1Z  plan-5  C15  0.020
 E1Z  plan-5  H9   0.020
 E1Z  plan-6  C10  0.020
 E1Z  plan-6  C11  0.020
 E1Z  plan-6  C12  0.020
 E1Z  plan-6  C13  0.020
 E1Z  plan-6  H11  0.020
 E1Z  plan-6  H12  0.020

