# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 20:49:58 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-(2-{4-[(4-carboxybutanoyl)amino]phenyl}ethyl)-1-methylpiperidinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+]1(CCCCC1)CCc2ccc(NC(=O)CCCC(O)=O)cc2
#
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
 GEP  GEP  1-(2-{4-[(4-carboxybutanoyl)amino]phenyl}ethyl)-1-methylpiperidinium  ligand  53  24  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GEP
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
 GEP  N1    N  NT    1  -0.393    5.4206   0.1089   0.0592
 GEP  C2    C  CH2   0  -0.335    5.7620  -1.2517   0.6033
 GEP  C3    C  CH2   0  -0.470    7.2533  -1.5258   0.6161
 GEP  C4    C  CH2   0  -0.442    7.8590  -1.3767  -0.7711
 GEP  C5    C  CH2   0  -0.478    7.5328  -0.0008  -1.3329
 GEP  C6    C  CH2   0  -0.325    6.0413   0.2691  -1.3073
 GEP  C7    C  CH3   0  -0.568    5.9029   1.1815   0.9705
 GEP  C8    C  CH2   0  -0.315    3.9308   0.2295  -0.1220
 GEP  C9    C  CH2   0  -0.571    3.1004   0.1224   1.1506
 GEP  C10   C  CR6   0   0.118    1.6447   0.2557   0.7918
 GEP  C11   C  CR16  0  -0.296    0.8372  -0.8626   0.6307
 GEP  C12   C  CR16  0  -0.298   -0.5030  -0.7592   0.2834
 GEP  C13   C  CR6   0   0.358   -1.0695   0.5000   0.0832
 GEP  C14   C  CR16  0  -0.333   -0.2610   1.6302   0.2332
 GEP  C15   C  CR16  0  -0.286    1.0709   1.5069   0.5816
 GEP  N16   N  NH1   0  -0.747   -2.4037   0.7215  -0.2694
 GEP  C17   C  C     0   0.561   -3.4397  -0.1561  -0.3138
 GEP  O18   O  O     0  -0.469   -3.3387  -1.3372  -0.0341
 GEP  C19   C  CH2   0  -0.593   -4.7439   0.4561  -0.7764
 GEP  C20   C  CH2   0  -0.420   -5.9617  -0.1763  -0.1158
 GEP  C21   C  CH2   0  -0.583   -7.2397   0.4343  -0.6656
 GEP  C22   C  C     0   0.551   -8.4897  -0.1307  -0.0510
 GEP  O23   O  OH1   0  -0.597   -9.5844   0.4157  -0.5718
 GEP  O24   O  O     0  -0.444   -8.5221  -0.9737   0.8107
 GEP  H21   H  HCH2  0   0.307    5.3487  -1.3208   1.6069
 GEP  H22   H  HCH2  0   0.295    5.2437  -1.9740  -0.0299
 GEP  H31   H  HCH2  0   0.279    7.3807  -2.5426   0.9903
 GEP  H32   H  HCH2  0   0.254    7.7581  -0.8719   1.3316
 GEP  H41   H  HCH2  0   0.235    7.4538  -2.1490  -1.4313
 GEP  H42   H  HCH2  0   0.258    8.9385  -1.5243  -0.7323
 GEP  H51   H  HCH2  0   0.280    7.8415   0.0782  -2.3765
 GEP  H52   H  HCH2  0   0.254    8.0829   0.7749  -0.7959
 GEP  H61   H  HCH2  0   0.295    5.5228  -0.4334  -1.9610
 GEP  H62   H  HCH2  0   0.306    5.8081   1.2777  -1.6471
 GEP  H71   H  HCH3  0   0.297    5.5079   2.1357   0.6313
 GEP  H72   H  HCH3  0   0.298    5.5682   0.9816   1.9837
 GEP  H73   H  HCH3  0   0.301    6.9858   1.2238   0.9645
 GEP  H81   H  HCH2  0   0.305    3.7597   1.1934  -0.6034
 GEP  H82   H  HCH2  0   0.308    3.6424  -0.5516  -0.8259
 GEP  H91   H  HCH2  0   0.282    3.2636  -0.8370   1.6417
 GEP  H92   H  HCH2  0   0.282    3.3716   0.9037   1.8625
 GEP  H11   H  HCR6  0   0.254    1.2550  -1.8504   0.7861
 GEP  H12   H  HCR6  0   0.280   -1.0892  -1.6565   0.1741
 GEP  H14   H  HCR6  0   0.271   -0.6818   2.6171   0.0803
 GEP  H15   H  HCR6  0   0.255    1.6675   2.4040   0.6995
 GEP  HN6   H  HNH1  0   0.415   -2.6298   1.6814  -0.4803
 GEP  H191  H  HCH2  0   0.261   -4.7464   1.5366  -0.6129
 GEP  H192  H  HCH2  0   0.280   -4.7971   0.3161  -1.8623
 GEP  H201  H  HCH2  0   0.243   -5.9586  -1.2529  -0.2874
 GEP  H202  H  HCH2  0   0.243   -5.9115  -0.0268   0.9647
 GEP  H211  H  HCH2  0   0.280   -7.2480   1.5183  -0.5126
 GEP  H212  H  HCH2  0   0.280   -7.2974   0.2937  -1.7497
 GEP  HO3   H  HOH1  0   0.479  -10.3736   0.0382  -0.1556

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
 GEP  N1   C2    single    1.505  0.020  1.505
 GEP  N1   C6    single    1.509  0.020  1.509
 GEP  N1   C7    single    1.488  0.020  1.488
 GEP  N1   C8    single    1.506  0.020  1.506
 GEP  C2   C3    single    1.516  0.020  1.516
 GEP  C2   H21   single    0.970  0.020  1.090
 GEP  C2   H22   single    0.970  0.020  1.090
 GEP  C3   C4    single    1.521  0.020  1.521
 GEP  C3   H31   single    0.970  0.020  1.090
 GEP  C3   H32   single    0.970  0.020  1.090
 GEP  C4   C5    single    1.522  0.020  1.522
 GEP  C4   H41   single    0.970  0.020  1.090
 GEP  C4   H42   single    0.970  0.020  1.090
 GEP  C5   C6    single    1.516  0.020  1.516
 GEP  C5   H51   single    0.970  0.020  1.090
 GEP  C5   H52   single    0.970  0.020  1.090
 GEP  C6   H61   single    0.970  0.020  1.090
 GEP  C6   H62   single    0.970  0.020  1.090
 GEP  C7   H71   single    0.970  0.020  1.090
 GEP  C7   H72   single    0.970  0.020  1.090
 GEP  C7   H73   single    0.970  0.020  1.090
 GEP  C8   C9    single    1.523  0.020  1.523
 GEP  C8   H81   single    0.970  0.020  1.090
 GEP  C8   H82   single    0.970  0.020  1.090
 GEP  C9   C10   single    1.505  0.020  1.505
 GEP  C9   H91   single    0.970  0.020  1.090
 GEP  C9   H92   single    0.970  0.020  1.090
 GEP  C10  C11   aromatic  1.389  0.020  1.389
 GEP  C10  C15   aromatic  1.392  0.020  1.392
 GEP  C11  C12   aromatic  1.388  0.020  1.388
 GEP  C11  H11   single    0.930  0.020  1.080
 GEP  C12  C13   aromatic  1.395  0.020  1.395
 GEP  C12  H12   single    0.930  0.020  1.080
 GEP  C13  C14   aromatic  1.398  0.020  1.398
 GEP  C13  N16   single    1.398  0.020  1.398
 GEP  C14  C15   aromatic  1.382  0.020  1.382
 GEP  C14  H14   single    0.930  0.020  1.080
 GEP  C15  H15   single    0.930  0.020  1.080
 GEP  N16  C17   single    1.359  0.020  1.359
 GEP  N16  HN6   single    0.860  0.020  1.020
 GEP  C17  O18   double    1.218  0.020  1.218
 GEP  C17  C19   single    1.513  0.020  1.513
 GEP  C19  C20   single    1.523  0.020  1.523
 GEP  C19  H191  single    0.970  0.020  1.090
 GEP  C19  H192  single    0.970  0.020  1.090
 GEP  C20  C21   single    1.519  0.020  1.519
 GEP  C20  H201  single    0.970  0.020  1.090
 GEP  C20  H202  single    0.970  0.020  1.090
 GEP  C21  C22   single    1.503  0.020  1.503
 GEP  C21  H211  single    0.970  0.020  1.090
 GEP  C21  H212  single    0.970  0.020  1.090
 GEP  C22  O23   single    1.330  0.020  1.330
 GEP  C22  O24   double    1.206  0.020  1.206
 GEP  O23  HO3   single    0.850  0.020  0.980

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
 GEP  C8    N1   C7    109.68  3.000
 GEP  C8    N1   C6    106.83  3.000
 GEP  C7    N1   C6    110.17  3.000
 GEP  C8    N1   C2    109.91  3.000
 GEP  C7    N1   C2    110.91  3.000
 GEP  C6    N1   C2    109.27  3.000
 GEP  H22   C2   H21   108.23  3.000
 GEP  H22   C2   C3    110.63  3.000
 GEP  H21   C2   C3    110.76  3.000
 GEP  H22   C2   N1    106.31  3.000
 GEP  H21   C2   N1    107.75  3.000
 GEP  C3    C2   N1    112.93  3.000
 GEP  H32   C3   H31   106.21  3.000
 GEP  H32   C3   C4    110.76  3.000
 GEP  H31   C3   C4    110.95  3.000
 GEP  H32   C3   C2    110.59  3.000
 GEP  H31   C3   C2    106.63  3.000
 GEP  C4    C3   C2    111.48  3.000
 GEP  H42   C4   H41   107.02  3.000
 GEP  H42   C4   C5    110.36  3.000
 GEP  H41   C4   C5    109.64  3.000
 GEP  H42   C4   C3    110.40  3.000
 GEP  H41   C4   C3    109.49  3.000
 GEP  C5    C4   C3    109.88  3.000
 GEP  H52   C5   H51   106.04  3.000
 GEP  H52   C5   C6    111.15  3.000
 GEP  H51   C5   C6    106.36  3.000
 GEP  H52   C5   C4    110.66  3.000
 GEP  H51   C5   C4    110.97  3.000
 GEP  C6    C5   C4    111.45  3.000
 GEP  H62   C6   H61   107.91  3.000
 GEP  H62   C6   C5    111.72  3.000
 GEP  H61   C6   C5    110.05  3.000
 GEP  H62   C6   N1    107.01  3.000
 GEP  H61   C6   N1    106.19  3.000
 GEP  C5    C6   N1    113.64  3.000
 GEP  H73   C7   H72   108.69  3.000
 GEP  H73   C7   H71   109.09  3.000
 GEP  H72   C7   H71   109.93  3.000
 GEP  H73   C7   N1    110.41  3.000
 GEP  H72   C7   N1    109.82  3.000
 GEP  H71   C7   N1    108.90  3.000
 GEP  H82   C8   H81   107.85  3.000
 GEP  H82   C8   C9    110.17  3.000
 GEP  H81   C8   C9    110.20  3.000
 GEP  H82   C8   N1    106.38  3.000
 GEP  H81   C8   N1    106.20  3.000
 GEP  C9    C8   N1    115.67  3.000
 GEP  H92   C9   H91   107.40  3.000
 GEP  H92   C9   C10   109.41  3.000
 GEP  H91   C9   C10   109.27  3.000
 GEP  H92   C9   C8    111.06  3.000
 GEP  H91   C9   C8    110.90  3.000
 GEP  C10   C9   C8    108.77  3.000
 GEP  C15   C10  C11   117.80  3.000
 GEP  C15   C10  C9    120.94  3.000
 GEP  C11   C10  C9    121.24  3.000
 GEP  H11   C11  C12   118.42  3.000
 GEP  H11   C11  C10   119.55  3.000
 GEP  C12   C11  C10   122.03  3.000
 GEP  H12   C12  C13   121.07  3.000
 GEP  H12   C12  C11   119.25  3.000
 GEP  C13   C12  C11   119.67  3.000
 GEP  N16   C13  C14   116.82  3.000
 GEP  N16   C13  C12   124.53  3.000
 GEP  C14   C13  C12   118.65  3.000
 GEP  H14   C14  C15   119.40  3.000
 GEP  H14   C14  C13   119.77  3.000
 GEP  C15   C14  C13   120.82  3.000
 GEP  H15   C15  C14   118.95  3.000
 GEP  H15   C15  C10   120.03  3.000
 GEP  C14   C15  C10   121.02  3.000
 GEP  HN6   N16  C17   115.92  3.000
 GEP  HN6   N16  C13   114.69  3.000
 GEP  C17   N16  C13   129.33  3.000
 GEP  C19   C17  O18   122.28  3.000
 GEP  C19   C17  N16   113.95  3.000
 GEP  O18   C17  N16   123.76  3.000
 GEP  H192  C19  H191  105.92  3.000
 GEP  H192  C19  C20   109.75  3.000
 GEP  H191  C19  C20   110.11  3.000
 GEP  H192  C19  C17   107.04  3.000
 GEP  H191  C19  C17   110.87  3.000
 GEP  C20   C19  C17   112.87  3.000
 GEP  H202  C20  H201  106.91  3.000
 GEP  H202  C20  C21   109.98  3.000
 GEP  H201  C20  C21   110.02  3.000
 GEP  H202  C20  C19   109.61  3.000
 GEP  H201  C20  C19   109.84  3.000
 GEP  C21   C20  C19   110.41  3.000
 GEP  H212  C21  H211  105.38  3.000
 GEP  H212  C21  C22   108.22  3.000
 GEP  H211  C21  C22   107.98  3.000
 GEP  H212  C21  C20   110.56  3.000
 GEP  H211  C21  C20   110.72  3.000
 GEP  C22   C21  C20   113.61  3.000
 GEP  O24   C22  O23   123.03  3.000
 GEP  O24   C22  C21   125.26  3.000
 GEP  O23   C22  C21   111.71  3.000
 GEP  HO3   O23  C22   110.01  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
 GEP  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 GEP  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 GEP  CONST_03  C14  C15  C10  C11     0.00   0.0  0
 GEP  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 GEP  CONST_05  C15  C10  C11  C12     0.00   0.0  0
 GEP  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 GEP  CONST_07  C12  C11  C10  C9    180.00   0.0  0
 GEP  CONST_08  C14  C15  C10  C9    180.00   0.0  0
 GEP  CONST_09  N16  C13  C12  C11   180.00   0.0  0
 GEP  CONST_10  N16  C13  C14  C15   180.00   0.0  0
 GEP  CONST_11  H12  C12  C11  C10   180.00   0.0  0
 GEP  CONST_12  H14  C14  C15  C10   180.00   0.0  0
 GEP  CONST_13  H15  C15  C10  C11   180.00   0.0  0
 GEP  CONST_14  H11  C11  C12  C13   180.00   0.0  0
 GEP  CONST_15  C17  N16  C13  C12     0.00   0.0  0
 GEP  CONST_16  C17  N16  C13  C14   180.00   0.0  0
 GEP  CONST_17  HN6  N16  C13  C12   180.00   0.0  0
 GEP  CONST_18  O18  C17  N16  C13     0.00   0.0  0
 GEP  CONST_19  C19  C17  N16  C13   180.00   0.0  0
 GEP  CONST_20  HO3  O23  C22  C21   180.00   0.0  0
 GEP  Var_01    C4   C3   C2   N1    -56.68  30.0  1
 GEP  Var_02    C4   C5   C6   N1     55.03  30.0  1
 GEP  Var_03    C5   C4   C3   C2     55.00  30.0  1
 GEP  Var_04    C6   C5   C4   C3    -54.03  30.0  1
 GEP  Var_05    C10  C9   C8   N1   -179.70  30.0  3
 GEP  Var_06    C11  C10  C9   C8     97.79  30.0  2
 GEP  Var_07    C20  C19  C17  N16  -146.99  30.0  3
 GEP  Var_08    C21  C20  C19  C17  -177.42  30.0  3
 GEP  Var_09    C22  C21  C20  C19  -179.45  30.0  3
 GEP  Var_10    O23  C22  C21  C20  -179.12  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
 GEP  chir_01  N1  C6  C2  C8  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
 GEP  plan-1  C9   0.020
 GEP  plan-1  C10  0.020
 GEP  plan-1  C11  0.020
 GEP  plan-1  C12  0.020
 GEP  plan-1  C13  0.020
 GEP  plan-1  C14  0.020
 GEP  plan-1  C15  0.020
 GEP  plan-1  N16  0.020
 GEP  plan-1  H11  0.020
 GEP  plan-1  H12  0.020
 GEP  plan-1  H14  0.020
 GEP  plan-1  H15  0.020
 GEP  plan-2  C13  0.020
 GEP  plan-2  N16  0.020
 GEP  plan-2  C17  0.020
 GEP  plan-2  O18  0.020
 GEP  plan-2  C19  0.020
 GEP  plan-2  HN6  0.020
 GEP  plan-3  C21  0.020
 GEP  plan-3  C22  0.020
 GEP  plan-3  O23  0.020
 GEP  plan-3  O24  0.020
 GEP  plan-3  HO3  0.020

