# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:10:57 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-(1,5-dimethyl-6-oxidanylidene-pyridin-3-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=C(C=C(C)C1=O)c2ccc(cc2)C(N)=O
#
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
 5TU  5TU  4-(1,5-dimethyl-6-oxidanylidene-pyridin-3-yl)benzamide  ligand  32  18  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5TU
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
 5TU  N1   N  NH2   0  -0.825  -5.4845  -0.8337  -0.6517
 5TU  C4   C  CR6   0  -0.116   3.0985   1.2348  -0.0726
 5TU  C5   C  CH3   0  -0.709   3.9123   2.4858  -0.1435
 5TU  C6   C  CR6   0   0.552   3.8201  -0.0156   0.0133
 5TU  C7   C  CR6   0   0.099  -0.4869   0.0399  -0.0573
 5TU  C8   C  CR16  0  -0.311  -1.2033   1.0981   0.5062
 5TU  C10  C  CR6   0  -0.057  -3.3082   0.0564  -0.0630
 5TU  C13  C  C     0   0.501  -4.8024   0.1326  -0.0202
 5TU  O1   O  O     0  -0.483  -5.3650   1.0451   0.5723
 5TU  C9   C  CR16  0  -0.251  -2.5862   1.1049   0.5026
 5TU  C11  C  CR16  0  -0.264  -2.5970  -1.0024  -0.6256
 5TU  C12  C  CR16  0  -0.305  -1.2134  -1.0066  -0.6295
 5TU  C2   C  CR6   0  -0.036   0.9831   0.0339  -0.0428
 5TU  C1   C  CR16  0  -0.002   1.6850  -1.1311   0.0371
 5TU  C3   C  CR16  0  -0.203   1.7404   1.2353  -0.0962
 5TU  N    N  NR6   0  -0.505   3.0372  -1.1592   0.0607
 5TU  C    C  CH3   0  -0.519   3.7323  -2.4354   0.1578
 5TU  H1   H  HNH2  0   0.414  -5.0517  -1.5707  -1.1778
 5TU  H2   H  HNH2  0   0.406  -6.4911  -0.8144  -0.6442
 5TU  H3   H  HCH3  0   0.245   4.5624   2.5873   0.7272
 5TU  H4   H  HCH3  0   0.245   4.5585   2.4912  -1.0231
 5TU  H5   H  HCH3  0   0.243   3.2712   3.3645  -0.1905
 5TU  H6   H  HCR6  0   0.259  -0.6797   1.9218   0.9740
 5TU  H7   H  HCR6  0   0.263  -3.1113   1.9356   0.9532
 5TU  H8   H  HCR6  0   0.251  -3.0973  -1.8477  -1.0794
 5TU  H9   H  HCR6  0   0.260  -0.6979  -1.8319  -1.1029
 5TU  H10  H  HCR6  0   0.303   1.1971  -2.0930   0.1079
 5TU  H11  H  HCR6  0   0.264   1.2199   2.1825  -0.1793
 5TU  H12  H  HCH3  0   0.262   4.3989  -2.5712  -0.6909
 5TU  H13  H  HCH3  0   0.262   4.3176  -2.4832   1.0737
 5TU  H14  H  HCH3  0   0.258   3.0016  -3.2378   0.1634
 5TU  O    O  O     0  -0.501   5.0444  -0.1060   0.0442

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
 5TU  N1   C13  single    1.341  0.020  1.341
 5TU  C13  C10  single    1.497  0.020  1.497
 5TU  C13  O1   double    1.225  0.020  1.225
 5TU  C11  C10  aromatic  1.394  0.020  1.394
 5TU  C11  C12  aromatic  1.384  0.020  1.384
 5TU  C10  C9   aromatic  1.393  0.020  1.393
 5TU  C12  C7   aromatic  1.397  0.020  1.397
 5TU  C9   C8   aromatic  1.383  0.020  1.383
 5TU  C7   C8   aromatic  1.397  0.020  1.397
 5TU  C7   C2   single    1.470  0.020  1.470
 5TU  C3   C2   single    1.421  0.020  1.421
 5TU  C3   C4   double    1.358  0.020  1.358
 5TU  C2   C1   double    1.362  0.020  1.362
 5TU  C5   C4   single    1.494  0.020  1.494
 5TU  C4   C6   single    1.446  0.020  1.446
 5TU  C1   N    single    1.353  0.020  1.353
 5TU  C6   N    single    1.387  0.020  1.387
 5TU  C6   O    double    1.228  0.020  1.228
 5TU  N    C    single    1.456  0.020  1.456
 5TU  N1   H1   single    0.860  0.020  1.020
 5TU  N1   H2   single    0.860  0.020  1.020
 5TU  C5   H3   single    0.970  0.020  1.090
 5TU  C5   H4   single    0.970  0.020  1.090
 5TU  C5   H5   single    0.970  0.020  1.090
 5TU  C8   H6   single    0.930  0.020  1.080
 5TU  C9   H7   single    0.930  0.020  1.080
 5TU  C11  H8   single    0.930  0.020  1.080
 5TU  C12  H9   single    0.930  0.020  1.080
 5TU  C1   H10  single    0.930  0.020  1.080
 5TU  C3   H11  single    0.930  0.020  1.080
 5TU  C    H12  single    0.970  0.020  1.090
 5TU  C    H13  single    0.970  0.020  1.090
 5TU  C    H14  single    0.970  0.020  1.090

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
 5TU  H2   N1   H1   116.68  3.000
 5TU  H2   N1   C13  119.42  3.000
 5TU  H1   N1   C13  123.84  3.000
 5TU  C3   C4   C6   120.02  3.000
 5TU  C6   C4   C5   117.06  3.000
 5TU  C3   C4   C5   122.92  3.000
 5TU  H5   C5   H4   108.05  3.000
 5TU  H5   C5   H3   108.07  3.000
 5TU  H4   C5   H3   106.85  3.000
 5TU  H5   C5   C4   110.92  3.000
 5TU  H4   C5   C4   111.40  3.000
 5TU  H3   C5   C4   111.37  3.000
 5TU  N    C6   O    120.08  3.000
 5TU  O    C6   C4   124.24  3.000
 5TU  N    C6   C4   115.68  3.000
 5TU  C2   C7   C12  121.41  3.000
 5TU  C2   C7   C8   120.80  3.000
 5TU  C12  C7   C8   117.79  3.000
 5TU  H6   C8   C9   118.76  3.000
 5TU  H6   C8   C7   120.19  3.000
 5TU  C9   C8   C7   121.04  3.000
 5TU  C11  C10  C9   118.10  3.000
 5TU  C9   C10  C13  117.87  3.000
 5TU  C11  C10  C13  124.02  3.000
 5TU  O1   C13  C10  120.68  3.000
 5TU  O1   C13  N1   122.08  3.000
 5TU  C10  C13  N1   117.24  3.000
 5TU  H7   C9   C10  119.72  3.000
 5TU  H7   C9   C8   119.23  3.000
 5TU  C10  C9   C8   121.04  3.000
 5TU  H8   C11  C12  117.31  3.000
 5TU  H8   C11  C10  121.78  3.000
 5TU  C12  C11  C10  120.90  3.000
 5TU  H9   C12  C11  118.68  3.000
 5TU  H9   C12  C7   120.19  3.000
 5TU  C11  C12  C7   121.12  3.000
 5TU  C3   C2   C1   116.78  3.000
 5TU  C1   C2   C7   121.28  3.000
 5TU  C3   C2   C7   121.94  3.000
 5TU  H10  C1   N    115.57  3.000
 5TU  H10  C1   C2   122.15  3.000
 5TU  N    C1   C2   122.27  3.000
 5TU  H11  C3   C2   119.06  3.000
 5TU  H11  C3   C4   118.80  3.000
 5TU  C2   C3   C4   122.13  3.000
 5TU  C    N    C1   119.77  3.000
 5TU  C    N    C6   117.09  3.000
 5TU  C1   N    C6   123.13  3.000
 5TU  H14  C    H13  108.99  3.000
 5TU  H14  C    H12  108.93  3.000
 5TU  H13  C    H12  108.76  3.000
 5TU  H14  C    N    109.07  3.000
 5TU  H13  C    N    110.57  3.000
 5TU  H12  C    N    110.48  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
 5TU  CONST_01  C10  C11  C12  C7     0.00   0.0  0
 5TU  CONST_02  C10  C9   C8   C7     0.00   0.0  0
 5TU  CONST_03  C11  C10  C9   C8     0.00   0.0  0
 5TU  CONST_04  C11  C12  C7   C8     0.00   0.0  0
 5TU  CONST_05  C12  C11  C10  C9     0.00   0.0  0
 5TU  CONST_06  C12  C7   C8   C9     0.00   0.0  0
 5TU  CONST_07  C2   C7   C8   C9   180.00   0.0  0
 5TU  CONST_08  C2   C7   C12  C11  180.00   0.0  0
 5TU  CONST_09  C1   N    C6   C4     0.00   0.0  0
 5TU  CONST_10  C13  C10  C9   C8   180.00   0.0  0
 5TU  CONST_11  C12  C11  C10  C13  180.00   0.0  0
 5TU  CONST_12  C    N    C6   C4   180.00   0.0  0
 5TU  CONST_13  O    C6   N    C1   180.00   0.0  0
 5TU  CONST_14  H8   C11  C12  C7   180.00   0.0  0
 5TU  CONST_15  H7   C9   C8   C7   180.00   0.0  0
 5TU  CONST_16  H9   C12  C7   C8   180.00   0.0  0
 5TU  CONST_17  H6   C8   C9   C10  180.00   0.0  0
 5TU  CONST_18  C    N    C6   O      0.00   0.0  0
 5TU  CONST_19  H1   N1   C13  C10    0.00   0.0  0
 5TU  CONST_20  H2   N1   C13  C10  180.00   0.0  0
 5TU  Var_01    C3   C2   C7   C8   -31.28  30.0  2
 5TU  Var_02    C11  C10  C13  N1    -5.11  30.0  2
 5TU  Var_03    H3   C5   C4   C6   -58.77  30.0  3
 5TU  Var_04    H12  C    N    C6   -59.04  30.0  3

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
 5TU  plan-1  C7   0.020
 5TU  plan-1  C8   0.020
 5TU  plan-1  C10  0.020
 5TU  plan-1  C13  0.020
 5TU  plan-1  C9   0.020
 5TU  plan-1  C11  0.020
 5TU  plan-1  C12  0.020
 5TU  plan-1  C2   0.020
 5TU  plan-1  H6   0.020
 5TU  plan-1  H7   0.020
 5TU  plan-1  H8   0.020
 5TU  plan-1  H9   0.020
 5TU  plan-2  C4   0.020
 5TU  plan-2  C5   0.020
 5TU  plan-2  C6   0.020
 5TU  plan-2  C7   0.020
 5TU  plan-2  C2   0.020
 5TU  plan-2  C1   0.020
 5TU  plan-2  C3   0.020
 5TU  plan-2  N    0.020
 5TU  plan-2  C    0.020
 5TU  plan-2  H10  0.020
 5TU  plan-2  H11  0.020
 5TU  plan-2  O    0.020
 5TU  plan-3  N1   0.020
 5TU  plan-3  C10  0.020
 5TU  plan-3  C13  0.020
 5TU  plan-3  O1   0.020
 5TU  plan-3  H1   0.020
 5TU  plan-3  H2   0.020

