# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:40:36 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-cyclopentyl-~{N}-(3-piperidin-1-ylphenyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCC1CCCC1)Nc2cccc(c2)N3CCCCC3
#
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
 5TE  5TE  3-cyclopentyl-~{N}-(3-piperidin-1-ylphenyl)propanamide  ligand  50  22  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5TE
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
 5TE  C1   C  CH2   0  -0.303   5.4609  -0.3338  -0.5096
 5TE  C2   C  CH2   0  -0.300   4.2000   1.2544   0.8229
 5TE  C3   C  CH2   0  -0.438   5.0563   2.4093   0.3313
 5TE  N1   N  NH1   0  -0.755  -0.5572  -0.5468   0.2854
 5TE  C4   C  CH2   0  -0.443   6.4535   1.9293  -0.0343
 5TE  C5   C  CR6   0   0.389   3.1014  -0.7402  -0.0454
 5TE  C6   C  CR16  0  -0.456   1.7865  -0.2785   0.0849
 5TE  C7   C  CR6   0   0.402   0.7018  -1.1472   0.1739
 5TE  C8   C  CR16  0  -0.353   0.9132  -2.5274   0.1212
 5TE  C9   C  CR16  0  -0.232   2.2142  -2.9838  -0.0163
 5TE  C10  C  CR16  0  -0.377   3.3008  -2.1263  -0.0913
 5TE  C11  C  C     0   0.563  -1.7829  -1.1115   0.4470
 5TE  C12  C  CH2   0  -0.603  -2.9011  -0.0964   0.5687
 5TE  C13  C  CH2   0  -0.409  -4.2621  -0.6477   0.1697
 5TE  C14  C  CR15  0  -0.233  -5.3773   0.3801   0.2958
 5TE  C15  C  CH2   0  -0.431  -6.7621  -0.1891  -0.0373
 5TE  C16  C  CH2   0  -0.444  -7.6379   1.0236  -0.4149
 5TE  C17  C  CH2   0  -0.448  -6.6668   2.2138  -0.5549
 5TE  C18  C  CH2   0  -0.431  -5.2787   1.5814  -0.6441
 5TE  O    O  O     0  -0.471  -1.9756  -2.3129   0.5056
 5TE  N    N  NT    0  -0.515   4.1465   0.1739  -0.1574
 5TE  C    C  CH2   0  -0.434   6.3569   0.7819  -1.0293
 5TE  H1   H  HCH2  0   0.205   5.9467  -0.8252   0.3489
 5TE  H2   H  HCH2  0   0.247   5.3530  -1.0887  -1.2888
 5TE  H3   H  HCH2  0   0.210   4.6056   0.8798   1.7762
 5TE  H4   H  HCH2  0   0.252   3.1954   1.6150   1.0321
 5TE  H5   H  HCH2  0   0.219   4.5788   2.8649  -0.5414
 5TE  H6   H  HCH2  0   0.235   5.0979   3.1737   1.1101
 5TE  H7   H  HNH1  0   0.413  -0.5427   0.4617   0.2642
 5TE  H8   H  HCH2  0   0.235   7.0491   2.7471  -0.4453
 5TE  H9   H  HCH2  0   0.214   6.9693   1.5869   0.8698
 5TE  H10  H  HCR6  0   0.268   1.5938   0.7878   0.0899
 5TE  H11  H  HCR6  0   0.271   0.0979  -3.2274   0.1791
 5TE  H12  H  HCR6  0   0.253   2.3891  -4.0518  -0.0528
 5TE  H13  H  HCR6  0   0.263   4.2926  -2.5469  -0.1708
 5TE  H14  H  HCH2  0   0.276  -2.9283   0.2412   1.6112
 5TE  H15  H  HCH2  0   0.262  -2.6562   0.7893  -0.0230
 5TE  H16  H  HCH2  0   0.219  -4.2258  -1.0088  -0.8634
 5TE  H17  H  HCH2  0   0.231  -4.5020  -1.5137   0.7910
 5TE  H18  H  HCR5  0   0.215  -5.3937   0.7574   1.3271
 5TE  H19  H  HCH2  0   0.215  -6.6722  -0.8698  -0.8891
 5TE  H20  H  HCH2  0   0.229  -7.1781  -0.7711   0.7869
 5TE  H21  H  HCH2  0   0.224  -8.1698   0.8393  -1.3493
 5TE  H22  H  HCH2  0   0.225  -8.3990   1.2221   0.3409
 5TE  H23  H  HCH2  0   0.227  -6.8981   2.8499  -1.4105
 5TE  H24  H  HCH2  0   0.220  -6.7179   2.8488   0.3327
 5TE  H25  H  HCH2  0   0.230  -4.4812   2.2802  -0.3842
 5TE  H26  H  HCH2  0   0.210  -5.0828   1.2277  -1.6629
 5TE  H27  H  HCH2  0   0.235   7.3438   0.3658  -1.2427
 5TE  H28  H  HCH2  0   0.219   5.9542   1.1479  -1.9785

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
 5TE  C18  C17  single    1.528  0.020  1.528
 5TE  C18  C14  single    1.528  0.020  1.528
 5TE  C17  C16  single    1.543  0.020  1.543
 5TE  C8   C9   aromatic  1.386  0.020  1.386
 5TE  C8   C7   aromatic  1.397  0.020  1.397
 5TE  C9   C10  aromatic  1.386  0.020  1.386
 5TE  C14  C13  single    1.522  0.020  1.522
 5TE  C14  C15  single    1.534  0.020  1.534
 5TE  C13  C12  single    1.522  0.020  1.522
 5TE  C16  C15  single    1.543  0.020  1.543
 5TE  N1   C7   single    1.399  0.020  1.399
 5TE  N1   C11  single    1.359  0.020  1.359
 5TE  C7   C6   aromatic  1.393  0.020  1.393
 5TE  C10  C5   aromatic  1.401  0.020  1.401
 5TE  C12  C11  single    1.515  0.020  1.515
 5TE  C11  O    double    1.218  0.020  1.218
 5TE  C6   C5   aromatic  1.400  0.020  1.400
 5TE  C5   N    single    1.393  0.020  1.393
 5TE  C1   N    single    1.452  0.020  1.452
 5TE  C1   C    single    1.522  0.020  1.522
 5TE  N    C2   single    1.460  0.020  1.460
 5TE  C2   C3   single    1.519  0.020  1.519
 5TE  C    C4   single    1.522  0.020  1.522
 5TE  C4   C3   single    1.522  0.020  1.522
 5TE  C1   H1   single    0.970  0.020  1.090
 5TE  C1   H2   single    0.970  0.020  1.090
 5TE  C2   H3   single    0.970  0.020  1.090
 5TE  C2   H4   single    0.970  0.020  1.090
 5TE  C3   H5   single    0.970  0.020  1.090
 5TE  C3   H6   single    0.970  0.020  1.090
 5TE  N1   H7   single    0.860  0.020  1.020
 5TE  C4   H8   single    0.970  0.020  1.090
 5TE  C4   H9   single    0.970  0.020  1.090
 5TE  C6   H10  single    0.930  0.020  1.080
 5TE  C8   H11  single    0.930  0.020  1.080
 5TE  C9   H12  single    0.930  0.020  1.080
 5TE  C10  H13  single    0.930  0.020  1.080
 5TE  C12  H14  single    0.970  0.020  1.090
 5TE  C12  H15  single    0.970  0.020  1.090
 5TE  C13  H16  single    0.970  0.020  1.090
 5TE  C13  H17  single    0.970  0.020  1.090
 5TE  C14  H18  single    0.970  0.020  1.090
 5TE  C15  H19  single    0.970  0.020  1.090
 5TE  C15  H20  single    0.970  0.020  1.090
 5TE  C16  H21  single    0.970  0.020  1.090
 5TE  C16  H22  single    0.970  0.020  1.090
 5TE  C17  H23  single    0.970  0.020  1.090
 5TE  C17  H24  single    0.970  0.020  1.090
 5TE  C18  H25  single    0.970  0.020  1.090
 5TE  C18  H26  single    0.970  0.020  1.090
 5TE  C    H27  single    0.970  0.020  1.090
 5TE  C    H28  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
 5TE  H2   C1   H1   106.95  3.000
 5TE  H2   C1   C    108.77  3.000
 5TE  H1   C1   C    109.47  3.000
 5TE  H2   C1   N    109.01  3.000
 5TE  H1   C1   N    111.46  3.000
 5TE  C    C1   N    111.05  3.000
 5TE  H4   C2   H3   106.63  3.000
 5TE  H4   C2   N    109.92  3.000
 5TE  H3   C2   N    110.05  3.000
 5TE  H4   C2   C3   109.32  3.000
 5TE  H3   C2   C3   109.33  3.000
 5TE  N    C2   C3   111.47  3.000
 5TE  H6   C3   H5   107.09  3.000
 5TE  H6   C3   C4   110.92  3.000
 5TE  H5   C3   C4   109.90  3.000
 5TE  H6   C3   C2   108.83  3.000
 5TE  H5   C3   C2   109.19  3.000
 5TE  C4   C3   C2   110.81  3.000
 5TE  H7   N1   C11  115.52  3.000
 5TE  H7   N1   C7   114.47  3.000
 5TE  C11  N1   C7   129.99  3.000
 5TE  H9   C4   H8   106.72  3.000
 5TE  H9   C4   C    109.50  3.000
 5TE  H8   C4   C    110.68  3.000
 5TE  H9   C4   C3   109.42  3.000
 5TE  H8   C4   C3   110.79  3.000
 5TE  C    C4   C3   109.67  3.000
 5TE  N    C5   C10  122.66  3.000
 5TE  N    C5   C6   119.73  3.000
 5TE  C10  C5   C6   117.59  3.000
 5TE  H10  C6   C7   118.37  3.000
 5TE  H10  C6   C5   119.48  3.000
 5TE  C7   C6   C5   122.13  3.000
 5TE  C8   C7   C6   119.74  3.000
 5TE  C6   C7   N1   115.99  3.000
 5TE  C8   C7   N1   124.26  3.000
 5TE  H11  C8   C9   120.16  3.000
 5TE  H11  C8   C7   121.73  3.000
 5TE  C9   C8   C7   118.11  3.000
 5TE  H12  C9   C10  118.80  3.000
 5TE  H12  C9   C8   118.68  3.000
 5TE  C10  C9   C8   122.52  3.000
 5TE  H13  C10  C9   118.87  3.000
 5TE  H13  C10  C5   121.21  3.000
 5TE  C9   C10  C5   119.91  3.000
 5TE  O    C11  C12  122.69  3.000
 5TE  O    C11  N1   123.93  3.000
 5TE  C12  C11  N1   113.38  3.000
 5TE  H15  C12  H14  105.71  3.000
 5TE  H15  C12  C13  110.61  3.000
 5TE  H14  C12  C13  109.81  3.000
 5TE  H15  C12  C11  109.51  3.000
 5TE  H14  C12  C11  107.52  3.000
 5TE  C13  C12  C11  113.35  3.000
 5TE  H17  C13  H16  106.40  3.000
 5TE  H17  C13  C14  109.11  3.000
 5TE  H16  C13  C14  108.98  3.000
 5TE  H17  C13  C12  109.53  3.000
 5TE  H16  C13  C12  109.71  3.000
 5TE  C14  C13  C12  112.90  3.000
 5TE  H18  C14  C18  107.96  3.000
 5TE  H18  C14  C15  108.54  3.000
 5TE  C18  C14  C15  102.49  3.000
 5TE  H18  C14  C13  108.71  3.000
 5TE  C15  C14  C13  113.14  3.000
 5TE  C18  C14  C13  115.63  3.000
 5TE  H20  C15  H19  106.71  3.000
 5TE  H20  C15  C16  112.80  3.000
 5TE  H19  C15  C16  110.19  3.000
 5TE  H20  C15  C14  112.21  3.000
 5TE  H19  C15  C14  109.02  3.000
 5TE  C16  C15  C14  105.90  3.000
 5TE  H22  C16  H21  106.51  3.000
 5TE  H22  C16  C17  111.21  3.000
 5TE  H21  C16  C17  111.08  3.000
 5TE  H22  C16  C15  111.69  3.000
 5TE  H21  C16  C15  110.71  3.000
 5TE  C17  C16  C15  105.74  3.000
 5TE  H24  C17  H23  106.76  3.000
 5TE  H24  C17  C18  109.30  3.000
 5TE  H23  C17  C18  112.84  3.000
 5TE  H24  C17  C16  110.20  3.000
 5TE  H23  C17  C16  112.80  3.000
 5TE  C18  C17  C16  104.94  3.000
 5TE  H26  C18  H25  107.29  3.000
 5TE  H26  C18  C17  110.50  3.000
 5TE  H25  C18  C17  112.63  3.000
 5TE  H26  C18  C14  109.24  3.000
 5TE  H25  C18  C14  113.81  3.000
 5TE  C17  C18  C14  103.34  3.000
 5TE  C5   N    C2   117.33  3.000
 5TE  C2   N    C1   112.85  3.000
 5TE  C5   N    C1   117.98  3.000
 5TE  H28  C    H27  106.89  3.000
 5TE  H28  C    C4   109.78  3.000
 5TE  H27  C    C4   110.96  3.000
 5TE  H28  C    C1   108.94  3.000
 5TE  H27  C    C1   108.62  3.000
 5TE  C4   C    C1   111.51  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
 5TE  CONST_01  C8   C9   C10  C5      0.00   0.0  0
 5TE  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 5TE  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 5TE  CONST_04  C9   C10  C5   C6      0.00   0.0  0
 5TE  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 5TE  CONST_06  C10  C5   C6   C7      0.00   0.0  0
 5TE  CONST_07  N    C5   C6   C7    180.00   0.0  0
 5TE  CONST_08  N    C5   C10  C9    180.00   0.0  0
 5TE  CONST_09  C9   C8   C7   N1    180.00   0.0  0
 5TE  CONST_10  C5   C6   C7   N1    180.00   0.0  0
 5TE  CONST_11  H12  C9   C10  C5    180.00   0.0  0
 5TE  CONST_12  H11  C8   C7   C6    180.00   0.0  0
 5TE  CONST_13  H13  C10  C5   C6    180.00   0.0  0
 5TE  CONST_14  H10  C6   C7   C8    180.00   0.0  0
 5TE  CONST_15  C11  N1   C7   C6    180.00   0.0  0
 5TE  CONST_16  C11  N1   C7   C8      0.00   0.0  0
 5TE  CONST_17  H7   N1   C7   C6      0.00   0.0  0
 5TE  CONST_18  C12  C11  N1   C7    180.00   0.0  0
 5TE  CONST_19  O    C11  N1   C7      0.00   0.0  0
 5TE  Var_01    C10  C5   N    C1      8.25  30.0  3
 5TE  Var_02    C3   C2   N    C1     57.17  30.0  1
 5TE  Var_03    C3   C4   C    C1    -54.03  30.0  1
 5TE  Var_04    C    C1   N    C2    -56.53  30.0  1
 5TE  Var_05    C    C4   C3   C2     54.03  30.0  1
 5TE  Var_06    N    C1   C    C4     55.13  30.0  1
 5TE  Var_07    N    C2   C3   C4    -55.62  30.0  1
 5TE  Var_08    C16  C17  C18  C14   -35.81  30.0  1
 5TE  Var_09    C17  C16  C15  C14    10.76  30.0  1
 5TE  Var_10    C18  C17  C16  C15    15.36  30.0  1
 5TE  Var_11    C14  C13  C12  C11  -180.00  30.0  2
 5TE  Var_12    C13  C12  C11  N1    155.80  30.0  2

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
 5TE  chir_01  C14  C18  C13  C15  positiv

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
 5TE  plan-1  N1   0.020
 5TE  plan-1  C7   0.020
 5TE  plan-1  C11  0.020
 5TE  plan-1  C12  0.020
 5TE  plan-1  O    0.020
 5TE  plan-1  H7   0.020
 5TE  plan-2  N1   0.020
 5TE  plan-2  C5   0.020
 5TE  plan-2  C6   0.020
 5TE  plan-2  C7   0.020
 5TE  plan-2  C8   0.020
 5TE  plan-2  C9   0.020
 5TE  plan-2  C10  0.020
 5TE  plan-2  N    0.020
 5TE  plan-2  H10  0.020
 5TE  plan-2  H11  0.020
 5TE  plan-2  H12  0.020
 5TE  plan-2  H13  0.020

