# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 10:35:51 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1ccc(cc1)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
 5YA  5YA  4-naphthalen-1-yl-~{N}-oxidanyl-benzamide  ligand  33  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5YA
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
 5YA  C1   C  CR16  0  -0.245   3.4083   2.3229  -0.4295
 5YA  C2   C  CR16  0  -0.311   2.0233   2.0791  -0.3685
 5YA  C3   C  CR6   0   0.063   1.5258   0.8172  -0.1482
 5YA  C4   C  CR66  0   0.101   2.4304  -0.2679   0.0531
 5YA  C5   C  CR66  0   0.116   3.8284  -0.0175  -0.0177
 5YA  C6   C  CR16  0  -0.324   4.2930   1.2945  -0.2669
 5YA  C7   C  CR16  0  -0.343   2.0000  -1.5836   0.3543
 5YA  C8   C  CR16  0  -0.251   2.9020  -2.5952   0.5446
 5YA  O1   O  O     0  -0.469  -4.9266   1.1756   0.1949
 5YA  C9   C  CR16  0  -0.259   4.2860  -2.3485   0.4472
 5YA  C10  C  CR16  0  -0.310   4.7356  -1.0859   0.1775
 5YA  C11  C  CR6   0   0.031   0.0594   0.6207  -0.1277
 5YA  C12  C  CR16  0  -0.283  -0.7335   1.3497   0.7584
 5YA  C13  C  CR16  0  -0.254  -2.1108   1.2104   0.7568
 5YA  N1   N  NH1   0  -0.376  -4.6958  -0.9951  -0.3840
 5YA  C14  C  CR6   0  -0.061  -2.7280   0.3238  -0.1207
 5YA  C15  C  CR16  0  -0.268  -1.9432  -0.3970  -1.0186
 5YA  C16  C  CR16  0  -0.283  -0.5659  -0.2479  -1.0211
 5YA  C17  C  C     0   0.491  -4.2171   0.2267  -0.0941
 5YA  O2   O  OH1   0  -0.538  -6.0308  -1.1874  -0.5499
 5YA  H1   H  HCR6  0   0.261   3.7636   3.3275  -0.6168
 5YA  H2   H  HCR6  0   0.258   1.3358   2.9019  -0.5209
 5YA  H3   H  HCR6  0   0.258   5.3604   1.4711  -0.3219
 5YA  H4   H  HCR6  0   0.258   0.9432  -1.7928   0.4507
 5YA  H5   H  HCR6  0   0.260   2.5507  -3.5916   0.7788
 5YA  H6   H  HCR6  0   0.260   4.9891  -3.1572   0.5965
 5YA  H7   H  HCR6  0   0.257   5.7983  -0.8845   0.1152
 5YA  H8   H  HCR6  0   0.261  -0.2659   2.0285   1.4606
 5YA  H9   H  HCR6  0   0.265  -2.7080   1.7849   1.4524
 5YA  H10  H  HNH1  0   0.424  -4.1150  -1.7957  -0.5851
 5YA  H11  H  HCR6  0   0.267  -2.3953  -1.0573  -1.7481
 5YA  H12  H  HCR6  0   0.269   0.0258  -0.7958  -1.7435
 5YA  H13  H  HOH1  0   0.479  -6.3810  -1.4469   0.3130

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
 5YA  O1   C17  double    1.220  0.020  1.220
 5YA  C15  C16  aromatic  1.385  0.020  1.385
 5YA  C15  C14  aromatic  1.393  0.020  1.393
 5YA  C16  C11  aromatic  1.394  0.020  1.394
 5YA  C17  C14  single    1.492  0.020  1.492
 5YA  C17  N1   single    1.344  0.020  1.344
 5YA  C14  C13  aromatic  1.392  0.020  1.392
 5YA  C11  C3   single    1.480  0.020  1.480
 5YA  C11  C12  aromatic  1.395  0.020  1.395
 5YA  C7   C8   aromatic  1.369  0.020  1.369
 5YA  C7   C4   aromatic  1.417  0.020  1.417
 5YA  C8   C9   aromatic  1.409  0.020  1.409
 5YA  C3   C4   aromatic  1.427  0.020  1.427
 5YA  C3   C2   aromatic  1.374  0.020  1.374
 5YA  N1   O2   single    1.359  0.020  1.359
 5YA  C4   C5   aromatic  1.422  0.020  1.422
 5YA  C13  C12  aromatic  1.384  0.020  1.384
 5YA  C2   C1   aromatic  1.408  0.020  1.408
 5YA  C9   C10  aromatic  1.367  0.020  1.367
 5YA  C5   C10  aromatic  1.415  0.020  1.415
 5YA  C5   C6   aromatic  1.414  0.020  1.414
 5YA  C1   C6   aromatic  1.366  0.020  1.366
 5YA  C1   H1   single    0.930  0.020  1.080
 5YA  C2   H2   single    0.930  0.020  1.080
 5YA  C6   H3   single    0.930  0.020  1.080
 5YA  C7   H4   single    0.930  0.020  1.080
 5YA  C8   H5   single    0.930  0.020  1.080
 5YA  C9   H6   single    0.930  0.020  1.080
 5YA  C10  H7   single    0.930  0.020  1.080
 5YA  C12  H8   single    0.930  0.020  1.080
 5YA  C13  H9   single    0.930  0.020  1.080
 5YA  N1   H10  single    0.860  0.020  1.020
 5YA  C15  H11  single    0.930  0.020  1.080
 5YA  C16  H12  single    0.930  0.020  1.080
 5YA  O2   H13  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
 5YA  H1   C1   C6   120.46  3.000
 5YA  H1   C1   C2   119.43  3.000
 5YA  C6   C1   C2   120.11  3.000
 5YA  H2   C2   C3   119.37  3.000
 5YA  H2   C2   C1   119.14  3.000
 5YA  C3   C2   C1   121.48  3.000
 5YA  C11  C3   C4   121.69  3.000
 5YA  C4   C3   C2   119.43  3.000
 5YA  C11  C3   C2   118.88  3.000
 5YA  C7   C4   C5   118.21  3.000
 5YA  C5   C4   C3   118.84  3.000
 5YA  C7   C4   C3   122.93  3.000
 5YA  C10  C5   C6   120.94  3.000
 5YA  C6   C5   C4   119.68  3.000
 5YA  C10  C5   C4   119.38  3.000
 5YA  H3   C6   C5   118.95  3.000
 5YA  H3   C6   C1   120.61  3.000
 5YA  C5   C6   C1   120.44  3.000
 5YA  H4   C7   C8   119.25  3.000
 5YA  H4   C7   C4   119.70  3.000
 5YA  C8   C7   C4   121.05  3.000
 5YA  H5   C8   C9   119.67  3.000
 5YA  H5   C8   C7   119.78  3.000
 5YA  C9   C8   C7   120.55  3.000
 5YA  H6   C9   C10  120.25  3.000
 5YA  H6   C9   C8   119.85  3.000
 5YA  C10  C9   C8   119.89  3.000
 5YA  H7   C10  C9   120.37  3.000
 5YA  H7   C10  C5   118.73  3.000
 5YA  C9   C10  C5   120.90  3.000
 5YA  C16  C11  C12  118.54  3.000
 5YA  C12  C11  C3   120.18  3.000
 5YA  C16  C11  C3   121.23  3.000
 5YA  H8   C12  C13  119.57  3.000
 5YA  H8   C12  C11  119.61  3.000
 5YA  C13  C12  C11  120.82  3.000
 5YA  H9   C13  C14  119.93  3.000
 5YA  H9   C13  C12  119.67  3.000
 5YA  C14  C13  C12  120.40  3.000
 5YA  H10  N1   O2   115.39  3.000
 5YA  H10  N1   C17  124.00  3.000
 5YA  O2   N1   C17  120.32  3.000
 5YA  C17  C14  C15  122.67  3.000
 5YA  C17  C14  C13  118.20  3.000
 5YA  C15  C14  C13  119.08  3.000
 5YA  H11  C15  C16  118.65  3.000
 5YA  H11  C15  C14  120.95  3.000
 5YA  C16  C15  C14  120.36  3.000
 5YA  H12  C16  C15  119.35  3.000
 5YA  H12  C16  C11  119.85  3.000
 5YA  C15  C16  C11  120.78  3.000
 5YA  C14  C17  N1   114.25  3.000
 5YA  N1   C17  O1   123.46  3.000
 5YA  C14  C17  O1   122.28  3.000
 5YA  H13  O2   N1   106.55  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
 5YA  CONST_01  C11  C3   C2   C1    180.00   0.0  0
 5YA  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 5YA  CONST_03  C4   C5   C6   C1      0.00   0.0  0
 5YA  CONST_04  C10  C5   C6   C1    180.00   0.0  0
 5YA  CONST_07  C7   C4   C3   C2    180.00   0.0  0
 5YA  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 5YA  CONST_09  C5   C6   C1   C2      0.00   0.0  0
 5YA  CONST_10  C15  C16  C11  C3    180.00   0.0  0
 5YA  CONST_11  C13  C12  C11  C3    180.00   0.0  0
 5YA  CONST_12  C8   C7   C4   C3    180.00   0.0  0
 5YA  CONST_13  C10  C5   C4   C3    180.00   0.0  0
 5YA  CONST_14  C6   C5   C4   C3      0.00   0.0  0
 5YA  CONST_15  C6   C1   C2   C3      0.00   0.0  0
 5YA  CONST_16  C9   C8   C7   C4      0.00   0.0  0
 5YA  CONST_19  C9   C10  C5   C4      0.00   0.0  0
 5YA  CONST_20  C8   C7   C4   C5      0.00   0.0  0
 5YA  CONST_21  C11  C3   C4   C5    180.00   0.0  0
 5YA  CONST_22  C8   C9   C10  C5      0.00   0.0  0
 5YA  CONST_23  C7   C4   C5   C6    180.00   0.0  0
 5YA  CONST_24  C9   C10  C5   C6    180.00   0.0  0
 5YA  CONST_25  C10  C9   C8   C7      0.00   0.0  0
 5YA  CONST_26  C11  C3   C4   C7      0.00   0.0  0
 5YA  CONST_27  C10  C5   C4   C7      0.00   0.0  0
 5YA  CONST_28  C14  C15  C16  C11     0.00   0.0  0
 5YA  CONST_29  C14  C13  C12  C11     0.00   0.0  0
 5YA  CONST_30  C15  C16  C11  C12     0.00   0.0  0
 5YA  CONST_31  C15  C14  C13  C12     0.00   0.0  0
 5YA  CONST_32  C16  C15  C14  C13     0.00   0.0  0
 5YA  CONST_33  C16  C11  C12  C13     0.00   0.0  0
 5YA  CONST_34  C17  C14  C13  C12   180.00   0.0  0
 5YA  CONST_35  C17  C14  C15  C16   180.00   0.0  0
 5YA  CONST_36  H3   C6   C1   C2    180.00   0.0  0
 5YA  CONST_37  H12  C16  C11  C3      0.00   0.0  0
 5YA  CONST_38  H8   C12  C11  C3      0.00   0.0  0
 5YA  CONST_39  H4   C7   C4   C3      0.00   0.0  0
 5YA  CONST_40  H1   C1   C2   C3    180.00   0.0  0
 5YA  CONST_41  H5   C8   C7   C4    180.00   0.0  0
 5YA  CONST_42  H2   C2   C3   C4    180.00   0.0  0
 5YA  CONST_43  H7   C10  C5   C4    180.00   0.0  0
 5YA  CONST_44  H6   C9   C10  C5    180.00   0.0  0
 5YA  CONST_45  H11  C15  C16  C11   180.00   0.0  0
 5YA  CONST_46  H9   C13  C12  C11   180.00   0.0  0
 5YA  CONST_47  O2   N1   C17  C14   180.00   0.0  0
 5YA  CONST_48  H10  N1   C17  C14     0.00   0.0  0
 5YA  CONST_49  O2   N1   C17  O1      0.00   0.0  0
 5YA  Var_01    C15  C14  C17  O1   -146.66  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
 5YA  plan-1  C3   0.020
 5YA  plan-1  C11  0.020
 5YA  plan-1  C12  0.020
 5YA  plan-1  C13  0.020
 5YA  plan-1  C14  0.020
 5YA  plan-1  C15  0.020
 5YA  plan-1  C16  0.020
 5YA  plan-1  C17  0.020
 5YA  plan-1  H8   0.020
 5YA  plan-1  H9   0.020
 5YA  plan-1  H11  0.020
 5YA  plan-1  H12  0.020
 5YA  plan-2  C1   0.020
 5YA  plan-2  C2   0.020
 5YA  plan-2  C3   0.020
 5YA  plan-2  C4   0.020
 5YA  plan-2  C5   0.020
 5YA  plan-2  C6   0.020
 5YA  plan-2  C7   0.020
 5YA  plan-2  C8   0.020
 5YA  plan-2  C9   0.020
 5YA  plan-2  C10  0.020
 5YA  plan-2  C11  0.020
 5YA  plan-2  H1   0.020
 5YA  plan-2  H2   0.020
 5YA  plan-2  H3   0.020
 5YA  plan-2  H4   0.020
 5YA  plan-2  H5   0.020
 5YA  plan-2  H6   0.020
 5YA  plan-2  H7   0.020
 5YA  plan-3  O1   0.020
 5YA  plan-3  N1   0.020
 5YA  plan-3  C14  0.020
 5YA  plan-3  C17  0.020
 5YA  plan-3  O2   0.020
 5YA  plan-3  H10  0.020

