# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:00:02 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: ~{N}-(1~{H}-benzotriazol-5-yl)-2-(2-methylphenoxy)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1OCC(=O)Nc2ccc3[nH]nnc3c2
#
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
 JV5  JV5  ~{N}-(1~{H}-benzotriazol-5-yl)-2-(2-methylphenoxy)ethanamide  ligand  35  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JV5
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
 JV5  C4   C  CR16  0  -0.258   5.5776  -1.8812   0.0424
 JV5  C5   C  CR16  0  -0.376   4.2411  -1.4979   0.1051
 JV5  C6   C  CR6   0   0.356   3.9034  -0.1530   0.0051
 JV5  C7   C  CH2   0  -0.308   1.5805  -0.5954   0.1436
 JV5  C8   C  C     0   0.503   0.2853   0.1936   0.0303
 JV5  C10  C  CR16  0  -0.302  -2.5573   1.1777   0.5157
 JV5  C13  C  CR56  0   0.148  -4.4159  -0.7806  -0.0310
 JV5  C1   C  CR6   0  -0.004   4.8958   0.8264  -0.1550
 JV5  C2   C  CR16  0  -0.286   6.2181   0.4111  -0.2134
 JV5  C3   C  CR16  0  -0.270   6.5707  -0.9319  -0.1170
 JV5  C9   C  CR6   0   0.362  -2.1466  -0.1619   0.2937
 JV5  C12  C  CR56  0   0.364  -4.8046   0.5433   0.1710
 JV5  N    N  NH1   0  -0.744  -0.7967  -0.5361   0.3964
 JV5  C    C  CH3   0  -0.709   4.5244   2.2761  -0.2561
 JV5  O    O  O2    0  -0.457   2.6360   0.3153   0.0530
 JV5  C11  C  CR16  0  -0.281  -3.8792   1.5495   0.4505
 JV5  C14  C  CR16  0  -0.381  -3.0700  -1.1501   0.0204
 JV5  N1   N  NR15  0  -0.529  -6.1489   0.4929   0.0337
 JV5  N2   N  N     0  -0.050  -6.5498  -0.7403  -0.2269
 JV5  N3   N  N     0  -0.334  -5.5379  -1.5214  -0.2721
 JV5  O1   O  O     0  -0.445   0.2479   1.3389  -0.3644
 JV5  H1   H  HCR6  0   0.257   5.8280  -2.9313   0.1203
 JV5  H2   H  HCR6  0   0.279   3.4850  -2.2608   0.2324
 JV5  H3   H  HCH2  0   0.262   1.5983  -1.1521   1.0885
 JV5  H4   H  HCH2  0   0.271   1.6052  -1.3337  -0.6690
 JV5  H6   H  HCR6  0   0.249   6.9924   1.1590  -0.3371
 JV5  H7   H  HCR6  0   0.250   7.6111  -1.2249  -0.1661
 JV5  H8   H  HNH1  0   0.421  -0.6338  -1.5037   0.6342
 JV5  H9   H  HCH3  0   0.243   4.0506   2.6359   0.6591
 JV5  H10  H  HCH3  0   0.241   5.4081   2.8871  -0.4331
 JV5  H11  H  HCH3  0   0.243   3.8203   2.4595  -1.0689
 JV5  H12  H  HCR6  0   0.286  -4.1767   2.5743   0.6238
 JV5  H13  H  HCR6  0   0.284  -2.7660  -2.1752  -0.1497
 JV5  H14  H  HNR5  0   0.435  -6.8288   1.2345   0.1100
 JV5  H5   H  HCR6  0   0.283  -1.8217   1.9291   0.7553

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
 JV5  C4   C5   aromatic  1.392  0.020  1.392
 JV5  C4   C3   aromatic  1.383  0.020  1.383
 JV5  C5   C6   aromatic  1.390  0.020  1.390
 JV5  C3   C2   aromatic  1.392  0.020  1.392
 JV5  C7   C8   single    1.521  0.020  1.521
 JV5  C7   O    single    1.397  0.020  1.397
 JV5  C6   C1   aromatic  1.403  0.020  1.403
 JV5  C6   O    single    1.352  0.020  1.352
 JV5  C2   C1   aromatic  1.387  0.020  1.387
 JV5  O1   C8   double    1.212  0.020  1.212
 JV5  C8   N    single    1.355  0.020  1.355
 JV5  C1   C    single    1.500  0.020  1.500
 JV5  N    C9   single    1.405  0.020  1.405
 JV5  C14  C9   aromatic  1.380  0.020  1.380
 JV5  C14  C13  aromatic  1.397  0.020  1.397
 JV5  C9   C10  aromatic  1.419  0.020  1.419
 JV5  C13  N3   aromatic  1.366  0.020  1.366
 JV5  C13  C12  aromatic  1.394  0.020  1.394
 JV5  N3   N2   aromatic  1.279  0.020  1.279
 JV5  C10  C11  aromatic  1.375  0.020  1.375
 JV5  C12  C11  aromatic  1.395  0.020  1.395
 JV5  C12  N1   aromatic  1.352  0.020  1.352
 JV5  N2   N1   aromatic  1.323  0.020  1.323
 JV5  C4   H1   single    0.930  0.020  1.080
 JV5  C5   H2   single    0.930  0.020  1.080
 JV5  C7   H3   single    0.970  0.020  1.090
 JV5  C7   H4   single    0.970  0.020  1.090
 JV5  C10  H5   single    0.930  0.020  1.080
 JV5  C2   H6   single    0.930  0.020  1.080
 JV5  C3   H7   single    0.930  0.020  1.080
 JV5  N    H8   single    0.860  0.020  1.020
 JV5  C    H9   single    0.970  0.020  1.090
 JV5  C    H10  single    0.970  0.020  1.090
 JV5  C    H11  single    0.970  0.020  1.090
 JV5  C11  H12  single    0.930  0.020  1.080
 JV5  C14  H13  single    0.930  0.020  1.080
 JV5  N1   H14  single    0.860  0.020  1.020

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
 JV5  H1   C4   C3   120.53  3.000
 JV5  H1   C4   C5   119.09  3.000
 JV5  C3   C4   C5   120.37  3.000
 JV5  H2   C5   C6   121.40  3.000
 JV5  H2   C5   C4   118.83  3.000
 JV5  C6   C5   C4   119.77  3.000
 JV5  O    C6   C1   115.16  3.000
 JV5  O    C6   C5   124.08  3.000
 JV5  C1   C6   C5   120.76  3.000
 JV5  H4   C7   H3   107.21  3.000
 JV5  H4   C7   O    111.91  3.000
 JV5  H3   C7   O    111.99  3.000
 JV5  H4   C7   C8   108.23  3.000
 JV5  H3   C7   C8   109.96  3.000
 JV5  O    C7   C8   107.48  3.000
 JV5  O1   C8   N    124.89  3.000
 JV5  N    C8   C7   112.36  3.000
 JV5  O1   C8   C7   122.74  3.000
 JV5  H5   C10  C11  118.55  3.000
 JV5  H5   C10  C9   119.68  3.000
 JV5  C11  C10  C9   121.76  3.000
 JV5  N3   C13  C14  130.88  3.000
 JV5  N3   C13  C12  108.15  3.000
 JV5  C14  C13  C12  120.96  3.000
 JV5  C    C1   C2   121.50  3.000
 JV5  C    C1   C6   120.47  3.000
 JV5  C2   C1   C6   118.03  3.000
 JV5  H6   C2   C3   119.53  3.000
 JV5  H6   C2   C1   118.64  3.000
 JV5  C3   C2   C1   121.83  3.000
 JV5  H7   C3   C2   120.12  3.000
 JV5  H7   C3   C4   120.65  3.000
 JV5  C2   C3   C4   119.23  3.000
 JV5  C14  C9   N    117.83  3.000
 JV5  C14  C9   C10  120.90  3.000
 JV5  N    C9   C10  121.23  3.000
 JV5  N1   C12  C11  134.96  3.000
 JV5  N1   C12  C13  103.12  3.000
 JV5  C11  C12  C13  121.92  3.000
 JV5  H8   N    C9   115.32  3.000
 JV5  H8   N    C8   116.80  3.000
 JV5  C9   N    C8   127.16  3.000
 JV5  H11  C    H10  107.96  3.000
 JV5  H11  C    H9   106.81  3.000
 JV5  H10  C    H9   107.68  3.000
 JV5  H11  C    C1   111.86  3.000
 JV5  H10  C    C1   110.63  3.000
 JV5  H9   C    C1   111.69  3.000
 JV5  C7   O    C6   119.00  3.000
 JV5  H12  C11  C12  122.22  3.000
 JV5  H12  C11  C10  120.89  3.000
 JV5  C12  C11  C10  116.88  3.000
 JV5  H13  C14  C9   121.42  3.000
 JV5  H13  C14  C13  121.02  3.000
 JV5  C9   C14  C13  117.56  3.000
 JV5  H14  N1   N2   119.73  3.000
 JV5  H14  N1   C12  129.41  3.000
 JV5  N2   N1   C12  110.86  3.000
 JV5  N3   N2   N1   109.67  3.000
 JV5  N2   N3   C13  108.20  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
 JV5  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 JV5  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 JV5  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 JV5  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 JV5  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 JV5  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 JV5  CONST_07  C13  C14  C9   C10     0.00   0.0  0
 JV5  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 JV5  CONST_09  N1   C12  C11  C10   180.00   0.0  0
 JV5  CONST_10  N1   N2   N3   C13     0.00   0.0  0
 JV5  CONST_11  N2   N1   C12  C13     0.00   0.0  0
 JV5  CONST_12  N3   C13  C14  C9    180.00   0.0  0
 JV5  CONST_13  C12  C13  C14  C9      0.00   0.0  0
 JV5  CONST_14  C12  C11  C10  C9      0.00   0.0  0
 JV5  CONST_15  N2   N3   C13  C12     0.00   0.0  0
 JV5  CONST_16  N3   N2   N1   C12     0.00   0.0  0
 JV5  CONST_17  C14  C9   C10  C11     0.00   0.0  0
 JV5  CONST_18  C14  C13  C12  C11     0.00   0.0  0
 JV5  CONST_19  N3   C13  C12  C11   180.00   0.0  0
 JV5  CONST_20  N2   N1   C12  C11   180.00   0.0  0
 JV5  CONST_21  N2   N3   C13  C14   180.00   0.0  0
 JV5  CONST_22  N1   C12  C13  C14   180.00   0.0  0
 JV5  CONST_23  N3   C13  C12  N1      0.00   0.0  0
 JV5  CONST_24  O    C6   C5   C4    180.00   0.0  0
 JV5  CONST_25  C    C1   C6   C5    180.00   0.0  0
 JV5  CONST_26  N    C9   C14  C13   180.00   0.0  0
 JV5  CONST_27  O    C6   C1   C2    180.00   0.0  0
 JV5  CONST_28  C    C1   C2   C3    180.00   0.0  0
 JV5  CONST_29  C11  C10  C9   N     180.00   0.0  0
 JV5  CONST_30  H6   C2   C3   C4    180.00   0.0  0
 JV5  CONST_31  H7   C3   C4   C5    180.00   0.0  0
 JV5  CONST_32  H1   C4   C5   C6    180.00   0.0  0
 JV5  CONST_33  H13  C14  C9   C10   180.00   0.0  0
 JV5  CONST_34  H12  C11  C12  C13   180.00   0.0  0
 JV5  CONST_35  H14  N1   C12  C13   180.00   0.0  0
 JV5  CONST_36  H2   C5   C6   C1    180.00   0.0  0
 JV5  CONST_37  H5   C10  C11  C12   180.00   0.0  0
 JV5  CONST_41  C9   N    C8   C7    180.00   0.0  0
 JV5  CONST_42  O1   C8   N    C9      0.00   0.0  0
 JV5  Var_01    C1   C6   O    C7    176.84  30.0  2
 JV5  Var_02    H9   C    C1   C6     63.29  30.0  2
 JV5  Var_03    C8   C7   O    C6   -174.07  30.0  2
 JV5  Var_04    O    C7   C8   N    -166.38  30.0  1

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
 JV5  plan-1  C4   0.020
 JV5  plan-1  C5   0.020
 JV5  plan-1  C6   0.020
 JV5  plan-1  C1   0.020
 JV5  plan-1  C2   0.020
 JV5  plan-1  C3   0.020
 JV5  plan-1  C    0.020
 JV5  plan-1  O    0.020
 JV5  plan-1  H1   0.020
 JV5  plan-1  H2   0.020
 JV5  plan-1  H6   0.020
 JV5  plan-1  H7   0.020
 JV5  plan-2  C10  0.020
 JV5  plan-2  C13  0.020
 JV5  plan-2  C9   0.020
 JV5  plan-2  C12  0.020
 JV5  plan-2  N    0.020
 JV5  plan-2  C11  0.020
 JV5  plan-2  C14  0.020
 JV5  plan-2  N1   0.020
 JV5  plan-2  N2   0.020
 JV5  plan-2  N3   0.020
 JV5  plan-2  H12  0.020
 JV5  plan-2  H13  0.020
 JV5  plan-2  H14  0.020
 JV5  plan-2  H5   0.020
 JV5  plan-3  C7   0.020
 JV5  plan-3  C8   0.020
 JV5  plan-3  C9   0.020
 JV5  plan-3  N    0.020
 JV5  plan-3  O1   0.020
 JV5  plan-3  H8   0.020

