# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 15:19:02 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: N-[(2R)-3-methylbutan-2-yl]-1H-benzotriazole-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](C)NC(=O)c1ccc2nn[nH]c2c1
#
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
 JVD  JVD  N-[(2R)-3-methylbutan-2-yl]-1H-benzotriazole-6-carboxamide  ligand  33  17  .  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_JVD
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
 JVD  C1   C  CR16  0  -0.306  -0.7854   1.1771   0.4511
 JVD  C2   C  CR16  0  -0.275  -2.0498   1.6701   0.6681
 JVD  C3   C  CR16  0  -0.309  -1.6239  -0.8825  -0.5438
 JVD  C4   C  CR6   0  -0.051  -0.5664  -0.0918  -0.1399
 JVD  C5   C  CR56  0   0.392  -2.9009  -0.3792  -0.3083
 JVD  C6   C  CR56  0   0.140  -3.1262   0.8654   0.2836
 JVD  C7   C  C     0   0.542   0.8152  -0.6201  -0.3929
 JVD  C10  C  CH3   0  -0.667   3.6203  -1.1545   1.6595
 JVD  C11  C  CH1   0  -0.222   4.0148   0.7029  -0.0569
 JVD  C12  C  CH1   0  -0.069   3.1789  -0.5261   0.3425
 JVD  N13  N  NR15  0  -0.534  -4.1515  -0.8392  -0.5373
 JVD  N14  N  N     0  -0.043  -5.0568   0.0345  -0.1286
 JVD  N15  N  N     0  -0.327  -4.4750   1.0603   0.3647
 JVD  N16  N  NH1   0  -0.646   1.7710  -0.1751   0.4352
 JVD  O17  O  O     0  -0.488   1.0179  -1.4153  -1.3014
 JVD  H1   H  HCR6  0   0.262   0.0578   1.8011   0.7174
 JVD  H2   H  HCR6  0   0.279  -2.2048   2.6447   1.1101
 JVD  H3   H  HCR6  0   0.284  -1.4645  -1.8442  -1.0110
 JVD  H4   H  HCH3  0   0.233   6.0632   1.2145  -0.5270
 JVD  H5   H  HCH3  0   0.233   5.9355   0.0325   0.7630
 JVD  H6   H  HCH3  0   0.218   5.6443  -0.4526  -0.9080
 JVD  H7   H  HCH3  0   0.226   2.4856   1.6526  -1.2984
 JVD  H8   H  HCH3  0   0.231   4.1277   2.1694  -1.6468
 JVD  H9   H  HCH3  0   0.216   3.5771   0.5835  -2.1803
 JVD  H10  H  HCH3  0   0.239   4.6385  -1.5348   1.5983
 JVD  H11  H  HCH3  0   0.224   3.5844  -0.4283   2.4748
 JVD  H12  H  HCH3  0   0.241   2.9732  -1.9915   1.9222
 JVD  H13  H  HCH1  0   0.216   3.9051   1.4531   0.7367
 JVD  H14  H  HCH1  0   0.243   3.2663  -1.2707  -0.4516
 JVD  H15  H  HNR5  0   0.437  -4.4474  -1.7083  -0.9563
 JVD  H16  H  HNH1  0   0.401   1.5058   0.3985   1.2210
 JVD  C8   C  CH3   0  -0.667   5.4946   0.3500  -0.1813
 JVD  C9   C  CH3   0  -0.655   3.5178   1.3095  -1.3659

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
 JVD  C10  C12  single    1.525  0.020  1.525
 JVD  C9   C11  single    1.526  0.020  1.526
 JVD  C12  C11  single    1.539  0.020  1.539
 JVD  C12  N16  single    1.454  0.020  1.454
 JVD  C11  C8   single    1.526  0.020  1.526
 JVD  N16  C7   single    1.341  0.020  1.341
 JVD  O17  C7   double    1.224  0.020  1.224
 JVD  C7   C4   single    1.501  0.020  1.501
 JVD  C4   C3   aromatic  1.381  0.020  1.381
 JVD  C4   C1   aromatic  1.417  0.020  1.417
 JVD  C3   C5   aromatic  1.393  0.020  1.393
 JVD  C1   C2   aromatic  1.374  0.020  1.374
 JVD  C5   N13  aromatic  1.352  0.020  1.352
 JVD  C5   C6   aromatic  1.396  0.020  1.396
 JVD  N13  N14  aromatic  1.323  0.020  1.323
 JVD  C2   C6   aromatic  1.398  0.020  1.398
 JVD  C6   N15  aromatic  1.365  0.020  1.365
 JVD  N14  N15  aromatic  1.278  0.020  1.278
 JVD  C1   H1   single    0.930  0.020  1.080
 JVD  C2   H2   single    0.930  0.020  1.080
 JVD  C3   H3   single    0.930  0.020  1.080
 JVD  C8   H4   single    0.970  0.020  1.090
 JVD  C8   H5   single    0.970  0.020  1.090
 JVD  C8   H6   single    0.970  0.020  1.090
 JVD  C9   H7   single    0.970  0.020  1.090
 JVD  C9   H8   single    0.970  0.020  1.090
 JVD  C9   H9   single    0.970  0.020  1.090
 JVD  C10  H10  single    0.970  0.020  1.090
 JVD  C10  H11  single    0.970  0.020  1.090
 JVD  C10  H12  single    0.970  0.020  1.090
 JVD  C11  H13  single    0.970  0.020  1.090
 JVD  C12  H14  single    0.970  0.020  1.090
 JVD  N13  H15  single    0.860  0.020  1.020
 JVD  N16  H16  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
 JVD  H1   C1   C4   119.91  3.000
 JVD  H1   C1   C2   118.10  3.000
 JVD  C4   C1   C2   121.96  3.000
 JVD  H2   C2   C6   121.40  3.000
 JVD  H2   C2   C1   121.31  3.000
 JVD  C6   C2   C1   117.29  3.000
 JVD  H3   C3   C5   122.00  3.000
 JVD  H3   C3   C4   121.52  3.000
 JVD  C5   C3   C4   116.48  3.000
 JVD  C7   C4   C3   117.02  3.000
 JVD  C3   C4   C1   121.09  3.000
 JVD  C7   C4   C1   121.87  3.000
 JVD  N13  C5   C6   103.05  3.000
 JVD  C6   C5   C3   122.80  3.000
 JVD  N13  C5   C3   134.15  3.000
 JVD  N15  C6   C5   108.17  3.000
 JVD  N15  C6   C2   131.47  3.000
 JVD  C5   C6   C2   120.36  3.000
 JVD  O17  C7   N16  123.77  3.000
 JVD  O17  C7   C4   120.42  3.000
 JVD  N16  C7   C4   115.81  3.000
 JVD  H12  C10  H11  108.12  3.000
 JVD  H12  C10  H10  107.50  3.000
 JVD  H11  C10  H10  107.75  3.000
 JVD  H12  C10  C12  110.65  3.000
 JVD  H11  C10  C12  111.17  3.000
 JVD  H10  C10  C12  111.48  3.000
 JVD  H13  C11  C12  107.69  3.000
 JVD  H13  C11  C9   108.42  3.000
 JVD  C12  C11  C9   111.29  3.000
 JVD  H13  C11  C8   108.29  3.000
 JVD  C12  C11  C8   111.29  3.000
 JVD  C9   C11  C8   109.74  3.000
 JVD  H14  C12  N16  106.77  3.000
 JVD  H14  C12  C11  108.20  3.000
 JVD  N16  C12  C11  110.47  3.000
 JVD  H14  C12  C10  108.90  3.000
 JVD  N16  C12  C10  108.96  3.000
 JVD  C11  C12  C10  113.33  3.000
 JVD  H15  N13  N14  119.76  3.000
 JVD  H15  N13  C5   129.38  3.000
 JVD  N14  N13  C5   110.86  3.000
 JVD  N15  N14  N13  109.74  3.000
 JVD  N14  N15  C6   108.19  3.000
 JVD  H16  N16  C12  116.21  3.000
 JVD  H16  N16  C7   118.86  3.000
 JVD  C12  N16  C7   124.81  3.000
 JVD  H6   C8   H5   107.87  3.000
 JVD  H6   C8   H4   107.45  3.000
 JVD  H5   C8   H4   107.14  3.000
 JVD  H6   C8   C11  110.90  3.000
 JVD  H5   C8   C11  112.90  3.000
 JVD  H4   C8   C11  110.36  3.000
 JVD  H9   C9   H8   107.54  3.000
 JVD  H9   C9   H7   107.86  3.000
 JVD  H8   C9   H7   107.30  3.000
 JVD  H9   C9   C11  110.95  3.000
 JVD  H8   C9   C11  110.61  3.000
 JVD  H7   C9   C11  112.37  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
 JVD  CONST_01  C5   C3   C4   C1      0.00   0.0  0
 JVD  CONST_02  C5   C6   C2   C1      0.00   0.0  0
 JVD  CONST_03  N15  C6   C2   C1    180.00   0.0  0
 JVD  CONST_04  C3   C4   C1   C2      0.00   0.0  0
 JVD  CONST_05  C3   C5   C6   C2      0.00   0.0  0
 JVD  CONST_06  N13  C5   C6   C2    180.00   0.0  0
 JVD  CONST_07  N14  N15  C6   C2    180.00   0.0  0
 JVD  CONST_08  N14  N13  C5   C3    180.00   0.0  0
 JVD  CONST_09  N15  C6   C5   C3    180.00   0.0  0
 JVD  CONST_10  N13  C5   C3   C4    180.00   0.0  0
 JVD  CONST_11  C6   C5   C3   C4      0.00   0.0  0
 JVD  CONST_12  C6   C2   C1   C4      0.00   0.0  0
 JVD  CONST_13  N15  N14  N13  C5      0.00   0.0  0
 JVD  CONST_14  N14  N15  C6   C5      0.00   0.0  0
 JVD  CONST_15  N14  N13  C5   C6      0.00   0.0  0
 JVD  CONST_16  N13  N14  N15  C6      0.00   0.0  0
 JVD  CONST_17  N15  C6   C5   N13     0.00   0.0  0
 JVD  CONST_18  C7   C4   C1   C2    180.00   0.0  0
 JVD  CONST_19  C7   C4   C3   C5    180.00   0.0  0
 JVD  CONST_20  H3   C3   C4   C1    180.00   0.0  0
 JVD  CONST_21  H1   C1   C4   C3    180.00   0.0  0
 JVD  CONST_22  H15  N13  C5   C3      0.00   0.0  0
 JVD  CONST_23  H2   C2   C1   C4    180.00   0.0  0
 JVD  CONST_24  C12  N16  C7   C4    180.00   0.0  0
 JVD  CONST_25  H16  N16  C7   C4      0.00   0.0  0
 JVD  CONST_26  O17  C7   N16  C12     0.00   0.0  0
 JVD  Var_01    N16  C7   C4   C1     28.07  30.0  2
 JVD  Var_02    H7   C9   C11  C8   -175.33  30.0  3
 JVD  Var_03    H4   C8   C11  C9     52.71  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JVD  chir_01  C12  C10  C11  N16  positiv

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
 JVD  plan-1  C1   0.020
 JVD  plan-1  C2   0.020
 JVD  plan-1  C3   0.020
 JVD  plan-1  C4   0.020
 JVD  plan-1  C5   0.020
 JVD  plan-1  C6   0.020
 JVD  plan-1  C7   0.020
 JVD  plan-1  N13  0.020
 JVD  plan-1  N14  0.020
 JVD  plan-1  N15  0.020
 JVD  plan-1  H1   0.020
 JVD  plan-1  H2   0.020
 JVD  plan-1  H3   0.020
 JVD  plan-1  H15  0.020
 JVD  plan-2  C4   0.020
 JVD  plan-2  C7   0.020
 JVD  plan-2  C12  0.020
 JVD  plan-2  N16  0.020
 JVD  plan-2  O17  0.020
 JVD  plan-2  H16  0.020

