# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:03:01 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: 4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)-N-(pyridin-4-ylmethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@]1(CN2CCC1CC2)C#Cc3ccc(Oc4ccc(cc4)C(=O)NCc5ccncc5)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
 5EL  5EL  4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)-N-(pyridin-4-ylmethyl)benzamide  ligand  61  34  .  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_5EL
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
 5EL  C1    C  CR16  0  -0.293    2.3440  -1.5532  -1.2679
 5EL  C2    C  CR16  0  -0.293    1.1235  -2.1852  -1.1075
 5EL  C3    C  CR6   0   0.304    0.6340  -2.4073   0.1724
 5EL  C4    C  CR16  0  -0.304    1.3483  -2.0012   1.2885
 5EL  C5    C  CR16  0  -0.297    2.5729  -1.3755   1.1233
 5EL  C6    C  CR6   0  -0.149    3.0840  -1.1408  -0.1554
 5EL  C7    C  CSP   0   0.091    4.3445  -0.4969  -0.3212
 5EL  C8    C  CSP   0   0.173    5.4081   0.0541  -0.4596
 5EL  C9    C  CT    0   0.087    6.7169   0.6971  -0.6262
 5EL  C10   C  CH2   0  -0.358    7.8104  -0.0578   0.2022
 5EL  N1    N  NT    0  -0.391    8.5954   0.8425   1.0203
 5EL  C11   C  CH2   0  -0.331    9.1537   1.9088   0.1944
 5EL  C12   C  CH2   0  -0.454    8.0402   2.8096  -0.3823
 5EL  C13   C  CH1   0  -0.282    6.6928   2.1429  -0.0904
 5EL  C14   C  CH2   0  -0.471    6.5023   2.1060   1.4269
 5EL  C15   C  CH2   0  -0.327    7.7382   1.4179   2.0521
 5EL  O1    O  OH1   0  -0.666    7.0350   0.7619  -2.0000
 5EL  O2    O  O2    0  -0.504   -0.5446  -3.0847   0.3528
 5EL  C16   C  CR6   0   0.369   -1.7251  -2.4699   0.0896
 5EL  C17   C  CR16  0  -0.317   -2.8548  -3.2852   0.0983
 5EL  C18   C  CR16  0  -0.259   -4.0993  -2.7339  -0.1296
 5EL  C19   C  CR6   0  -0.047   -4.2432  -1.3722  -0.3959
 5EL  C20   C  CR16  0  -0.282   -3.1051  -0.5717  -0.3944
 5EL  C21   C  CR16  0  -0.328   -1.8490  -1.1064  -0.1506
 5EL  C22   C  C     0   0.542   -5.6142  -0.8358  -0.6204
 5EL  O3    O  O     0  -0.480   -6.6038  -1.4054  -0.1814
 5EL  N2    N  NH1   0  -0.657   -5.7079   0.3034  -1.3318
 5EL  C23   C  CH2   0  -0.342   -6.9830   0.9241  -1.5823
 5EL  C24   C  CR6   0   0.189   -7.5983   1.5568  -0.3607
 5EL  C25   C  CR16  0  -0.374   -8.9785   1.6125  -0.2133
 5EL  C26   C  CR16  0  -0.061   -9.5148   2.2418   0.8995
 5EL  N3    N  N     0  -0.412   -8.7786   2.8028   1.8519
 5EL  C27   C  CR16  0  -0.061   -7.4589   2.7470   1.7089
 5EL  C28   C  CR16  0  -0.355   -6.8255   2.1435   0.6339
 5EL  H1    H  HCR6  0   0.268    2.7305  -1.3816  -2.2634
 5EL  H2    H  HCR6  0   0.285    0.5620  -2.5099  -1.9743
 5EL  H4    H  HCR6  0   0.280    0.9560  -2.1811   2.2809
 5EL  H5    H  HCR6  0   0.267    3.1357  -1.0644   1.9932
 5EL  H101  H  HCH2  0   0.251    7.3512  -0.8033   0.8547
 5EL  H102  H  HCH2  0   0.254    8.4686  -0.5952  -0.4868
 5EL  H13   H  HCH1  0   0.252    5.8773   2.6927  -0.5650
 5EL  HA    H  HOH1  0   0.449    7.1501  -0.1350  -2.3328
 5EL  H111  H  HCH2  0   0.240    9.8547   2.4877   0.7992
 5EL  H112  H  HCH2  0   0.237    9.7341   1.4463  -0.6072
 5EL  H151  H  HCH2  0   0.241    7.4377   0.6223   2.7374
 5EL  H152  H  HCH2  0   0.240    8.3329   2.1255   2.6335
 5EL  H121  H  HCH2  0   0.235    8.0445   3.7927   0.0941
 5EL  H122  H  HCH2  0   0.245    8.1812   2.9797  -1.4490
 5EL  H141  H  HCH2  0   0.247    6.3917   3.1269   1.7977
 5EL  H142  H  HCH2  0   0.242    5.5820   1.5794   1.6894
 5EL  H17   H  HCR6  0   0.276   -2.7511  -4.3459   0.2876
 5EL  H21   H  HCR6  0   0.287   -0.9898  -0.4498  -0.1396
 5EL  H18   H  HCR6  0   0.265   -4.9706  -3.3746  -0.1129
 5EL  H20   H  HCR6  0   0.264   -3.1759   0.4969  -0.5545
 5EL  HB    H  HNH1  0   0.414   -4.8959   0.6905  -1.7808
 5EL  H231  H  HCH2  0   0.290   -6.8237   1.6960  -2.3362
 5EL  H232  H  HCH2  0   0.263   -7.6826   0.2053  -2.0147
 5EL  H25   H  HCR6  0   0.265   -9.6352   1.1666  -0.9499
 5EL  H28   H  HCR6  0   0.259   -5.7444   2.1330   0.5850
 5EL  H26   H  HCR6  0   0.263  -10.5908   2.2877   1.0279
 5EL  H27   H  HCR6  0   0.262   -6.8679   3.2078   2.4929

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
 5EL  C1   C2    aromatic  1.384  0.020  1.384
 5EL  C1   C6    aromatic  1.398  0.020  1.398
 5EL  C2   C3    aromatic  1.388  0.020  1.388
 5EL  C3   C4    aromatic  1.386  0.020  1.386
 5EL  C3   O2    single    1.371  0.020  1.371
 5EL  C4   C5    aromatic  1.385  0.020  1.385
 5EL  C5   C6    aromatic  1.397  0.020  1.397
 5EL  C6   C7    single    1.425  0.020  1.425
 5EL  C7   C8    triple    1.206  0.020  1.206
 5EL  C8   C9    single    1.468  0.020  1.468
 5EL  C9   C10   single    1.566  0.020  1.566
 5EL  C9   C13   single    1.542  0.020  1.542
 5EL  C9   O1    single    1.412  0.020  1.412
 5EL  C10  N1    single    1.448  0.020  1.448
 5EL  N1   C11   single    1.460  0.020  1.460
 5EL  N1   C15   single    1.460  0.020  1.460
 5EL  C11  C12   single    1.544  0.020  1.544
 5EL  C12  C13   single    1.531  0.020  1.531
 5EL  C13  C14   single    1.530  0.020  1.530
 5EL  C14  C15   single    1.547  0.020  1.547
 5EL  O2   C16   single    1.357  0.020  1.357
 5EL  C16  C17   aromatic  1.393  0.020  1.393
 5EL  C16  C21   aromatic  1.390  0.020  1.390
 5EL  C17  C18   aromatic  1.380  0.020  1.380
 5EL  C18  C19   aromatic  1.395  0.020  1.395
 5EL  C19  C20   aromatic  1.391  0.020  1.391
 5EL  C19  C22   single    1.489  0.020  1.489
 5EL  C20  C21   aromatic  1.387  0.020  1.387
 5EL  C22  O3    double    1.223  0.020  1.223
 5EL  C22  N2    single    1.346  0.020  1.346
 5EL  N2   C23   single    1.440  0.020  1.440
 5EL  C23  C24   single    1.507  0.020  1.507
 5EL  C24  C25   aromatic  1.389  0.020  1.389
 5EL  C24  C28   aromatic  1.390  0.020  1.390
 5EL  C25  C26   aromatic  1.386  0.020  1.386
 5EL  C26  N3    aromatic  1.328  0.020  1.328
 5EL  N3   C27   aromatic  1.329  0.020  1.329
 5EL  C27  C28   aromatic  1.386  0.020  1.386
 5EL  C1   H1    single    0.930  0.020  1.080
 5EL  C2   H2    single    0.930  0.020  1.080
 5EL  C4   H4    single    0.930  0.020  1.080
 5EL  C5   H5    single    0.930  0.020  1.080
 5EL  C10  H101  single    0.970  0.020  1.090
 5EL  C10  H102  single    0.970  0.020  1.090
 5EL  C13  H13   single    0.970  0.020  1.090
 5EL  O1   HA    single    0.850  0.020  0.980
 5EL  C11  H111  single    0.970  0.020  1.090
 5EL  C11  H112  single    0.970  0.020  1.090
 5EL  C15  H151  single    0.970  0.020  1.090
 5EL  C15  H152  single    0.970  0.020  1.090
 5EL  C12  H121  single    0.970  0.020  1.090
 5EL  C12  H122  single    0.970  0.020  1.090
 5EL  C14  H141  single    0.970  0.020  1.090
 5EL  C14  H142  single    0.970  0.020  1.090
 5EL  C17  H17   single    0.930  0.020  1.080
 5EL  C21  H21   single    0.930  0.020  1.080
 5EL  C18  H18   single    0.930  0.020  1.080
 5EL  C20  H20   single    0.930  0.020  1.080
 5EL  N2   HB    single    0.860  0.020  1.020
 5EL  C23  H231  single    0.970  0.020  1.090
 5EL  C23  H232  single    0.970  0.020  1.090
 5EL  C25  H25   single    0.930  0.020  1.080
 5EL  C28  H28   single    0.930  0.020  1.080
 5EL  C26  H26   single    0.930  0.020  1.080
 5EL  C27  H27   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
 5EL  H1    C1   C6    119.76  3.000
 5EL  H1    C1   C2    119.62  3.000
 5EL  C6    C1   C2    120.61  3.000
 5EL  H2    C2   C3    120.48  3.000
 5EL  H2    C2   C1    120.11  3.000
 5EL  C3    C2   C1    119.41  3.000
 5EL  O2    C3   C4    118.80  3.000
 5EL  O2    C3   C2    120.23  3.000
 5EL  C4    C3   C2    120.92  3.000
 5EL  H4    C4   C5    120.33  3.000
 5EL  H4    C4   C3    120.20  3.000
 5EL  C5    C4   C3    119.47  3.000
 5EL  H5    C5   C6    119.83  3.000
 5EL  H5    C5   C4    119.60  3.000
 5EL  C6    C5   C4    120.57  3.000
 5EL  C7    C6   C5    120.40  3.000
 5EL  C7    C6   C1    120.58  3.000
 5EL  C5    C6   C1    119.02  3.000
 5EL  C8    C7   C6    180.00  3.000
 5EL  C9    C8   C7    180.00  3.000
 5EL  O1    C9   C13   107.37  3.000
 5EL  O1    C9   C10   112.31  3.000
 5EL  C13   C9   C10   106.21  3.000
 5EL  O1    C9   C8    109.36  3.000
 5EL  C13   C9   C8    110.94  3.000
 5EL  C10   C9   C8    110.58  3.000
 5EL  H102  C10  H101  107.10  3.000
 5EL  H102  C10  N1    109.58  3.000
 5EL  H101  C10  N1    108.35  3.000
 5EL  H102  C10  C9    108.89  3.000
 5EL  H101  C10  C9    110.59  3.000
 5EL  N1    C10  C9    112.20  3.000
 5EL  C15   N1   C11   109.67  3.000
 5EL  C15   N1   C10   109.03  3.000
 5EL  C11   N1   C10   109.99  3.000
 5EL  H112  C11  H111  106.85  3.000
 5EL  H112  C11  C12   110.86  3.000
 5EL  H111  C11  C12   111.13  3.000
 5EL  H112  C11  N1    108.01  3.000
 5EL  H111  C11  N1    108.63  3.000
 5EL  C12   C11  N1    111.20  3.000
 5EL  H122  C12  H121  106.61  3.000
 5EL  H122  C12  C13   111.63  3.000
 5EL  H121  C12  C13   108.19  3.000
 5EL  H122  C12  C11   111.31  3.000
 5EL  H121  C12  C11   111.06  3.000
 5EL  C13   C12  C11   108.02  3.000
 5EL  H13   C13  C14   110.50  3.000
 5EL  H13   C13  C12   110.79  3.000
 5EL  C14   C13  C12   108.01  3.000
 5EL  H13   C13  C9    109.43  3.000
 5EL  C14   C13  C9    108.90  3.000
 5EL  C12   C13  C9    109.16  3.000
 5EL  H142  C14  H141  106.49  3.000
 5EL  H142  C14  C15   111.20  3.000
 5EL  H141  C14  C15   111.08  3.000
 5EL  H142  C14  C13   110.79  3.000
 5EL  H141  C14  C13   109.08  3.000
 5EL  C15   C14  C13   108.19  3.000
 5EL  H152  C15  H151  106.73  3.000
 5EL  H152  C15  C14   111.23  3.000
 5EL  H151  C15  C14   110.97  3.000
 5EL  H152  C15  N1    108.18  3.000
 5EL  H151  C15  N1    108.54  3.000
 5EL  C14   C15  N1    111.04  3.000
 5EL  HA    O1   C9    108.68  3.000
 5EL  C16   O2   C3    119.89  3.000
 5EL  C21   C16  C17   120.19  3.000
 5EL  C21   C16  O2    123.75  3.000
 5EL  C17   C16  O2    116.05  3.000
 5EL  H17   C17  C18   120.45  3.000
 5EL  H17   C17  C16   119.79  3.000
 5EL  C18   C17  C16   119.76  3.000
 5EL  H18   C18  C19   119.87  3.000
 5EL  H18   C18  C17   119.16  3.000
 5EL  C19   C18  C17   120.96  3.000
 5EL  C22   C19  C20   123.09  3.000
 5EL  C22   C19  C18   118.38  3.000
 5EL  C20   C19  C18   118.49  3.000
 5EL  H20   C20  C21   117.75  3.000
 5EL  H20   C20  C19   120.94  3.000
 5EL  C21   C20  C19   121.28  3.000
 5EL  H21   C21  C20   119.17  3.000
 5EL  H21   C21  C16   121.53  3.000
 5EL  C20   C21  C16   119.30  3.000
 5EL  N2    C22  O3    121.82  3.000
 5EL  N2    C22  C19   116.65  3.000
 5EL  O3    C22  C19   121.53  3.000
 5EL  HB    N2   C23   118.13  3.000
 5EL  HB    N2   C22   120.37  3.000
 5EL  C23   N2   C22   121.22  3.000
 5EL  H232  C23  H231  106.59  3.000
 5EL  H232  C23  C24   109.61  3.000
 5EL  H231  C23  C24   108.83  3.000
 5EL  H232  C23  N2    110.64  3.000
 5EL  H231  C23  N2    107.22  3.000
 5EL  C24   C23  N2    113.67  3.000
 5EL  C28   C24  C25   117.37  3.000
 5EL  C28   C24  C23   122.03  3.000
 5EL  C25   C24  C23   120.57  3.000
 5EL  H25   C25  C26   119.89  3.000
 5EL  H25   C25  C24   120.92  3.000
 5EL  C26   C25  C24   119.19  3.000
 5EL  H26   C26  N3    116.56  3.000
 5EL  H26   C26  C25   119.87  3.000
 5EL  N3    C26  C25   123.57  3.000
 5EL  C27   N3   C26   117.11  3.000
 5EL  H27   C27  C28   119.78  3.000
 5EL  H27   C27  N3    116.47  3.000
 5EL  C28   C27  N3    123.76  3.000
 5EL  H28   C28  C27   119.72  3.000
 5EL  H28   C28  C24   121.28  3.000
 5EL  C27   C28  C24   119.00  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
 5EL  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 5EL  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 5EL  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 5EL  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 5EL  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 5EL  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 5EL  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 5EL  CONST_08  C19  C20  C21  C16     0.00   0.0  0
 5EL  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 5EL  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 5EL  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 5EL  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 5EL  CONST_13  N3   C26  C25  C24     0.00   0.0  0
 5EL  CONST_14  N3   C27  C28  C24     0.00   0.0  0
 5EL  CONST_15  C27  C28  C24  C25     0.00   0.0  0
 5EL  CONST_16  C27  N3   C26  C25     0.00   0.0  0
 5EL  CONST_17  C28  C24  C25  C26     0.00   0.0  0
 5EL  CONST_18  C28  C27  N3   C26     0.00   0.0  0
 5EL  CONST_19  O2   C3   C2   C1    180.00   0.0  0
 5EL  CONST_20  C7   C6   C1   C2    180.00   0.0  0
 5EL  CONST_21  C7   C6   C5   C4    180.00   0.0  0
 5EL  CONST_22  O2   C3   C4   C5    180.00   0.0  0
 5EL  CONST_23  C18  C17  C16  O2    180.00   0.0  0
 5EL  CONST_24  C20  C21  C16  O2    180.00   0.0  0
 5EL  CONST_25  C22  C19  C18  C17   180.00   0.0  0
 5EL  CONST_26  C22  C19  C20  C21   180.00   0.0  0
 5EL  CONST_27  C26  C25  C24  C23   180.00   0.0  0
 5EL  CONST_28  C27  C28  C24  C23   180.00   0.0  0
 5EL  CONST_29  H5   C5   C6   C1    180.00   0.0  0
 5EL  CONST_30  H4   C4   C3   C2    180.00   0.0  0
 5EL  CONST_31  H1   C1   C2   C3    180.00   0.0  0
 5EL  CONST_32  H2   C2   C3   C4    180.00   0.0  0
 5EL  CONST_33  H18  C18  C17  C16   180.00   0.0  0
 5EL  CONST_34  H20  C20  C21  C16   180.00   0.0  0
 5EL  CONST_35  H21  C21  C16  C17   180.00   0.0  0
 5EL  CONST_36  H17  C17  C18  C19   180.00   0.0  0
 5EL  CONST_37  H26  C26  C25  C24   180.00   0.0  0
 5EL  CONST_38  H27  C27  C28  C24   180.00   0.0  0
 5EL  CONST_39  H28  C28  C24  C25   180.00   0.0  0
 5EL  CONST_40  H25  C25  C26  N3    180.00   0.0  0
 5EL  CONST_41  C23  N2   C22  C19   180.00   0.0  0
 5EL  CONST_42  HB   N2   C22  C19     0.00   0.0  0
 5EL  CONST_43  C23  N2   C22  O3      0.00   0.0  0
 5EL  Var_01    C11  N1   C10  C9    -53.82  30.0  1
 5EL  Var_02    C12  C11  N1   C10    65.53  30.0  1
 5EL  Var_03    C14  C15  N1   C10   -55.31  30.0  3
 5EL  Var_04    C13  C12  C11  N1     -9.56  30.0  1
 5EL  Var_05    C13  C14  C15  N1     -8.54  30.0  3
 5EL  Var_06    C17  C16  O2   C3    170.38  30.0  2
 5EL  Var_07    O3   C22  C19  C18    23.42  30.0  2
 5EL  Var_08    C25  C24  C23  N2   -148.77  30.0  2
 5EL  Var_09    C24  C23  N2   C22    71.18  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
 5EL  chir_01  C9   C10  C13  O1  negativ
 5EL  chir_02  C13  C14  C12  C9  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
 5EL  plan-1  C1   0.020
 5EL  plan-1  C2   0.020
 5EL  plan-1  C3   0.020
 5EL  plan-1  C4   0.020
 5EL  plan-1  C5   0.020
 5EL  plan-1  C6   0.020
 5EL  plan-1  C7   0.020
 5EL  plan-1  C8   0.020
 5EL  plan-1  O2   0.020
 5EL  plan-1  H1   0.020
 5EL  plan-1  H2   0.020
 5EL  plan-1  H4   0.020
 5EL  plan-1  H5   0.020
 5EL  plan-2  O2   0.020
 5EL  plan-2  C16  0.020
 5EL  plan-2  C17  0.020
 5EL  plan-2  C18  0.020
 5EL  plan-2  C19  0.020
 5EL  plan-2  C20  0.020
 5EL  plan-2  C21  0.020
 5EL  plan-2  C22  0.020
 5EL  plan-2  H17  0.020
 5EL  plan-2  H21  0.020
 5EL  plan-2  H18  0.020
 5EL  plan-2  H20  0.020
 5EL  plan-3  C23  0.020
 5EL  plan-3  C24  0.020
 5EL  plan-3  C25  0.020
 5EL  plan-3  C26  0.020
 5EL  plan-3  N3   0.020
 5EL  plan-3  C27  0.020
 5EL  plan-3  C28  0.020
 5EL  plan-3  H25  0.020
 5EL  plan-3  H28  0.020
 5EL  plan-3  H26  0.020
 5EL  plan-3  H27  0.020
 5EL  plan-4  C19  0.020
 5EL  plan-4  C22  0.020
 5EL  plan-4  O3   0.020
 5EL  plan-4  N2   0.020
 5EL  plan-4  C23  0.020
 5EL  plan-4  HB   0.020

