# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 12:01:49 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-(benzotriazol-1-yl)-~{N}-[4-(1~{H}-imidazol-4-yl)phenyl]-~{N}-(thiophen-3-ylmethyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cn1nnc2ccccc12)N(Cc3cscc3)c4ccc(cc4)c5c[nH]cn5
#
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
 Y6G  Y6G  2-(benzotriazol-1-yl)-~{N}-[4-(1~{H}-imidazol-4-yl)phenyl]-~{N}-(thiophen-3-ylmethyl)ethanamide  ligand  48  30  .  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_Y6G
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
 Y6G  O01  O  O     0  -0.458  -22.9951  -39.3965   3.4406
 Y6G  C02  C  C     0   0.530  -23.6012  -40.4080   3.1442
 Y6G  C03  C  CH2   0  -0.448  -22.8794  -41.5907   2.4964
 Y6G  N04  N  NR5   0  -0.380  -21.5128  -41.2568   2.2247
 Y6G  C05  C  CR56  0   0.394  -21.0083  -40.4964   1.2248
 Y6G  C06  C  CR16  0  -0.290  -21.5682  -39.8637   0.1132
 Y6G  C07  C  CR16  0  -0.260  -20.6894  -39.1806  -0.6973
 Y6G  C08  C  CR16  0  -0.268  -19.3055  -39.1242  -0.4226
 Y6G  C09  C  CR16  0  -0.289  -18.7628  -39.7511   0.6753
 Y6G  C10  C  CR56  0   0.123  -19.6431  -40.4473   1.5106
 Y6G  N11  N  N     0  -0.318  -19.4253  -41.1586   2.6565
 Y6G  N12  N  N     0  -0.059  -20.5442  -41.6180   3.0619
 Y6G  N13  N  NT    0  -0.528  -24.9304  -40.5670   3.3235
 Y6G  C14  C  CH2   0  -0.426  -25.7198  -39.4926   3.9254
 Y6G  C15  C  CR5   0   0.186  -25.8816  -39.6630   5.4071
 Y6G  C16  C  CR15  0  -0.519  -24.9931  -39.2008   6.3339
 Y6G  S17  S  S2    0   0.215  -25.4613  -39.6123   7.9278
 Y6G  C18  C  CR15  0  -0.465  -26.8705  -40.4128   7.3707
 Y6G  C19  C  CR15  0  -0.203  -26.9655  -40.3627   6.0146
 Y6G  C20  C  CR6   0   0.218  -25.5850  -41.8093   3.0993
 Y6G  C21  C  CR16  0  -0.230  -26.3565  -41.9949   1.9595
 Y6G  C22  C  CR16  0  -0.310  -27.0135  -43.1955   1.7494
 Y6G  C23  C  CR6   0   0.063  -26.9136  -44.2395   2.6717
 Y6G  C24  C  CR5   0   0.138  -27.6013  -45.5060   2.4351
 Y6G  C25  C  CR15  0  -0.104  -27.6409  -46.6204   3.2375
 Y6G  N26  N  NR15  0  -0.566  -28.4057  -47.5213   2.5668
 Y6G  C27  C  CR15  0   0.098  -28.7977  -46.9486   1.4110
 Y6G  N28  N  N     0  -0.452  -28.3317  -45.7342   1.2992
 Y6G  C29  C  CR16  0  -0.349  -26.1407  -44.0363   3.8173
 Y6G  C30  C  CR16  0  -0.217  -25.4893  -42.8347   4.0333
 Y6G  H1   H  HCH2  0   0.313  -23.3713  -41.8871   1.5683
 Y6G  H2   H  HCH2  0   0.328  -22.8855  -42.4615   3.1518
 Y6G  H3   H  HCR6  0   0.281  -22.6278  -39.9030  -0.1021
 Y6G  H4   H  HCR6  0   0.267  -21.0679  -38.6695  -1.5726
 Y6G  H5   H  HCR6  0   0.263  -18.6629  -38.5725  -1.0956
 Y6G  H6   H  HCR6  0   0.271  -17.7028  -39.7087   0.8873
 Y6G  H7   H  HCH2  0   0.279  -25.2426  -38.5429   3.6931
 Y6G  H8   H  HCH2  0   0.282  -26.6957  -39.4903   3.4384
 Y6G  H9   H  HCR5  0   0.292  -24.0874  -38.6413   6.1552
 Y6G  H10  H  HCR5  0   0.293  -27.5529  -40.8720   8.0691
 Y6G  H11  H  HCR5  0   0.265  -27.7813  -40.8029   5.4574
 Y6G  H12  H  HCR6  0   0.265  -26.4400  -41.1981   1.2304
 Y6G  H13  H  HCR6  0   0.252  -27.6075  -43.3269   0.8550
 Y6G  H14  H  HCR5  0   0.292  -27.2065  -46.8433   4.1975
 Y6G  H15  H  HNR5  0   0.424  -28.6353  -48.4520   2.8796
 Y6G  H16  H  HCR5  0   0.281  -29.4183  -47.4606   0.6920
 Y6G  H18  H  HCR6  0   0.252  -26.0412  -44.8200   4.5577
 Y6G  H19  H  HCR6  0   0.270  -24.9006  -42.6923   4.9310

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
 Y6G  C08  C07  aromatic  1.412  0.020  1.412
 Y6G  C08  C09  aromatic  1.376  0.020  1.376
 Y6G  C07  C06  aromatic  1.377  0.020  1.377
 Y6G  C06  C05  aromatic  1.396  0.020  1.396
 Y6G  C09  C10  aromatic  1.399  0.020  1.399
 Y6G  N28  C27  aromatic  1.306  0.020  1.306
 Y6G  N28  C24  aromatic  1.370  0.020  1.370
 Y6G  C10  C05  aromatic  1.396  0.020  1.396
 Y6G  C10  N11  aromatic  1.366  0.020  1.366
 Y6G  C05  N04  aromatic  1.354  0.020  1.354
 Y6G  C27  N26  aromatic  1.348  0.020  1.348
 Y6G  C22  C21  aromatic  1.385  0.020  1.385
 Y6G  C22  C23  aromatic  1.397  0.020  1.397
 Y6G  C21  C20  aromatic  1.389  0.020  1.389
 Y6G  N11  N12  aromatic  1.276  0.020  1.276
 Y6G  C24  C23  single    1.461  0.020  1.461
 Y6G  C24  C25  aromatic  1.374  0.020  1.374
 Y6G  N04  C03  single    1.433  0.020  1.433
 Y6G  N04  N12  aromatic  1.330  0.020  1.330
 Y6G  N26  C25  aromatic  1.359  0.020  1.359
 Y6G  C23  C29  aromatic  1.397  0.020  1.397
 Y6G  C03  C02  single    1.530  0.020  1.530
 Y6G  C20  N13  single    1.422  0.020  1.422
 Y6G  C20  C30  aromatic  1.390  0.020  1.390
 Y6G  C02  N13  single    1.351  0.020  1.351
 Y6G  C02  O01  double    1.216  0.020  1.216
 Y6G  N13  C14  single    1.463  0.020  1.463
 Y6G  C29  C30  aromatic  1.384  0.020  1.384
 Y6G  C14  C15  single    1.500  0.020  1.500
 Y6G  C15  C19  aromatic  1.426  0.020  1.426
 Y6G  C15  C16  aromatic  1.365  0.020  1.365
 Y6G  C19  C18  aromatic  1.360  0.020  1.360
 Y6G  C16  S17  aromatic  1.711  0.020  1.711
 Y6G  C18  S17  aromatic  1.714  0.020  1.714
 Y6G  C03  H1   single    0.970  0.020  1.090
 Y6G  C03  H2   single    0.970  0.020  1.090
 Y6G  C06  H3   single    0.930  0.020  1.080
 Y6G  C07  H4   single    0.930  0.020  1.080
 Y6G  C08  H5   single    0.930  0.020  1.080
 Y6G  C09  H6   single    0.930  0.020  1.080
 Y6G  C14  H7   single    0.970  0.020  1.090
 Y6G  C14  H8   single    0.970  0.020  1.090
 Y6G  C16  H9   single    0.930  0.020  1.080
 Y6G  C18  H10  single    0.930  0.020  1.080
 Y6G  C19  H11  single    0.930  0.020  1.080
 Y6G  C21  H12  single    0.930  0.020  1.080
 Y6G  C22  H13  single    0.930  0.020  1.080
 Y6G  C25  H14  single    0.930  0.020  1.080
 Y6G  N26  H15  single    0.860  0.020  1.020
 Y6G  C27  H16  single    0.930  0.020  1.080
 Y6G  C29  H18  single    0.930  0.020  1.080
 Y6G  C30  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
 Y6G  N13  C02  C03  115.44  3.000
 Y6G  N13  C02  O01  123.79  3.000
 Y6G  C03  C02  O01  120.75  3.000
 Y6G  H2   C03  H1   106.97  3.000
 Y6G  H2   C03  N04  107.79  3.000
 Y6G  H1   C03  N04  109.39  3.000
 Y6G  H2   C03  C02  111.13  3.000
 Y6G  H1   C03  C02  110.95  3.000
 Y6G  N04  C03  C02  110.50  3.000
 Y6G  N12  N04  C05  110.24  3.000
 Y6G  N12  N04  C03  120.79  3.000
 Y6G  C05  N04  C03  128.79  3.000
 Y6G  C10  C05  C06  122.64  3.000
 Y6G  C10  C05  N04  103.48  3.000
 Y6G  C06  C05  N04  133.88  3.000
 Y6G  H3   C06  C07  121.73  3.000
 Y6G  H3   C06  C05  122.32  3.000
 Y6G  C07  C06  C05  115.94  3.000
 Y6G  H4   C07  C08  118.78  3.000
 Y6G  H4   C07  C06  119.16  3.000
 Y6G  C08  C07  C06  122.07  3.000
 Y6G  H5   C08  C09  119.64  3.000
 Y6G  H5   C08  C07  118.79  3.000
 Y6G  C09  C08  C07  121.58  3.000
 Y6G  H6   C09  C10  121.27  3.000
 Y6G  H6   C09  C08  121.67  3.000
 Y6G  C10  C09  C08  117.06  3.000
 Y6G  N11  C10  C09  131.26  3.000
 Y6G  N11  C10  C05  108.02  3.000
 Y6G  C09  C10  C05  120.71  3.000
 Y6G  N12  N11  C10  108.32  3.000
 Y6G  N11  N12  N04  109.93  3.000
 Y6G  C20  N13  C14  117.27  3.000
 Y6G  C14  N13  C02  119.95  3.000
 Y6G  C20  N13  C02  122.34  3.000
 Y6G  H8   C14  H7   107.18  3.000
 Y6G  H8   C14  C15  110.16  3.000
 Y6G  H7   C14  C15  110.94  3.000
 Y6G  H8   C14  N13  107.50  3.000
 Y6G  H7   C14  N13  108.46  3.000
 Y6G  C15  C14  N13  112.41  3.000
 Y6G  C19  C15  C16  111.82  3.000
 Y6G  C16  C15  C14  124.20  3.000
 Y6G  C19  C15  C14  123.95  3.000
 Y6G  H9   C16  S17  120.55  3.000
 Y6G  H9   C16  C15  127.54  3.000
 Y6G  S17  C16  C15  111.90  3.000
 Y6G  C18  S17  C16   91.98  3.000
 Y6G  H10  C18  C19  128.08  3.000
 Y6G  H10  C18  S17  120.56  3.000
 Y6G  C19  C18  S17  111.36  3.000
 Y6G  H11  C19  C18  123.46  3.000
 Y6G  H11  C19  C15  123.61  3.000
 Y6G  C18  C19  C15  112.93  3.000
 Y6G  C30  C20  C21  119.41  3.000
 Y6G  C30  C20  N13  120.45  3.000
 Y6G  C21  C20  N13  120.12  3.000
 Y6G  H12  C21  C22  119.94  3.000
 Y6G  H12  C21  C20  119.80  3.000
 Y6G  C22  C21  C20  120.26  3.000
 Y6G  H13  C22  C23  119.64  3.000
 Y6G  H13  C22  C21  119.43  3.000
 Y6G  C23  C22  C21  120.93  3.000
 Y6G  C29  C23  C24  121.31  3.000
 Y6G  C29  C23  C22  118.19  3.000
 Y6G  C24  C23  C22  120.50  3.000
 Y6G  N28  C24  C25  109.51  3.000
 Y6G  C25  C24  C23  128.49  3.000
 Y6G  N28  C24  C23  122.00  3.000
 Y6G  H14  C25  N26  121.99  3.000
 Y6G  H14  C25  C24  132.60  3.000
 Y6G  N26  C25  C24  105.41  3.000
 Y6G  H15  N26  C27  126.28  3.000
 Y6G  H15  N26  C25  125.95  3.000
 Y6G  C27  N26  C25  107.77  3.000
 Y6G  H16  C27  N28  126.13  3.000
 Y6G  H16  C27  N26  122.48  3.000
 Y6G  N28  C27  N26  111.39  3.000
 Y6G  C27  N28  C24  105.92  3.000
 Y6G  H18  C29  C30  118.59  3.000
 Y6G  H18  C29  C23  120.42  3.000
 Y6G  C30  C29  C23  120.99  3.000
 Y6G  H19  C30  C29  119.96  3.000
 Y6G  H19  C30  C20  119.83  3.000
 Y6G  C29  C30  C20  120.21  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
 Y6G  CONST_01  C07  C06  C05  N04  180.00   0.0  0
 Y6G  CONST_02  C09  C10  C05  N04  180.00   0.0  0
 Y6G  CONST_03  N11  C10  C05  N04    0.00   0.0  0
 Y6G  CONST_04  C10  N11  N12  N04    0.00   0.0  0
 Y6G  CONST_05  C08  C07  C06  C05    0.00   0.0  0
 Y6G  CONST_06  C08  C09  C10  C05    0.00   0.0  0
 Y6G  CONST_07  N12  N11  C10  C05    0.00   0.0  0
 Y6G  CONST_08  N11  N12  N04  C05    0.00   0.0  0
 Y6G  CONST_09  C09  C08  C07  C06    0.00   0.0  0
 Y6G  CONST_10  C09  C10  C05  C06    0.00   0.0  0
 Y6G  CONST_11  N11  C10  C05  C06  180.00   0.0  0
 Y6G  CONST_12  N12  N04  C05  C06  180.00   0.0  0
 Y6G  CONST_13  C10  C09  C08  C07    0.00   0.0  0
 Y6G  CONST_14  C10  C05  C06  C07    0.00   0.0  0
 Y6G  CONST_15  N11  C10  C09  C08  180.00   0.0  0
 Y6G  CONST_16  N12  N11  C10  C09  180.00   0.0  0
 Y6G  CONST_17  N12  N04  C05  C10    0.00   0.0  0
 Y6G  CONST_18  S17  C18  C19  C15    0.00   0.0  0
 Y6G  CONST_19  C18  S17  C16  C15    0.00   0.0  0
 Y6G  CONST_20  C18  C19  C15  C16    0.00   0.0  0
 Y6G  CONST_21  C19  C18  S17  C16    0.00   0.0  0
 Y6G  CONST_22  C19  C15  C16  S17    0.00   0.0  0
 Y6G  CONST_23  C23  C22  C21  C20    0.00   0.0  0
 Y6G  CONST_24  C23  C29  C30  C20    0.00   0.0  0
 Y6G  CONST_25  C24  C23  C22  C21  180.00   0.0  0
 Y6G  CONST_26  C29  C23  C22  C21    0.00   0.0  0
 Y6G  CONST_27  C29  C30  C20  C21    0.00   0.0  0
 Y6G  CONST_28  C30  C20  C21  C22    0.00   0.0  0
 Y6G  CONST_29  N28  C24  C23  C22    0.00   0.0  0
 Y6G  CONST_30  C25  C24  C23  C22  180.00   0.0  0
 Y6G  CONST_31  C30  C29  C23  C22    0.00   0.0  0
 Y6G  CONST_32  C27  N28  C24  C23  180.00   0.0  0
 Y6G  CONST_33  N26  C25  C24  C23  180.00   0.0  0
 Y6G  CONST_34  N26  C27  N28  C24    0.00   0.0  0
 Y6G  CONST_35  C30  C29  C23  C24  180.00   0.0  0
 Y6G  CONST_36  C27  N26  C25  C24    0.00   0.0  0
 Y6G  CONST_37  C27  N28  C24  C25    0.00   0.0  0
 Y6G  CONST_38  C29  C23  C24  C25    0.00   0.0  0
 Y6G  CONST_39  N28  C27  N26  C25    0.00   0.0  0
 Y6G  CONST_40  N28  C24  C25  N26    0.00   0.0  0
 Y6G  CONST_41  C29  C23  C24  N28  180.00   0.0  0
 Y6G  CONST_42  C06  C05  N04  C03    0.00   0.0  0
 Y6G  CONST_43  C10  C05  N04  C03  180.00   0.0  0
 Y6G  CONST_44  N11  N12  N04  C03  180.00   0.0  0
 Y6G  CONST_45  C22  C21  C20  N13  180.00   0.0  0
 Y6G  CONST_46  C29  C30  C20  N13  180.00   0.0  0
 Y6G  CONST_47  C18  C19  C15  C14  180.00   0.0  0
 Y6G  CONST_48  S17  C16  C15  C14  180.00   0.0  0
 Y6G  CONST_49  H3   C06  C05  N04    0.00   0.0  0
 Y6G  CONST_50  H4   C07  C06  C05  180.00   0.0  0
 Y6G  CONST_51  H6   C09  C10  C05  180.00   0.0  0
 Y6G  CONST_52  H5   C08  C07  C06  180.00   0.0  0
 Y6G  CONST_53  H10  C18  C19  C15  180.00   0.0  0
 Y6G  CONST_54  H11  C19  C15  C16  180.00   0.0  0
 Y6G  CONST_55  H9   C16  S17  C18  180.00   0.0  0
 Y6G  CONST_56  H13  C22  C21  C20  180.00   0.0  0
 Y6G  CONST_57  H18  C29  C30  C20  180.00   0.0  0
 Y6G  CONST_58  H19  C30  C20  C21  180.00   0.0  0
 Y6G  CONST_59  H12  C21  C22  C23  180.00   0.0  0
 Y6G  CONST_60  H14  C25  C24  C23    0.00   0.0  0
 Y6G  CONST_61  H16  C27  N28  C24  180.00   0.0  0
 Y6G  CONST_62  H15  N26  C25  C24  180.00   0.0  0
 Y6G  CONST_67  C20  N13  C02  O01  180.00   0.0  0
 Y6G  CONST_68  C20  N13  C02  C03    0.00   0.0  0
 Y6G  CONST_69  C14  N13  C02  O01    0.00   0.0  0
 Y6G  CONST_70  C14  N13  C02  C03  180.00   0.0  0
 Y6G  Var_01    C05  N04  C03  C02  -76.94  30.0  1
 Y6G  Var_02    C19  C15  C14  N13  -90.91  30.0  2
 Y6G  Var_03    C20  N13  C14  C15   78.22  30.0  2
 Y6G  Var_04    N04  C03  C02  O01   -4.79  30.0  2

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
 Y6G  plan-1  C14  0.020
 Y6G  plan-1  C15  0.020
 Y6G  plan-1  C16  0.020
 Y6G  plan-1  S17  0.020
 Y6G  plan-1  C18  0.020
 Y6G  plan-1  C19  0.020
 Y6G  plan-1  H9   0.020
 Y6G  plan-1  H10  0.020
 Y6G  plan-1  H11  0.020
 Y6G  plan-2  C23  0.020
 Y6G  plan-2  C24  0.020
 Y6G  plan-2  C25  0.020
 Y6G  plan-2  N26  0.020
 Y6G  plan-2  C27  0.020
 Y6G  plan-2  N28  0.020
 Y6G  plan-2  H14  0.020
 Y6G  plan-2  H15  0.020
 Y6G  plan-2  H16  0.020
 Y6G  plan-3  N13  0.020
 Y6G  plan-3  C20  0.020
 Y6G  plan-3  C21  0.020
 Y6G  plan-3  C22  0.020
 Y6G  plan-3  C23  0.020
 Y6G  plan-3  C24  0.020
 Y6G  plan-3  C29  0.020
 Y6G  plan-3  C30  0.020
 Y6G  plan-3  H12  0.020
 Y6G  plan-3  H13  0.020
 Y6G  plan-3  H18  0.020
 Y6G  plan-3  H19  0.020
 Y6G  plan-4  C03  0.020
 Y6G  plan-4  N04  0.020
 Y6G  plan-4  C05  0.020
 Y6G  plan-4  C06  0.020
 Y6G  plan-4  C07  0.020
 Y6G  plan-4  C08  0.020
 Y6G  plan-4  C09  0.020
 Y6G  plan-4  C10  0.020
 Y6G  plan-4  N11  0.020
 Y6G  plan-4  N12  0.020
 Y6G  plan-4  H3   0.020
 Y6G  plan-4  H4   0.020
 Y6G  plan-4  H5   0.020
 Y6G  plan-4  H6   0.020
 Y6G  plan-5  O01  0.020
 Y6G  plan-5  C02  0.020
 Y6G  plan-5  C03  0.020
 Y6G  plan-5  N13  0.020
 Y6G  plan-5  C14  0.020
 Y6G  plan-5  C20  0.020

