# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 15:07:07 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-(benzotriazol-1-yl)-~{N}-(4-pyridin-3-ylphenyl)-~{N}-(thiophen-3-ylmethyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cn1nnc2ccccc12)N(Cc3cscc3)c4ccc(cc4)c5cccnc5
#
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
 Y6D  Y6D  2-(benzotriazol-1-yl)-~{N}-(4-pyridin-3-ylphenyl)-~{N}-(thiophen-3-ylmethyl)ethanamide  ligand  50  31  .  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_Y6D
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
 Y6D  C10  C  CR56  0   0.125  -19.7154  -40.7208   0.8951
 Y6D  C14  C  CH2   0  -0.374  -25.1077  -40.3737   4.6465
 Y6D  C21  C  CR16  0  -0.226  -26.2402  -42.0737   2.1803
 Y6D  C22  C  CR16  0  -0.310  -27.0473  -43.0829   1.6854
 Y6D  C30  C  CR16  0  -0.309  -26.0307  -44.6424   3.1969
 Y6D  C31  C  CR16  0  -0.234  -25.2272  -43.6319   3.7023
 Y6D  O01  O  O     0  -0.451  -22.5073  -40.2382   3.7338
 Y6D  C02  C  C     0   0.531  -23.2237  -41.1193   3.3035
 Y6D  C03  C  CH2   0  -0.452  -22.7089  -42.1080   2.2571
 Y6D  N04  N  NR5   0  -0.379  -21.4178  -41.7058   1.7850
 Y6D  C05  C  CR56  0   0.393  -21.1106  -40.7471   0.8795
 Y6D  C06  C  CR16  0  -0.290  -21.8707  -39.9203   0.0499
 Y6D  C07  C  CR16  0  -0.260  -21.1592  -39.0678  -0.7643
 Y6D  C08  C  CR16  0  -0.267  -19.7478  -39.0313  -0.7614
 Y6D  C09  C  CR16  0  -0.289  -19.0074  -39.8501   0.0601
 Y6D  N11  N  N     0  -0.318  -19.2854  -41.6412   1.8088
 Y6D  N12  N  N     0  -0.057  -20.3079  -42.2015   2.3258
 Y6D  N13  N  NT    0  -0.547  -24.5067  -41.2958   3.6967
 Y6D  C15  C  CR5   0   0.172  -24.9824  -40.8003   6.0814
 Y6D  C16  C  CR15  0  -0.535  -24.0941  -41.7085   6.5737
 Y6D  S17  S  S2    0   0.214  -24.2348  -41.8840   8.2735
 Y6D  C18  C  CR15  0  -0.458  -25.4961  -40.7279   8.3464
 Y6D  C19  C  CR15  0  -0.207  -25.7922  -40.2382   7.1132
 Y6D  C20  C  CR6   0   0.230  -25.3230  -42.3456   3.1890
 Y6D  C23  C  CR6   0   0.092  -26.9530  -44.3835   2.1837
 Y6D  C24  C  CR6   0  -0.006  -27.8092  -45.4563   1.6464
 Y6D  C25  C  CR16  0  -0.191  -28.1077  -45.5491   0.2887
 Y6D  C26  C  CR16  0  -0.314  -28.9182  -46.5779  -0.1595
 Y6D  C27  C  CR16  0  -0.068  -29.4052  -47.4892   0.7653
 Y6D  N28  N  N     0  -0.394  -29.1369  -47.4146   2.0638
 Y6D  C29  C  CR16  0  -0.097  -28.3631  -46.4248   2.4845
 Y6D  H1   H  HCH2  0   0.279  -24.6590  -39.3881   4.5121
 Y6D  H2   H  HCH2  0   0.277  -26.1629  -40.2679   4.3887
 Y6D  H3   H  HCR6  0   0.272  -26.3203  -41.0699   1.7819
 Y6D  H4   H  HCR6  0   0.264  -27.7672  -42.8500   0.9110
 Y6D  H5   H  HCR6  0   0.264  -25.9203  -45.6452   3.5883
 Y6D  H6   H  HCR6  0   0.274  -24.5129  -43.8496   4.4856
 Y6D  H7   H  HCH2  0   0.314  -23.3930  -42.1877   1.4111
 Y6D  H8   H  HCH2  0   0.331  -22.6159  -43.1062   2.6863
 Y6D  H9   H  HCR6  0   0.281  -22.9525  -39.9428   0.0442
 Y6D  H10  H  HCR6  0   0.267  -21.6961  -38.4027  -1.4277
 Y6D  H11  H  HCR6  0   0.264  -19.2433  -38.3405  -1.4235
 Y6D  H12  H  HCR6  0   0.271  -17.9259  -39.8237   0.0640
 Y6D  H13  H  HCR5  0   0.290  -23.3580  -42.2859   6.0351
 Y6D  H14  H  HCR5  0   0.294  -25.9579  -40.4766   9.2887
 Y6D  H15  H  HCR5  0   0.264  -26.5638  -39.5012   6.9350
 Y6D  H16  H  HCR6  0   0.272  -27.6974  -44.8353  -0.4150
 Y6D  H17  H  HCR6  0   0.273  -29.1620  -46.6792  -1.2081
 Y6D  H18  H  HCR6  0   0.266  -30.0371  -48.3104   0.4460
 Y6D  H19  H  HCR6  0   0.262  -28.1812  -46.3822   3.5538

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
 Y6D  C07  C08  aromatic  1.412  0.020  1.412
 Y6D  C07  C06  aromatic  1.377  0.020  1.377
 Y6D  C08  C09  aromatic  1.376  0.020  1.376
 Y6D  C26  C25  aromatic  1.384  0.020  1.384
 Y6D  C26  C27  aromatic  1.387  0.020  1.387
 Y6D  C06  C05  aromatic  1.396  0.020  1.396
 Y6D  C09  C10  aromatic  1.399  0.020  1.399
 Y6D  C25  C24  aromatic  1.393  0.020  1.393
 Y6D  C27  N28  aromatic  1.328  0.020  1.328
 Y6D  C05  C10  aromatic  1.395  0.020  1.395
 Y6D  C05  N04  aromatic  1.354  0.020  1.354
 Y6D  C10  N11  aromatic  1.366  0.020  1.366
 Y6D  C24  C23  single    1.474  0.020  1.474
 Y6D  C24  C29  aromatic  1.395  0.020  1.395
 Y6D  C22  C23  aromatic  1.396  0.020  1.396
 Y6D  C22  C21  aromatic  1.384  0.020  1.384
 Y6D  N28  C29  aromatic  1.325  0.020  1.325
 Y6D  N04  C03  single    1.432  0.020  1.432
 Y6D  N04  N12  aromatic  1.331  0.020  1.331
 Y6D  N11  N12  aromatic  1.275  0.020  1.275
 Y6D  C23  C30  aromatic  1.394  0.020  1.394
 Y6D  C21  C20  aromatic  1.390  0.020  1.390
 Y6D  C03  C02  single    1.529  0.020  1.529
 Y6D  C30  C31  aromatic  1.386  0.020  1.386
 Y6D  C20  C31  aromatic  1.388  0.020  1.388
 Y6D  C20  N13  single    1.424  0.020  1.424
 Y6D  C02  O01  double    1.214  0.020  1.214
 Y6D  C02  N13  single    1.354  0.020  1.354
 Y6D  N13  C14  single    1.454  0.020  1.454
 Y6D  C14  C15  single    1.502  0.020  1.502
 Y6D  C15  C16  aromatic  1.362  0.020  1.362
 Y6D  C15  C19  aromatic  1.427  0.020  1.427
 Y6D  C16  S17  aromatic  1.715  0.020  1.715
 Y6D  C19  C18  aromatic  1.360  0.020  1.360
 Y6D  S17  C18  aromatic  1.712  0.020  1.712
 Y6D  C14  H1   single    0.970  0.020  1.090
 Y6D  C14  H2   single    0.970  0.020  1.090
 Y6D  C21  H3   single    0.930  0.020  1.080
 Y6D  C22  H4   single    0.930  0.020  1.080
 Y6D  C30  H5   single    0.930  0.020  1.080
 Y6D  C31  H6   single    0.930  0.020  1.080
 Y6D  C03  H7   single    0.970  0.020  1.090
 Y6D  C03  H8   single    0.970  0.020  1.090
 Y6D  C06  H9   single    0.930  0.020  1.080
 Y6D  C07  H10  single    0.930  0.020  1.080
 Y6D  C08  H11  single    0.930  0.020  1.080
 Y6D  C09  H12  single    0.930  0.020  1.080
 Y6D  C16  H13  single    0.930  0.020  1.080
 Y6D  C18  H14  single    0.930  0.020  1.080
 Y6D  C19  H15  single    0.930  0.020  1.080
 Y6D  C25  H16  single    0.930  0.020  1.080
 Y6D  C26  H17  single    0.930  0.020  1.080
 Y6D  C27  H18  single    0.930  0.020  1.080
 Y6D  C29  H19  single    0.930  0.020  1.080

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
 Y6D  N11  C10  C09  131.23  3.000
 Y6D  N11  C10  C05  108.02  3.000
 Y6D  C09  C10  C05  120.74  3.000
 Y6D  H2   C14  H1   106.32  3.000
 Y6D  H2   C14  C15  109.50  3.000
 Y6D  H1   C14  C15  109.86  3.000
 Y6D  H2   C14  N13  107.87  3.000
 Y6D  H1   C14  N13  108.81  3.000
 Y6D  C15  C14  N13  114.17  3.000
 Y6D  H3   C21  C20  119.80  3.000
 Y6D  H3   C21  C22  120.09  3.000
 Y6D  C20  C21  C22  120.11  3.000
 Y6D  H4   C22  C23  120.04  3.000
 Y6D  H4   C22  C21  119.13  3.000
 Y6D  C23  C22  C21  120.82  3.000
 Y6D  H5   C30  C23  120.16  3.000
 Y6D  H5   C30  C31  118.97  3.000
 Y6D  C23  C30  C31  120.86  3.000
 Y6D  H6   C31  C20  119.98  3.000
 Y6D  H6   C31  C30  119.98  3.000
 Y6D  C20  C31  C30  120.03  3.000
 Y6D  N13  C02  C03  115.70  3.000
 Y6D  N13  C02  O01  123.43  3.000
 Y6D  C03  C02  O01  120.87  3.000
 Y6D  H8   C03  H7   106.96  3.000
 Y6D  H8   C03  N04  108.05  3.000
 Y6D  H7   C03  N04  109.28  3.000
 Y6D  H8   C03  C02  110.57  3.000
 Y6D  H7   C03  C02  111.52  3.000
 Y6D  N04  C03  C02  110.33  3.000
 Y6D  N12  N04  C05  110.26  3.000
 Y6D  N12  N04  C03  120.89  3.000
 Y6D  C05  N04  C03  128.59  3.000
 Y6D  C06  C05  N04  133.87  3.000
 Y6D  N04  C05  C10  103.46  3.000
 Y6D  C06  C05  C10  122.66  3.000
 Y6D  H9   C06  C07  121.76  3.000
 Y6D  H9   C06  C05  122.35  3.000
 Y6D  C07  C06  C05  115.89  3.000
 Y6D  H10  C07  C08  118.78  3.000
 Y6D  H10  C07  C06  119.12  3.000
 Y6D  C08  C07  C06  122.09  3.000
 Y6D  H11  C08  C09  119.63  3.000
 Y6D  H11  C08  C07  118.78  3.000
 Y6D  C09  C08  C07  121.59  3.000
 Y6D  H12  C09  C08  121.70  3.000
 Y6D  H12  C09  C10  121.27  3.000
 Y6D  C08  C09  C10  117.02  3.000
 Y6D  N12  N11  C10  108.34  3.000
 Y6D  N11  N12  N04  109.90  3.000
 Y6D  C20  N13  C02  122.42  3.000
 Y6D  C02  N13  C14  119.93  3.000
 Y6D  C20  N13  C14  117.63  3.000
 Y6D  C19  C15  C16  111.80  3.000
 Y6D  C19  C15  C14  122.10  3.000
 Y6D  C16  C15  C14  126.08  3.000
 Y6D  H13  C16  S17  119.73  3.000
 Y6D  H13  C16  C15  128.37  3.000
 Y6D  S17  C16  C15  111.90  3.000
 Y6D  C18  S17  C16   91.92  3.000
 Y6D  H14  C18  C19  127.95  3.000
 Y6D  H14  C18  S17  120.64  3.000
 Y6D  C19  C18  S17  111.41  3.000
 Y6D  H15  C19  C18  123.38  3.000
 Y6D  H15  C19  C15  123.65  3.000
 Y6D  C18  C19  C15  112.97  3.000
 Y6D  N13  C20  C31  120.79  3.000
 Y6D  N13  C20  C21  119.53  3.000
 Y6D  C31  C20  C21  119.67  3.000
 Y6D  C24  C23  C30  120.93  3.000
 Y6D  C30  C23  C22  118.49  3.000
 Y6D  C24  C23  C22  120.58  3.000
 Y6D  C29  C24  C25  117.00  3.000
 Y6D  C29  C24  C23  121.12  3.000
 Y6D  C25  C24  C23  121.88  3.000
 Y6D  H16  C25  C26  120.08  3.000
 Y6D  H16  C25  C24  120.54  3.000
 Y6D  C26  C25  C24  119.37  3.000
 Y6D  H17  C26  C27  120.39  3.000
 Y6D  H17  C26  C25  121.04  3.000
 Y6D  C27  C26  C25  118.56  3.000
 Y6D  H18  C27  N28  116.63  3.000
 Y6D  H18  C27  C26  120.40  3.000
 Y6D  N28  C27  C26  122.97  3.000
 Y6D  C29  N28  C27  118.06  3.000
 Y6D  H19  C29  N28  116.10  3.000
 Y6D  H19  C29  C24  119.86  3.000
 Y6D  N28  C29  C24  124.03  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
 Y6D  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 Y6D  CONST_02  C07  C06  C05  C10    0.00   0.0  0
 Y6D  CONST_03  N12  N04  C05  C10    0.00   0.0  0
 Y6D  CONST_04  N04  N12  N11  C10    0.00   0.0  0
 Y6D  CONST_05  C24  C23  C22  C21  180.00   0.0  0
 Y6D  CONST_06  C30  C23  C22  C21    0.00   0.0  0
 Y6D  CONST_07  C30  C31  C20  C21    0.00   0.0  0
 Y6D  CONST_10  C31  C30  C23  C22    0.00   0.0  0
 Y6D  CONST_11  C31  C20  C21  C22    0.00   0.0  0
 Y6D  CONST_14  C24  C23  C30  C31  180.00   0.0  0
 Y6D  CONST_15  C07  C06  C05  N04  180.00   0.0  0
 Y6D  CONST_16  C09  C10  C05  N04  180.00   0.0  0
 Y6D  CONST_17  N11  C10  C05  N04    0.00   0.0  0
 Y6D  CONST_18  C08  C07  C06  C05    0.00   0.0  0
 Y6D  CONST_19  C08  C09  C10  C05    0.00   0.0  0
 Y6D  CONST_20  N12  N11  C10  C05    0.00   0.0  0
 Y6D  CONST_21  N11  N12  N04  C05    0.00   0.0  0
 Y6D  CONST_22  C09  C08  C07  C06    0.00   0.0  0
 Y6D  CONST_23  C09  C10  C05  C06    0.00   0.0  0
 Y6D  CONST_24  N11  C10  C05  C06  180.00   0.0  0
 Y6D  CONST_25  N12  N04  C05  C06  180.00   0.0  0
 Y6D  CONST_26  N11  C10  C09  C08  180.00   0.0  0
 Y6D  CONST_27  N12  N11  C10  C09  180.00   0.0  0
 Y6D  CONST_28  C18  S17  C16  C15    0.00   0.0  0
 Y6D  CONST_29  S17  C18  C19  C15    0.00   0.0  0
 Y6D  CONST_30  C18  C19  C15  C16    0.00   0.0  0
 Y6D  CONST_31  C19  C18  S17  C16    0.00   0.0  0
 Y6D  CONST_32  C19  C15  C16  S17    0.00   0.0  0
 Y6D  CONST_33  C23  C22  C21  C20    0.00   0.0  0
 Y6D  CONST_34  C23  C30  C31  C20    0.00   0.0  0
 Y6D  CONST_35  C26  C25  C24  C23  180.00   0.0  0
 Y6D  CONST_36  N28  C29  C24  C23  180.00   0.0  0
 Y6D  CONST_37  C27  C26  C25  C24    0.00   0.0  0
 Y6D  CONST_38  C27  N28  C29  C24    0.00   0.0  0
 Y6D  CONST_39  N28  C27  C26  C25    0.00   0.0  0
 Y6D  CONST_40  N28  C29  C24  C25    0.00   0.0  0
 Y6D  CONST_41  C29  C24  C25  C26    0.00   0.0  0
 Y6D  CONST_42  C29  N28  C27  C26    0.00   0.0  0
 Y6D  CONST_43  C03  N04  C05  C10  180.00   0.0  0
 Y6D  CONST_44  S17  C16  C15  C14  180.00   0.0  0
 Y6D  CONST_45  C18  C19  C15  C14  180.00   0.0  0
 Y6D  CONST_46  N13  C20  C21  C22  180.00   0.0  0
 Y6D  CONST_47  N13  C20  C31  C30  180.00   0.0  0
 Y6D  CONST_48  C06  C05  N04  C03    0.00   0.0  0
 Y6D  CONST_49  N11  N12  N04  C03  180.00   0.0  0
 Y6D  CONST_50  H11  C08  C09  C10  180.00   0.0  0
 Y6D  CONST_51  H9   C06  C05  C10  180.00   0.0  0
 Y6D  CONST_52  H6   C31  C20  C21  180.00   0.0  0
 Y6D  CONST_53  H5   C30  C23  C22  180.00   0.0  0
 Y6D  CONST_54  H4   C22  C23  C30  180.00   0.0  0
 Y6D  CONST_55  H3   C21  C20  C31  180.00   0.0  0
 Y6D  CONST_56  H10  C07  C06  C05  180.00   0.0  0
 Y6D  CONST_57  H12  C09  C10  C05  180.00   0.0  0
 Y6D  CONST_58  H14  C18  C19  C15  180.00   0.0  0
 Y6D  CONST_59  H15  C19  C15  C16  180.00   0.0  0
 Y6D  CONST_60  H13  C16  S17  C18  180.00   0.0  0
 Y6D  CONST_61  H16  C25  C24  C23    0.00   0.0  0
 Y6D  CONST_62  H19  C29  C24  C23    0.00   0.0  0
 Y6D  CONST_63  H17  C26  C25  C24  180.00   0.0  0
 Y6D  CONST_64  H18  C27  C26  C25  180.00   0.0  0
 Y6D  CONST_69  C20  N13  C02  O01  180.00   0.0  0
 Y6D  CONST_70  C20  N13  C02  C03    0.00   0.0  0
 Y6D  CONST_71  C03  C02  N13  C14  180.00   0.0  0
 Y6D  CONST_72  O01  C02  N13  C14    0.00   0.0  0
 Y6D  Var_01    C05  N04  C03  C02  -78.94  30.0  2
 Y6D  Var_02    C16  C15  C14  N13   18.97  30.0  2
 Y6D  Var_03    C20  N13  C14  C15   89.24  30.0  2
 Y6D  Var_04    N04  C03  C02  O01   -8.01  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
 Y6D  plan-1  C14  0.020
 Y6D  plan-1  C15  0.020
 Y6D  plan-1  C16  0.020
 Y6D  plan-1  S17  0.020
 Y6D  plan-1  C18  0.020
 Y6D  plan-1  C19  0.020
 Y6D  plan-1  H13  0.020
 Y6D  plan-1  H14  0.020
 Y6D  plan-1  H15  0.020
 Y6D  plan-2  C21  0.020
 Y6D  plan-2  C22  0.020
 Y6D  plan-2  C30  0.020
 Y6D  plan-2  C31  0.020
 Y6D  plan-2  N13  0.020
 Y6D  plan-2  C20  0.020
 Y6D  plan-2  C23  0.020
 Y6D  plan-2  C24  0.020
 Y6D  plan-2  H3   0.020
 Y6D  plan-2  H4   0.020
 Y6D  plan-2  H5   0.020
 Y6D  plan-2  H6   0.020
 Y6D  plan-3  C23  0.020
 Y6D  plan-3  C24  0.020
 Y6D  plan-3  C25  0.020
 Y6D  plan-3  C26  0.020
 Y6D  plan-3  C27  0.020
 Y6D  plan-3  N28  0.020
 Y6D  plan-3  C29  0.020
 Y6D  plan-3  H16  0.020
 Y6D  plan-3  H17  0.020
 Y6D  plan-3  H18  0.020
 Y6D  plan-3  H19  0.020
 Y6D  plan-4  C10  0.020
 Y6D  plan-4  C03  0.020
 Y6D  plan-4  N04  0.020
 Y6D  plan-4  C05  0.020
 Y6D  plan-4  C06  0.020
 Y6D  plan-4  C07  0.020
 Y6D  plan-4  C08  0.020
 Y6D  plan-4  C09  0.020
 Y6D  plan-4  N11  0.020
 Y6D  plan-4  N12  0.020
 Y6D  plan-4  H9   0.020
 Y6D  plan-4  H10  0.020
 Y6D  plan-4  H11  0.020
 Y6D  plan-4  H12  0.020
 Y6D  plan-5  C14  0.020
 Y6D  plan-5  O01  0.020
 Y6D  plan-5  C02  0.020
 Y6D  plan-5  C03  0.020
 Y6D  plan-5  N13  0.020
 Y6D  plan-5  C20  0.020

