# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:43:04 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 3-[1-[4-(methylaminomethyl)phenyl]piperidin-4-yl]-1-pyrrolidin-1-yl-propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1ccc(cc1)N2CCC(CC2)CCC(=O)N3CCCC3
#
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
 5T0  5T0  3-[1-[4-(methylaminomethyl)phenyl]piperidin-4-yl]-1-pyrrolidin-1-yl-propan-1-one  ligand  55  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5T0
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
 5T0  C14  C  CR16  0  -0.301   4.8444   1.4428   0.6329
 5T0  C13  C  CR16  0  -0.317   3.4966   1.1291   0.6620
 5T0  C15  C  CR6   0   0.060   5.7580   0.6825  -0.0917
 5T0  C17  C  CR16  0  -0.347   3.9120  -0.7344  -0.7764
 5T0  C16  C  CR16  0  -0.278   5.2624  -0.4149  -0.7863
 5T0  C8   C  CH2   0  -0.415  -0.1824  -1.9310  -0.0607
 5T0  C10  C  CH2   0  -0.296   0.6880   0.7986  -0.1961
 5T0  C9   C  CH2   0  -0.307   1.1956  -1.5364  -0.5710
 5T0  N1   N  NT    0  -0.507   1.6342  -0.2888   0.0246
 5T0  C12  C  CR6   0   0.349   2.9911   0.0287  -0.0457
 5T0  C11  C  CH2   0  -0.432  -0.6933   0.4551   0.3350
 5T0  C1   C  CH2   0  -0.474  -7.3105   2.0573  -0.4169
 5T0  C2   C  CH2   0  -0.485  -8.2540   0.8628  -0.3244
 5T0  C3   C  CH2   0  -0.258  -7.4470  -0.1611   0.4662
 5T0  C4   C  C     0   0.575  -5.0515  -0.6672   0.4393
 5T0  C6   C  CH2   0  -0.395  -2.5836  -1.2548   0.2670
 5T0  C7   C  CH1   0  -0.241  -1.2203  -0.8367  -0.2804
 5T0  O    O  O     0  -0.515  -5.2377  -1.6981   1.0783
 5T0  N    N  NT    0  -0.477  -6.0664   0.1477   0.1087
 5T0  C    C  CH2   0  -0.268  -5.9478   1.4063  -0.6205
 5T0  C18  C  CH2   0  -0.319   7.2190   1.0395  -0.1275
 5T0  N2   N  NH1   0  -0.584   8.0612  -0.1096   0.1428
 5T0  C19  C  CH3   0  -0.519   9.4717   0.2149   0.0945
 5T0  H1   H  HCR6  0   0.243   5.1933   2.2983   1.2006
 5T0  H2   H  HCR6  0   0.254   2.8368   1.7347   1.2697
 5T0  H3   H  HCR6  0   0.261   3.5860  -1.5869  -1.3559
 5T0  H4   H  HCR6  0   0.240   5.9409  -1.0342  -1.3605
 5T0  H5   H  HCH2  0   0.233  -0.4895  -2.8534  -0.5606
 5T0  H6   H  HCH2  0   0.216  -0.1143  -2.1554   1.0088
 5T0  H7   H  HCH2  0   0.252   1.0435   1.7027   0.2932
 5T0  H8   H  HCH2  0   0.208   0.6167   1.0283  -1.2711
 5T0  H9   H  HCH2  0   0.247   1.9014  -2.3254  -0.3083
 5T0  H10  H  HCH2  0   0.204   1.1783  -1.4743  -1.6716
 5T0  H11  H  HCH2  0   0.216  -0.6470   0.3494   1.4245
 5T0  H12  H  HCH2  0   0.238  -1.3582   1.2960   0.1239
 5T0  H14  H  HCH2  0   0.251  -9.2027   1.1001   0.1552
 5T0  H15  H  HCH2  0   0.233  -7.6001  -0.0470   1.5434
 5T0  H18  H  HCH2  0   0.217  -2.5018  -1.4248   1.3445
 5T0  H19  H  HCH2  0   0.227  -2.8585  -2.2159  -0.1762
 5T0  H20  H  HCH1  0   0.211  -1.3210  -0.6788  -1.3633
 5T0  H21  H  HCH2  0   0.239  -5.7513   1.2263  -1.6823
 5T0  H22  H  HCH2  0   0.229   7.4830   1.4139  -1.1233
 5T0  H23  H  HCH2  0   0.206   7.4019   1.8772   0.5645
 5T0  H24  H  HNH1  0   0.342   7.8338  -0.4732   1.0599
 5T0  H26  H  HCH3  0   0.193   9.7688   1.0377   0.7601
 5T0  H27  H  HCH3  0   0.233  10.0622  -0.6611   0.3629
 5T0  H28  H  HCH3  0   0.222   9.7500   0.5030  -0.9213
 5T0  H29  H  HCH2  0   0.239  -7.3185   2.6214   0.5183
 5T0  H30  H  HCH2  0   0.238  -8.4733   0.4773  -1.3224
 5T0  H31  H  HCH2  0   0.243  -7.6998  -1.1885   0.2032
 5T0  H32  H  HCH2  0   0.251  -5.1348   2.0208  -0.2323
 5T0  C5   C  CH2   0  -0.607  -3.6743  -0.2336  -0.0184
 5T0  H13  H  HCH2  0   0.251  -7.5601   2.7476  -1.2218
 5T0  H16  H  HCH2  0   0.259  -3.7052  -0.0104  -1.0905
 5T0  H17  H  HCH2  0   0.268  -3.4405   0.7200   0.4658

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
 5T0  O    C4   double    1.227  0.020  1.227
 5T0  C3   C2   single    1.525  0.020  1.525
 5T0  C3   N    single    1.459  0.020  1.459
 5T0  C2   C1   single    1.525  0.020  1.525
 5T0  C4   N    single    1.343  0.020  1.343
 5T0  C4   C5   single    1.515  0.020  1.515
 5T0  N    C    single    1.459  0.020  1.459
 5T0  C6   C5   single    1.521  0.020  1.521
 5T0  C6   C7   single    1.527  0.020  1.527
 5T0  C8   C9   single    1.522  0.020  1.522
 5T0  C8   C7   single    1.524  0.020  1.524
 5T0  C1   C    single    1.524  0.020  1.524
 5T0  C9   N1   single    1.450  0.020  1.450
 5T0  C7   C11  single    1.525  0.020  1.525
 5T0  C11  C10  single    1.519  0.020  1.519
 5T0  N1   C12  single    1.395  0.020  1.395
 5T0  N1   C10  single    1.458  0.020  1.458
 5T0  C12  C13  aromatic  1.403  0.020  1.403
 5T0  C12  C17  aromatic  1.402  0.020  1.402
 5T0  C13  C14  aromatic  1.384  0.020  1.384
 5T0  C17  C16  aromatic  1.388  0.020  1.388
 5T0  C14  C15  aromatic  1.392  0.020  1.392
 5T0  C16  C15  aromatic  1.390  0.020  1.390
 5T0  C15  C18  single    1.504  0.020  1.504
 5T0  C18  N2   single    1.450  0.020  1.450
 5T0  N2   C19  single    1.448  0.020  1.448
 5T0  C14  H1   single    0.930  0.020  1.080
 5T0  C13  H2   single    0.930  0.020  1.080
 5T0  C17  H3   single    0.930  0.020  1.080
 5T0  C16  H4   single    0.930  0.020  1.080
 5T0  C8   H5   single    0.970  0.020  1.090
 5T0  C8   H6   single    0.970  0.020  1.090
 5T0  C10  H7   single    0.970  0.020  1.090
 5T0  C10  H8   single    0.970  0.020  1.090
 5T0  C9   H9   single    0.970  0.020  1.090
 5T0  C9   H10  single    0.970  0.020  1.090
 5T0  C11  H11  single    0.970  0.020  1.090
 5T0  C11  H12  single    0.970  0.020  1.090
 5T0  C1   H13  single    0.970  0.020  1.090
 5T0  C2   H14  single    0.970  0.020  1.090
 5T0  C3   H15  single    0.970  0.020  1.090
 5T0  C5   H16  single    0.970  0.020  1.090
 5T0  C5   H17  single    0.970  0.020  1.090
 5T0  C6   H18  single    0.970  0.020  1.090
 5T0  C6   H19  single    0.970  0.020  1.090
 5T0  C7   H20  single    0.970  0.020  1.090
 5T0  C    H21  single    0.970  0.020  1.090
 5T0  C18  H22  single    0.970  0.020  1.090
 5T0  C18  H23  single    0.970  0.020  1.090
 5T0  N2   H24  single    0.890  0.020  1.040
 5T0  C19  H26  single    0.970  0.020  1.090
 5T0  C19  H27  single    0.970  0.020  1.090
 5T0  C19  H28  single    0.970  0.020  1.090
 5T0  C1   H29  single    0.970  0.020  1.090
 5T0  C2   H30  single    0.970  0.020  1.090
 5T0  C3   H31  single    0.970  0.020  1.090
 5T0  C    H32  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
 5T0  H1   C14  C15  119.49  3.000
 5T0  H1   C14  C13  118.76  3.000
 5T0  C15  C14  C13  121.75  3.000
 5T0  H2   C13  C12  120.17  3.000
 5T0  H2   C13  C14  118.60  3.000
 5T0  C12  C13  C14  121.21  3.000
 5T0  C18  C15  C16  121.44  3.000
 5T0  C18  C15  C14  121.34  3.000
 5T0  C16  C15  C14  117.21  3.000
 5T0  H3   C17  C12  120.71  3.000
 5T0  H3   C17  C16  118.10  3.000
 5T0  C12  C17  C16  121.18  3.000
 5T0  H4   C16  C17  118.79  3.000
 5T0  H4   C16  C15  119.53  3.000
 5T0  C17  C16  C15  121.67  3.000
 5T0  H6   C8   H5   106.93  3.000
 5T0  H6   C8   C7   109.28  3.000
 5T0  H5   C8   C7   110.40  3.000
 5T0  H6   C8   C9   108.93  3.000
 5T0  H5   C8   C9   108.66  3.000
 5T0  C7   C8   C9   112.47  3.000
 5T0  H8   C10  H7   106.67  3.000
 5T0  H8   C10  C11  109.24  3.000
 5T0  H7   C10  C11  109.13  3.000
 5T0  H8   C10  N1   110.19  3.000
 5T0  H7   C10  N1   109.86  3.000
 5T0  C11  C10  N1   111.62  3.000
 5T0  H10  C9   H9   106.94  3.000
 5T0  H10  C9   N1   111.48  3.000
 5T0  H9   C9   N1   109.13  3.000
 5T0  H10  C9   C8   109.59  3.000
 5T0  H9   C9   C8   108.52  3.000
 5T0  N1   C9   C8   111.05  3.000
 5T0  C12  N1   C9   117.97  3.000
 5T0  C12  N1   C10  116.98  3.000
 5T0  C9   N1   C10  112.52  3.000
 5T0  N1   C12  C17  122.77  3.000
 5T0  C17  C12  C13  116.97  3.000
 5T0  N1   C12  C13  120.24  3.000
 5T0  H12  C11  H11  106.98  3.000
 5T0  H12  C11  C7   111.33  3.000
 5T0  H11  C11  C7   109.52  3.000
 5T0  H12  C11  C10  108.17  3.000
 5T0  H11  C11  C10  109.33  3.000
 5T0  C7   C11  C10  111.39  3.000
 5T0  H29  C1   H13  107.68  3.000
 5T0  H29  C1   C    109.97  3.000
 5T0  H13  C1   C    112.14  3.000
 5T0  H29  C1   C2   110.37  3.000
 5T0  H13  C1   C2   113.55  3.000
 5T0  C    C1   C2   103.11  3.000
 5T0  H30  C2   H14  107.72  3.000
 5T0  H30  C2   C3   110.06  3.000
 5T0  H14  C2   C3   112.27  3.000
 5T0  H30  C2   C1   110.20  3.000
 5T0  H14  C2   C1   113.26  3.000
 5T0  C3   C2   C1   103.30  3.000
 5T0  H31  C3   H15  107.66  3.000
 5T0  H31  C3   N    111.09  3.000
 5T0  H15  C3   N    110.59  3.000
 5T0  H31  C3   C2   112.64  3.000
 5T0  H15  C3   C2   111.50  3.000
 5T0  N    C3   C2   103.39  3.000
 5T0  N    C4   O    121.55  3.000
 5T0  N    C4   C5   116.04  3.000
 5T0  O    C4   C5   122.40  3.000
 5T0  H19  C6   H18  106.35  3.000
 5T0  H19  C6   C7   108.65  3.000
 5T0  H18  C6   C7   109.19  3.000
 5T0  H19  C6   C5   109.49  3.000
 5T0  H18  C6   C5   110.04  3.000
 5T0  C7   C6   C5   112.89  3.000
 5T0  H20  C7   C6   108.10  3.000
 5T0  H20  C7   C11  107.91  3.000
 5T0  C6   C7   C11  113.31  3.000
 5T0  H20  C7   C8   107.91  3.000
 5T0  C11  C7   C8   108.34  3.000
 5T0  C6   C7   C8   111.08  3.000
 5T0  C    N    C4   125.80  3.000
 5T0  C    N    C3   112.45  3.000
 5T0  C4   N    C3   121.75  3.000
 5T0  H32  C    H21  107.71  3.000
 5T0  H32  C    N    111.63  3.000
 5T0  H21  C    N    110.94  3.000
 5T0  H32  C    C1   112.23  3.000
 5T0  H21  C    C1   111.12  3.000
 5T0  N    C    C1   103.24  3.000
 5T0  H23  C18  H22  105.71  3.000
 5T0  H23  C18  N2   112.90  3.000
 5T0  H22  C18  N2   107.47  3.000
 5T0  H23  C18  C15  109.06  3.000
 5T0  H22  C18  C15  109.67  3.000
 5T0  N2   C18  C15  111.81  3.000
 5T0  H24  N2   C19  109.23  3.000
 5T0  H24  N2   C18  108.85  3.000
 5T0  C19  N2   C18  112.45  3.000
 5T0  H28  C19  H27  107.64  3.000
 5T0  H28  C19  H26  107.27  3.000
 5T0  H27  C19  H26  107.82  3.000
 5T0  H28  C19  N2   109.78  3.000
 5T0  H27  C19  N2   109.84  3.000
 5T0  H26  C19  N2   114.25  3.000
 5T0  H17  C5   H16  105.15  3.000
 5T0  H17  C5   C6   110.40  3.000
 5T0  H16  C5   C6   109.91  3.000
 5T0  H17  C5   C4   108.05  3.000
 5T0  H16  C5   C4   109.18  3.000
 5T0  C6   C5   C4   113.77  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
 5T0  CONST_01  C17  C12  C13  C14     0.00   0.0  0
 5T0  CONST_02  C17  C16  C15  C14     0.00   0.0  0
 5T0  CONST_03  C16  C17  C12  C13     0.00   0.0  0
 5T0  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 5T0  CONST_05  C12  C13  C14  C15     0.00   0.0  0
 5T0  CONST_06  C12  C17  C16  C15     0.00   0.0  0
 5T0  CONST_07  N1   C12  C13  C14   180.00   0.0  0
 5T0  CONST_08  N1   C12  C17  C16   180.00   0.0  0
 5T0  CONST_09  C18  C15  C14  C13   180.00   0.0  0
 5T0  CONST_10  C18  C15  C16  C17   180.00   0.0  0
 5T0  CONST_11  H4   C16  C15  C14   180.00   0.0  0
 5T0  CONST_12  H3   C17  C12  C13   180.00   0.0  0
 5T0  CONST_13  H2   C13  C14  C15   180.00   0.0  0
 5T0  CONST_14  H1   C14  C15  C16   180.00   0.0  0
 5T0  CONST_15  O    C4   N    C3      0.00   0.0  0
 5T0  CONST_16  C5   C4   N    C3    180.00   0.0  0
 5T0  CONST_17  C    N    C4   C5      0.00   0.0  0
 5T0  CONST_18  C    N    C4   O     180.00   0.0  0
 5T0  Var_01    C9   N1   C12  C13  -171.61  30.0  2
 5T0  Var_02    C12  N1   C9   C8    162.99  30.0  1
 5T0  Var_03    C11  C10  N1   C9     57.06  30.0  1
 5T0  Var_04    C7   C8   C9   N1     55.39  30.0  1
 5T0  Var_05    C7   C11  C10  N1    -56.26  30.0  1
 5T0  Var_06    N    C3   C2   C1    -30.07  30.0  1
 5T0  Var_07    C3   N    C    C1     13.22  30.0  1
 5T0  Var_08    C    N    C3   C2     10.64  30.0  1
 5T0  Var_09    N    C    C1   C2    -31.54  30.0  1
 5T0  Var_10    C    C1   C2   C3     38.38  30.0  1
 5T0  Var_11    N2   C18  C15  C14   131.33  30.0  2
 5T0  Var_12    C19  N2   C18  C15   179.24  30.0  3
 5T0  Var_13    C7   C6   C5   C4    176.39  30.0  1
 5T0  Var_14    N    C4   C5   C6   -174.52  30.0  1
 5T0  Var_15    H26  C19  N2   C18    55.26  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
 5T0  chir_01  C7  C6  C8  C11  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
 5T0  plan-1  C3   0.020
 5T0  plan-1  C4   0.020
 5T0  plan-1  O    0.020
 5T0  plan-1  N    0.020
 5T0  plan-1  C    0.020
 5T0  plan-1  C5   0.020
 5T0  plan-2  C14  0.020
 5T0  plan-2  C13  0.020
 5T0  plan-2  C15  0.020
 5T0  plan-2  C17  0.020
 5T0  plan-2  C16  0.020
 5T0  plan-2  N1   0.020
 5T0  plan-2  C12  0.020
 5T0  plan-2  C18  0.020
 5T0  plan-2  H1   0.020
 5T0  plan-2  H2   0.020
 5T0  plan-2  H3   0.020
 5T0  plan-2  H4   0.020

