# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 05:47:08 2022
#   Inital geometry file: a 148 line input string
#   Ligand name: 5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1oc2ccc(cc2c1)N3CCN(CCCCc4c[nH]c5ccc(cc45)C#N)CC3
#
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
 YG7  YG7  5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide  ligand  60  33  .  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_YG7
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
 YG7  C10  C  CH2   0  -0.306  154.2903  166.0811  150.1012
 YG7  C13  C  CH2   0  -0.449  151.8446  169.5527  148.9476
 YG7  C15  C  CR6   0   0.357  156.4988  165.0798  150.2823
 YG7  C17  C  CR5   0   0.004  151.6939  172.6862  149.2354
 YG7  C20  C  CR56  0   0.041  152.5938  173.7568  149.5514
 YG7  C21  C  CR56  0   0.097  158.4345  164.2385  151.4302
 YG7  C22  C  CR15  0  -0.068  150.8883  172.5499  150.3295
 YG7  C24  C  CR16  0  -0.323  156.8367  162.6582  150.4902
 YG7  C26  C  CR15  0  -0.368  159.6611  164.0969  152.1555
 YG7  C28  C  CR16  0  -0.288  152.9563  175.2604  151.4697
 YG7  C08  C  CH2   0  -0.291  153.5016  166.9985  149.1892
 YG7  C09  C  CH2   0  -0.277  155.4110  168.3602  148.8960
 YG7  C11  C  CH2   0  -0.318  156.2261  167.4549  149.8024
 YG7  C14  C  CH2   0  -0.450  151.0637  170.5185  148.0586
 YG7  C16  C  CH2   0  -0.522  151.6451  171.9279  147.9476
 YG7  C18  C  CR16  0  -0.455  157.6714  165.3251  150.9885
 YG7  C19  C  CR16  0  -0.324  156.1075  163.7385  150.0424
 YG7  C23  C  CR56  0   0.341  158.0034  162.9385  151.1831
 YG7  C25  C  CR56  0   0.377  152.2677  174.2166  150.8510
 YG7  C27  C  CR16  0  -0.363  153.6389  174.3631  148.8604
 YG7  C29  C  CR5   0   0.247  159.8694  162.7653  152.2809
 YG7  C30  C  CR6   0  -0.004  154.3269  175.4009  149.4776
 YG7  C31  C  CR16  0  -0.273  153.9873  175.8477  150.7738
 YG7  C32  C  C     0   0.442  160.9854  162.0531  152.9345
 YG7  C33  C  CSP   0   0.037  155.4015  176.0344  148.7896
 YG7  N03  N  NT    0  -0.423  154.0078  168.3556  149.2601
 YG7  N04  N  NT    0  -0.512  155.7052  166.1046  149.7566
 YG7  N05  N  NR15  0  -0.687  151.2314  173.4648  151.2918
 YG7  N06  N  NH2   0  -0.811  160.9327  160.7148  152.8985
 YG7  N07  N  NS    0  -0.265  156.2722  176.5513  148.2368
 YG7  O01  O  O     0  -0.464  158.8765  162.0444  151.6970
 YG7  O02  O  O     0  -0.466  161.8835  162.6907  153.4653
 YG7  H1   H  HCH2  0   0.214  154.1422  166.3917  151.1467
 YG7  H2   H  HCH2  0   0.252  153.8940  165.0724  150.0040
 YG7  H3   H  HCH2  0   0.221  151.9051  169.9333  149.9703
 YG7  H4   H  HCH2  0   0.231  151.2757  168.6215  148.9997
 YG7  H5   H  HCR5  0   0.287  150.0807  171.8570  150.5068
 YG7  H6   H  HCR6  0   0.271  156.5161  161.6448  150.2881
 YG7  H7   H  HCR5  0   0.271  160.2998  164.8804  152.5302
 YG7  H8   H  HCR6  0   0.273  152.6937  175.6002  152.4629
 YG7  H9   H  HCH2  0   0.243  152.4583  166.9705  149.5055
 YG7  H10  H  HCH2  0   0.192  153.5405  166.6067  148.1576
 YG7  H11  H  HCH2  0   0.192  155.5604  168.0418  147.8496
 YG7  H12  H  HCH2  0   0.239  155.7995  169.3775  148.9805
 YG7  H13  H  HCH2  0   0.250  157.2590  167.4594  149.4507
 YG7  H14  H  HCH2  0   0.210  156.2229  167.8617  150.8256
 YG7  H15  H  HCH2  0   0.185  153.1996  168.9366  147.3864
 YG7  H16  H  HCH2  0   0.228  153.8112  170.2226  148.4173
 YG7  H17  H  HCH2  0   0.231  150.0343  170.5821  148.4218
 YG7  H18  H  HCH2  0   0.231  150.9951  170.0976  147.0513
 YG7  H19  H  HCH2  0   0.236  152.6502  171.8842  147.5197
 YG7  H20  H  HCH2  0   0.250  151.0509  172.4891  147.2192
 YG7  H21  H  HCR6  0   0.270  158.0028  166.3311  151.2066
 YG7  H22  H  HCR6  0   0.268  155.2143  163.5455  149.4633
 YG7  H23  H  HCR6  0   0.266  153.9142  174.0379  147.8646
 YG7  H24  H  HCR6  0   0.271  154.5458  176.6599  151.2188
 YG7  H28  H  HNR5  0   0.414  150.7859  173.5530  152.1907
 YG7  H29  H  HNH2  0   0.409  161.6679  160.1765  153.3275
 YG7  H30  H  HNH2  0   0.413  160.1840  160.2068  152.4585
 YG7  C12  C  CH2   0  -0.250  153.2526  169.2831  148.4344

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
 YG7  C33  C30  single    1.425  0.020  1.425
 YG7  C33  N07  triple    1.154  0.020  1.154
 YG7  C16  C14  single    1.529  0.020  1.529
 YG7  C16  C17  single    1.495  0.020  1.495
 YG7  C27  C30  aromatic  1.390  0.020  1.390
 YG7  C27  C20  aromatic  1.392  0.020  1.392
 YG7  C14  C13  single    1.527  0.020  1.527
 YG7  C30  C31  aromatic  1.412  0.020  1.412
 YG7  C17  C20  aromatic  1.434  0.020  1.434
 YG7  C17  C22  aromatic  1.366  0.020  1.366
 YG7  C20  C25  aromatic  1.417  0.020  1.417
 YG7  C31  C28  aromatic  1.376  0.020  1.376
 YG7  C22  N05  aromatic  1.371  0.020  1.371
 YG7  C24  C19  aromatic  1.378  0.020  1.378
 YG7  C24  C23  aromatic  1.386  0.020  1.386
 YG7  C25  C28  aromatic  1.395  0.020  1.395
 YG7  C25  N05  aromatic  1.354  0.020  1.354
 YG7  C12  C13  single    1.523  0.020  1.523
 YG7  C12  N03  single    1.453  0.020  1.453
 YG7  C19  C15  aromatic  1.418  0.020  1.418
 YG7  C09  N03  single    1.450  0.020  1.450
 YG7  C09  C11  single    1.518  0.020  1.518
 YG7  N03  C08  single    1.450  0.020  1.450
 YG7  C08  C10  single    1.515  0.020  1.515
 YG7  C23  O01  aromatic  1.351  0.020  1.351
 YG7  C23  C21  aromatic  1.392  0.020  1.392
 YG7  O01  C29  aromatic  1.359  0.020  1.359
 YG7  C11  N04  single    1.448  0.020  1.448
 YG7  C15  N04  single    1.399  0.020  1.399
 YG7  C15  C18  aromatic  1.391  0.020  1.391
 YG7  N04  C10  single    1.456  0.020  1.456
 YG7  N06  C32  single    1.340  0.020  1.340
 YG7  C21  C18  aromatic  1.399  0.020  1.399
 YG7  C21  C26  aromatic  1.432  0.020  1.432
 YG7  C29  C32  single    1.477  0.020  1.477
 YG7  C29  C26  aromatic  1.354  0.020  1.354
 YG7  C32  O02  double    1.223  0.020  1.223
 YG7  C10  H1   single    0.970  0.020  1.090
 YG7  C10  H2   single    0.970  0.020  1.090
 YG7  C13  H3   single    0.970  0.020  1.090
 YG7  C13  H4   single    0.970  0.020  1.090
 YG7  C22  H5   single    0.930  0.020  1.080
 YG7  C24  H6   single    0.930  0.020  1.080
 YG7  C26  H7   single    0.930  0.020  1.080
 YG7  C28  H8   single    0.930  0.020  1.080
 YG7  C08  H9   single    0.970  0.020  1.090
 YG7  C08  H10  single    0.970  0.020  1.090
 YG7  C09  H11  single    0.970  0.020  1.090
 YG7  C09  H12  single    0.970  0.020  1.090
 YG7  C11  H13  single    0.970  0.020  1.090
 YG7  C11  H14  single    0.970  0.020  1.090
 YG7  C12  H15  single    0.970  0.020  1.090
 YG7  C12  H16  single    0.970  0.020  1.090
 YG7  C14  H17  single    0.970  0.020  1.090
 YG7  C14  H18  single    0.970  0.020  1.090
 YG7  C16  H19  single    0.970  0.020  1.090
 YG7  C16  H20  single    0.970  0.020  1.090
 YG7  C18  H21  single    0.930  0.020  1.080
 YG7  C19  H22  single    0.930  0.020  1.080
 YG7  C27  H23  single    0.930  0.020  1.080
 YG7  C31  H24  single    0.930  0.020  1.080
 YG7  N05  H28  single    0.860  0.020  1.020
 YG7  N06  H29  single    0.860  0.020  1.020
 YG7  N06  H30  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
 YG7  H2   C10  H1   107.31  3.000
 YG7  H2   C10  N04  110.34  3.000
 YG7  H1   C10  N04  110.54  3.000
 YG7  H2   C10  C08  108.54  3.000
 YG7  H1   C10  C08  109.32  3.000
 YG7  N04  C10  C08  110.70  3.000
 YG7  H4   C13  H3   106.32  3.000
 YG7  H4   C13  C14  107.49  3.000
 YG7  H3   C13  C14  110.65  3.000
 YG7  H4   C13  C12  110.29  3.000
 YG7  H3   C13  C12  109.02  3.000
 YG7  C14  C13  C12  112.87  3.000
 YG7  N04  C15  C19  118.23  3.000
 YG7  N04  C15  C18  122.68  3.000
 YG7  C19  C15  C18  119.05  3.000
 YG7  C16  C17  C22  128.33  3.000
 YG7  C22  C17  C20  105.56  3.000
 YG7  C16  C17  C20  126.08  3.000
 YG7  C27  C20  C25  119.14  3.000
 YG7  C25  C20  C17  107.46  3.000
 YG7  C27  C20  C17  133.40  3.000
 YG7  C23  C21  C18  120.02  3.000
 YG7  C18  C21  C26  134.73  3.000
 YG7  C23  C21  C26  105.25  3.000
 YG7  H5   C22  N05  120.03  3.000
 YG7  H5   C22  C17  129.60  3.000
 YG7  N05  C22  C17  110.37  3.000
 YG7  H6   C24  C23  122.17  3.000
 YG7  H6   C24  C19  121.11  3.000
 YG7  C23  C24  C19  116.71  3.000
 YG7  H7   C26  C29  126.27  3.000
 YG7  H7   C26  C21  127.71  3.000
 YG7  C29  C26  C21  106.02  3.000
 YG7  H8   C28  C31  120.82  3.000
 YG7  H8   C28  C25  121.48  3.000
 YG7  C31  C28  C25  117.71  3.000
 YG7  H10  C08  H9   107.19  3.000
 YG7  H10  C08  N03  111.44  3.000
 YG7  H9   C08  N03  110.11  3.000
 YG7  H10  C08  C10  109.22  3.000
 YG7  H9   C08  C10  107.93  3.000
 YG7  N03  C08  C10  110.83  3.000
 YG7  H12  C09  H11  107.09  3.000
 YG7  H12  C09  N03  109.13  3.000
 YG7  H11  C09  N03  111.60  3.000
 YG7  H12  C09  C11  108.55  3.000
 YG7  H11  C09  C11  108.74  3.000
 YG7  N03  C09  C11  111.58  3.000
 YG7  H14  C11  H13  107.50  3.000
 YG7  H14  C11  N04  111.89  3.000
 YG7  H13  C11  N04  109.52  3.000
 YG7  H14  C11  C09  109.44  3.000
 YG7  H13  C11  C09  108.26  3.000
 YG7  N04  C11  C09  110.12  3.000
 YG7  H18  C14  H17  105.62  3.000
 YG7  H18  C14  C16  108.17  3.000
 YG7  H17  C14  C16  109.18  3.000
 YG7  H18  C14  C13  108.95  3.000
 YG7  H17  C14  C13  108.95  3.000
 YG7  C16  C14  C13  115.52  3.000
 YG7  H20  C16  H19  105.01  3.000
 YG7  H20  C16  C14  108.33  3.000
 YG7  H19  C16  C14  109.95  3.000
 YG7  H20  C16  C17  109.32  3.000
 YG7  H19  C16  C17  109.11  3.000
 YG7  C14  C16  C17  114.67  3.000
 YG7  H21  C18  C21  119.45  3.000
 YG7  H21  C18  C15  121.66  3.000
 YG7  C21  C18  C15  118.89  3.000
 YG7  H22  C19  C24  118.10  3.000
 YG7  H22  C19  C15  119.16  3.000
 YG7  C24  C19  C15  122.72  3.000
 YG7  O01  C23  C24  126.90  3.000
 YG7  O01  C23  C21  110.51  3.000
 YG7  C24  C23  C21  122.59  3.000
 YG7  N05  C25  C28  130.45  3.000
 YG7  N05  C25  C20  107.13  3.000
 YG7  C28  C25  C20  122.42  3.000
 YG7  H23  C27  C30  120.44  3.000
 YG7  H23  C27  C20  121.10  3.000
 YG7  C30  C27  C20  118.46  3.000
 YG7  O01  C29  C32  119.12  3.000
 YG7  C32  C29  C26  129.19  3.000
 YG7  O01  C29  C26  111.69  3.000
 YG7  C33  C30  C31  118.94  3.000
 YG7  C31  C30  C27  121.65  3.000
 YG7  C33  C30  C27  119.41  3.000
 YG7  H24  C31  C30  119.40  3.000
 YG7  H24  C31  C28  119.97  3.000
 YG7  C30  C31  C28  120.63  3.000
 YG7  O02  C32  N06  124.16  3.000
 YG7  O02  C32  C29  119.72  3.000
 YG7  N06  C32  C29  116.11  3.000
 YG7  N07  C33  C30  180.00  3.000
 YG7  C12  N03  C09  111.00  3.000
 YG7  C09  N03  C08  109.18  3.000
 YG7  C12  N03  C08  112.83  3.000
 YG7  C11  N04  C15  117.86  3.000
 YG7  C15  N04  C10  116.77  3.000
 YG7  C11  N04  C10  110.92  3.000
 YG7  H28  N05  C25  125.49  3.000
 YG7  H28  N05  C22  125.03  3.000
 YG7  C25  N05  C22  109.48  3.000
 YG7  H30  N06  H29  117.36  3.000
 YG7  H30  N06  C32  123.05  3.000
 YG7  H29  N06  C32  119.59  3.000
 YG7  C29  O01  C23  106.53  3.000
 YG7  H16  C12  H15  106.21  3.000
 YG7  H16  C12  N03  106.96  3.000
 YG7  H15  C12  N03  111.32  3.000
 YG7  H16  C12  C13  109.01  3.000
 YG7  H15  C12  C13  109.32  3.000
 YG7  N03  C12  C13  113.71  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
 YG7  CONST_01  C23  C24  C19  C15     0.00   0.0  0
 YG7  CONST_02  C23  C21  C18  C15     0.00   0.0  0
 YG7  CONST_03  C26  C21  C18  C15   180.00   0.0  0
 YG7  CONST_04  C30  C27  C20  C17   180.00   0.0  0
 YG7  CONST_05  C28  C25  C20  C17   180.00   0.0  0
 YG7  CONST_06  N05  C25  C20  C17     0.00   0.0  0
 YG7  CONST_07  C25  N05  C22  C17     0.00   0.0  0
 YG7  CONST_08  C31  C30  C27  C20     0.00   0.0  0
 YG7  CONST_09  N05  C22  C17  C20     0.00   0.0  0
 YG7  CONST_10  C31  C28  C25  C20     0.00   0.0  0
 YG7  CONST_11  C22  N05  C25  C20     0.00   0.0  0
 YG7  CONST_12  C19  C24  C23  C21     0.00   0.0  0
 YG7  CONST_13  C29  O01  C23  C21     0.00   0.0  0
 YG7  CONST_14  C19  C15  C18  C21     0.00   0.0  0
 YG7  CONST_15  O01  C29  C26  C21     0.00   0.0  0
 YG7  CONST_16  C27  C20  C17  C22   180.00   0.0  0
 YG7  CONST_17  C25  C20  C17  C22     0.00   0.0  0
 YG7  CONST_18  C28  C25  N05  C22   180.00   0.0  0
 YG7  CONST_19  C18  C15  C19  C24     0.00   0.0  0
 YG7  CONST_20  C29  O01  C23  C24   180.00   0.0  0
 YG7  CONST_21  C18  C21  C23  C24     0.00   0.0  0
 YG7  CONST_22  C26  C21  C23  C24   180.00   0.0  0
 YG7  CONST_23  O01  C23  C21  C26     0.00   0.0  0
 YG7  CONST_24  C23  O01  C29  C26     0.00   0.0  0
 YG7  CONST_25  C27  C30  C31  C28     0.00   0.0  0
 YG7  CONST_26  C27  C20  C25  C28     0.00   0.0  0
 YG7  CONST_27  O01  C23  C21  C18   180.00   0.0  0
 YG7  CONST_28  C29  C26  C21  C18   180.00   0.0  0
 YG7  CONST_29  O01  C23  C24  C19   180.00   0.0  0
 YG7  CONST_30  C29  C26  C21  C23     0.00   0.0  0
 YG7  CONST_31  C30  C27  C20  C25     0.00   0.0  0
 YG7  CONST_32  C30  C31  C28  C25     0.00   0.0  0
 YG7  CONST_33  N05  C25  C20  C27   180.00   0.0  0
 YG7  CONST_34  N05  C25  C28  C31   180.00   0.0  0
 YG7  CONST_35  N04  C15  C18  C21   180.00   0.0  0
 YG7  CONST_36  N04  C15  C19  C24   180.00   0.0  0
 YG7  CONST_37  C33  C30  C27  C20   180.00   0.0  0
 YG7  CONST_38  C32  C29  C26  C21   180.00   0.0  0
 YG7  CONST_39  C33  C30  C31  C28   180.00   0.0  0
 YG7  CONST_40  C27  C20  C17  C16     0.00   0.0  0
 YG7  CONST_41  C25  C20  C17  C16   180.00   0.0  0
 YG7  CONST_42  N05  C22  C17  C16   180.00   0.0  0
 YG7  CONST_43  C32  C29  O01  C23   180.00   0.0  0
 YG7  CONST_44  H6   C24  C19  C15   180.00   0.0  0
 YG7  CONST_45  H23  C27  C20  C17     0.00   0.0  0
 YG7  CONST_46  H28  N05  C22  C17   180.00   0.0  0
 YG7  CONST_47  H5   C22  C17  C20   180.00   0.0  0
 YG7  CONST_48  H8   C28  C25  C20   180.00   0.0  0
 YG7  CONST_49  H21  C18  C21  C26     0.00   0.0  0
 YG7  CONST_50  H22  C19  C15  C18   180.00   0.0  0
 YG7  CONST_51  H7   C26  C21  C18     0.00   0.0  0
 YG7  CONST_52  H24  C31  C28  C25   180.00   0.0  0
 YG7  CONST_53  H29  N06  C32  C29   180.00   0.0  0
 YG7  CONST_54  H30  N06  C32  C29     0.00   0.0  0
 YG7  Var_01    C09  N03  C08  C10    58.02  30.0  1
 YG7  Var_02    C09  C11  N04  C10   -55.76  30.0  1
 YG7  Var_03    C19  C15  N04  C10    54.53  30.0  2
 YG7  Var_04    C08  C10  N04  C15  -164.82  30.0  1
 YG7  Var_05    C11  C09  N03  C08   -58.24  30.0  1
 YG7  Var_06    N04  C11  C09  N03    57.46  30.0  1
 YG7  Var_07    N04  C10  C08  N03   -57.61  30.0  1
 YG7  Var_08    C14  C16  C17  C20   154.94  30.0  1
 YG7  Var_09    N06  C32  C29  C26  -179.63  30.0  2
 YG7  Var_10    C17  C16  C14  C13   -62.61  30.0  1
 YG7  Var_11    N03  C12  C13  C14  -179.43  30.0  1
 YG7  Var_12    C16  C14  C13  C12   -62.79  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
 YG7  plan-1  C17  0.020
 YG7  plan-1  C20  0.020
 YG7  plan-1  C22  0.020
 YG7  plan-1  C28  0.020
 YG7  plan-1  C16  0.020
 YG7  plan-1  C25  0.020
 YG7  plan-1  C27  0.020
 YG7  plan-1  C30  0.020
 YG7  plan-1  C31  0.020
 YG7  plan-1  C33  0.020
 YG7  plan-1  N05  0.020
 YG7  plan-1  N07  0.020
 YG7  plan-1  H5   0.020
 YG7  plan-1  H8   0.020
 YG7  plan-1  H23  0.020
 YG7  plan-1  H24  0.020
 YG7  plan-1  H28  0.020
 YG7  plan-2  C15  0.020
 YG7  plan-2  C21  0.020
 YG7  plan-2  C24  0.020
 YG7  plan-2  C26  0.020
 YG7  plan-2  C18  0.020
 YG7  plan-2  C19  0.020
 YG7  plan-2  C23  0.020
 YG7  plan-2  C29  0.020
 YG7  plan-2  C32  0.020
 YG7  plan-2  N04  0.020
 YG7  plan-2  O01  0.020
 YG7  plan-2  H6   0.020
 YG7  plan-2  H7   0.020
 YG7  plan-2  H21  0.020
 YG7  plan-2  H22  0.020
 YG7  plan-3  C29  0.020
 YG7  plan-3  C32  0.020
 YG7  plan-3  N06  0.020
 YG7  plan-3  O02  0.020
 YG7  plan-3  H29  0.020
 YG7  plan-3  H30  0.020

