# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 17:26:11 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: 2-(benzotriazol-1-yl)-~{N}-[(3-chlorophenyl)methyl]-~{N}-[4-(2-oxidanylidene-1~{H}-pyridin-3-yl)phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(CN(C(=O)Cn2nnc3ccccc23)c4ccc(cc4)C5=CC=CNC5=O)c1
#
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
 Y67  Y67  2-(benzotriazol-1-yl)-~{N}-[(3-chlorophenyl)methyl]-~{N}-[4-(2-oxidanylidene-1~{H}-pyridin-3-yl)phenyl]ethanamide  ligand  54  34  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y67
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
 Y67  C02   C   C     0   0.533  -23.1190  -41.0241   2.8577
 Y67  C03   C   CH2   0  -0.449  -22.4824  -42.1205   2.0008
 Y67  C05   C   CR56  0   0.396  -20.8296  -40.8073   0.6436
 Y67  C06   C   CR16  0  -0.290  -21.5590  -40.0020  -0.2332
 Y67  C07   C   CR16  0  -0.261  -20.8173  -39.1833  -1.0552
 Y67  C08   C   CR16  0  -0.267  -19.4061  -39.1590  -1.0142
 Y67  C09   C   CR16  0  -0.289  -18.6962  -39.9569  -0.1467
 Y67  C10   C   CR56  0   0.123  -19.4353  -40.7936   0.6965
 Y67  N12   N   N     0  -0.058  -20.0822  -42.2169   2.1617
 Y67  C14   C   CH2   0  -0.400  -25.1804  -40.1961   3.8924
 Y67  C15   C   CR6   0   0.106  -25.7157  -40.7632   5.1805
 Y67  C16   C   CR16  0  -0.288  -27.0800  -40.9483   5.3609
 Y67  C17   C   CR16  0  -0.245  -27.5664  -41.4884   6.5446
 Y67  C18   C   CR16  0  -0.224  -26.6967  -41.8551   7.5591
 Y67  C19   C   CR6   0  -0.022  -25.3349  -41.6675   7.3686
 Y67  C21   C   CR16  0  -0.249  -24.8353  -41.1280   6.1962
 Y67  C22   C   CR6   0   0.232  -25.1618  -42.3427   2.7200
 Y67  C23   C   CR16  0  -0.238  -26.0436  -42.2524   1.6494
 Y67  C24   C   CR16  0  -0.290  -26.7831  -43.3560   1.2604
 Y67  C25   C   CR6   0   0.115  -26.6631  -44.5712   1.9391
 Y67  C26   C   CR6   0  -0.191  -27.4781  -45.7437   1.5740
 Y67  C27   C   CR16  0  -0.158  -28.1208  -46.4808   2.5301
 Y67  C28   C   CR16  0  -0.382  -28.8987  -47.6155   2.2121
 Y67  C29   C   CR16  0   0.051  -28.9980  -47.9664   0.9061
 Y67  C31   C   CR6   0   0.520  -27.5776  -46.1299   0.1786
 Y67  C33   C   CR16  0  -0.310  -25.7744  -44.6457   3.0115
 Y67  C34   C   CR16  0  -0.226  -25.0376  -43.5407   3.4087
 Y67  O01   O   O     0  -0.457  -22.4632  -40.0732   3.2346
 Y67  N04   N   NR5   0  -0.381  -21.1719  -41.7273   1.5758
 Y67  N11   N   N     0  -0.319  -19.0400  -41.6854   1.6533
 Y67  N13   N   NT    0  -0.540  -24.4322  -41.1942   3.1343
 Y67  CL20  CL  CL    0  -0.129  -24.2350  -42.1175   8.6320
 Y67  N30   N   NR16  0  -0.656  -28.3603  -47.2469  -0.0424
 Y67  O32   O   O     0  -0.481  -27.0304  -45.5674  -0.7636
 Y67  H1    H   HCH2  0   0.312  -23.0937  -42.3487   1.1258
 Y67  H2    H   HCH2  0   0.330  -22.3857  -43.0441   2.5717
 Y67  H3    H   HCR6  0   0.281  -22.6404  -40.0146  -0.2681
 Y67  H4    H   HCR6  0   0.267  -21.3290  -38.5354  -1.7546
 Y67  H5    H   HCR6  0   0.263  -18.8769  -38.4946  -1.6840
 Y67  H6    H   HCR6  0   0.271  -17.6151  -39.9395  -0.1139
 Y67  H7    H   HCH2  0   0.288  -24.5201  -39.3533   4.0870
 Y67  H8    H   HCH2  0   0.280  -26.0049  -39.8316   3.2760
 Y67  H9    H   HCR6  0   0.261  -27.7688  -40.6704   4.5726
 Y67  H10   H   HCR6  0   0.268  -28.6307  -41.6297   6.6786
 Y67  H11   H   HCR6  0   0.279  -27.0707  -42.2786   8.4813
 Y67  H12   H   HCR6  0   0.277  -23.7683  -40.9912   6.0699
 Y67  H13   H   HCR6  0   0.268  -26.1494  -41.3143   1.1188
 Y67  H14   H   HCR6  0   0.256  -27.4704  -43.2611   0.4318
 Y67  H16   H   HCR6  0   0.275  -28.0443  -46.1780   3.5679
 Y67  H17   H   HCR6  0   0.277  -29.4077  -48.1827   2.9757
 Y67  H18   H   HCR6  0   0.312  -29.5720  -48.8114   0.5550
 Y67  H19   H   HCR6  0   0.261  -25.6510  -45.5806   3.5435
 Y67  H20   H   HCR6  0   0.272  -24.3609  -43.6127   4.2509
 Y67  H15   H   HNR6  0   0.422  -28.4486  -47.5403  -1.0067

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
 Y67  C07  C08   aromatic  1.412  0.020  1.412
 Y67  C07  C06   aromatic  1.377  0.020  1.377
 Y67  C08  C09   aromatic  1.376  0.020  1.376
 Y67  O32  C31   double    1.226  0.020  1.226
 Y67  N30  C31   single    1.382  0.020  1.382
 Y67  N30  C29   single    1.351  0.020  1.351
 Y67  C06  C05   aromatic  1.396  0.020  1.396
 Y67  C31  C26   single    1.451  0.020  1.451
 Y67  C09  C10   aromatic  1.399  0.020  1.399
 Y67  C29  C28   double    1.356  0.020  1.356
 Y67  C05  C10   aromatic  1.395  0.020  1.395
 Y67  C05  N04   aromatic  1.354  0.020  1.354
 Y67  C10  N11   aromatic  1.366  0.020  1.366
 Y67  C24  C23   aromatic  1.384  0.020  1.384
 Y67  C24  C25   aromatic  1.397  0.020  1.397
 Y67  C26  C25   single    1.474  0.020  1.474
 Y67  C26  C27   double    1.368  0.020  1.368
 Y67  C23  C22   aromatic  1.390  0.020  1.390
 Y67  C25  C33   aromatic  1.395  0.020  1.395
 Y67  N04  C03   single    1.433  0.020  1.433
 Y67  N04  N12   aromatic  1.331  0.020  1.331
 Y67  C28  C27   single    1.412  0.020  1.412
 Y67  N11  N12   aromatic  1.276  0.020  1.276
 Y67  C03  C02   single    1.530  0.020  1.530
 Y67  C22  N13   single    1.422  0.020  1.422
 Y67  C22  C34   aromatic  1.387  0.020  1.387
 Y67  C33  C34   aromatic  1.386  0.020  1.386
 Y67  C02  N13   single    1.353  0.020  1.353
 Y67  C02  O01   double    1.215  0.020  1.215
 Y67  N13  C14   single    1.460  0.020  1.460
 Y67  C14  C15   single    1.506  0.020  1.506
 Y67  C15  C16   aromatic  1.389  0.020  1.389
 Y67  C15  C21   aromatic  1.393  0.020  1.393
 Y67  C16  C17   aromatic  1.389  0.020  1.389
 Y67  C21  C19   aromatic  1.384  0.020  1.384
 Y67  C17  C18   aromatic  1.386  0.020  1.386
 Y67  C19  C18   aromatic  1.388  0.020  1.388
 Y67  C19  CL20  single    1.734  0.020  1.734
 Y67  C03  H1    single    0.970  0.020  1.090
 Y67  C03  H2    single    0.970  0.020  1.090
 Y67  C06  H3    single    0.930  0.020  1.080
 Y67  C07  H4    single    0.930  0.020  1.080
 Y67  C08  H5    single    0.930  0.020  1.080
 Y67  C09  H6    single    0.930  0.020  1.080
 Y67  C14  H7    single    0.970  0.020  1.090
 Y67  C14  H8    single    0.970  0.020  1.090
 Y67  C16  H9    single    0.930  0.020  1.080
 Y67  C17  H10   single    0.930  0.020  1.080
 Y67  C18  H11   single    0.930  0.020  1.080
 Y67  C21  H12   single    0.930  0.020  1.080
 Y67  C23  H13   single    0.930  0.020  1.080
 Y67  C24  H14   single    0.930  0.020  1.080
 Y67  C27  H16   single    0.930  0.020  1.080
 Y67  C28  H17   single    0.930  0.020  1.080
 Y67  C29  H18   single    0.930  0.020  1.080
 Y67  C33  H19   single    0.930  0.020  1.080
 Y67  C34  H20   single    0.930  0.020  1.080
 Y67  N30  H15   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
 Y67  N13   C02  O01  123.98  3.000
 Y67  O01   C02  C03  120.65  3.000
 Y67  N13   C02  C03  115.36  3.000
 Y67  H2    C03  H1   107.00  3.000
 Y67  H2    C03  N04  107.86  3.000
 Y67  H1    C03  N04  109.38  3.000
 Y67  H2    C03  C02  110.53  3.000
 Y67  H1    C03  C02  111.45  3.000
 Y67  N04   C03  C02  110.49  3.000
 Y67  N04   C05  C10  103.49  3.000
 Y67  N04   C05  C06  133.81  3.000
 Y67  C10   C05  C06  122.70  3.000
 Y67  H3    C06  C07  121.73  3.000
 Y67  H3    C06  C05  122.39  3.000
 Y67  C07   C06  C05  115.87  3.000
 Y67  H4    C07  C08  118.76  3.000
 Y67  H4    C07  C06  119.16  3.000
 Y67  C08   C07  C06  122.09  3.000
 Y67  H5    C08  C09  119.61  3.000
 Y67  H5    C08  C07  118.79  3.000
 Y67  C09   C08  C07  121.60  3.000
 Y67  H6    C09  C10  121.29  3.000
 Y67  H6    C09  C08  121.70  3.000
 Y67  C10   C09  C08  117.01  3.000
 Y67  N11   C10  C09  131.26  3.000
 Y67  N11   C10  C05  108.01  3.000
 Y67  C09   C10  C05  120.73  3.000
 Y67  N11   N12  N04  109.89  3.000
 Y67  H8    C14  H7   107.49  3.000
 Y67  H8    C14  N13  108.79  3.000
 Y67  H7    C14  N13  108.15  3.000
 Y67  H8    C14  C15  109.88  3.000
 Y67  H7    C14  C15  110.76  3.000
 Y67  N13   C14  C15  111.65  3.000
 Y67  C21   C15  C16  119.43  3.000
 Y67  C21   C15  C14  119.85  3.000
 Y67  C16   C15  C14  120.71  3.000
 Y67  H9    C16  C17  119.83  3.000
 Y67  H9    C16  C15  119.74  3.000
 Y67  C17   C16  C15  120.43  3.000
 Y67  H10   C17  C18  119.48  3.000
 Y67  H10   C17  C16  120.05  3.000
 Y67  C18   C17  C16  120.47  3.000
 Y67  H11   C18  C19  120.62  3.000
 Y67  H11   C18  C17  120.72  3.000
 Y67  C19   C18  C17  118.66  3.000
 Y67  CL20  C19  C21  119.30  3.000
 Y67  CL20  C19  C18  119.16  3.000
 Y67  C21   C19  C18  121.55  3.000
 Y67  H12   C21  C19  120.24  3.000
 Y67  H12   C21  C15  120.30  3.000
 Y67  C19   C21  C15  119.46  3.000
 Y67  N13   C22  C34  120.44  3.000
 Y67  C34   C22  C23  119.69  3.000
 Y67  N13   C22  C23  119.82  3.000
 Y67  H13   C23  C24  120.05  3.000
 Y67  H13   C23  C22  119.71  3.000
 Y67  C24   C23  C22  120.24  3.000
 Y67  H14   C24  C25  120.23  3.000
 Y67  H14   C24  C23  119.02  3.000
 Y67  C25   C24  C23  120.73  3.000
 Y67  C33   C25  C26  120.02  3.000
 Y67  C33   C25  C24  118.34  3.000
 Y67  C26   C25  C24  121.61  3.000
 Y67  C31   C26  C27  119.77  3.000
 Y67  C27   C26  C25  121.03  3.000
 Y67  C31   C26  C25  119.20  3.000
 Y67  H16   C27  C28  118.63  3.000
 Y67  H16   C27  C26  119.05  3.000
 Y67  C28   C27  C26  122.32  3.000
 Y67  H17   C28  C29  120.74  3.000
 Y67  H17   C28  C27  121.53  3.000
 Y67  C29   C28  C27  117.72  3.000
 Y67  H18   C29  N30  116.07  3.000
 Y67  H18   C29  C28  123.67  3.000
 Y67  N30   C29  C28  120.27  3.000
 Y67  O32   C31  N30  120.05  3.000
 Y67  N30   C31  C26  114.06  3.000
 Y67  O32   C31  C26  125.88  3.000
 Y67  H19   C33  C34  119.14  3.000
 Y67  H19   C33  C25  119.77  3.000
 Y67  C34   C33  C25  121.09  3.000
 Y67  H20   C34  C33  120.14  3.000
 Y67  H20   C34  C22  119.96  3.000
 Y67  C33   C34  C22  119.90  3.000
 Y67  N12   N04  C05  110.25  3.000
 Y67  N12   N04  C03  121.16  3.000
 Y67  C05   N04  C03  128.47  3.000
 Y67  N12   N11  C10  108.34  3.000
 Y67  C22   N13  C14  116.14  3.000
 Y67  C14   N13  C02  121.18  3.000
 Y67  C22   N13  C02  122.68  3.000
 Y67  H15   N30  C31  115.86  3.000
 Y67  H15   N30  C29  118.27  3.000
 Y67  C31   N30  C29  125.86  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
 Y67  CONST_01  C08   C07  C06  C05     0.00   0.0  0
 Y67  CONST_02  C08   C09  C10  C05     0.00   0.0  0
 Y67  CONST_03  N12   N11  C10  C05     0.00   0.0  0
 Y67  CONST_04  N11   N12  N04  C05     0.00   0.0  0
 Y67  CONST_05  C09   C08  C07  C06     0.00   0.0  0
 Y67  CONST_06  C09   C10  C05  C06     0.00   0.0  0
 Y67  CONST_07  N11   C10  C05  C06   180.00   0.0  0
 Y67  CONST_08  N12   N04  C05  C06   180.00   0.0  0
 Y67  CONST_09  C10   C09  C08  C07     0.00   0.0  0
 Y67  CONST_10  C10   C05  C06  C07     0.00   0.0  0
 Y67  CONST_11  N04   C05  C06  C07   180.00   0.0  0
 Y67  CONST_12  N11   C10  C09  C08   180.00   0.0  0
 Y67  CONST_13  N04   C05  C10  C09   180.00   0.0  0
 Y67  CONST_14  N12   N11  C10  C09   180.00   0.0  0
 Y67  CONST_15  N12   N04  C05  C10     0.00   0.0  0
 Y67  CONST_16  N04   N12  N11  C10     0.00   0.0  0
 Y67  CONST_17  C18   C17  C16  C15     0.00   0.0  0
 Y67  CONST_18  C18   C19  C21  C15     0.00   0.0  0
 Y67  CONST_19  C19   C21  C15  C16     0.00   0.0  0
 Y67  CONST_20  C19   C18  C17  C16     0.00   0.0  0
 Y67  CONST_21  C21   C15  C16  C17     0.00   0.0  0
 Y67  CONST_22  C21   C19  C18  C17     0.00   0.0  0
 Y67  CONST_23  C25   C24  C23  C22     0.00   0.0  0
 Y67  CONST_24  C25   C33  C34  C22     0.00   0.0  0
 Y67  CONST_25  C33   C25  C24  C23     0.00   0.0  0
 Y67  CONST_26  C33   C34  C22  C23     0.00   0.0  0
 Y67  CONST_27  C34   C22  C23  C24     0.00   0.0  0
 Y67  CONST_28  C34   C33  C25  C24     0.00   0.0  0
 Y67  CONST_29  N11   C10  C05  N04     0.00   0.0  0
 Y67  CONST_30  C26   C25  C24  C23   180.00   0.0  0
 Y67  CONST_31  C34   C33  C25  C26   180.00   0.0  0
 Y67  CONST_32  C29   N30  C31  C26     0.00   0.0  0
 Y67  CONST_33  C06   C05  N04  C03     0.00   0.0  0
 Y67  CONST_34  C10   C05  N04  C03   180.00   0.0  0
 Y67  CONST_35  N11   N12  N04  C03   180.00   0.0  0
 Y67  CONST_36  C17   C16  C15  C14   180.00   0.0  0
 Y67  CONST_37  C19   C21  C15  C14   180.00   0.0  0
 Y67  CONST_38  CL20  C19  C21  C15   180.00   0.0  0
 Y67  CONST_39  CL20  C19  C18  C17   180.00   0.0  0
 Y67  CONST_40  N13   C22  C23  C24   180.00   0.0  0
 Y67  CONST_41  N13   C22  C34  C33   180.00   0.0  0
 Y67  CONST_42  O32   C31  N30  C29   180.00   0.0  0
 Y67  CONST_43  H4    C07  C06  C05   180.00   0.0  0
 Y67  CONST_44  H6    C09  C10  C05   180.00   0.0  0
 Y67  CONST_45  H5    C08  C07  C06   180.00   0.0  0
 Y67  CONST_46  H3    C06  C07  C08   180.00   0.0  0
 Y67  CONST_47  H10   C17  C16  C15   180.00   0.0  0
 Y67  CONST_48  H12   C21  C15  C16   180.00   0.0  0
 Y67  CONST_49  H11   C18  C17  C16   180.00   0.0  0
 Y67  CONST_50  H9    C16  C17  C18   180.00   0.0  0
 Y67  CONST_51  H14   C24  C23  C22   180.00   0.0  0
 Y67  CONST_52  H19   C33  C34  C22   180.00   0.0  0
 Y67  CONST_53  H20   C34  C22  C23   180.00   0.0  0
 Y67  CONST_54  H13   C23  C24  C25   180.00   0.0  0
 Y67  CONST_55  H15   N30  C31  C26   180.00   0.0  0
 Y67  CONST_60  C22   N13  C02  C03     0.00   0.0  0
 Y67  CONST_61  O01   C02  N13  C22   180.00   0.0  0
 Y67  CONST_62  C14   N13  C02  C03   180.00   0.0  0
 Y67  CONST_63  O01   C02  N13  C14     0.00   0.0  0
 Y67  Var_01    C31   C26  C25  C24    48.03  30.0  1
 Y67  Var_02    C05   N04  C03  C02   -73.04  30.0  2
 Y67  Var_03    C22   N13  C14  C15    61.37  30.0  1
 Y67  Var_04    N13   C14  C15  C16  -111.39  30.0  2
 Y67  Var_05    N04   C03  C02  O01    -9.44  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
 Y67  plan-1  C14   0.020
 Y67  plan-1  C15   0.020
 Y67  plan-1  C16   0.020
 Y67  plan-1  C17   0.020
 Y67  plan-1  C18   0.020
 Y67  plan-1  C19   0.020
 Y67  plan-1  C21   0.020
 Y67  plan-1  CL20  0.020
 Y67  plan-1  H9    0.020
 Y67  plan-1  H10   0.020
 Y67  plan-1  H11   0.020
 Y67  plan-1  H12   0.020
 Y67  plan-2  C22   0.020
 Y67  plan-2  C23   0.020
 Y67  plan-2  C24   0.020
 Y67  plan-2  C25   0.020
 Y67  plan-2  C26   0.020
 Y67  plan-2  C33   0.020
 Y67  plan-2  C34   0.020
 Y67  plan-2  N13   0.020
 Y67  plan-2  H13   0.020
 Y67  plan-2  H14   0.020
 Y67  plan-2  H19   0.020
 Y67  plan-2  H20   0.020
 Y67  plan-3  C25   0.020
 Y67  plan-3  C26   0.020
 Y67  plan-3  C27   0.020
 Y67  plan-3  C28   0.020
 Y67  plan-3  C29   0.020
 Y67  plan-3  C31   0.020
 Y67  plan-3  N30   0.020
 Y67  plan-3  O32   0.020
 Y67  plan-3  H16   0.020
 Y67  plan-3  H17   0.020
 Y67  plan-3  H18   0.020
 Y67  plan-3  H15   0.020
 Y67  plan-4  C03   0.020
 Y67  plan-4  C05   0.020
 Y67  plan-4  C06   0.020
 Y67  plan-4  C07   0.020
 Y67  plan-4  C08   0.020
 Y67  plan-4  C09   0.020
 Y67  plan-4  C10   0.020
 Y67  plan-4  N12   0.020
 Y67  plan-4  N04   0.020
 Y67  plan-4  N11   0.020
 Y67  plan-4  H3    0.020
 Y67  plan-4  H4    0.020
 Y67  plan-4  H5    0.020
 Y67  plan-4  H6    0.020
 Y67  plan-5  C02   0.020
 Y67  plan-5  C03   0.020
 Y67  plan-5  C14   0.020
 Y67  plan-5  C22   0.020
 Y67  plan-5  O01   0.020
 Y67  plan-5  N13   0.020

