# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 02:40:03 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 1-[2-(1H-indol-5-yloxy)ethyl]piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1CCN(CCOc2ccc3[nH]ccc3c2)CC1
#
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
 58Z  58Z  '1-[2-(1H-indol-5-yloxy)ethyl]piperidine-4-carboxylic acid'  ligand  40  21  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_58Z
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
 58Z  O21   O  O      0  -0.607   5.8203   1.7028  -1.0687
 58Z  C19   C  C      0   0.427   5.2716   1.5168   0.0364
 58Z  O20   O  OC    -1  -0.617   5.4033   2.2367   1.0485
 58Z  C16   C  CH1    0  -0.392   4.3769   0.2697   0.1874
 58Z  C15   C  CH2    0  -0.415   3.9358  -0.3418  -1.1350
 58Z  C14   C  CH2    0  -0.277   3.0604  -1.5640  -0.9087
 58Z  C17   C  CH2    0  -0.417   3.1445   0.5289   1.0473
 58Z  C18   C  CH2    0  -0.284   2.2922  -0.7217   1.1916
 58Z  N13   N  NT     0  -0.409   1.8939  -1.2508  -0.1005
 58Z  C12   C  CH2    0  -0.291   1.0235  -2.4015   0.0166
 58Z  C11   C  CH2    0  -0.207  -0.3607  -2.0832   0.5400
 58Z  O10   O  O2     0  -0.478  -0.9733  -1.1644  -0.3411
 58Z  C3    C  CR6    0   0.385  -2.2245  -0.7219  -0.0652
 58Z  C2    C  CR16   0  -0.406  -2.9901  -1.1930   1.0193
 58Z  C4    C  CR16   0  -0.462  -2.7352   0.2396  -0.9231
 58Z  C5    C  CR56   0   0.076  -4.0233   0.7343  -0.7029
 58Z  C7    C  CR15   0  -0.427  -4.8415   1.6990  -1.3695
 58Z  C8    C  CR15   0  -0.024  -6.0192   1.7578  -0.6786
 58Z  N9    N  NR15   0  -0.681  -5.9848   0.8939   0.3746
 58Z  C6    C  CR56   0   0.328  -4.7772   0.2495   0.3896
 58Z  C1    C  CR16   0  -0.290  -4.2667  -0.7115   1.2525
 58Z  H16   H  HCH1   0   0.213   4.9838  -0.4839   0.7146
 58Z  H15   H  HCH2   0   0.202   3.3744   0.3969  -1.7164
 58Z  H15A  H  HCH2   0   0.218   4.7983  -0.6312  -1.7375
 58Z  H14   H  HCH2   0   0.227   2.7181  -1.9580  -1.8696
 58Z  H14A  H  HCH2   0   0.175   3.6687  -2.3606  -0.4401
 58Z  H17   H  HCH2   0   0.222   3.4363   0.8790   2.0376
 58Z  H17A  H  HCH2   0   0.204   2.5390   1.3204   0.5924
 58Z  H18   H  HCH2   0   0.176   2.8545  -1.4789   1.7707
 58Z  H18A  H  HCH2   0   0.232   1.4033  -0.4794   1.7785
 58Z  H12   H  HCH2   0   0.236   0.9228  -2.8582  -0.9721
 58Z  H12A  H  HCH2   0   0.199   1.4482  -3.1815   0.6729
 58Z  H11   H  HCH2   0   0.229  -0.9298  -3.0188   0.5949
 58Z  H11A  H  HCH2   0   0.221  -0.3190  -1.6743   1.5558
 58Z  H2    H  HCR6   0   0.271  -2.5947  -1.9440   1.6890
 58Z  H4    H  HCR6   0   0.246  -2.1355   0.5984  -1.7514
 58Z  H7    H  HCR5   0   0.245  -4.5908   2.2727  -2.2475
 58Z  H8    H  HCR5   0   0.280  -6.8941   2.3605  -0.8627
 58Z  H1    H  HCR6   0   0.262  -4.8434  -1.0856   2.0889
 58Z  HN9   H  HNR5   0   0.408  -6.7371   0.7480   1.0260

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
 58Z  C19  O21   deloc     1.248  0.020  1.248
 58Z  C16  C19   single    1.542  0.020  1.542
 58Z  C19  O20   deloc     1.249  0.020  1.249
 58Z  C17  C16   single    1.525  0.020  1.525
 58Z  C15  C16   single    1.522  0.020  1.522
 58Z  C16  H16   single    0.970  0.020  1.090
 58Z  C14  C15   single    1.520  0.020  1.520
 58Z  C15  H15   single    0.970  0.020  1.090
 58Z  C15  H15A  single    0.970  0.020  1.090
 58Z  N13  C14   single    1.453  0.020  1.453
 58Z  C14  H14   single    0.970  0.020  1.090
 58Z  C14  H14A  single    0.970  0.020  1.090
 58Z  C18  C17   single    1.520  0.020  1.520
 58Z  C17  H17   single    0.970  0.020  1.090
 58Z  C17  H17A  single    0.970  0.020  1.090
 58Z  N13  C18   single    1.452  0.020  1.452
 58Z  C18  H18   single    0.970  0.020  1.090
 58Z  C18  H18A  single    0.970  0.020  1.090
 58Z  C12  N13   single    1.448  0.020  1.448
 58Z  C12  C11   single    1.514  0.020  1.514
 58Z  C12  H12   single    0.970  0.020  1.090
 58Z  C12  H12A  single    0.970  0.020  1.090
 58Z  O10  C11   single    1.413  0.020  1.413
 58Z  C11  H11   single    0.970  0.020  1.090
 58Z  C11  H11A  single    0.970  0.020  1.090
 58Z  O10  C3    single    1.355  0.020  1.355
 58Z  C3   C4    aromatic  1.386  0.020  1.386
 58Z  C3   C2    aromatic  1.409  0.020  1.409
 58Z  C2   C1    aromatic  1.384  0.020  1.384
 58Z  C2   H2    single    0.930  0.020  1.080
 58Z  C4   C5    aromatic  1.397  0.020  1.397
 58Z  C4   H4    single    0.930  0.020  1.080
 58Z  C5   C7    aromatic  1.430  0.020  1.430
 58Z  C5   C6    aromatic  1.413  0.020  1.413
 58Z  C7   C8    aromatic  1.367  0.020  1.367
 58Z  C7   H7    single    0.930  0.020  1.080
 58Z  C8   N9    aromatic  1.363  0.020  1.363
 58Z  C8   H8    single    0.930  0.020  1.080
 58Z  C6   N9    aromatic  1.369  0.020  1.369
 58Z  C1   C6    aromatic  1.389  0.020  1.389
 58Z  C1   H1    single    0.930  0.020  1.080
 58Z  N9   HN9   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
 58Z  C16   C19  O20  116.61  3.000
 58Z  O20   C19  O21  125.83  3.000
 58Z  C16   C19  O21  117.54  3.000
 58Z  H16   C16  C17  106.95  3.000
 58Z  H16   C16  C15  107.49  3.000
 58Z  C17   C16  C15  108.90  3.000
 58Z  H16   C16  C19  106.28  3.000
 58Z  C15   C16  C19  114.07  3.000
 58Z  C17   C16  C19  112.74  3.000
 58Z  H15A  C15  H15  106.92  3.000
 58Z  H15A  C15  C14  108.91  3.000
 58Z  H15   C15  C14  109.04  3.000
 58Z  H15A  C15  C16  110.93  3.000
 58Z  H15   C15  C16  109.80  3.000
 58Z  C14   C15  C16  111.13  3.000
 58Z  H14A  C14  H14  106.55  3.000
 58Z  H14A  C14  N13  111.16  3.000
 58Z  H14   C14  N13  108.37  3.000
 58Z  H14A  C14  C15  108.98  3.000
 58Z  H14   C14  C15  109.82  3.000
 58Z  N13   C14  C15  111.82  3.000
 58Z  H17A  C17  H17  107.05  3.000
 58Z  H17A  C17  C18  108.90  3.000
 58Z  H17   C17  C18  109.15  3.000
 58Z  H17A  C17  C16  109.59  3.000
 58Z  H17   C17  C16  110.52  3.000
 58Z  C18   C17  C16  111.51  3.000
 58Z  H18A  C18  H18  106.51  3.000
 58Z  H18A  C18  N13  109.61  3.000
 58Z  H18   C18  N13  110.84  3.000
 58Z  H18A  C18  C17  108.95  3.000
 58Z  H18   C18  C17  109.12  3.000
 58Z  N13   C18  C17  111.66  3.000
 58Z  C12   N13  C18  112.50  3.000
 58Z  C12   N13  C14  110.88  3.000
 58Z  C18   N13  C14  110.68  3.000
 58Z  H12A  C12  H12  106.12  3.000
 58Z  H12A  C12  C11  107.14  3.000
 58Z  H12   C12  C11  108.44  3.000
 58Z  H12A  C12  N13  112.23  3.000
 58Z  H12   C12  N13  108.31  3.000
 58Z  C11   C12  N13  114.25  3.000
 58Z  H11A  C11  H11  106.96  3.000
 58Z  H11A  C11  O10  110.61  3.000
 58Z  H11   C11  O10  111.16  3.000
 58Z  H11A  C11  C12  111.36  3.000
 58Z  H11   C11  C12  108.21  3.000
 58Z  O10   C11  C12  108.52  3.000
 58Z  C3    O10  C11  119.05  3.000
 58Z  C4    C3   C2   120.54  3.000
 58Z  C2    C3   O10  123.32  3.000
 58Z  C4    C3   O10  116.14  3.000
 58Z  H2    C2   C1   118.33  3.000
 58Z  H2    C2   C3   120.69  3.000
 58Z  C1    C2   C3   120.98  3.000
 58Z  H4    C4   C5   120.89  3.000
 58Z  H4    C4   C3   119.92  3.000
 58Z  C5    C4   C3   119.19  3.000
 58Z  C6    C5   C7   106.66  3.000
 58Z  C6    C5   C4   119.48  3.000
 58Z  C7    C5   C4   133.86  3.000
 58Z  H7    C7   C8   126.09  3.000
 58Z  H7    C7   C5   127.27  3.000
 58Z  C8    C7   C5   106.64  3.000
 58Z  H8    C8   N9   120.45  3.000
 58Z  H8    C8   C7   129.57  3.000
 58Z  N9    C8   C7   109.98  3.000
 58Z  HN9   N9   C6   125.77  3.000
 58Z  HN9   N9   C8   125.01  3.000
 58Z  C6    N9   C8   109.22  3.000
 58Z  C1    C6   N9   131.06  3.000
 58Z  C1    C6   C5   121.45  3.000
 58Z  N9    C6   C5   107.50  3.000
 58Z  H1    C1   C6   121.55  3.000
 58Z  H1    C1   C2   120.09  3.000
 58Z  C6    C1   C2   118.36  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
 58Z  CONST_01  C7   C5   C4   C3    180.00   0.0  0
 58Z  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 58Z  CONST_03  C6   C1   C2   C3      0.00   0.0  0
 58Z  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 58Z  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 58Z  CONST_06  N9   C6   C1   C2    180.00   0.0  0
 58Z  CONST_07  C1   C2   C3   C4      0.00   0.0  0
 58Z  CONST_08  C8   C7   C5   C4    180.00   0.0  0
 58Z  CONST_09  N9   C6   C5   C4    180.00   0.0  0
 58Z  CONST_10  C1   C6   C5   C4      0.00   0.0  0
 58Z  CONST_11  N9   C8   C7   C5      0.00   0.0  0
 58Z  CONST_12  C8   N9   C6   C5      0.00   0.0  0
 58Z  CONST_13  N9   C6   C5   C7      0.00   0.0  0
 58Z  CONST_14  C1   C6   C5   C7    180.00   0.0  0
 58Z  CONST_15  C6   N9   C8   C7      0.00   0.0  0
 58Z  CONST_16  C6   C5   C7   C8      0.00   0.0  0
 58Z  CONST_17  C1   C6   N9   C8    180.00   0.0  0
 58Z  CONST_18  C5   C4   C3   O10   180.00   0.0  0
 58Z  CONST_19  C1   C2   C3   O10   180.00   0.0  0
 58Z  CONST_20  H1   C1   C2   C3    180.00   0.0  0
 58Z  CONST_21  H4   C4   C3   C2    180.00   0.0  0
 58Z  CONST_22  H2   C2   C3   C4    180.00   0.0  0
 58Z  CONST_23  H7   C7   C5   C4      0.00   0.0  0
 58Z  CONST_24  H8   C8   C7   C5    180.00   0.0  0
 58Z  CONST_25  HN9  N9   C6   C5    180.00   0.0  0
 58Z  Var_01    N13  C18  C17  C16   -56.48  30.0  1
 58Z  Var_02    N13  C14  C15  C16    57.04  30.0  1
 58Z  Var_03    C18  N13  C14  C15   -58.81  30.0  1
 58Z  Var_04    C17  C18  N13  C14    58.38  30.0  1
 58Z  Var_05    C11  C12  N13  C14  -165.63  30.0  2
 58Z  Var_06    C4   C3   O10  C11   176.13  30.0  2
 58Z  Var_07    O10  C11  C12  N13    59.63  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
 58Z  chir_01  C16  C19  C17  C15  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
 58Z  plan-1  O10  0.020
 58Z  plan-1  C3   0.020
 58Z  plan-1  C2   0.020
 58Z  plan-1  C4   0.020
 58Z  plan-1  C5   0.020
 58Z  plan-1  C7   0.020
 58Z  plan-1  C8   0.020
 58Z  plan-1  N9   0.020
 58Z  plan-1  C6   0.020
 58Z  plan-1  C1   0.020
 58Z  plan-1  H2   0.020
 58Z  plan-1  H4   0.020
 58Z  plan-1  H7   0.020
 58Z  plan-1  H8   0.020
 58Z  plan-1  H1   0.020
 58Z  plan-1  HN9  0.020
 58Z  plan-2  O21  0.020
 58Z  plan-2  C19  0.020
 58Z  plan-2  O20  0.020
 58Z  plan-2  C16  0.020

