# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 17:31:19 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: N'-[(E)-(3,4-dimethoxyphenyl)methylidene]-2-(naphthalen-1-yl)acetohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(\C=N\NC(=O)Cc2cccc3ccccc23)cc1OC
#
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
 YUS  YUS  N'-[(E)-(3,4-dimethoxyphenyl)methylidene]-2-(naphthalen-1-yl)acetohydrazide  ligand  46  26  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YUS
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
 YUS  O1   O  O2    0  -0.454  161.7370  162.9606  170.2136
 YUS  C1   C  C1    0  -0.068  161.9735  166.8313  166.1828
 YUS  C2   C  CR6   0   0.058  161.9113  165.8161  167.2258
 YUS  N1   N  N     0  -0.201  162.3156  168.0255  166.4539
 YUS  C7   C  CR6   0   0.341  162.1002  165.1673  169.5481
 YUS  C6   C  CH3   0  -0.437  161.4356  161.6101  169.9280
 YUS  C5   C  CR6   0   0.310  161.7704  163.8349  169.1972
 YUS  C4   C  CR16  0  -0.371  161.5119  163.5270  167.8724
 YUS  C3   C  CR16  0  -0.320  161.5802  164.5141  166.8918
 YUS  C8   C  CH3   0  -0.436  162.6566  166.6945  171.2643
 YUS  C9   C  CR16  0  -0.433  162.1708  166.1338  168.5681
 YUS  C10  C  CH2   0  -0.612  162.9906  170.5700  167.1480
 YUS  C11  C  CR6   0   0.083  161.8179  170.5193  168.0981
 YUS  C12  C  CR66  0   0.092  162.0477  170.4018  169.5018
 YUS  C13  C  CR16  0  -0.332  163.3459  170.3198  170.0636
 YUS  C14  C  CR16  0  -0.243  163.5294  170.2118  171.4163
 YUS  N    N  NH1   0  -0.475  162.3422  168.9325  165.4645
 YUS  C    C  C     0   0.512  162.6486  170.2332  165.7149
 YUS  O    O  O     0  -0.455  162.6522  171.0547  164.8169
 YUS  C15  C  CR16  0  -0.260  162.4239  170.1799  172.2878
 YUS  C16  C  CR16  0  -0.306  161.1567  170.2627  171.7805
 YUS  C17  C  CR66  0   0.108  160.9354  170.3782  170.3882
 YUS  C18  C  CR16  0  -0.331  159.6242  170.4789  169.8684
 YUS  C19  C  CR16  0  -0.240  159.4286  170.6089  168.5241
 YUS  C20  C  CR16  0  -0.317  160.5287  170.6336  167.6440
 YUS  H1   H  H     0   0.248  161.7092  166.5163  165.1701
 YUS  H2   H  HCH3  0   0.260  161.4723  161.0796  170.8762
 YUS  H3   H  HCH3  0   0.230  160.4366  161.4961  169.4991
 YUS  H4   H  HCH3  0   0.229  162.1650  161.1650  169.2461
 YUS  H5   H  HCR6  0   0.284  161.2551  162.5180  167.5803
 YUS  H6   H  HCR6  0   0.256  161.3743  164.2510  165.8616
 YUS  H7   H  HCH3  0   0.258  162.7932  166.6575  172.3423
 YUS  H8   H  HCH3  0   0.226  163.5844  167.0428  170.8033
 YUS  H9   H  HCH3  0   0.229  161.8628  167.4114  171.0359
 YUS  H10  H  HCR6  0   0.284  162.4219  167.1552  168.8208
 YUS  H11  H  HCH2  0   0.273  163.7744  169.8880  167.4803
 YUS  H12  H  HCH2  0   0.289  163.4231  171.5731  167.1484
 YUS  H13  H  HCR6  0   0.253  164.2174  170.3510  169.4238
 YUS  H14  H  HCR6  0   0.258  164.5321  170.1535  171.8194
 YUS  H15  H  HNH1  0   0.397  162.0903  168.6711  164.5146
 YUS  H16  H  HCR6  0   0.257  162.5807  170.0935  173.3552
 YUS  H17  H  HCR6  0   0.255  160.2989  170.2439  172.4423
 YUS  H18  H  HCR6  0   0.254  158.7836  170.4574  170.5515
 YUS  H19  H  HCR6  0   0.256  158.4277  170.6934  168.1215
 YUS  H20  H  HCR6  0   0.252  160.3274  170.7436  166.5853
 YUS  O2   O  O2    0  -0.461  162.3234  165.3831  170.8556

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
 YUS  O    C    double    1.217  0.020  1.217
 YUS  N    C    single    1.360  0.020  1.360
 YUS  N    N1   single    1.342  0.020  1.342
 YUS  C    C10  single    1.511  0.020  1.511
 YUS  C1   N1   double    1.271  0.020  1.271
 YUS  C1   C2   single    1.457  0.020  1.457
 YUS  C3   C2   aromatic  1.384  0.020  1.384
 YUS  C3   C4   aromatic  1.393  0.020  1.393
 YUS  C10  C11  single    1.510  0.020  1.510
 YUS  C2   C9   aromatic  1.404  0.020  1.404
 YUS  C20  C11  aromatic  1.372  0.020  1.372
 YUS  C20  C19  aromatic  1.409  0.020  1.409
 YUS  C4   C5   aromatic  1.384  0.020  1.384
 YUS  C11  C12  aromatic  1.427  0.020  1.427
 YUS  C19  C18  aromatic  1.365  0.020  1.365
 YUS  C9   C7   aromatic  1.378  0.020  1.378
 YUS  C5   C7   aromatic  1.417  0.020  1.417
 YUS  C5   O1   single    1.341  0.020  1.341
 YUS  C12  C13  aromatic  1.417  0.020  1.417
 YUS  C12  C17  aromatic  1.422  0.020  1.422
 YUS  C7   O2   single    1.344  0.020  1.344
 YUS  C18  C17  aromatic  1.414  0.020  1.414
 YUS  C6   O1   single    1.413  0.020  1.413
 YUS  C13  C14  aromatic  1.369  0.020  1.369
 YUS  C17  C16  aromatic  1.415  0.020  1.415
 YUS  O2   C8   single    1.413  0.020  1.413
 YUS  C14  C15  aromatic  1.408  0.020  1.408
 YUS  C16  C15  aromatic  1.367  0.020  1.367
 YUS  C1   H1   single    0.930  0.020  1.080
 YUS  C6   H2   single    0.970  0.020  1.090
 YUS  C6   H3   single    0.970  0.020  1.090
 YUS  C6   H4   single    0.970  0.020  1.090
 YUS  C4   H5   single    0.930  0.020  1.080
 YUS  C3   H6   single    0.930  0.020  1.080
 YUS  C8   H7   single    0.970  0.020  1.090
 YUS  C8   H8   single    0.970  0.020  1.090
 YUS  C8   H9   single    0.970  0.020  1.090
 YUS  C9   H10  single    0.930  0.020  1.080
 YUS  C10  H11  single    0.970  0.020  1.090
 YUS  C10  H12  single    0.970  0.020  1.090
 YUS  C13  H13  single    0.930  0.020  1.080
 YUS  C14  H14  single    0.930  0.020  1.080
 YUS  N    H15  single    0.860  0.020  1.020
 YUS  C15  H16  single    0.930  0.020  1.080
 YUS  C16  H17  single    0.930  0.020  1.080
 YUS  C18  H18  single    0.930  0.020  1.080
 YUS  C19  H19  single    0.930  0.020  1.080
 YUS  C20  H20  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
 YUS  C5   O1   C6   118.38  3.000
 YUS  H1   C1   N1   122.23  3.000
 YUS  H1   C1   C2   116.88  3.000
 YUS  N1   C1   C2   120.89  3.000
 YUS  C9   C2   C3   119.20  3.000
 YUS  C9   C2   C1   121.27  3.000
 YUS  C3   C2   C1   119.53  3.000
 YUS  N    N1   C1   118.87  3.000
 YUS  C9   C7   C5   119.69  3.000
 YUS  C5   C7   O2   115.51  3.000
 YUS  C9   C7   O2   124.80  3.000
 YUS  H4   C6   H3   108.82  3.000
 YUS  H4   C6   H2   108.83  3.000
 YUS  H3   C6   H2   108.80  3.000
 YUS  H4   C6   O1   111.90  3.000
 YUS  H3   C6   O1   111.96  3.000
 YUS  H2   C6   O1   106.44  3.000
 YUS  C4   C5   C7   119.32  3.000
 YUS  C7   C5   O1   115.54  3.000
 YUS  C4   C5   O1   125.14  3.000
 YUS  H5   C4   C3   118.86  3.000
 YUS  H5   C4   C5   120.68  3.000
 YUS  C3   C4   C5   120.46  3.000
 YUS  H6   C3   C4   119.22  3.000
 YUS  H6   C3   C2   120.23  3.000
 YUS  C4   C3   C2   120.55  3.000
 YUS  H9   C8   H8   108.61  3.000
 YUS  H9   C8   H7   108.70  3.000
 YUS  H8   C8   H7   108.81  3.000
 YUS  H9   C8   O2   112.13  3.000
 YUS  H8   C8   O2   111.95  3.000
 YUS  H7   C8   O2   106.54  3.000
 YUS  H10  C9   C7   120.53  3.000
 YUS  H10  C9   C2   118.68  3.000
 YUS  C7   C9   C2   120.79  3.000
 YUS  H12  C10  H11  106.83  3.000
 YUS  H12  C10  C    107.13  3.000
 YUS  H11  C10  C    108.18  3.000
 YUS  H12  C10  C11  109.76  3.000
 YUS  H11  C10  C11  110.21  3.000
 YUS  C    C10  C11  114.42  3.000
 YUS  C20  C11  C12  118.93  3.000
 YUS  C12  C11  C10  119.77  3.000
 YUS  C20  C11  C10  121.25  3.000
 YUS  C17  C12  C13  117.93  3.000
 YUS  C17  C12  C11  119.23  3.000
 YUS  C13  C12  C11  122.84  3.000
 YUS  H13  C13  C14  118.60  3.000
 YUS  H13  C13  C12  120.13  3.000
 YUS  C14  C13  C12  121.27  3.000
 YUS  H14  C14  C15  119.71  3.000
 YUS  H14  C14  C13  119.76  3.000
 YUS  C15  C14  C13  120.53  3.000
 YUS  H15  N    C    118.27  3.000
 YUS  H15  N    N1   120.66  3.000
 YUS  C    N    N1   121.01  3.000
 YUS  O    C    N    120.70  3.000
 YUS  N    C    C10  116.03  3.000
 YUS  O    C    C10  123.27  3.000
 YUS  H16  C15  C16  120.33  3.000
 YUS  H16  C15  C14  119.90  3.000
 YUS  C16  C15  C14  119.77  3.000
 YUS  H17  C16  C17  118.60  3.000
 YUS  H17  C16  C15  120.40  3.000
 YUS  C17  C16  C15  121.00  3.000
 YUS  C18  C17  C16  120.84  3.000
 YUS  C16  C17  C12  119.50  3.000
 YUS  C18  C17  C12  119.66  3.000
 YUS  H18  C18  C19  120.79  3.000
 YUS  H18  C18  C17  119.09  3.000
 YUS  C19  C18  C17  120.12  3.000
 YUS  H19  C19  C20  119.23  3.000
 YUS  H19  C19  C18  120.43  3.000
 YUS  C20  C19  C18  120.34  3.000
 YUS  H20  C20  C19  117.85  3.000
 YUS  H20  C20  C11  120.44  3.000
 YUS  C19  C20  C11  121.70  3.000
 YUS  C8   O2   C7   118.00  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
 YUS  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 YUS  CONST_02  C5   C7   C9   C2      0.00   0.0  0
 YUS  CONST_03  C3   C2   C9   C7      0.00   0.0  0
 YUS  CONST_04  C3   C4   C5   C7      0.00   0.0  0
 YUS  CONST_05  C9   C2   C3   C4      0.00   0.0  0
 YUS  CONST_06  C9   C7   C5   C4      0.00   0.0  0
 YUS  CONST_07  C18  C19  C20  C11     0.00   0.0  0
 YUS  CONST_08  C14  C13  C12  C11   180.00   0.0  0
 YUS  CONST_09  C18  C17  C12  C11     0.00   0.0  0
 YUS  CONST_10  C16  C17  C12  C11   180.00   0.0  0
 YUS  CONST_11  C19  C20  C11  C12     0.00   0.0  0
 YUS  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 YUS  CONST_13  C19  C18  C17  C12     0.00   0.0  0
 YUS  CONST_14  C15  C16  C17  C12     0.00   0.0  0
 YUS  CONST_15  C20  C11  C12  C13   180.00   0.0  0
 YUS  CONST_16  C18  C17  C12  C13   180.00   0.0  0
 YUS  CONST_17  C16  C17  C12  C13     0.00   0.0  0
 YUS  CONST_18  C16  C15  C14  C13     0.00   0.0  0
 YUS  CONST_19  C17  C12  C13  C14     0.00   0.0  0
 YUS  CONST_20  C17  C16  C15  C14     0.00   0.0  0
 YUS  CONST_21  C18  C17  C16  C15   180.00   0.0  0
 YUS  CONST_22  C19  C18  C17  C16   180.00   0.0  0
 YUS  CONST_23  C20  C11  C12  C17     0.00   0.0  0
 YUS  CONST_24  C20  C19  C18  C17     0.00   0.0  0
 YUS  CONST_25  C3   C4   C5   O1    180.00   0.0  0
 YUS  CONST_26  C9   C7   C5   O1    180.00   0.0  0
 YUS  CONST_27  C2   C9   C7   O2    180.00   0.0  0
 YUS  CONST_28  C4   C5   C7   O2    180.00   0.0  0
 YUS  CONST_29  C4   C3   C2   C1    180.00   0.0  0
 YUS  CONST_30  C7   C9   C2   C1    180.00   0.0  0
 YUS  CONST_31  C19  C20  C11  C10   180.00   0.0  0
 YUS  CONST_32  C13  C12  C11  C10     0.00   0.0  0
 YUS  CONST_33  C17  C12  C11  C10   180.00   0.0  0
 YUS  CONST_34  H5   C4   C3   C2    180.00   0.0  0
 YUS  CONST_35  H6   C3   C4   C5    180.00   0.0  0
 YUS  CONST_36  H10  C9   C7   C5    180.00   0.0  0
 YUS  CONST_37  H19  C19  C20  C11   180.00   0.0  0
 YUS  CONST_38  H13  C13  C12  C11     0.00   0.0  0
 YUS  CONST_39  H20  C20  C11  C12   180.00   0.0  0
 YUS  CONST_40  H14  C14  C13  C12   180.00   0.0  0
 YUS  CONST_41  H18  C18  C17  C12   180.00   0.0  0
 YUS  CONST_42  H17  C16  C17  C12   180.00   0.0  0
 YUS  CONST_43  H16  C15  C14  C13   180.00   0.0  0
 YUS  CONST_44  O    C    N    N1    180.00   0.0  0
 YUS  CONST_45  C10  C    N    N1      0.00   0.0  0
 YUS  CONST_46  H15  N    C    C10   180.00   0.0  0
 YUS  Var_01    C3   C2   C1   N1   -177.78  30.0  2
 YUS  Var_02    C4   C5   O1   C6      1.00  30.0  2
 YUS  Var_03    C9   C7   O2   C8     -0.05  30.0  2
 YUS  Var_04    C    C10  C11  C12   160.58  30.0  1
 YUS  Var_05    O    C    C10  C11   110.16  30.0  2
 YUS  Var_06    H7   C8   O2   C7    179.90  30.0  3
 YUS  Var_07    H2   C6   O1   C5    179.34  30.0  3
 YUS  Var_08    C    N    N1   C1    177.30  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
 YUS  plan-1  O1   0.020
 YUS  plan-1  C1   0.020
 YUS  plan-1  C2   0.020
 YUS  plan-1  C7   0.020
 YUS  plan-1  C5   0.020
 YUS  plan-1  C4   0.020
 YUS  plan-1  C3   0.020
 YUS  plan-1  C9   0.020
 YUS  plan-1  H5   0.020
 YUS  plan-1  H6   0.020
 YUS  plan-1  H10  0.020
 YUS  plan-1  O2   0.020
 YUS  plan-2  C10  0.020
 YUS  plan-2  C11  0.020
 YUS  plan-2  C12  0.020
 YUS  plan-2  C13  0.020
 YUS  plan-2  C14  0.020
 YUS  plan-2  C15  0.020
 YUS  plan-2  C16  0.020
 YUS  plan-2  C17  0.020
 YUS  plan-2  C18  0.020
 YUS  plan-2  C19  0.020
 YUS  plan-2  C20  0.020
 YUS  plan-2  H13  0.020
 YUS  plan-2  H14  0.020
 YUS  plan-2  H16  0.020
 YUS  plan-2  H17  0.020
 YUS  plan-2  H18  0.020
 YUS  plan-2  H19  0.020
 YUS  plan-2  H20  0.020
 YUS  plan-3  N1   0.020
 YUS  plan-3  C10  0.020
 YUS  plan-3  N    0.020
 YUS  plan-3  C    0.020
 YUS  plan-3  O    0.020
 YUS  plan-3  H15  0.020
 YUS  plan-4  C1   0.020
 YUS  plan-4  C2   0.020
 YUS  plan-4  N1   0.020
 YUS  plan-4  N    0.020
 YUS  plan-4  H1   0.020

