# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 10:43:26 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 1-ethyl-3-(2-{[3-(1-methylethyl)[1,2,4]triazolo[4,3-a]pyridin-6-yl]sulfanyl}benzyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)NCc1ccccc1Sc2ccc3nnc(C(C)C)n3c2
#
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
 YIX  YIX  1-ethyl-3-(2-{[3-(1-methylethyl)[1,2,4]triazolo[4,3-a]pyridin-6-yl]sulfanyl}benzyl)urea  ligand  49  26  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YIX
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
 YIX  C1    C  CH3   0  -0.701   1.4631   3.7695   1.5754
 YIX  C2    C  CH2   0  -0.261   1.4318   3.0871   0.2210
 YIX  N3    N  NH1   0  -0.674   1.6614   1.6659   0.3704
 YIX  C4    C  C     0   0.773   1.5658   0.8081  -0.6751
 YIX  O5    O  O     0  -0.554   1.1075   1.1438  -1.7655
 YIX  N6    N  NH1   0  -0.669   1.9823  -0.4608  -0.4227
 YIX  C7    C  CH2   0  -0.328   1.9977  -1.4804  -1.4476
 YIX  C8    C  CR6   0   0.120   2.0599  -2.8413  -0.8099
 YIX  C9    C  CR16  0  -0.278   3.3055  -3.3815  -0.5051
 YIX  C10   C  CR16  0  -0.239   3.4305  -4.6237   0.1013
 YIX  C11   C  CR16  0  -0.257   2.2948  -5.3518   0.4200
 YIX  C12   C  CR16  0  -0.222   1.0423  -4.8287   0.1328
 YIX  C13   C  CR6   0  -0.200   0.9194  -3.5821  -0.4742
 YIX  S14   S  S2    0   0.054  -0.7236  -3.0521  -0.8987
 YIX  C15   C  CR6   0  -0.237  -0.9316  -1.6173   0.1077
 YIX  C16   C  CR16  0  -0.115  -0.7227  -1.6681   1.5212
 YIX  C17   C  CR16  0  -0.361  -0.9390  -0.5735   2.2914
 YIX  C18   C  CR56  0   0.481  -1.3966   0.6135   1.6703
 YIX  N19   N  N     0  -0.358  -1.6851   1.7986   2.1535
 YIX  N20   N  N     0  -0.324  -2.0647   2.5703   1.1147
 YIX  C21   C  CR5   0   0.460  -2.0167   1.8798   0.0091
 YIX  C22   C  CH1   0  -0.366  -2.3617   2.3375  -1.3677
 YIX  C23   C  CH3   0  -0.650  -3.6997   1.7461  -1.8243
 YIX  C24   C  CH3   0  -0.649  -2.3924   3.8590  -1.4454
 YIX  N25   N  N     0  -0.557  -1.6005   0.6132   0.3099
 YIX  C26   C  CR16  0   0.025  -1.3588  -0.4756  -0.4804
 YIX  H11C  H  HCH3  0   0.239   1.2668   4.8347   1.4600
 YIX  H12C  H  HCH3  0   0.236   0.7027   3.3561   2.2378
 YIX  H13C  H  HCH3  0   0.227   2.4363   3.6622   2.0575
 YIX  H21C  H  HCH2  0   0.234   0.4584   3.2512  -0.2414
 YIX  H22C  H  HCH2  0   0.224   2.1788   3.5399  -0.4396
 YIX  H3    H  HNH1  0   0.384   2.1418   1.3679   1.2041
 YIX  H6    H  HNH1  0   0.390   2.4720  -0.6624   0.4339
 YIX  H71C  H  HCH2  0   0.259   1.1019  -1.3904  -2.0618
 YIX  H72C  H  HCH2  0   0.252   2.8566  -1.3622  -2.1166
 YIX  H9    H  HCR6  0   0.262   4.1975  -2.8218  -0.7605
 YIX  H10   H  HCR6  0   0.266   4.4130  -5.0209   0.3191
 YIX  H11   H  HCR6  0   0.266   2.3783  -6.3211   0.8935
 YIX  H12   H  HCR6  0   0.273   0.1512  -5.3898   0.3826
 YIX  H16   H  HCR6  0   0.284  -0.3827  -2.5912   1.9712
 YIX  H26   H  HCR6  0   0.321  -1.5061  -0.3639  -1.5438
 YIX  H17   H  HCR6  0   0.289  -0.7823  -0.5844   3.3605
 YIX  H22   H  HCH1  0   0.264  -1.5723   1.9782  -2.0370
 YIX  H231  H  HCH3  0   0.233  -4.5165   2.1339  -1.2137
 YIX  H232  H  HCH3  0   0.244  -3.8940   2.0198  -2.8614
 YIX  H233  H  HCH3  0   0.235  -3.7236   0.6574  -1.7639
 YIX  H241  H  HCH3  0   0.229  -3.1696   4.2718  -0.8021
 YIX  H242  H  HCH3  0   0.238  -1.4405   4.3003  -1.1504
 YIX  H243  H  HCH3  0   0.238  -2.6026   4.1705  -2.4684

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
 YIX  C1   C2    single    1.517  0.020  1.517
 YIX  C2   N3    single    1.447  0.020  1.447
 YIX  N3   C4    single    1.356  0.020  1.356
 YIX  C4   O5    double    1.230  0.020  1.230
 YIX  C4   N6    single    1.359  0.020  1.359
 YIX  N6   C7    single    1.446  0.020  1.446
 YIX  C7   C8    single    1.504  0.020  1.504
 YIX  C8   C9    aromatic  1.392  0.020  1.392
 YIX  C8   C13   aromatic  1.401  0.020  1.401
 YIX  C9   C10   aromatic  1.388  0.020  1.388
 YIX  C10  C11   aromatic  1.386  0.020  1.386
 YIX  C11  C12   aromatic  1.387  0.020  1.387
 YIX  C12  C13   aromatic  1.392  0.020  1.392
 YIX  C13  S14   single    1.778  0.020  1.778
 YIX  S14  C15   single    1.765  0.020  1.765
 YIX  C15  C16   aromatic  1.430  0.020  1.430
 YIX  C15  C26   aromatic  1.353  0.020  1.353
 YIX  C16  C17   aromatic  1.356  0.020  1.356
 YIX  C17  C18   aromatic  1.416  0.020  1.416
 YIX  C18  N19   aromatic  1.312  0.020  1.312
 YIX  C18  N25   aromatic  1.376  0.020  1.376
 YIX  N19  N20   aromatic  1.349  0.020  1.349
 YIX  N20  C21   aromatic  1.304  0.020  1.304
 YIX  C21  C22   single    1.491  0.020  1.491
 YIX  C21  N25   aromatic  1.367  0.020  1.367
 YIX  C22  C23   single    1.532  0.020  1.532
 YIX  C22  C24   single    1.524  0.020  1.524
 YIX  N25  C26   aromatic  1.367  0.020  1.367
 YIX  C1   H11C  single    0.970  0.020  1.090
 YIX  C1   H12C  single    0.970  0.020  1.090
 YIX  C1   H13C  single    0.970  0.020  1.090
 YIX  C2   H21C  single    0.970  0.020  1.090
 YIX  C2   H22C  single    0.970  0.020  1.090
 YIX  N3   H3    single    0.860  0.020  1.020
 YIX  N6   H6    single    0.860  0.020  1.020
 YIX  C7   H71C  single    0.970  0.020  1.090
 YIX  C7   H72C  single    0.970  0.020  1.090
 YIX  C9   H9    single    0.930  0.020  1.080
 YIX  C10  H10   single    0.930  0.020  1.080
 YIX  C11  H11   single    0.930  0.020  1.080
 YIX  C12  H12   single    0.930  0.020  1.080
 YIX  C16  H16   single    0.930  0.020  1.080
 YIX  C26  H26   single    0.930  0.020  1.080
 YIX  C17  H17   single    0.930  0.020  1.080
 YIX  C22  H22   single    0.970  0.020  1.090
 YIX  C23  H231  single    0.970  0.020  1.090
 YIX  C23  H232  single    0.970  0.020  1.090
 YIX  C23  H233  single    0.970  0.020  1.090
 YIX  C24  H241  single    0.970  0.020  1.090
 YIX  C24  H242  single    0.970  0.020  1.090
 YIX  C24  H243  single    0.970  0.020  1.090

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
 YIX  H13C  C1   H12C  108.44  3.000
 YIX  H13C  C1   H11C  107.67  3.000
 YIX  H12C  C1   H11C  108.04  3.000
 YIX  H13C  C1   C2    111.63  3.000
 YIX  H12C  C1   C2    110.96  3.000
 YIX  H11C  C1   C2    109.98  3.000
 YIX  H22C  C2   H21C  106.92  3.000
 YIX  H22C  C2   N3    111.10  3.000
 YIX  H21C  C2   N3    109.46  3.000
 YIX  H22C  C2   C1    109.79  3.000
 YIX  H21C  C2   C1    109.24  3.000
 YIX  N3    C2   C1    110.26  3.000
 YIX  H3    N3   C4    118.99  3.000
 YIX  H3    N3   C2    116.85  3.000
 YIX  C4    N3   C2    122.04  3.000
 YIX  N6    C4   O5    122.27  3.000
 YIX  N6    C4   N3    115.21  3.000
 YIX  O5    C4   N3    122.51  3.000
 YIX  H6    N6   C7    117.17  3.000
 YIX  H6    N6   C4    119.59  3.000
 YIX  C7    N6   C4    122.01  3.000
 YIX  H72C  C7   H71C  106.95  3.000
 YIX  H72C  C7   C8    108.92  3.000
 YIX  H71C  C7   C8    110.34  3.000
 YIX  H72C  C7   N6    111.42  3.000
 YIX  H71C  C7   N6    109.42  3.000
 YIX  C8    C7   N6    109.75  3.000
 YIX  C13   C8   C9    118.10  3.000
 YIX  C13   C8   C7    123.12  3.000
 YIX  C9    C8   C7    118.76  3.000
 YIX  H9    C9   C10   119.42  3.000
 YIX  H9    C9   C8    118.99  3.000
 YIX  C10   C9   C8    121.59  3.000
 YIX  H10   C10  C11   120.33  3.000
 YIX  H10   C10  C9    119.88  3.000
 YIX  C11   C10  C9    119.78  3.000
 YIX  H11   C11  C12   119.87  3.000
 YIX  H11   C11  C10   120.52  3.000
 YIX  C12   C11  C10   119.61  3.000
 YIX  H12   C12  C13   119.49  3.000
 YIX  H12   C12  C11   120.01  3.000
 YIX  C13   C12  C11   120.51  3.000
 YIX  S14   C13  C12   116.92  3.000
 YIX  S14   C13  C8    122.52  3.000
 YIX  C12   C13  C8    120.41  3.000
 YIX  C15   S14  C13   102.42  3.000
 YIX  C26   C15  C16   120.37  3.000
 YIX  C26   C15  S14   118.38  3.000
 YIX  C16   C15  S14   121.17  3.000
 YIX  H16   C16  C17   120.19  3.000
 YIX  H16   C16  C15   119.17  3.000
 YIX  C17   C16  C15   120.64  3.000
 YIX  H17   C17  C18   119.31  3.000
 YIX  H17   C17  C16   122.05  3.000
 YIX  C18   C17  C16   118.64  3.000
 YIX  N25   C18  N19   109.38  3.000
 YIX  N25   C18  C17   118.79  3.000
 YIX  N19   C18  C17   131.83  3.000
 YIX  N20   N19  C18   107.16  3.000
 YIX  C21   N20  N19   109.85  3.000
 YIX  N25   C21  C22   123.92  3.000
 YIX  N25   C21  N20   108.38  3.000
 YIX  C22   C21  N20   127.70  3.000
 YIX  H22   C22  C24   108.11  3.000
 YIX  H22   C22  C23   108.69  3.000
 YIX  C24   C22  C23   110.64  3.000
 YIX  H22   C22  C21   107.26  3.000
 YIX  C24   C22  C21   110.99  3.000
 YIX  C23   C22  C21   111.01  3.000
 YIX  H233  C23  H232  107.42  3.000
 YIX  H233  C23  H231  107.90  3.000
 YIX  H232  C23  H231  108.05  3.000
 YIX  H233  C23  C22   112.82  3.000
 YIX  H232  C23  C22   110.01  3.000
 YIX  H231  C23  C22   110.47  3.000
 YIX  H243  C24  H242  107.87  3.000
 YIX  H243  C24  H241  107.96  3.000
 YIX  H242  C24  H241  108.03  3.000
 YIX  H243  C24  C22   109.70  3.000
 YIX  H242  C24  C22   111.89  3.000
 YIX  H241  C24  C22   111.25  3.000
 YIX  C26   N25  C21   131.67  3.000
 YIX  C26   N25  C18   123.08  3.000
 YIX  C21   N25  C18   105.22  3.000
 YIX  H26   C26  N25   117.59  3.000
 YIX  H26   C26  C15   123.95  3.000
 YIX  N25   C26  C15   118.46  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
 YIX  CONST_01  C11   C10  C9   C8      0.00   0.0  0
 YIX  CONST_02  C11   C12  C13  C8      0.00   0.0  0
 YIX  CONST_03  C12   C13  C8   C9      0.00   0.0  0
 YIX  CONST_04  C12   C11  C10  C9      0.00   0.0  0
 YIX  CONST_05  C13   C8   C9   C10     0.00   0.0  0
 YIX  CONST_06  C13   C12  C11  C10     0.00   0.0  0
 YIX  CONST_07  C18   C17  C16  C15     0.00   0.0  0
 YIX  CONST_08  C18   N25  C26  C15     0.00   0.0  0
 YIX  CONST_09  C21   N25  C26  C15   180.00   0.0  0
 YIX  CONST_10  N25   C26  C15  C16     0.00   0.0  0
 YIX  CONST_11  N19   C18  C17  C16   180.00   0.0  0
 YIX  CONST_12  N25   C18  C17  C16     0.00   0.0  0
 YIX  CONST_13  C26   C15  C16  C17     0.00   0.0  0
 YIX  CONST_14  N20   N19  C18  C17   180.00   0.0  0
 YIX  CONST_15  C21   N25  C18  C17   180.00   0.0  0
 YIX  CONST_16  C26   N25  C18  C17     0.00   0.0  0
 YIX  CONST_17  C21   N20  N19  C18     0.00   0.0  0
 YIX  CONST_18  N20   C21  N25  C18     0.00   0.0  0
 YIX  CONST_19  C21   N25  C18  N19     0.00   0.0  0
 YIX  CONST_20  C26   N25  C18  N19   180.00   0.0  0
 YIX  CONST_21  N25   C21  N20  N19     0.00   0.0  0
 YIX  CONST_22  N25   C18  N19  N20     0.00   0.0  0
 YIX  CONST_23  C26   N25  C21  N20   180.00   0.0  0
 YIX  CONST_24  C10   C9   C8   C7    180.00   0.0  0
 YIX  CONST_25  C12   C13  C8   C7    180.00   0.0  0
 YIX  CONST_26  S14   C13  C8   C9    180.00   0.0  0
 YIX  CONST_27  S14   C13  C12  C11   180.00   0.0  0
 YIX  CONST_28  C17   C16  C15  S14   180.00   0.0  0
 YIX  CONST_29  N25   C26  C15  S14   180.00   0.0  0
 YIX  CONST_30  C22   C21  N25  C18   180.00   0.0  0
 YIX  CONST_31  C22   C21  N20  N19   180.00   0.0  0
 YIX  CONST_32  C26   N25  C21  C22     0.00   0.0  0
 YIX  CONST_33  H10   C10  C9   C8    180.00   0.0  0
 YIX  CONST_34  H12   C12  C13  C8    180.00   0.0  0
 YIX  CONST_35  H11   C11  C10  C9    180.00   0.0  0
 YIX  CONST_36  H9    C9   C10  C11   180.00   0.0  0
 YIX  CONST_37  H17   C17  C16  C15   180.00   0.0  0
 YIX  CONST_38  H26   C26  C15  C16   180.00   0.0  0
 YIX  CONST_39  H16   C16  C17  C18   180.00   0.0  0
 YIX  CONST_40  O5    C4   N3   C2      0.00   0.0  0
 YIX  CONST_41  C7    N6   C4   O5      0.00   0.0  0
 YIX  CONST_42  N6    C4   N3   C2    180.00   0.0  0
 YIX  CONST_43  C7    N6   C4   N3    180.00   0.0  0
 YIX  CONST_44  H3    N3   C4   O5    180.00   0.0  0
 YIX  CONST_45  H6    N6   C4   O5    180.00   0.0  0
 YIX  Var_01    C16   C15  S14  C13   -53.84  30.0  2
 YIX  Var_02    C9    C8   C7   N6    -87.61  30.0  2
 YIX  Var_03    C23   C22  C21  N20  -106.14  30.0  2
 YIX  Var_04    C8    C7   N6   C4   -161.52  30.0  3
 YIX  Var_05    H231  C23  C22  C21    65.71  30.0  3
 YIX  Var_06    H241  C24  C22  C21   -63.11  30.0  3
 YIX  Var_07    C4    N3   C2   C1    174.03  30.0  3
 YIX  Var_08    H11C  C1   C2   N3   -178.69  30.0  3

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
 YIX  plan-1  C7   0.020
 YIX  plan-1  C8   0.020
 YIX  plan-1  C9   0.020
 YIX  plan-1  C10  0.020
 YIX  plan-1  C11  0.020
 YIX  plan-1  C12  0.020
 YIX  plan-1  C13  0.020
 YIX  plan-1  S14  0.020
 YIX  plan-1  H9   0.020
 YIX  plan-1  H10  0.020
 YIX  plan-1  H11  0.020
 YIX  plan-1  H12  0.020
 YIX  plan-2  S14  0.020
 YIX  plan-2  C15  0.020
 YIX  plan-2  C16  0.020
 YIX  plan-2  C17  0.020
 YIX  plan-2  C18  0.020
 YIX  plan-2  N19  0.020
 YIX  plan-2  N20  0.020
 YIX  plan-2  C21  0.020
 YIX  plan-2  C22  0.020
 YIX  plan-2  N25  0.020
 YIX  plan-2  C26  0.020
 YIX  plan-2  H16  0.020
 YIX  plan-2  H26  0.020
 YIX  plan-2  H17  0.020
 YIX  plan-3  C2   0.020
 YIX  plan-3  N3   0.020
 YIX  plan-3  C4   0.020
 YIX  plan-3  O5   0.020
 YIX  plan-3  N6   0.020
 YIX  plan-3  C7   0.020
 YIX  plan-3  H3   0.020
 YIX  plan-3  H6   0.020

