# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 19:38:25 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 1-{4-[(2-methoxyethyl)amino]piperidin-1-yl}ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCNC1CCN(CC1)C(C)=O
#
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
 JJ7  JJ7  1-{4-[(2-methoxyethyl)amino]piperidin-1-yl}ethan-1-one  ligand  34  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JJ7
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
 JJ7  C01   C  CH3   0  -0.805   3.8898  -1.8630  -0.2875
 JJ7  C02   C  C     0   0.514   3.5254  -0.4164  -0.5339
 JJ7  O03   O  O     0  -0.511   4.0890   0.2254  -1.4136
 JJ7  N04   N  NT    0  -0.432   2.5727   0.1271   0.2551
 JJ7  C05   C  CH2   0  -0.317   2.0843   1.4744   0.0217
 JJ7  C06   C  CH2   0  -0.450   0.6410   1.4435  -0.4640
 JJ7  C07   C  CH1   0  -0.043  -0.2582   0.6829   0.5060
 JJ7  C08   C  CH2   0  -0.433   0.3253  -0.7045   0.7645
 JJ7  C09   C  CH2   0  -0.322   1.7759  -0.6058   1.2216
 JJ7  N10   N  NH1   0  -0.601  -1.6031   0.6043  -0.0370
 JJ7  C11   C  CH2   0  -0.304  -2.6073   0.1901   0.9244
 JJ7  C12   C  CH2   0  -0.158  -4.0015   0.2314   0.3396
 JJ7  O13   O  O2    0  -0.481  -4.1189  -0.6965  -0.7086
 JJ7  C14   C  CH3   0  -0.394  -5.4020  -0.7001  -1.2765
 JJ7  H011  H  HCH3  0   0.263   3.0489  -2.5287  -0.4885
 JJ7  H012  H  HCH3  0   0.267   4.7058  -2.1388  -0.9503
 JJ7  H013  H  HCH3  0   0.264   4.2078  -2.0391   0.7403
 JJ7  H051  H  HCH2  0   0.239   2.1486   2.0372   0.9589
 JJ7  H052  H  HCH2  0   0.264   2.7255   1.9729  -0.6992
 JJ7  H061  H  HCH2  0   0.240   0.2810   2.4697  -0.5820
 JJ7  H062  H  HCH2  0   0.228   0.5963   0.9702  -1.4494
 JJ7  H071  H  HCH1  0   0.188  -0.2453   1.2301   1.4676
 JJ7  H081  H  HCH2  0   0.243  -0.2431  -1.2348   1.5318
 JJ7  H082  H  HCH2  0   0.224   0.2666  -1.2997  -0.1521
 JJ7  H091  H  HCH2  0   0.275   2.1889  -1.5956   1.3920
 JJ7  H092  H  HCH2  0   0.243   1.8240  -0.0789   2.1804
 JJ7  H101  H  HNH1  0   0.339  -1.8591   1.5240  -0.3804
 JJ7  H111  H  HCH2  0   0.228  -2.3935  -0.8268   1.2628
 JJ7  H112  H  HCH2  0   0.198  -2.6155   0.8203   1.8284
 JJ7  H121  H  HCH2  0   0.206  -4.7242   0.0134   1.1389
 JJ7  H122  H  HCH2  0   0.195  -4.2268   1.2498  -0.0147
 JJ7  H143  H  HCH3  0   0.201  -6.1778  -0.9605  -0.5454
 JJ7  H141  H  HCH3  0   0.201  -5.6651   0.2737  -1.7081
 JJ7  H142  H  HCH3  0   0.231  -5.4188  -1.4428  -2.0735

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
 JJ7  O03  C02   double  1.226  0.020  1.226
 JJ7  C05  C06   single  1.523  0.020  1.523
 JJ7  C05  N04   single  1.452  0.020  1.452
 JJ7  C02  N04   single  1.351  0.020  1.351
 JJ7  C02  C01   single  1.512  0.020  1.512
 JJ7  C06  C07   single  1.526  0.020  1.526
 JJ7  N04  C09   single  1.451  0.020  1.451
 JJ7  C07  C08   single  1.527  0.020  1.527
 JJ7  C07  N10   single  1.453  0.020  1.453
 JJ7  C09  C08   single  1.524  0.020  1.524
 JJ7  C11  N10   single  1.451  0.020  1.451
 JJ7  C11  C12   single  1.512  0.020  1.512
 JJ7  O13  C14   single  1.403  0.020  1.403
 JJ7  O13  C12   single  1.405  0.020  1.405
 JJ7  C01  H011  single  0.970  0.020  1.090
 JJ7  C01  H012  single  0.970  0.020  1.090
 JJ7  C01  H013  single  0.970  0.020  1.090
 JJ7  C05  H051  single  0.970  0.020  1.090
 JJ7  C05  H052  single  0.970  0.020  1.090
 JJ7  C06  H061  single  0.970  0.020  1.090
 JJ7  C06  H062  single  0.970  0.020  1.090
 JJ7  C07  H071  single  0.970  0.020  1.090
 JJ7  C08  H081  single  0.970  0.020  1.090
 JJ7  C08  H082  single  0.970  0.020  1.090
 JJ7  C09  H091  single  0.970  0.020  1.090
 JJ7  C09  H092  single  0.970  0.020  1.090
 JJ7  N10  H101  single  0.890  0.020  1.040
 JJ7  C11  H111  single  0.970  0.020  1.090
 JJ7  C11  H112  single  0.970  0.020  1.090
 JJ7  C12  H121  single  0.970  0.020  1.090
 JJ7  C12  H122  single  0.970  0.020  1.090
 JJ7  C14  H143  single  0.970  0.020  1.090
 JJ7  C14  H141  single  0.970  0.020  1.090
 JJ7  C14  H142  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
 JJ7  H013  C01  H012  108.36  3.000
 JJ7  H013  C01  H011  107.45  3.000
 JJ7  H012  C01  H011  108.15  3.000
 JJ7  H013  C01  C02   112.24  3.000
 JJ7  H012  C01  C02   108.92  3.000
 JJ7  H011  C01  C02   111.59  3.000
 JJ7  N04   C02  O03   122.18  3.000
 JJ7  N04   C02  C01   117.36  3.000
 JJ7  O03   C02  C01   120.46  3.000
 JJ7  C09   N04  C05   113.01  3.000
 JJ7  C09   N04  C02   124.95  3.000
 JJ7  C05   N04  C02   121.11  3.000
 JJ7  H052  C05  H051  107.31  3.000
 JJ7  H052  C05  C06   110.92  3.000
 JJ7  H051  C05  C06   109.81  3.000
 JJ7  H052  C05  N04   109.52  3.000
 JJ7  H051  C05  N04   108.64  3.000
 JJ7  C06   C05  N04   110.56  3.000
 JJ7  H062  C06  H061  107.18  3.000
 JJ7  H062  C06  C07   109.44  3.000
 JJ7  H061  C06  C07   110.01  3.000
 JJ7  H062  C06  C05   109.56  3.000
 JJ7  H061  C06  C05   109.10  3.000
 JJ7  C07   C06  C05   111.46  3.000
 JJ7  H071  C07  N10   111.25  3.000
 JJ7  H071  C07  C08   107.32  3.000
 JJ7  N10   C07  C08   111.59  3.000
 JJ7  H071  C07  C06   107.41  3.000
 JJ7  N10   C07  C06   109.57  3.000
 JJ7  C08   C07  C06   109.59  3.000
 JJ7  H082  C08  H081  107.24  3.000
 JJ7  H082  C08  C09   109.72  3.000
 JJ7  H081  C08  C09   108.42  3.000
 JJ7  H082  C08  C07   109.37  3.000
 JJ7  H081  C08  C07   111.17  3.000
 JJ7  C09   C08  C07   110.83  3.000
 JJ7  H092  C09  H091  106.52  3.000
 JJ7  H092  C09  C08   109.60  3.000
 JJ7  H091  C09  C08   110.49  3.000
 JJ7  H092  C09  N04   108.42  3.000
 JJ7  H091  C09  N04   110.85  3.000
 JJ7  C08   C09  N04   110.83  3.000
 JJ7  H101  N10  C11   107.97  3.000
 JJ7  H101  N10  C07   108.12  3.000
 JJ7  C11   N10  C07   114.12  3.000
 JJ7  H112  C11  H111  106.24  3.000
 JJ7  H112  C11  C12   107.14  3.000
 JJ7  H111  C11  C12   109.00  3.000
 JJ7  H112  C11  N10   112.67  3.000
 JJ7  H111  C11  N10   109.60  3.000
 JJ7  C12   C11  N10   111.97  3.000
 JJ7  H122  C12  H121  106.42  3.000
 JJ7  H122  C12  O13   110.71  3.000
 JJ7  H121  C12  O13   110.89  3.000
 JJ7  H122  C12  C11   109.77  3.000
 JJ7  H121  C12  C11   108.63  3.000
 JJ7  O13   C12  C11   110.34  3.000
 JJ7  C14   O13  C12   112.34  3.000
 JJ7  H142  C14  H141  108.27  3.000
 JJ7  H142  C14  H143  108.34  3.000
 JJ7  H141  C14  H143  107.65  3.000
 JJ7  H142  C14  O13   108.17  3.000
 JJ7  H141  C14  O13   112.10  3.000
 JJ7  H143  C14  O13   112.18  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
 JJ7  CONST_01  C05   N04  C02  C01  180.00   0.0  0
 JJ7  CONST_02  C09   N04  C02  C01    0.00   0.0  0
 JJ7  CONST_03  C05   N04  C02  O03    0.00   0.0  0
 JJ7  CONST_04  C09   N04  C02  O03  180.00   0.0  0
 JJ7  Var_01    C07   C06  C05  N04   55.39  30.0  1
 JJ7  Var_02    C07   C08  C09  N04  -56.03  30.0  1
 JJ7  Var_03    C08   C09  N04  C05   58.67  30.0  1
 JJ7  Var_04    C09   N04  C05  C06  -58.10  30.0  1
 JJ7  Var_05    C12   C11  N10  C07  175.42  30.0  1
 JJ7  Var_06    H011  C01  C02  N04   64.18  30.0  3
 JJ7  Var_07    O13   C12  C11  N10   64.23  30.0  3
 JJ7  Var_08    H143  C14  O13  C12  -60.27  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
 JJ7  chir_01  C07  C06  C08  N10  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
 JJ7  plan-1  C01  0.020
 JJ7  plan-1  C02  0.020
 JJ7  plan-1  O03  0.020
 JJ7  plan-1  N04  0.020
 JJ7  plan-1  C05  0.020
 JJ7  plan-1  C09  0.020

