# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 21:36:56 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: (~{E})-3-dibenzofuran-4-yl-~{N}-oxidanyl-prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)/C=C/c1cccc2c1oc3ccccc23
#
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
 T56  T56  "(E)-3-dibenzofuran-4-yl-N-oxidanyl-prop-2-enamide"
  ligand  30  19  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T56
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
 T56  C02  C  C     0   0.534   96.5451  -90.4854   6.3442
 T56  C03  C  C1    0  -0.417   97.3651  -90.1981   7.5427
 T56  C04  C  C1    0  -0.230   98.6855  -90.4003   7.5285
 T56  C05  C  CR6   0   0.052   99.6003  -90.1606   8.6387
 T56  C06  C  CR16  0  -0.340   99.2254  -89.5874   9.8589
 T56  C07  C  CR16  0  -0.240  100.1330  -89.3780  10.8921
 T56  C08  C  CR16  0  -0.379  101.4692  -89.7316  10.7600
 T56  C09  C  CR56  0   0.092  101.8773  -90.3023   9.5621
 T56  C10  C  CR56  0   0.073  103.1295  -90.7962   9.0393
 T56  C11  C  CR16  0  -0.364  104.4300  -90.8969   9.5227
 T56  C12  C  CR16  0  -0.254  105.3957  -91.4499   8.6964
 T56  C13  C  CR16  0  -0.266  105.0751  -91.8947   7.4104
 T56  C14  C  CR16  0  -0.341  103.7833  -91.8023   6.9106
 T56  C15  C  CR56  0   0.357  102.8378  -91.2490   7.7521
 T56  C17  C  CR56  0   0.320  100.9461  -90.5015   8.5399
 T56  N18  N  NH1   0  -0.394   95.2269  -90.2843   6.5654
 T56  O01  O  O     0  -0.467   96.9952  -90.8924   5.2866
 T56  O16  O  O     0  -0.479  101.5221  -91.0722   7.4531
 T56  O19  O  OH1   0  -0.537   94.3496  -90.3350   5.5267
 T56  H1   H  H     0   0.275   96.8570  -89.8301   8.4269
 T56  H2   H  H     0   0.266   99.1252  -90.7816   6.6131
 T56  H3   H  HCR6  0   0.264   98.1966  -89.2890  10.0115
 T56  H4   H  HCR6  0   0.264   99.7863  -88.9288  11.8130
 T56  H5   H  HCR6  0   0.263  102.1707  -89.5654  11.5671
 T56  H6   H  HCR6  0   0.259  104.6815  -90.5531  10.5177
 T56  H7   H  HCR6  0   0.260  106.4144  -91.5395   9.0491
 T56  H8   H  HCR6  0   0.265  105.8504  -92.3216   6.7880
 T56  H9   H  HCR6  0   0.273  103.5329  -92.1460   5.9158
 T56  H10  H  HNH1  0   0.415   94.8881  -89.7855   7.3766
 T56  H11  H  HOH1  0   0.476   93.9471  -91.2130   5.5573

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
 T56  O19  N18  single    1.361  0.020  1.361
 T56  O01  C02  double    1.219  0.020  1.219
 T56  C02  N18  single    1.352  0.020  1.352
 T56  C02  C03  single    1.480  0.020  1.480
 T56  C14  C13  aromatic  1.388  0.020  1.388
 T56  C14  C15  aromatic  1.381  0.020  1.381
 T56  O16  C15  aromatic  1.361  0.020  1.361
 T56  O16  C17  aromatic  1.356  0.020  1.356
 T56  C13  C12  aromatic  1.398  0.020  1.398
 T56  C04  C03  double    1.336  0.020  1.336
 T56  C04  C05  single    1.458  0.020  1.458
 T56  C15  C10  aromatic  1.395  0.020  1.395
 T56  C17  C05  aromatic  1.392  0.020  1.392
 T56  C17  C09  aromatic  1.397  0.020  1.397
 T56  C05  C06  aromatic  1.399  0.020  1.399
 T56  C12  C11  aromatic  1.386  0.020  1.386
 T56  C10  C09  aromatic  1.444  0.020  1.444
 T56  C10  C11  aromatic  1.391  0.020  1.391
 T56  C09  C08  aromatic  1.388  0.020  1.388
 T56  C06  C07  aromatic  1.391  0.020  1.391
 T56  C08  C07  aromatic  1.388  0.020  1.388
 T56  C03  H1   single    0.930  0.020  1.080
 T56  C04  H2   single    0.930  0.020  1.080
 T56  C06  H3   single    0.930  0.020  1.080
 T56  C07  H4   single    0.930  0.020  1.080
 T56  C08  H5   single    0.930  0.020  1.080
 T56  C11  H6   single    0.930  0.020  1.080
 T56  C12  H7   single    0.930  0.020  1.080
 T56  C13  H8   single    0.930  0.020  1.080
 T56  C14  H9   single    0.930  0.020  1.080
 T56  N18  H10  single    0.890  0.020  1.040
 T56  O19  H11  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
 T56  O01  C02  N18  123.48  3.000
 T56  N18  C02  C03  112.26  3.000
 T56  O01  C02  C03  124.23  3.000
 T56  H1   C03  C04  121.55  3.000
 T56  H1   C03  C02  117.81  3.000
 T56  C04  C03  C02  120.63  3.000
 T56  H2   C04  C05  116.48  3.000
 T56  H2   C04  C03  117.57  3.000
 T56  C05  C04  C03  125.94  3.000
 T56  C17  C05  C06  114.91  3.000
 T56  C06  C05  C04  124.28  3.000
 T56  C17  C05  C04  120.81  3.000
 T56  H3   C06  C07  118.31  3.000
 T56  H3   C06  C05  119.38  3.000
 T56  C07  C06  C05  122.31  3.000
 T56  H4   C07  C08  119.69  3.000
 T56  H4   C07  C06  119.05  3.000
 T56  C08  C07  C06  121.26  3.000
 T56  H5   C08  C09  121.07  3.000
 T56  H5   C08  C07  120.91  3.000
 T56  C09  C08  C07  118.01  3.000
 T56  C17  C09  C10  105.33  3.000
 T56  C10  C09  C08  135.07  3.000
 T56  C17  C09  C08  119.61  3.000
 T56  C15  C10  C11  119.50  3.000
 T56  C11  C10  C09  135.21  3.000
 T56  C15  C10  C09  105.29  3.000
 T56  H6   C11  C12  120.86  3.000
 T56  H6   C11  C10  120.90  3.000
 T56  C12  C11  C10  118.24  3.000
 T56  H7   C12  C13  119.31  3.000
 T56  H7   C12  C11  119.66  3.000
 T56  C13  C12  C11  121.04  3.000
 T56  H8   C13  C14  119.08  3.000
 T56  H8   C13  C12  119.37  3.000
 T56  C14  C13  C12  121.56  3.000
 T56  H9   C14  C15  121.94  3.000
 T56  H9   C14  C13  121.69  3.000
 T56  C15  C14  C13  116.37  3.000
 T56  O16  C15  C14  125.45  3.000
 T56  O16  C15  C10  111.26  3.000
 T56  C14  C15  C10  123.29  3.000
 T56  O16  C17  C09  111.30  3.000
 T56  C09  C17  C05  123.89  3.000
 T56  O16  C17  C05  124.80  3.000
 T56  H10  N18  O19  114.52  3.000
 T56  H10  N18  C02  122.12  3.000
 T56  O19  N18  C02  119.89  3.000
 T56  C17  O16  C15  106.82  3.000
 T56  H11  O19  N18  106.15  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
 T56  CONST_01  C15  O16  C17  C05   180.00   0.0  0
 T56  CONST_02  C10  C09  C17  C05   180.00   0.0  0
 T56  CONST_03  C08  C09  C17  C05     0.00   0.0  0
 T56  CONST_04  C08  C07  C06  C05     0.00   0.0  0
 T56  CONST_05  O16  C17  C05  C06   180.00   0.0  0
 T56  CONST_06  C09  C17  C05  C06     0.00   0.0  0
 T56  CONST_07  C09  C08  C07  C06     0.00   0.0  0
 T56  CONST_08  C17  C05  C06  C07     0.00   0.0  0
 T56  CONST_09  C17  C09  C08  C07     0.00   0.0  0
 T56  CONST_10  C10  C09  C08  C07   180.00   0.0  0
 T56  CONST_11  O16  C17  C09  C08   180.00   0.0  0
 T56  CONST_12  C15  C10  C09  C08   180.00   0.0  0
 T56  CONST_13  C11  C10  C09  C08     0.00   0.0  0
 T56  CONST_14  C15  O16  C17  C09     0.00   0.0  0
 T56  CONST_15  C14  C15  C10  C09   180.00   0.0  0
 T56  CONST_16  O16  C15  C10  C09     0.00   0.0  0
 T56  CONST_17  C12  C11  C10  C09   180.00   0.0  0
 T56  CONST_18  C13  C14  C15  C10     0.00   0.0  0
 T56  CONST_19  C17  O16  C15  C10     0.00   0.0  0
 T56  CONST_20  O16  C17  C09  C10     0.00   0.0  0
 T56  CONST_21  C13  C12  C11  C10     0.00   0.0  0
 T56  CONST_22  C14  C13  C12  C11     0.00   0.0  0
 T56  CONST_23  C14  C15  C10  C11     0.00   0.0  0
 T56  CONST_24  O16  C15  C10  C11   180.00   0.0  0
 T56  CONST_25  C17  C09  C10  C11   180.00   0.0  0
 T56  CONST_26  C15  C14  C13  C12     0.00   0.0  0
 T56  CONST_27  C15  C10  C11  C12     0.00   0.0  0
 T56  CONST_28  O16  C15  C14  C13   180.00   0.0  0
 T56  CONST_29  C17  O16  C15  C14   180.00   0.0  0
 T56  CONST_30  C17  C09  C10  C15     0.00   0.0  0
 T56  CONST_31  O16  C17  C05  C04     0.00   0.0  0
 T56  CONST_32  C09  C17  C05  C04   180.00   0.0  0
 T56  CONST_33  C07  C06  C05  C04   180.00   0.0  0
 T56  CONST_34  H4   C07  C06  C05   180.00   0.0  0
 T56  CONST_35  H5   C08  C07  C06   180.00   0.0  0
 T56  CONST_36  H3   C06  C07  C08   180.00   0.0  0
 T56  CONST_37  H6   C11  C10  C09     0.00   0.0  0
 T56  CONST_38  H4   C07  C08  C09   180.00   0.0  0
 T56  CONST_39  H9   C14  C15  C10   180.00   0.0  0
 T56  CONST_40  H5   C08  C09  C10     0.00   0.0  0
 T56  CONST_41  H7   C12  C11  C10   180.00   0.0  0
 T56  CONST_42  H8   C13  C12  C11   180.00   0.0  0
 T56  CONST_43  H9   C14  C13  C12   180.00   0.0  0
 T56  CONST_44  H6   C11  C12  C13   180.00   0.0  0
 T56  CONST_45  H7   C12  C13  C14   180.00   0.0  0
 T56  CONST_46  H8   C13  C14  C15   180.00   0.0  0
 T56  CONST_47  H6   C11  C10  C15   180.00   0.0  0
 T56  CONST_48  H3   C06  C05  C17   180.00   0.0  0
 T56  CONST_49  H5   C08  C09  C17   180.00   0.0  0
 T56  CONST_50  H9   C14  C15  O16     0.00   0.0  0
 T56  CONST_51  O19  N18  C02  C03   180.00   0.0  0
 T56  CONST_52  O19  N18  C02  O01     0.00   0.0  0
 T56  CONST_53  H10  N18  C02  C03     0.00   0.0  0
 T56  CONST_54  H10  N18  C02  O01   180.00   0.0  0
 T56  Var_01    C17  C05  C04  C03   175.22  30.0  2
 T56  Var_02    C06  C05  C04  C03    -4.81  30.0  2
 T56  Var_03    H2   C04  C05  C06   175.47  30.0  2
 T56  Var_04    H2   C04  C05  C17    -4.50  30.0  2
 T56  Var_05    C05  C04  C03  C02  -179.86   0.0  2
 T56  Var_06    H1   C03  C04  C05    -0.45   0.0  2
 T56  Var_07    O01  C02  C03  C04    -1.17  30.0  2
 T56  Var_08    N18  C02  C03  C04   176.93  30.0  2
 T56  Var_09    H2   C04  C03  C02    -0.14   0.0  2
 T56  Var_10    H1   C03  C02  N18    -2.50  30.0  2
 T56  Var_11    H1   C03  C02  O01   179.40  30.0  2
 T56  Var_12    H2   C04  C03  H1    179.27   0.0  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
 T56  plan-1  C04  0.020
 T56  plan-1  C05  0.020
 T56  plan-1  C06  0.020
 T56  plan-1  C07  0.020
 T56  plan-1  C08  0.020
 T56  plan-1  C09  0.020
 T56  plan-1  C10  0.020
 T56  plan-1  C11  0.020
 T56  plan-1  C12  0.020
 T56  plan-1  C13  0.020
 T56  plan-1  C14  0.020
 T56  plan-1  C15  0.020
 T56  plan-1  C17  0.020
 T56  plan-1  O16  0.020
 T56  plan-1  H3   0.020
 T56  plan-1  H4   0.020
 T56  plan-1  H5   0.020
 T56  plan-1  H6   0.020
 T56  plan-1  H7   0.020
 T56  plan-1  H8   0.020
 T56  plan-1  H9   0.020
 T56  plan-2  C02  0.020
 T56  plan-2  C03  0.020
 T56  plan-2  N18  0.020
 T56  plan-2  O01  0.020
 T56  plan-2  O19  0.020
 T56  plan-2  H10  0.020
 T56  plan-3  C02  0.020
 T56  plan-3  C03  0.020
 T56  plan-3  C04  0.020
 T56  plan-3  C05  0.020
 T56  plan-3  H1   0.020
 T56  plan-3  H2   0.020

