# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:45:03 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: 5-[(E)-(hydroxyimino)methyl]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1cc(ccc1C)\C=N\O)c2cccc3ccccc23
#
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
 Y96  Y96  5-[(E)-(hydroxyimino)methyl]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide  ligand  45  25  .  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_Y96
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
 Y96  O    O  O     0  -0.471  49.4139  31.0931  -0.9705
 Y96  C    C  C     0   0.496  49.9522  31.6354  -0.0175
 Y96  C13  C  CR6   0  -0.055  49.7669  33.0902   0.2826
 Y96  C19  C  CR6   0   0.086  48.4898  33.6618   0.3188
 Y96  C20  C  CH3   0  -0.729  47.2354  32.8633   0.1162
 Y96  C18  C  CR16  0  -0.280  48.4017  35.0304   0.5759
 Y96  C17  C  CR16  0  -0.275  49.5228  35.8160   0.7686
 Y96  C15  C  CR6   0   0.068  50.7944  35.2462   0.7203
 Y96  C21  C  C1    0  -0.088  52.0220  36.0157   0.9104
 Y96  N22  N  N     0  -0.114  51.9816  37.2587   1.1623
 Y96  O23  O  OH1   0  -0.544  53.2178  37.8085   1.3068
 Y96  C14  C  CR16  0  -0.341  50.8949  33.8789   0.4832
 Y96  N    N  NH1   0  -0.639  50.7633  30.9822   0.8330
 Y96  C1   C  CH1   0  -0.142  51.0908  29.5808   0.6790
 Y96  C12  C  CH3   0  -0.675  51.5920  29.0455   2.0182
 Y96  C2   C  CR6   0   0.115  52.1137  29.3383  -0.4158
 Y96  C7   C  CR66  0   0.099  52.1861  28.0692  -1.0635
 Y96  C8   C  CR16  0  -0.342  51.3093  26.9961  -0.7627
 Y96  C9   C  CR16  0  -0.248  51.4102  25.7934  -1.4090
 Y96  C10  C  CR16  0  -0.261  52.3951  25.5906  -2.3956
 Y96  C11  C  CR16  0  -0.311  53.2588  26.6027  -2.7103
 Y96  C6   C  CR66  0   0.111  53.1809  27.8558  -2.0579
 Y96  C5   C  CR16  0  -0.333  54.0809  28.8969  -2.3827
 Y96  C4   C  CR16  0  -0.243  53.9981  30.1001  -1.7432
 Y96  C3   C  CR16  0  -0.339  53.0126  30.3141  -0.7595
 Y96  H1   H  HCH3  0   0.246  47.2309  31.9518   0.7143
 Y96  H2   H  HCH3  0   0.246  46.3623  33.4500   0.3978
 Y96  H3   H  HCH3  0   0.255  47.1153  32.5659  -0.9254
 Y96  H4   H  HCR6  0   0.259  47.4227  35.4908   0.6287
 Y96  H5   H  HCR6  0   0.260  49.4083  36.8756   0.9563
 Y96  H6   H  H     0   0.244  52.9663  35.4766   0.8267
 Y96  H7   H  HOH1  0   0.478  53.0470  38.7372   1.4976
 Y96  H8   H  HCR6  0   0.270  51.8808  33.4295   0.4364
 Y96  H9   H  HNH1  0   0.411  51.1293  31.4731   1.6339
 Y96  H10  H  HCH1  0   0.257  50.1643  29.0644   0.4176
 Y96  H11  H  HCH3  0   0.250  50.8260  29.1469   2.7872
 Y96  H12  H  HCH3  0   0.250  51.8546  27.9920   1.9395
 Y96  H13  H  HCH3  0   0.239  52.4833  29.5872   2.3389
 Y96  H14  H  HCR6  0   0.250  50.5431  27.1125  -0.0086
 Y96  H15  H  HCR6  0   0.260  50.7280  24.9911  -1.1595
 Y96  H16  H  HCR6  0   0.258  52.4641  24.6358  -2.9004
 Y96  H17  H  HCR6  0   0.256  54.0204  26.4585  -3.4676
 Y96  H18  H  HCR6  0   0.255  54.8335  28.7252  -3.1425
 Y96  H19  H  HCR6  0   0.256  54.6863  30.8989  -1.9876
 Y96  H20  H  HCR6  0   0.254  52.9722  31.2796  -0.2717

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
 Y96  C10  C11  aromatic  1.367  0.020  1.367
 Y96  C10  C9   aromatic  1.409  0.020  1.409
 Y96  C11  C6   aromatic  1.415  0.020  1.415
 Y96  C9   C8   aromatic  1.369  0.020  1.369
 Y96  C6   C5   aromatic  1.414  0.020  1.414
 Y96  C6   C7   aromatic  1.423  0.020  1.423
 Y96  C8   C7   aromatic  1.418  0.020  1.418
 Y96  C5   C4   aromatic  1.365  0.020  1.365
 Y96  C7   C2   aromatic  1.427  0.020  1.427
 Y96  O    C    double    1.221  0.020  1.221
 Y96  O23  N22  single    1.361  0.020  1.361
 Y96  C21  N22  double    1.269  0.020  1.269
 Y96  C21  C15  single    1.461  0.020  1.461
 Y96  C4   C3   aromatic  1.409  0.020  1.409
 Y96  C14  C15  aromatic  1.391  0.020  1.391
 Y96  C14  C13  aromatic  1.391  0.020  1.391
 Y96  C15  C17  aromatic  1.394  0.020  1.394
 Y96  C    C13  single    1.497  0.020  1.497
 Y96  C    N    single    1.345  0.020  1.345
 Y96  C2   C3   aromatic  1.371  0.020  1.371
 Y96  C2   C1   single    1.518  0.020  1.518
 Y96  C13  C19  aromatic  1.400  0.020  1.400
 Y96  C17  C18  aromatic  1.383  0.020  1.383
 Y96  C19  C18  aromatic  1.395  0.020  1.395
 Y96  C19  C20  single    1.501  0.020  1.501
 Y96  N    C1   single    1.447  0.020  1.447
 Y96  C1   C12  single    1.527  0.020  1.527
 Y96  C20  H1   single    0.970  0.020  1.090
 Y96  C20  H2   single    0.970  0.020  1.090
 Y96  C20  H3   single    0.970  0.020  1.090
 Y96  C18  H4   single    0.930  0.020  1.080
 Y96  C17  H5   single    0.930  0.020  1.080
 Y96  C21  H6   single    0.930  0.020  1.080
 Y96  O23  H7   single    0.850  0.020  0.980
 Y96  C14  H8   single    0.930  0.020  1.080
 Y96  N    H9   single    0.860  0.020  1.020
 Y96  C1   H10  single    0.970  0.020  1.090
 Y96  C12  H11  single    0.970  0.020  1.090
 Y96  C12  H12  single    0.970  0.020  1.090
 Y96  C12  H13  single    0.970  0.020  1.090
 Y96  C8   H14  single    0.930  0.020  1.080
 Y96  C9   H15  single    0.930  0.020  1.080
 Y96  C10  H16  single    0.930  0.020  1.080
 Y96  C11  H17  single    0.930  0.020  1.080
 Y96  C5   H18  single    0.930  0.020  1.080
 Y96  C4   H19  single    0.930  0.020  1.080
 Y96  C3   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
 Y96  N    C    C13  114.83  3.000
 Y96  N    C    O    122.94  3.000
 Y96  C13  C    O    122.23  3.000
 Y96  C14  C13  C19  120.31  3.000
 Y96  C19  C13  C    121.00  3.000
 Y96  C14  C13  C    118.66  3.000
 Y96  C18  C19  C20  119.60  3.000
 Y96  C20  C19  C13  122.81  3.000
 Y96  C18  C19  C13  117.58  3.000
 Y96  H3   C20  H2   107.81  3.000
 Y96  H3   C20  H1   107.20  3.000
 Y96  H2   C20  H1   107.78  3.000
 Y96  H3   C20  C19  111.49  3.000
 Y96  H2   C20  C19  110.40  3.000
 Y96  H1   C20  C19  111.97  3.000
 Y96  H4   C18  C17  118.99  3.000
 Y96  H4   C18  C19  118.88  3.000
 Y96  C17  C18  C19  122.13  3.000
 Y96  H5   C17  C15  120.17  3.000
 Y96  H5   C17  C18  119.65  3.000
 Y96  C15  C17  C18  120.17  3.000
 Y96  C14  C15  C21  118.62  3.000
 Y96  C14  C15  C17  118.25  3.000
 Y96  C21  C15  C17  123.13  3.000
 Y96  H6   C21  N22  121.81  3.000
 Y96  H6   C21  C15  117.20  3.000
 Y96  N22  C21  C15  120.99  3.000
 Y96  O23  N22  C21  112.82  3.000
 Y96  H7   O23  N22  104.44  3.000
 Y96  H8   C14  C15  118.70  3.000
 Y96  H8   C14  C13  119.74  3.000
 Y96  C15  C14  C13  121.55  3.000
 Y96  H9   N    C1   118.28  3.000
 Y96  H9   N    C    119.01  3.000
 Y96  C1   N    C    122.65  3.000
 Y96  H10  C1   C2   108.87  3.000
 Y96  H10  C1   C12  108.82  3.000
 Y96  C2   C1   C12  110.82  3.000
 Y96  H10  C1   N    106.93  3.000
 Y96  C12  C1   N    108.69  3.000
 Y96  C2   C1   N    112.58  3.000
 Y96  H13  C12  H12  107.73  3.000
 Y96  H13  C12  H11  108.69  3.000
 Y96  H12  C12  H11  108.09  3.000
 Y96  H13  C12  C1   110.60  3.000
 Y96  H12  C12  C1   110.80  3.000
 Y96  H11  C12  C1   110.82  3.000
 Y96  C3   C2   C7   119.09  3.000
 Y96  C3   C2   C1   120.61  3.000
 Y96  C7   C2   C1   120.25  3.000
 Y96  C6   C7   C8   117.85  3.000
 Y96  C8   C7   C2   123.06  3.000
 Y96  C6   C7   C2   119.09  3.000
 Y96  H14  C8   C9   118.42  3.000
 Y96  H14  C8   C7   120.30  3.000
 Y96  C9   C8   C7   121.27  3.000
 Y96  H15  C9   C10  119.70  3.000
 Y96  H15  C9   C8   119.73  3.000
 Y96  C10  C9   C8   120.57  3.000
 Y96  H16  C10  C11  120.36  3.000
 Y96  H16  C10  C9   119.89  3.000
 Y96  C11  C10  C9   119.75  3.000
 Y96  H17  C11  C6   118.60  3.000
 Y96  H17  C11  C10  120.42  3.000
 Y96  C6   C11  C10  120.98  3.000
 Y96  C5   C6   C11  120.74  3.000
 Y96  C5   C6   C7   119.68  3.000
 Y96  C11  C6   C7   119.58  3.000
 Y96  H18  C5   C4   120.69  3.000
 Y96  H18  C5   C6   119.13  3.000
 Y96  C4   C5   C6   120.18  3.000
 Y96  H19  C4   C3   119.37  3.000
 Y96  H19  C4   C5   120.41  3.000
 Y96  C3   C4   C5   120.22  3.000
 Y96  H20  C3   C4   118.44  3.000
 Y96  H20  C3   C2   119.84  3.000
 Y96  C4   C3   C2   121.72  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
 Y96  CONST_01  C17  C15  C14  C13     0.00   0.0  0
 Y96  CONST_02  C17  C18  C19  C13     0.00   0.0  0
 Y96  CONST_03  C15  C14  C13  C19     0.00   0.0  0
 Y96  CONST_04  C15  C17  C18  C19     0.00   0.0  0
 Y96  CONST_05  C14  C15  C17  C18     0.00   0.0  0
 Y96  CONST_06  C14  C13  C19  C18     0.00   0.0  0
 Y96  CONST_07  C11  C6   C7   C2    180.00   0.0  0
 Y96  CONST_08  C5   C6   C7   C2      0.00   0.0  0
 Y96  CONST_09  C9   C8   C7   C2    180.00   0.0  0
 Y96  CONST_10  C5   C4   C3   C2      0.00   0.0  0
 Y96  CONST_11  C10  C11  C6   C7      0.00   0.0  0
 Y96  CONST_12  C4   C5   C6   C7      0.00   0.0  0
 Y96  CONST_13  C10  C9   C8   C7      0.00   0.0  0
 Y96  CONST_14  C4   C3   C2   C7      0.00   0.0  0
 Y96  CONST_15  C11  C10  C9   C8      0.00   0.0  0
 Y96  CONST_16  C11  C6   C7   C8      0.00   0.0  0
 Y96  CONST_17  C5   C6   C7   C8    180.00   0.0  0
 Y96  CONST_18  C3   C2   C7   C8    180.00   0.0  0
 Y96  CONST_19  C6   C11  C10  C9      0.00   0.0  0
 Y96  CONST_20  C6   C7   C8   C9      0.00   0.0  0
 Y96  CONST_21  C5   C6   C11  C10   180.00   0.0  0
 Y96  CONST_22  C4   C5   C6   C11   180.00   0.0  0
 Y96  CONST_23  C3   C4   C5   C6      0.00   0.0  0
 Y96  CONST_24  C3   C2   C7   C6      0.00   0.0  0
 Y96  CONST_25  C15  C14  C13  C     180.00   0.0  0
 Y96  CONST_26  C18  C19  C13  C     180.00   0.0  0
 Y96  CONST_27  C21  C15  C14  C13   180.00   0.0  0
 Y96  CONST_28  C14  C13  C19  C20   180.00   0.0  0
 Y96  CONST_29  C17  C18  C19  C20   180.00   0.0  0
 Y96  CONST_30  C21  C15  C17  C18   180.00   0.0  0
 Y96  CONST_31  C6   C7   C2   C1    180.00   0.0  0
 Y96  CONST_32  C8   C7   C2   C1      0.00   0.0  0
 Y96  CONST_33  C4   C3   C2   C1    180.00   0.0  0
 Y96  CONST_34  H4   C18  C19  C13   180.00   0.0  0
 Y96  CONST_35  H8   C14  C13  C19   180.00   0.0  0
 Y96  CONST_36  H5   C17  C18  C19   180.00   0.0  0
 Y96  CONST_37  H14  C8   C7   C2      0.00   0.0  0
 Y96  CONST_38  H19  C4   C3   C2    180.00   0.0  0
 Y96  CONST_39  H17  C11  C6   C7    180.00   0.0  0
 Y96  CONST_40  H18  C5   C6   C7    180.00   0.0  0
 Y96  CONST_41  H15  C9   C8   C7    180.00   0.0  0
 Y96  CONST_42  H20  C3   C2   C7    180.00   0.0  0
 Y96  CONST_43  H16  C10  C9   C8    180.00   0.0  0
 Y96  CONST_44  C1   N    C    C13   180.00   0.0  0
 Y96  CONST_45  H9   N    C    C13     0.00   0.0  0
 Y96  CONST_46  C1   N    C    O       0.00   0.0  0
 Y96  Var_01    C14  C13  C    O    -128.88  30.0  2
 Y96  Var_02    N22  C21  C15  C17     1.59  30.0  2
 Y96  Var_03    H1   C20  C19  C13    47.53  30.0  2

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
 Y96  chir_01  C1  C2  N  C12  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
 Y96  plan-1  C    0.020
 Y96  plan-1  C13  0.020
 Y96  plan-1  C19  0.020
 Y96  plan-1  C20  0.020
 Y96  plan-1  C18  0.020
 Y96  plan-1  C17  0.020
 Y96  plan-1  C15  0.020
 Y96  plan-1  C21  0.020
 Y96  plan-1  C14  0.020
 Y96  plan-1  H4   0.020
 Y96  plan-1  H5   0.020
 Y96  plan-1  H8   0.020
 Y96  plan-2  C1   0.020
 Y96  plan-2  C2   0.020
 Y96  plan-2  C7   0.020
 Y96  plan-2  C8   0.020
 Y96  plan-2  C9   0.020
 Y96  plan-2  C10  0.020
 Y96  plan-2  C11  0.020
 Y96  plan-2  C6   0.020
 Y96  plan-2  C5   0.020
 Y96  plan-2  C4   0.020
 Y96  plan-2  C3   0.020
 Y96  plan-2  H14  0.020
 Y96  plan-2  H15  0.020
 Y96  plan-2  H16  0.020
 Y96  plan-2  H17  0.020
 Y96  plan-2  H18  0.020
 Y96  plan-2  H19  0.020
 Y96  plan-2  H20  0.020
 Y96  plan-3  O    0.020
 Y96  plan-3  C    0.020
 Y96  plan-3  C13  0.020
 Y96  plan-3  N    0.020
 Y96  plan-3  C1   0.020
 Y96  plan-3  H9   0.020
 Y96  plan-4  C15  0.020
 Y96  plan-4  C21  0.020
 Y96  plan-4  N22  0.020
 Y96  plan-4  O23  0.020
 Y96  plan-4  H6   0.020

