# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:52:27 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-(4-phenylphenoxy)-~{N}-(3-piperidin-1-ylpropyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(COc1ccc(cc1)c2ccccc2)NCCCN3CCCCC3
#
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
 E5H  E5H  2-(4-phenylphenoxy)-~{N}-(3-piperidin-1-ylpropyl)ethanamide  ligand  54  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E5H
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
 E5H  O01  O  O     0  -0.483    0.9787  -2.4979  -0.3307
 E5H  C02  C  C     0   0.514    1.0002  -1.2872  -0.1937
 E5H  N03  N  NH1   0  -0.645    2.1264  -0.5697  -0.1051
 E5H  C04  C  CH2   0  -0.231    3.4443  -1.1708  -0.1443
 E5H  C05  C  CH2   0  -0.505    4.5199  -0.1028  -0.0310
 E5H  C06  C  CH2   0  -0.249    5.9098  -0.7218  -0.1194
 E5H  N07  N  NT    0  -0.420    6.9702   0.1901   0.2616
 E5H  C08  C  CH2   0  -0.283    7.1317   1.2867  -0.6795
 E5H  C09  C  CH2   0  -0.435    8.1701   2.2858  -0.1907
 E5H  C10  C  CH2   0  -0.439    9.5059   1.6027   0.0702
 E5H  C11  C  CH2   0  -0.437    9.3048   0.4094   0.9954
 E5H  C12  C  CH2   0  -0.277    8.2252  -0.5165   0.4558
 E5H  C13  C  CH2   0  -0.305   -0.2661  -0.4482  -0.0949
 E5H  O14  O  O2    0  -0.462   -1.3602  -1.3054  -0.2686
 E5H  C15  C  CR6   0   0.376   -2.6040  -0.7934  -0.1784
 E5H  C16  C  CR16  0  -0.363   -2.8949   0.5483   0.0492
 E5H  C17  C  CR16  0  -0.297   -4.2185   0.9627   0.1272
 E5H  C18  C  CR6   0   0.066   -5.2775   0.0710  -0.0157
 E5H  C19  C  CR6   0   0.095   -6.6794   0.5226   0.0788
 E5H  C25  C  CR16  0  -0.293   -4.9627  -1.2717  -0.2484
 E5H  C26  C  CR16  0  -0.332   -3.6532  -1.7013  -0.3294
 E5H  H1   H  HNH1  0   0.406    2.0641   0.4299   0.0097
 E5H  H2   H  HCH2  0   0.235    3.5498  -1.8888   0.6736
 E5H  H3   H  HCH2  0   0.235    3.5666  -1.7304  -1.0759
 E5H  H4   H  HCH2  0   0.241    4.3719   0.6384  -0.8203
 E5H  H5   H  HCH2  0   0.236    4.4255   0.4187   0.9258
 E5H  H6   H  HCH2  0   0.226    5.9493  -1.5748   0.5652
 E5H  H7   H  HCH2  0   0.190    6.0642  -1.1325  -1.1330
 E5H  H9   H  HCH2  0   0.181    7.4256   0.9123  -1.6778
 E5H  H10  H  HCH2  0   0.237    6.1756   1.7973  -0.8070
 E5H  H11  H  HCH2  0   0.229    8.2777   3.0826  -0.9298
 E5H  H12  H  HCH2  0   0.214    7.8086   2.7515   0.7313
 E5H  H13  H  HCH2  0   0.209    9.9318   1.2597  -0.8791
 E5H  H14  H  HCH2  0   0.229   10.2220   2.3076   0.4986
 E5H  H15  H  HCH2  0   0.228   10.2344  -0.1516   1.1152
 E5H  H16  H  HCH2  0   0.213    9.0113   0.7592   1.9898
 E5H  H17  H  HCH2  0   0.231    8.0572  -1.3364   1.1586
 E5H  H18  H  HCH2  0   0.181    8.5801  -0.9738  -0.4864
 E5H  H19  H  HCH2  0   0.265   -0.2905   0.0461   0.8842
 E5H  H20  H  HCH2  0   0.263   -0.2446   0.3407  -0.8565
 E5H  H21  H  HCR6  0   0.282   -2.1141   1.2857   0.1749
 E5H  H22  H  HCR6  0   0.258   -4.4156   2.0091   0.3244
 E5H  H26  H  HCR6  0   0.256   -5.7546  -1.9967  -0.3888
 E5H  H27  H  HCR6  0   0.265   -3.4330  -2.7449  -0.5170
 E5H  C1   C  CR16  0  -0.316   -7.6509  -0.2797   0.6817
 E5H  C2   C  CR16  0  -0.239   -8.9687   0.1439   0.7722
 E5H  C3   C  CR16  0  -0.269   -9.3429   1.3813   0.2649
 E5H  C4   C  CR16  0  -0.240   -8.3862   2.1901  -0.3346
 E5H  C5   C  CR16  0  -0.314   -7.0693   1.7642  -0.4281
 E5H  H8   H  HCR6  0   0.253   -7.3734  -1.2373   1.1048
 E5H  H23  H  HCR6  0   0.256   -9.7036  -0.4924   1.2486
 E5H  H24  H  HCR6  0   0.256  -10.3710   1.7120   0.3356
 E5H  H25  H  HCR6  0   0.257   -8.6668   3.1536  -0.7399
 E5H  H28  H  HCR6  0   0.252   -6.3412   2.3979  -0.9198

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
 E5H  C09  C10  single    1.523  0.020  1.523
 E5H  C09  C08  single    1.522  0.020  1.522
 E5H  C10  C11  single    1.523  0.020  1.523
 E5H  C17  C16  aromatic  1.389  0.020  1.389
 E5H  C17  C18  aromatic  1.392  0.020  1.392
 E5H  C08  N07  single    1.454  0.020  1.454
 E5H  C16  C15  aromatic  1.392  0.020  1.392
 E5H  C19  C18  single    1.476  0.020  1.476
 E5H  C18  C25  aromatic  1.399  0.020  1.399
 E5H  C11  C12  single    1.521  0.020  1.521
 E5H  N07  C12  single    1.453  0.020  1.453
 E5H  N07  C06  single    1.450  0.020  1.450
 E5H  C15  O14  single    1.348  0.020  1.348
 E5H  C15  C26  aromatic  1.396  0.020  1.396
 E5H  O14  C13  single    1.401  0.020  1.401
 E5H  C05  C04  single    1.520  0.020  1.520
 E5H  C05  C06  single    1.524  0.020  1.524
 E5H  C25  C26  aromatic  1.381  0.020  1.381
 E5H  N03  C04  single    1.449  0.020  1.449
 E5H  N03  C02  single    1.338  0.020  1.338
 E5H  C13  C02  single    1.522  0.020  1.522
 E5H  C02  O01  double    1.219  0.020  1.219
 E5H  N03  H1   single    0.860  0.020  1.020
 E5H  C04  H2   single    0.970  0.020  1.090
 E5H  C04  H3   single    0.970  0.020  1.090
 E5H  C05  H4   single    0.970  0.020  1.090
 E5H  C05  H5   single    0.970  0.020  1.090
 E5H  C06  H6   single    0.970  0.020  1.090
 E5H  C06  H7   single    0.970  0.020  1.090
 E5H  C08  H9   single    0.970  0.020  1.090
 E5H  C08  H10  single    0.970  0.020  1.090
 E5H  C09  H11  single    0.970  0.020  1.090
 E5H  C09  H12  single    0.970  0.020  1.090
 E5H  C10  H13  single    0.970  0.020  1.090
 E5H  C10  H14  single    0.970  0.020  1.090
 E5H  C11  H15  single    0.970  0.020  1.090
 E5H  C11  H16  single    0.970  0.020  1.090
 E5H  C12  H17  single    0.970  0.020  1.090
 E5H  C12  H18  single    0.970  0.020  1.090
 E5H  C13  H19  single    0.970  0.020  1.090
 E5H  C13  H20  single    0.970  0.020  1.090
 E5H  C16  H21  single    0.930  0.020  1.080
 E5H  C17  H22  single    0.930  0.020  1.080
 E5H  C25  H26  single    0.930  0.020  1.080
 E5H  C26  H27  single    0.930  0.020  1.080
 E5H  C19  C1   aromatic  1.397  0.020  1.397
 E5H  C1   C2   aromatic  1.387  0.020  1.387
 E5H  C2   C3   aromatic  1.389  0.020  1.389
 E5H  C3   C4   aromatic  1.389  0.020  1.389
 E5H  C4   C5   aromatic  1.387  0.020  1.387
 E5H  C5   C19  aromatic  1.397  0.020  1.397
 E5H  C1   H8   single    0.930  0.020  1.080
 E5H  C2   H23  single    0.930  0.020  1.080
 E5H  C3   H24  single    0.930  0.020  1.080
 E5H  C4   H25  single    0.930  0.020  1.080
 E5H  C5   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
 E5H  C13  C02  N03  113.59  3.000
 E5H  C13  C02  O01  122.70  3.000
 E5H  N03  C02  O01  123.71  3.000
 E5H  H1   N03  C04  118.07  3.000
 E5H  H1   N03  C02  119.16  3.000
 E5H  C04  N03  C02  122.76  3.000
 E5H  H3   C04  H2   106.88  3.000
 E5H  H3   C04  C05  110.11  3.000
 E5H  H2   C04  C05  109.72  3.000
 E5H  H3   C04  N03  109.69  3.000
 E5H  H2   C04  N03  109.87  3.000
 E5H  C05  C04  N03  110.49  3.000
 E5H  H5   C05  H4   107.26  3.000
 E5H  H5   C05  C06  108.86  3.000
 E5H  H4   C05  C06  110.92  3.000
 E5H  H5   C05  C04  109.82  3.000
 E5H  H4   C05  C04  109.08  3.000
 E5H  C06  C05  C04  110.83  3.000
 E5H  H7   C06  H6   106.22  3.000
 E5H  H7   C06  N07  111.89  3.000
 E5H  H6   C06  N07  107.43  3.000
 E5H  H7   C06  C05  109.38  3.000
 E5H  H6   C06  C05  108.25  3.000
 E5H  N07  C06  C05  113.35  3.000
 E5H  C12  N07  C08  110.93  3.000
 E5H  C12  N07  C06  111.16  3.000
 E5H  C08  N07  C06  112.68  3.000
 E5H  H10  C08  H9   106.60  3.000
 E5H  H10  C08  C09  109.16  3.000
 E5H  H9   C08  C09  109.33  3.000
 E5H  H10  C08  N07  109.34  3.000
 E5H  H9   C08  N07  111.00  3.000
 E5H  C09  C08  N07  111.29  3.000
 E5H  H12  C09  H11  106.99  3.000
 E5H  H12  C09  C10  109.65  3.000
 E5H  H11  C09  C10  110.90  3.000
 E5H  H12  C09  C08  108.95  3.000
 E5H  H11  C09  C08  109.20  3.000
 E5H  C10  C09  C08  111.05  3.000
 E5H  H14  C10  H13  106.68  3.000
 E5H  H14  C10  C11  110.73  3.000
 E5H  H13  C10  C11  109.41  3.000
 E5H  H14  C10  C09  110.66  3.000
 E5H  H13  C10  C09  109.45  3.000
 E5H  C11  C10  C09  109.85  3.000
 E5H  H16  C11  H15  107.02  3.000
 E5H  H16  C11  C12  109.07  3.000
 E5H  H15  C11  C12  109.28  3.000
 E5H  H16  C11  C10  109.69  3.000
 E5H  H15  C11  C10  110.89  3.000
 E5H  C12  C11  C10  110.80  3.000
 E5H  H18  C12  H17  106.68  3.000
 E5H  H18  C12  C11  109.04  3.000
 E5H  H17  C12  C11  109.73  3.000
 E5H  H18  C12  N07  111.37  3.000
 E5H  H17  C12  N07  108.54  3.000
 E5H  C11  C12  N07  111.37  3.000
 E5H  H20  C13  H19  107.22  3.000
 E5H  H20  C13  O14  111.67  3.000
 E5H  H19  C13  O14  111.66  3.000
 E5H  H20  C13  C02  109.58  3.000
 E5H  H19  C13  C02  108.95  3.000
 E5H  O14  C13  C02  107.73  3.000
 E5H  C15  O14  C13  118.69  3.000
 E5H  C26  C15  C16  119.19  3.000
 E5H  C26  C15  O14  116.06  3.000
 E5H  C16  C15  O14  124.75  3.000
 E5H  H21  C16  C17  118.56  3.000
 E5H  H21  C16  C15  121.70  3.000
 E5H  C17  C16  C15  119.74  3.000
 E5H  H22  C17  C18  119.96  3.000
 E5H  H22  C17  C16  118.16  3.000
 E5H  C18  C17  C16  121.87  3.000
 E5H  C25  C18  C19  121.21  3.000
 E5H  C25  C18  C17  117.45  3.000
 E5H  C19  C18  C17  121.34  3.000
 E5H  C5   C19  C1   118.24  3.000
 E5H  C5   C19  C18  120.93  3.000
 E5H  C1   C19  C18  120.84  3.000
 E5H  H26  C25  C26  118.53  3.000
 E5H  H26  C25  C18  119.99  3.000
 E5H  C26  C25  C18  121.47  3.000
 E5H  H27  C26  C25  120.19  3.000
 E5H  H27  C26  C15  119.53  3.000
 E5H  C25  C26  C15  120.28  3.000
 E5H  H8   C1   C2   119.21  3.000
 E5H  H8   C1   C19  119.88  3.000
 E5H  C2   C1   C19  120.90  3.000
 E5H  H23  C2   C3   120.11  3.000
 E5H  H23  C2   C1   119.61  3.000
 E5H  C3   C2   C1   120.28  3.000
 E5H  H24  C3   C4   120.31  3.000
 E5H  H24  C3   C2   120.29  3.000
 E5H  C4   C3   C2   119.41  3.000
 E5H  H25  C4   C5   119.62  3.000
 E5H  H25  C4   C3   120.10  3.000
 E5H  C5   C4   C3   120.28  3.000
 E5H  H28  C5   C4   119.28  3.000
 E5H  H28  C5   C19  119.81  3.000
 E5H  C4   C5   C19  120.89  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
 E5H  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 E5H  CONST_02  C18  C25  C26  C15     0.00   0.0  0
 E5H  CONST_03  C19  C18  C17  C16   180.00   0.0  0
 E5H  CONST_04  C25  C18  C17  C16     0.00   0.0  0
 E5H  CONST_05  C25  C26  C15  C16     0.00   0.0  0
 E5H  CONST_06  C26  C15  C16  C17     0.00   0.0  0
 E5H  CONST_09  C26  C25  C18  C17     0.00   0.0  0
 E5H  CONST_10  C2   C1   C19  C18   180.00   0.0  0
 E5H  CONST_11  C4   C5   C19  C18   180.00   0.0  0
 E5H  CONST_12  C26  C25  C18  C19   180.00   0.0  0
 E5H  CONST_13  C3   C2   C1   C19     0.00   0.0  0
 E5H  CONST_14  C3   C4   C5   C19     0.00   0.0  0
 E5H  CONST_17  C4   C5   C19  C1      0.00   0.0  0
 E5H  CONST_18  C4   C3   C2   C1      0.00   0.0  0
 E5H  CONST_19  C5   C19  C1   C2      0.00   0.0  0
 E5H  CONST_20  C5   C4   C3   C2      0.00   0.0  0
 E5H  CONST_21  C17  C16  C15  O14   180.00   0.0  0
 E5H  CONST_22  C25  C26  C15  O14   180.00   0.0  0
 E5H  CONST_23  H22  C17  C16  C15   180.00   0.0  0
 E5H  CONST_24  H26  C25  C26  C15   180.00   0.0  0
 E5H  CONST_25  H27  C26  C15  C16   180.00   0.0  0
 E5H  CONST_26  H21  C16  C17  C18   180.00   0.0  0
 E5H  CONST_27  H8   C1   C19  C18     0.00   0.0  0
 E5H  CONST_28  H28  C5   C19  C18     0.00   0.0  0
 E5H  CONST_29  H23  C2   C1   C19   180.00   0.0  0
 E5H  CONST_30  H25  C4   C5   C19   180.00   0.0  0
 E5H  CONST_31  H24  C3   C2   C1    180.00   0.0  0
 E5H  CONST_32  C04  N03  C02  O01     0.00   0.0  0
 E5H  CONST_33  C13  C02  N03  C04   180.00   0.0  0
 E5H  CONST_34  H1   N03  C02  O01   180.00   0.0  0
 E5H  Var_01    C10  C09  C08  N07    56.33  30.0  1
 E5H  Var_02    C10  C11  C12  N07   -56.75  30.0  1
 E5H  Var_03    C11  C10  C09  C08   -52.75  30.0  1
 E5H  Var_04    C11  C12  N07  C08    59.73  30.0  1
 E5H  Var_05    C12  C11  C10  C09    52.86  30.0  1
 E5H  Var_06    C12  N07  C08  C09   -59.43  30.0  1
 E5H  Var_07    C08  N07  C06  C05   -67.78  30.0  2
 E5H  Var_08    C16  C15  O14  C13     1.48  30.0  3
 E5H  Var_09    N07  C06  C05  C04  -167.68  30.0  3
 E5H  Var_10    H19  C13  O14  C15    58.29  30.0  3
 E5H  Var_11    O14  C13  C02  O01    -3.41  30.0  1
 E5H  Var_12    C05  C04  N03  C02   179.63  30.0  3
 E5H  Var_13    C06  C05  C04  N03  -178.06  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
 E5H  plan-1  O14  0.020
 E5H  plan-1  C15  0.020
 E5H  plan-1  C16  0.020
 E5H  plan-1  C17  0.020
 E5H  plan-1  C18  0.020
 E5H  plan-1  C19  0.020
 E5H  plan-1  C25  0.020
 E5H  plan-1  C26  0.020
 E5H  plan-1  H21  0.020
 E5H  plan-1  H22  0.020
 E5H  plan-1  H26  0.020
 E5H  plan-1  H27  0.020
 E5H  plan-2  C18  0.020
 E5H  plan-2  C19  0.020
 E5H  plan-2  C1   0.020
 E5H  plan-2  C2   0.020
 E5H  plan-2  C3   0.020
 E5H  plan-2  C4   0.020
 E5H  plan-2  C5   0.020
 E5H  plan-2  H8   0.020
 E5H  plan-2  H23  0.020
 E5H  plan-2  H24  0.020
 E5H  plan-2  H25  0.020
 E5H  plan-2  H28  0.020
 E5H  plan-3  O01  0.020
 E5H  plan-3  C02  0.020
 E5H  plan-3  N03  0.020
 E5H  plan-3  C04  0.020
 E5H  plan-3  C13  0.020
 E5H  plan-3  H1   0.020

