# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 18:42:27 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 4-methyl-~{N}-oxidanyl-3-[(phenylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1NCc2ccccc2)C(=O)NO
#
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
 T34  T34  4-methyl-~{N}-oxidanyl-3-[(phenylmethyl)amino]benzamide  ligand  35  19  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T34
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
 T34  O1   O  OH1   0  -0.540   5.7715   1.6421   0.1488
 T34  N2   N  NH1   0  -0.378   4.7454   0.7670   0.3220
 T34  C3   C  C     0   0.486   3.5958   0.9234  -0.3583
 T34  O4   O  O     0  -0.473   3.3361   1.9217  -1.0104
 T34  C5   C  CR6   0  -0.047   2.6440  -0.2169  -0.2119
 T34  C6   C  CR16  0  -0.314   3.0724  -1.5334  -0.1052
 T34  C7   C  CR16  0  -0.289   2.1228  -2.5438  -0.0020
 T34  C8   C  CR6   0   0.045   0.7640  -2.2796   0.0079
 T34  C9   C  CR6   0   0.347   0.3296  -0.9392  -0.1088
 T34  C10  C  CR16  0  -0.380   1.2820   0.0732  -0.2353
 T34  C11  C  CH3   0  -0.754  -0.2369  -3.3861   0.1456
 T34  N12  N  NH1   0  -0.691  -1.0180  -0.6703  -0.0607
 T34  C13  C  CH2   0  -0.336  -1.5432   0.6504  -0.3204
 T34  C14  C  CR6   0   0.083  -3.0355   0.6652  -0.1276
 T34  C15  C  CR16  0  -0.284  -3.5947   0.2542   1.0819
 T34  C16  C  CR16  0  -0.240  -4.9690   0.2739   1.2661
 T34  C17  C  CR16  0  -0.267  -5.8057   0.7052   0.2426
 T34  C18  C  CR16  0  -0.239  -5.2578   1.1137  -0.9645
 T34  C19  C  CR16  0  -0.312  -3.8798   1.0902  -1.1471
 T34  H1   H  HOH1  0   0.478   5.6721   2.3185   0.8321
 T34  H2   H  HNH1  0   0.421   4.9607  -0.0473   0.8776
 T34  H3   H  HCR6  0   0.254   4.1223  -1.7945  -0.1315
 T34  H4   H  HCR6  0   0.251   2.4547  -3.5725   0.0744
 T34  H5   H  HCR6  0   0.272   0.9728   1.1034  -0.3499
 T34  H6   H  HCH3  0   0.249  -0.9108  -3.2138   0.9882
 T34  H7   H  HCH3  0   0.248  -0.8630  -3.4843  -0.7460
 T34  H8   H  HCH3  0   0.260   0.2552  -4.3442   0.3008
 T34  H9   H  HNH1  0   0.387  -1.6173  -1.4169  -0.3759
 T34  H10  H  HCH2  0   0.252  -1.0843   1.3557   0.3789
 T34  H11  H  HCH2  0   0.240  -1.2955   1.0093  -1.3282
 T34  H12  H  HCR6  0   0.252  -2.9504  -0.0826   1.8853
 T34  H13  H  HCR6  0   0.256  -5.3889  -0.0475   2.2105
 T34  H14  H  HCR6  0   0.256  -6.8783   0.7202   0.3874
 T34  H15  H  HCR6  0   0.256  -5.9005   1.4467  -1.7694
 T34  H16  H  HCR6  0   0.254  -3.4589   1.4066  -2.0941

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
 T34  C17  C18  aromatic  1.387  0.020  1.387
 T34  C17  C16  aromatic  1.391  0.020  1.391
 T34  C18  C19  aromatic  1.390  0.020  1.390
 T34  C16  C15  aromatic  1.387  0.020  1.387
 T34  C19  C14  aromatic  1.390  0.020  1.390
 T34  C15  C14  aromatic  1.394  0.020  1.394
 T34  C14  C13  single    1.505  0.020  1.505
 T34  C13  N12  single    1.445  0.020  1.445
 T34  O4   C3   double    1.220  0.020  1.220
 T34  N12  C9   single    1.375  0.020  1.375
 T34  C10  C9   aromatic  1.396  0.020  1.396
 T34  C10  C5   aromatic  1.393  0.020  1.393
 T34  C3   C5   single    1.493  0.020  1.493
 T34  C3   N2   single    1.345  0.020  1.345
 T34  C9   C8   aromatic  1.414  0.020  1.414
 T34  C5   C6   aromatic  1.389  0.020  1.389
 T34  O1   N2   single    1.360  0.020  1.360
 T34  C8   C11  single    1.498  0.020  1.498
 T34  C8   C7   aromatic  1.384  0.020  1.384
 T34  C6   C7   aromatic  1.390  0.020  1.390
 T34  O1   H1   single    0.850  0.020  0.980
 T34  N2   H2   single    0.860  0.020  1.020
 T34  C6   H3   single    0.930  0.020  1.080
 T34  C7   H4   single    0.930  0.020  1.080
 T34  C10  H5   single    0.930  0.020  1.080
 T34  C11  H6   single    0.970  0.020  1.090
 T34  C11  H7   single    0.970  0.020  1.090
 T34  C11  H8   single    0.970  0.020  1.090
 T34  N12  H9   single    0.890  0.020  1.040
 T34  C13  H10  single    0.970  0.020  1.090
 T34  C13  H11  single    0.970  0.020  1.090
 T34  C15  H12  single    0.930  0.020  1.080
 T34  C16  H13  single    0.930  0.020  1.080
 T34  C17  H14  single    0.930  0.020  1.080
 T34  C18  H15  single    0.930  0.020  1.080
 T34  C19  H16  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
 T34  H1   O1   N2   106.42  3.000
 T34  H2   N2   C3   123.69  3.000
 T34  H2   N2   O1   115.37  3.000
 T34  C3   N2   O1   120.39  3.000
 T34  C5   C3   O4   122.80  3.000
 T34  C5   C3   N2   113.99  3.000
 T34  O4   C3   N2   123.19  3.000
 T34  C10  C5   C6   120.03  3.000
 T34  C6   C5   C3   122.36  3.000
 T34  C10  C5   C3   117.57  3.000
 T34  H3   C6   C7   119.28  3.000
 T34  H3   C6   C5   121.75  3.000
 T34  C7   C6   C5   118.95  3.000
 T34  H4   C7   C8   118.77  3.000
 T34  H4   C7   C6   119.08  3.000
 T34  C8   C7   C6   122.15  3.000
 T34  C11  C8   C9   120.16  3.000
 T34  C11  C8   C7   121.02  3.000
 T34  C9   C8   C7   118.81  3.000
 T34  N12  C9   C10  122.01  3.000
 T34  C10  C9   C8   119.04  3.000
 T34  N12  C9   C8   118.92  3.000
 T34  H5   C10  C9   120.36  3.000
 T34  H5   C10  C5   118.66  3.000
 T34  C9   C10  C5   120.98  3.000
 T34  H8   C11  H7   107.22  3.000
 T34  H8   C11  H6   107.92  3.000
 T34  H7   C11  H6   106.84  3.000
 T34  H8   C11  C8   111.17  3.000
 T34  H7   C11  C8   111.95  3.000
 T34  H6   C11  C8   111.50  3.000
 T34  H9   N12  C13  113.87  3.000
 T34  H9   N12  C9   115.27  3.000
 T34  C13  N12  C9   121.92  3.000
 T34  H11  C13  H10  106.34  3.000
 T34  H11  C13  C14  109.76  3.000
 T34  H10  C13  C14  109.13  3.000
 T34  H11  C13  N12  112.44  3.000
 T34  H10  C13  N12  108.78  3.000
 T34  C14  C13  N12  110.27  3.000
 T34  C19  C14  C15  118.86  3.000
 T34  C15  C14  C13  120.39  3.000
 T34  C19  C14  C13  120.75  3.000
 T34  H12  C15  C16  119.68  3.000
 T34  H12  C15  C14  119.76  3.000
 T34  C16  C15  C14  120.56  3.000
 T34  H13  C16  C17  120.05  3.000
 T34  H13  C16  C15  119.75  3.000
 T34  C17  C16  C15  120.20  3.000
 T34  H14  C17  C18  120.25  3.000
 T34  H14  C17  C16  120.14  3.000
 T34  C18  C17  C16  119.61  3.000
 T34  H15  C18  C19  119.74  3.000
 T34  H15  C18  C17  120.21  3.000
 T34  C19  C18  C17  120.06  3.000
 T34  H16  C19  C18  119.66  3.000
 T34  H16  C19  C14  119.62  3.000
 T34  C18  C19  C14  120.72  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
 T34  CONST_01  C8   C9   C10  C5      0.00   0.0  0
 T34  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 T34  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 T34  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 T34  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 T34  CONST_06  C10  C5   C6   C7      0.00   0.0  0
 T34  CONST_07  C17  C18  C19  C14     0.00   0.0  0
 T34  CONST_08  C17  C16  C15  C14     0.00   0.0  0
 T34  CONST_09  C18  C17  C16  C15     0.00   0.0  0
 T34  CONST_10  C18  C19  C14  C15     0.00   0.0  0
 T34  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 T34  CONST_12  C19  C14  C15  C16     0.00   0.0  0
 T34  CONST_13  C9   C10  C5   C3    180.00   0.0  0
 T34  CONST_14  C7   C6   C5   C3    180.00   0.0  0
 T34  CONST_15  N12  C9   C10  C5    180.00   0.0  0
 T34  CONST_16  C11  C8   C7   C6    180.00   0.0  0
 T34  CONST_17  N12  C9   C8   C7    180.00   0.0  0
 T34  CONST_18  C11  C8   C9   C10   180.00   0.0  0
 T34  CONST_19  C18  C19  C14  C13   180.00   0.0  0
 T34  CONST_20  C16  C15  C14  C13   180.00   0.0  0
 T34  CONST_21  H4   C7   C6   C5    180.00   0.0  0
 T34  CONST_22  H5   C10  C5   C6    180.00   0.0  0
 T34  CONST_23  H3   C6   C7   C8    180.00   0.0  0
 T34  CONST_24  H15  C18  C19  C14   180.00   0.0  0
 T34  CONST_25  H13  C16  C15  C14   180.00   0.0  0
 T34  CONST_26  H14  C17  C16  C15   180.00   0.0  0
 T34  CONST_27  H16  C19  C14  C15   180.00   0.0  0
 T34  CONST_28  H12  C15  C16  C17   180.00   0.0  0
 T34  CONST_29  C13  N12  C9   C8    180.00   0.0  0
 T34  CONST_30  C13  N12  C9   C10     0.00   0.0  0
 T34  CONST_32  C5   C3   N2   O1    180.00   0.0  0
 T34  CONST_33  H2   N2   C3   C5      0.00   0.0  0
 T34  CONST_34  O4   C3   N2   O1      0.00   0.0  0
 T34  Var_01    C10  C5   C3   N2    147.16  30.0  2
 T34  Var_02    C14  C13  N12  C9   -177.05  30.0  1
 T34  Var_03    C19  C14  C13  N12  -124.35  30.0  2
 T34  Var_04    H6   C11  C8   C7    124.55  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
 T34  plan-1  C3   0.020
 T34  plan-1  C5   0.020
 T34  plan-1  C6   0.020
 T34  plan-1  C7   0.020
 T34  plan-1  C8   0.020
 T34  plan-1  C9   0.020
 T34  plan-1  C10  0.020
 T34  plan-1  C11  0.020
 T34  plan-1  N12  0.020
 T34  plan-1  H3   0.020
 T34  plan-1  H4   0.020
 T34  plan-1  H5   0.020
 T34  plan-2  C13  0.020
 T34  plan-2  C14  0.020
 T34  plan-2  C15  0.020
 T34  plan-2  C16  0.020
 T34  plan-2  C17  0.020
 T34  plan-2  C18  0.020
 T34  plan-2  C19  0.020
 T34  plan-2  H12  0.020
 T34  plan-2  H13  0.020
 T34  plan-2  H14  0.020
 T34  plan-2  H15  0.020
 T34  plan-2  H16  0.020
 T34  plan-3  O1   0.020
 T34  plan-3  N2   0.020
 T34  plan-3  C3   0.020
 T34  plan-3  O4   0.020
 T34  plan-3  C5   0.020
 T34  plan-3  H2   0.020
 T34  plan-4  C9   0.020
 T34  plan-4  N12  0.020
 T34  plan-4  C13  0.020
 T34  plan-4  H9   0.020

