# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 21:59:44 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 1-{2-[5-(2-methoxyethoxy)-1H-benzimidazol-1-yl]quinolin-8-yl}piperidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOc1ccc2n(cnc2c1)c3ccc4cccc(N5CCC(N)CC5)c4n3
#
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
 34U  34U  1-{2-[5-(2-methoxyethoxy)-1H-benzimidazol-1-yl]quinolin-8-yl}piperidin-4-amine  ligand  58  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_34U
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
 34U  C01  C  CH3   0  -0.396   8.2070  -1.0659   0.5977
 34U  O02  O  O2    0  -0.483   6.8107  -0.9142   0.5774
 34U  C03  C  CH2   0  -0.160   6.2707  -1.0899  -0.7051
 34U  C04  C  CH2   0  -0.220   4.7775  -0.9024  -0.6587
 34U  O05  O  O2    0  -0.477   4.5061   0.4396  -0.3025
 34U  C06  C  CR6   0   0.392   3.2234   0.8391  -0.1678
 34U  C07  C  CR16  0  -0.432   3.0345   2.1353   0.2959
 34U  C08  C  CR56  0   0.134   1.7324   2.5902   0.4520
 34U  C09  C  CR56  0   0.308   0.6371   1.7659   0.1551
 34U  C10  C  CR16  0  -0.267   0.8180   0.4742  -0.3141
 34U  C11  C  CR16  0  -0.391   2.1204   0.0235  -0.4712
 34U  N12  N  NR5   0  -0.629  -0.4776   2.5525   0.4186
 34U  C13  C  CR15  0   0.118   0.0060   3.7584   0.8536
 34U  N14  N  N     0  -0.459   1.2976   3.8241   0.8895
 34U  C15  C  CR6   0   0.513  -1.8240   2.1942   0.2791
 34U  N16  N  N     0  -0.464  -2.0687   0.9269   0.1450
 34U  C17  C  CR66  0   0.177  -3.3374   0.5044  -0.0325
 34U  C18  C  CR66  0   0.079  -4.4197   1.4149  -0.0755
 34U  C19  C  CR16  0  -0.342  -5.7302   0.9576  -0.3234
 34U  C20  C  CR16  0  -0.247  -5.9419  -0.3766  -0.5302
 34U  C21  C  CR16  0  -0.354  -4.8759  -1.2938  -0.4676
 34U  C22  C  CR6   0   0.305  -3.5802  -0.8945  -0.2117
 34U  N23  N  NT    0  -0.486  -2.5011  -1.7866  -0.1673
 34U  C24  C  CH2   0  -0.303  -1.9321  -1.9869   1.1657
 34U  C25  C  CH2   0  -0.441  -0.6072  -2.7307   1.1069
 34U  C26  C  CH1   0  -0.088  -0.7206  -4.0412   0.3412
 34U  C27  C  CH2   0  -0.439  -1.3575  -3.7645  -1.0190
 34U  C28  C  CH2   0  -0.316  -2.6887  -3.0465  -0.8655
 34U  N29  N  NH2   0  -0.789   0.5755  -4.6996   0.2881
 34U  C30  C  CR16  0  -0.182  -4.1143   2.7851   0.0934
 34U  C31  C  CR16  0  -0.378  -2.8266   3.1931   0.2655
 34U  H1   H  HCH3  0   0.234   8.5481  -0.9051   1.6196
 34U  H2   H  HCH3  0   0.204   8.5179  -2.0692   0.2827
 34U  H3   H  HCH3  0   0.205   8.7087  -0.3394  -0.0527
 34U  H4   H  HCH2  0   0.211   6.7151  -0.3872  -1.4247
 34U  H5   H  HCH2  0   0.213   6.4688  -2.1013  -1.0876
 34U  H6   H  HCH2  0   0.233   4.3682  -1.1412  -1.6464
 34U  H7   H  HCH2  0   0.229   4.3304  -1.5944   0.0648
 34U  H8   H  HCR6  0   0.263   3.8799   2.7707   0.5282
 34U  H9   H  HCR6  0   0.286  -0.0179  -0.1705  -0.5394
 34U  H10  H  HCR6  0   0.272   2.2639  -0.9842  -0.8364
 34U  H11  H  HCR5  0   0.302  -0.6531   4.5598   1.1501
 34U  H12  H  HCR6  0   0.260  -6.5455   1.6690  -0.3607
 34U  H13  H  HCR6  0   0.261  -6.9384  -0.7463  -0.7329
 34U  H14  H  HCR6  0   0.271  -5.0987  -2.3411  -0.6199
 34U  H15  H  HCH2  0   0.257  -1.7843  -1.0192   1.6415
 34U  H16  H  HCH2  0   0.211  -2.6375  -2.5558   1.7930
 34U  H17  H  HCH2  0   0.215   0.1429  -2.0957   0.6243
 34U  H18  H  HCH2  0   0.238  -0.2598  -2.9166   2.1258
 34U  H19  H  HCH1  0   0.213  -1.3981  -4.7003   0.8988
 34U  H20  H  HCH2  0   0.213  -0.6796  -3.1492  -1.6212
 34U  H21  H  HCH2  0   0.233  -1.5161  -4.7013  -1.5600
 34U  H22  H  HCH2  0   0.203  -3.3915  -3.7108  -0.3356
 34U  H23  H  HCH2  0   0.250  -3.1196  -2.8457  -1.8480
 34U  H24  H  HNH2  0   0.343   0.4922  -5.5706  -0.2235
 34U  H25  H  HNH2  0   0.329   1.2167  -4.1304  -0.2541
 34U  H27  H  HCR6  0   0.279  -4.9135   3.5146   0.0642
 34U  H28  H  HCR6  0   0.289  -2.5940   4.2436   0.3608

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
 34U  C01  O02  single    1.405  0.020  1.405
 34U  O02  C03  single    1.403  0.020  1.403
 34U  C03  C04  single    1.506  0.020  1.506
 34U  C04  O05  single    1.415  0.020  1.415
 34U  O05  C06  single    1.350  0.020  1.350
 34U  C07  C06  aromatic  1.390  0.020  1.390
 34U  C07  C08  aromatic  1.388  0.020  1.388
 34U  C06  C11  aromatic  1.405  0.020  1.405
 34U  N14  C08  aromatic  1.379  0.020  1.379
 34U  N14  C13  aromatic  1.294  0.020  1.294
 34U  C08  C09  aromatic  1.403  0.020  1.403
 34U  C13  N12  aromatic  1.370  0.020  1.370
 34U  C11  C10  aromatic  1.387  0.020  1.387
 34U  C09  N12  aromatic  1.390  0.020  1.390
 34U  C09  C10  aromatic  1.386  0.020  1.386
 34U  N12  C15  single    1.400  0.020  1.400
 34U  N29  C26  single    1.455  0.020  1.455
 34U  C25  C26  single    1.522  0.020  1.522
 34U  C25  C24  single    1.521  0.020  1.521
 34U  C15  C31  aromatic  1.415  0.020  1.415
 34U  C15  N16  aromatic  1.298  0.020  1.298
 34U  C31  C30  aromatic  1.362  0.020  1.362
 34U  C26  C27  single    1.527  0.020  1.527
 34U  C24  N23  single    1.463  0.020  1.463
 34U  N16  C17  aromatic  1.349  0.020  1.349
 34U  C30  C18  aromatic  1.414  0.020  1.414
 34U  N23  C22  single    1.401  0.020  1.401
 34U  N23  C28  single    1.453  0.020  1.453
 34U  C27  C28  single    1.520  0.020  1.520
 34U  C17  C18  aromatic  1.415  0.020  1.415
 34U  C17  C22  aromatic  1.431  0.020  1.431
 34U  C18  C19  aromatic  1.410  0.020  1.410
 34U  C22  C21  aromatic  1.380  0.020  1.380
 34U  C19  C20  aromatic  1.367  0.020  1.367
 34U  C21  C20  aromatic  1.408  0.020  1.408
 34U  C01  H1   single    0.970  0.020  1.090
 34U  C01  H2   single    0.970  0.020  1.090
 34U  C01  H3   single    0.970  0.020  1.090
 34U  C03  H4   single    0.970  0.020  1.090
 34U  C03  H5   single    0.970  0.020  1.090
 34U  C04  H6   single    0.970  0.020  1.090
 34U  C04  H7   single    0.970  0.020  1.090
 34U  C07  H8   single    0.930  0.020  1.080
 34U  C10  H9   single    0.930  0.020  1.080
 34U  C11  H10  single    0.930  0.020  1.080
 34U  C13  H11  single    0.930  0.020  1.080
 34U  C19  H12  single    0.930  0.020  1.080
 34U  C20  H13  single    0.930  0.020  1.080
 34U  C21  H14  single    0.930  0.020  1.080
 34U  C24  H15  single    0.970  0.020  1.090
 34U  C24  H16  single    0.970  0.020  1.090
 34U  C25  H17  single    0.970  0.020  1.090
 34U  C25  H18  single    0.970  0.020  1.090
 34U  C26  H19  single    0.970  0.020  1.090
 34U  C27  H20  single    0.970  0.020  1.090
 34U  C27  H21  single    0.970  0.020  1.090
 34U  C28  H22  single    0.970  0.020  1.090
 34U  C28  H23  single    0.970  0.020  1.090
 34U  N29  H24  single    0.890  0.020  1.040
 34U  N29  H25  single    0.890  0.020  1.040
 34U  C30  H27  single    0.930  0.020  1.080
 34U  C31  H28  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
 34U  H3   C01  H2   107.82  3.000
 34U  H3   C01  H1   108.38  3.000
 34U  H2   C01  H1   108.40  3.000
 34U  H3   C01  O02  112.01  3.000
 34U  H2   C01  O02  112.11  3.000
 34U  H1   C01  O02  108.00  3.000
 34U  C03  O02  C01  112.48  3.000
 34U  H5   C03  H4   106.71  3.000
 34U  H5   C03  C04  107.70  3.000
 34U  H4   C03  C04  109.96  3.000
 34U  H5   C03  O02  111.35  3.000
 34U  H4   C03  O02  111.27  3.000
 34U  C04  C03  O02  109.76  3.000
 34U  H7   C04  H6   107.76  3.000
 34U  H7   C04  O05  110.76  3.000
 34U  H6   C04  O05  111.23  3.000
 34U  H7   C04  C03  110.25  3.000
 34U  H6   C04  C03  108.39  3.000
 34U  O05  C04  C03  108.43  3.000
 34U  C06  O05  C04  119.20  3.000
 34U  C11  C06  C07  120.46  3.000
 34U  C11  C06  O05  123.54  3.000
 34U  C07  C06  O05  116.00  3.000
 34U  H8   C07  C08  121.06  3.000
 34U  H8   C07  C06  120.86  3.000
 34U  C08  C07  C06  118.08  3.000
 34U  N14  C08  C09  110.28  3.000
 34U  C09  C08  C07  121.07  3.000
 34U  N14  C08  C07  128.64  3.000
 34U  N12  C09  C10  134.14  3.000
 34U  C10  C09  C08  121.16  3.000
 34U  N12  C09  C08  104.69  3.000
 34U  H9   C10  C11  120.63  3.000
 34U  H9   C10  C09  121.74  3.000
 34U  C11  C10  C09  117.62  3.000
 34U  H10  C11  C10  117.75  3.000
 34U  H10  C11  C06  120.65  3.000
 34U  C10  C11  C06  121.61  3.000
 34U  C15  N12  C13  126.60  3.000
 34U  C15  N12  C09  127.42  3.000
 34U  C13  N12  C09  105.98  3.000
 34U  H11  C13  N14  124.36  3.000
 34U  H11  C13  N12  121.69  3.000
 34U  N14  C13  N12  113.95  3.000
 34U  C13  N14  C08  105.10  3.000
 34U  C31  C15  N16  123.69  3.000
 34U  N16  C15  N12  116.20  3.000
 34U  C31  C15  N12  120.10  3.000
 34U  C17  N16  C15  119.79  3.000
 34U  C22  C17  C18  119.70  3.000
 34U  C22  C17  N16  118.83  3.000
 34U  C18  C17  N16  121.46  3.000
 34U  C30  C18  C19  122.41  3.000
 34U  C19  C18  C17  120.50  3.000
 34U  C30  C18  C17  117.05  3.000
 34U  H12  C19  C20  121.31  3.000
 34U  H12  C19  C18  119.53  3.000
 34U  C20  C19  C18  119.15  3.000
 34U  H13  C20  C21  118.89  3.000
 34U  H13  C20  C19  120.30  3.000
 34U  C21  C20  C19  120.81  3.000
 34U  H14  C21  C22  119.99  3.000
 34U  H14  C21  C20  117.95  3.000
 34U  C22  C21  C20  122.06  3.000
 34U  N23  C22  C21  123.02  3.000
 34U  C21  C22  C17  117.74  3.000
 34U  N23  C22  C17  119.20  3.000
 34U  C28  N23  C24  111.68  3.000
 34U  C28  N23  C22  115.96  3.000
 34U  C24  N23  C22  114.56  3.000
 34U  H16  C24  H15  107.28  3.000
 34U  H16  C24  C25  109.10  3.000
 34U  H15  C24  C25  109.49  3.000
 34U  H16  C24  N23  109.89  3.000
 34U  H15  C24  N23  109.23  3.000
 34U  C25  C24  N23  111.75  3.000
 34U  H18  C25  H17  106.98  3.000
 34U  H18  C25  C26  110.26  3.000
 34U  H17  C25  C26  109.18  3.000
 34U  H18  C25  C24  108.92  3.000
 34U  H17  C25  C24  109.29  3.000
 34U  C26  C25  C24  112.07  3.000
 34U  H19  C26  N29  107.26  3.000
 34U  H19  C26  C27  107.69  3.000
 34U  N29  C26  C27  114.90  3.000
 34U  H19  C26  C25  107.91  3.000
 34U  C27  C26  C25  108.85  3.000
 34U  N29  C26  C25  109.98  3.000
 34U  H21  C27  H20  107.40  3.000
 34U  H21  C27  C28  109.13  3.000
 34U  H20  C27  C28  109.39  3.000
 34U  H21  C27  C26  110.24  3.000
 34U  H20  C27  C26  109.46  3.000
 34U  C28  C27  C26  111.15  3.000
 34U  H23  C28  H22  106.96  3.000
 34U  H23  C28  C27  109.98  3.000
 34U  H22  C28  C27  108.79  3.000
 34U  H23  C28  N23  108.91  3.000
 34U  H22  C28  N23  111.95  3.000
 34U  C27  C28  N23  110.19  3.000
 34U  H25  N29  H24  105.33  3.000
 34U  H25  N29  C26  109.19  3.000
 34U  H24  N29  C26  109.52  3.000
 34U  H27  C30  C31  119.98  3.000
 34U  H27  C30  C18  119.37  3.000
 34U  C31  C30  C18  120.64  3.000
 34U  H28  C31  C30  120.41  3.000
 34U  H28  C31  C15  122.21  3.000
 34U  C30  C31  C15  117.36  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
 34U  CONST_01  N14  C08  C07  C06   180.00   0.0  0
 34U  CONST_02  C09  C08  C07  C06     0.00   0.0  0
 34U  CONST_03  C09  C10  C11  C06     0.00   0.0  0
 34U  CONST_04  C10  C11  C06  C07     0.00   0.0  0
 34U  CONST_05  C13  N14  C08  C07   180.00   0.0  0
 34U  CONST_06  N12  C09  C08  C07   180.00   0.0  0
 34U  CONST_07  C10  C09  C08  C07     0.00   0.0  0
 34U  CONST_08  C11  C06  C07  C08     0.00   0.0  0
 34U  CONST_09  N12  C13  N14  C08     0.00   0.0  0
 34U  CONST_10  C13  N12  C09  C08     0.00   0.0  0
 34U  CONST_11  C15  N12  C09  C08   180.00   0.0  0
 34U  CONST_12  C11  C10  C09  C08     0.00   0.0  0
 34U  CONST_13  C13  N14  C08  C09     0.00   0.0  0
 34U  CONST_14  N14  C13  N12  C09     0.00   0.0  0
 34U  CONST_16  N16  C15  N12  C09     0.00   0.0  0
 34U  CONST_17  N14  C08  C09  C10   180.00   0.0  0
 34U  CONST_18  C13  N12  C09  C10   180.00   0.0  0
 34U  CONST_19  C15  N12  C09  C10     0.00   0.0  0
 34U  CONST_20  N12  C09  C10  C11   180.00   0.0  0
 34U  CONST_21  N14  C08  C09  N12     0.00   0.0  0
 34U  CONST_22  C30  C31  C15  N12   180.00   0.0  0
 34U  CONST_23  C17  N16  C15  N12   180.00   0.0  0
 34U  CONST_26  C15  N12  C13  N14   180.00   0.0  0
 34U  CONST_27  C18  C30  C31  C15     0.00   0.0  0
 34U  CONST_28  C18  C17  N16  C15     0.00   0.0  0
 34U  CONST_29  C22  C17  N16  C15   180.00   0.0  0
 34U  CONST_30  C30  C31  C15  N16     0.00   0.0  0
 34U  CONST_31  C30  C18  C17  N16     0.00   0.0  0
 34U  CONST_32  C19  C18  C17  N16   180.00   0.0  0
 34U  CONST_33  C21  C22  C17  N16   180.00   0.0  0
 34U  CONST_34  C31  C15  N16  C17     0.00   0.0  0
 34U  CONST_35  C31  C30  C18  C17     0.00   0.0  0
 34U  CONST_36  C20  C19  C18  C17     0.00   0.0  0
 34U  CONST_37  C20  C21  C22  C17     0.00   0.0  0
 34U  CONST_38  C21  C22  C17  C18     0.00   0.0  0
 34U  CONST_39  C21  C20  C19  C18     0.00   0.0  0
 34U  CONST_40  C31  C30  C18  C19   180.00   0.0  0
 34U  CONST_41  C22  C17  C18  C19     0.00   0.0  0
 34U  CONST_42  C22  C21  C20  C19     0.00   0.0  0
 34U  CONST_43  C30  C18  C19  C20   180.00   0.0  0
 34U  CONST_44  C30  C18  C17  C22   180.00   0.0  0
 34U  CONST_45  N23  C22  C17  N16     0.00   0.0  0
 34U  CONST_46  N23  C22  C17  C18   180.00   0.0  0
 34U  CONST_47  N23  C22  C21  C20   180.00   0.0  0
 34U  CONST_48  C08  C07  C06  O05   180.00   0.0  0
 34U  CONST_49  C10  C11  C06  O05   180.00   0.0  0
 34U  CONST_50  H9   C10  C11  C06   180.00   0.0  0
 34U  CONST_51  H10  C11  C06  C07   180.00   0.0  0
 34U  CONST_52  H11  C13  N14  C08   180.00   0.0  0
 34U  CONST_53  H8   C07  C08  C09   180.00   0.0  0
 34U  CONST_54  H28  C31  C15  N12     0.00   0.0  0
 34U  CONST_55  H27  C30  C31  C15   180.00   0.0  0
 34U  CONST_56  H12  C19  C18  C17   180.00   0.0  0
 34U  CONST_57  H14  C21  C22  C17   180.00   0.0  0
 34U  CONST_58  H13  C20  C19  C18   180.00   0.0  0
 34U  Var_01    C24  N23  C22  C17    71.73  30.0  1
 34U  Var_02    C25  C24  N23  C22  -168.39  30.0  1
 34U  Var_03    C27  C28  N23  C22   166.65  30.0  1
 34U  Var_04    C26  C25  C24  N23   -53.77  30.0  1
 34U  Var_05    C26  C27  C28  N23    59.11  30.0  1
 34U  Var_06    C07  C06  O05  C04   174.60  30.0  2
 34U  Var_07    H6   C04  O05  C06    62.39  30.0  1
 34U  Var_08    C04  C03  O02  C01  -179.49  30.0  3
 34U  Var_09    O05  C04  C03  O02    64.67  30.0  3
 34U  Var_10    H1   C01  O02  C03   179.41  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 34U  chir_01  C26  N29  C25  C27  negativ

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
 34U  plan-1  O05  0.020
 34U  plan-1  C06  0.020
 34U  plan-1  C07  0.020
 34U  plan-1  C08  0.020
 34U  plan-1  C09  0.020
 34U  plan-1  C10  0.020
 34U  plan-1  C11  0.020
 34U  plan-1  N12  0.020
 34U  plan-1  C13  0.020
 34U  plan-1  N14  0.020
 34U  plan-1  C15  0.020
 34U  plan-1  H8   0.020
 34U  plan-1  H9   0.020
 34U  plan-1  H10  0.020
 34U  plan-1  H11  0.020
 34U  plan-2  N12  0.020
 34U  plan-2  C15  0.020
 34U  plan-2  N16  0.020
 34U  plan-2  C17  0.020
 34U  plan-2  C18  0.020
 34U  plan-2  C19  0.020
 34U  plan-2  C20  0.020
 34U  plan-2  C21  0.020
 34U  plan-2  C22  0.020
 34U  plan-2  N23  0.020
 34U  plan-2  C30  0.020
 34U  plan-2  C31  0.020
 34U  plan-2  H12  0.020
 34U  plan-2  H13  0.020
 34U  plan-2  H14  0.020
 34U  plan-2  H27  0.020
 34U  plan-2  H28  0.020

