# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:59:33 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 2-[(2-aminoethyl)amino]-N-[(1R)-1-(3-methoxyphenyl)ethyl]-4-(pyridin-4-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)[C@@H](C)NC(=O)c2ccc(cc2NCCN)c3ccncc3
#
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
 J0G  J0G  2-[(2-aminoethyl)amino]-N-[(1R)-1-(3-methoxyphenyl)ethyl]-4-(pyridin-4-yl)benzamide  ligand  55  29  .  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_J0G
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
 J0G  N1   N  NH1   0  -0.641  -1.7244   0.5460   0.5332
 J0G  N3   N  N     0  -0.406   6.6181  -3.3110  -0.3486
 J0G  C4   C  CR6   0   0.405   1.8367   1.0886  -0.1152
 J0G  C5   C  CR6   0  -0.145   0.5907   0.4074  -0.1029
 J0G  C6   C  CR16  0  -0.274   0.5798  -0.9838  -0.1710
 J0G  C7   C  C     0   0.564  -0.6897   1.1652  -0.0607
 J0G  C8   C  CH1   0  -0.179  -3.0463   1.1437   0.6448
 J0G  C10  C  CR16  0  -0.422  -5.0299   0.0412  -0.4189
 J0G  C13  C  CR16  0  -0.224  -5.1155  -1.9131   1.5274
 J0G  C15  C  CH3   0  -0.437  -7.9155  -1.8176  -1.6018
 J0G  C17  C  CR6   0   0.168   4.2292  -1.8425  -0.2571
 J0G  C20  C  CR16  0  -0.060   6.5180  -2.1948   0.3642
 J0G  C21  C  CR16  0  -0.377   5.3633  -1.4329   0.4413
 J0G  C22  C  CH2   0  -0.311   2.8898   4.6662  -0.0802
 J0G  C1   C  CR16  0  -0.342   1.7407  -1.7305  -0.2264
 J0G  O1   O  O     0  -0.510  -0.7988   2.2888  -0.5513
 J0G  C2   C  CR6   0   0.124   2.9709  -1.0735  -0.2074
 J0G  C3   C  CR16  0  -0.429   3.0077   0.3125  -0.1541
 J0G  N4   N  NH2   0  -0.800   4.1330   5.3937  -0.2623
 J0G  C9   C  CR6   0   0.176  -4.0958   0.0564   0.6030
 J0G  C11  C  CR6   0   0.403  -6.0191  -0.9452  -0.4738
 J0G  C12  C  CR16  0  -0.395  -6.0594  -1.9327   0.5058
 J0G  C14  C  CR16  0  -0.338  -4.1430  -0.9312   1.5888
 J0G  C16  C  CH2   0  -0.273   3.1460   3.1722  -0.2031
 J0G  C18  C  CR16  0  -0.377   4.3355  -3.0149  -1.0031
 J0G  C19  C  CR16  0  -0.060   5.5385  -3.7020  -1.0162
 J0G  C23  C  CH3   0  -0.645  -3.1679   2.0095   1.8963
 J0G  H1   H  HNH1  0   0.408  -1.5454  -0.2845   1.0747
 J0G  H2   H  HCR6  0   0.257  -0.3656  -1.5111  -0.2043
 J0G  H3   H  HCH1  0   0.269  -3.1804   1.7823  -0.2287
 J0G  H4   H  HCR6  0   0.260  -5.0034   0.8020  -1.1908
 J0G  H5   H  HCR6  0   0.261  -5.1519  -2.6820   2.2881
 J0G  H6   H  HCH3  0   0.260  -8.5007  -1.5527  -2.4790
 J0G  H7   H  HCH3  0   0.229  -7.5248  -2.8300  -1.7337
 J0G  H8   H  HCH3  0   0.229  -8.5685  -1.8036  -0.7255
 J0G  H9   H  HCR6  0   0.266   7.4022  -1.8880   0.9121
 J0G  H10  H  HCR6  0   0.268   5.3504  -0.5439   1.0580
 J0G  H11  H  HCH2  0   0.232   2.5072   4.8759   0.9210
 J0G  H12  H  HCH2  0   0.202   2.0976   4.9565  -0.7858
 J0G  H13  H  HCR6  0   0.255   1.6854  -2.8097  -0.2657
 J0G  H14  H  HNH1  0   0.392   1.0620   2.9278  -0.3110
 J0G  H15  H  HCR6  0   0.273   3.9678   0.8102  -0.1807
 J0G  H16  H  HNH2  0   0.344   4.3967   5.3793  -1.2395
 J0G  H17  H  HNH2  0   0.354   3.9921   6.3676  -0.0297
 J0G  H19  H  HCR6  0   0.280  -6.8056  -2.7150   0.4952
 J0G  H20  H  HCR6  0   0.254  -3.4316  -0.9399   2.4060
 J0G  H21  H  HCH2  0   0.220   3.6261   2.9564  -1.1681
 J0G  H22  H  HCH2  0   0.229   3.8556   2.8790   0.5753
 J0G  H23  H  HCR6  0   0.270   3.5039  -3.3865  -1.5869
 J0G  H24  H  HCR6  0   0.266   5.6310  -4.6113  -1.5998
 J0G  H25  H  HCH3  0   0.228  -3.0288   1.4208   2.8037
 J0G  H26  H  HCH3  0   0.242  -2.4205   2.8029   1.8861
 J0G  H27  H  HCH3  0   0.238  -4.1538   2.4727   1.9426
 J0G  O2   O  O2    0  -0.472  -6.8807  -0.8592  -1.5046
 J0G  N2   N  NH1   0  -0.706   1.9101   2.4437  -0.0567

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
 J0G  C22  N4   single    1.452  0.020  1.452
 J0G  C22  C16  single    1.521  0.020  1.521
 J0G  C16  N2   single    1.442  0.020  1.442
 J0G  N2   C4   single    1.358  0.020  1.358
 J0G  C23  C8   single    1.527  0.020  1.527
 J0G  C4   C3   aromatic  1.405  0.020  1.405
 J0G  C4   C5   aromatic  1.420  0.020  1.420
 J0G  C3   C2   aromatic  1.387  0.020  1.387
 J0G  C8   N1   single    1.455  0.020  1.455
 J0G  C8   C9   single    1.512  0.020  1.512
 J0G  O1   C7   double    1.231  0.020  1.231
 J0G  C7   N1   single    1.344  0.020  1.344
 J0G  C7   C5   single    1.488  0.020  1.488
 J0G  C5   C6   aromatic  1.393  0.020  1.393
 J0G  C2   C17  single    1.475  0.020  1.475
 J0G  C2   C1   aromatic  1.395  0.020  1.395
 J0G  C17  C18  aromatic  1.394  0.020  1.394
 J0G  C17  C21  aromatic  1.393  0.020  1.393
 J0G  C18  C19  aromatic  1.385  0.020  1.385
 J0G  C21  C20  aromatic  1.386  0.020  1.386
 J0G  C6   C1   aromatic  1.381  0.020  1.381
 J0G  C19  N3   aromatic  1.328  0.020  1.328
 J0G  C20  N3   aromatic  1.328  0.020  1.328
 J0G  C9   C10  aromatic  1.385  0.020  1.385
 J0G  C9   C14  aromatic  1.396  0.020  1.396
 J0G  C10  C11  aromatic  1.398  0.020  1.398
 J0G  C15  O2   single    1.414  0.020  1.414
 J0G  C14  C13  aromatic  1.383  0.020  1.383
 J0G  C11  O2   single    1.346  0.020  1.346
 J0G  C11  C12  aromatic  1.391  0.020  1.391
 J0G  C13  C12  aromatic  1.391  0.020  1.391
 J0G  N1   H1   single    0.860  0.020  1.020
 J0G  C6   H2   single    0.930  0.020  1.080
 J0G  C8   H3   single    0.970  0.020  1.090
 J0G  C10  H4   single    0.930  0.020  1.080
 J0G  C13  H5   single    0.930  0.020  1.080
 J0G  C15  H6   single    0.970  0.020  1.090
 J0G  C15  H7   single    0.970  0.020  1.090
 J0G  C15  H8   single    0.970  0.020  1.090
 J0G  C20  H9   single    0.930  0.020  1.080
 J0G  C21  H10  single    0.930  0.020  1.080
 J0G  C22  H11  single    0.970  0.020  1.090
 J0G  C22  H12  single    0.970  0.020  1.090
 J0G  C1   H13  single    0.930  0.020  1.080
 J0G  N2   H14  single    0.890  0.020  1.040
 J0G  C3   H15  single    0.930  0.020  1.080
 J0G  N4   H16  single    0.890  0.020  1.040
 J0G  N4   H17  single    0.890  0.020  1.040
 J0G  C12  H19  single    0.930  0.020  1.080
 J0G  C14  H20  single    0.930  0.020  1.080
 J0G  C16  H21  single    0.970  0.020  1.090
 J0G  C16  H22  single    0.970  0.020  1.090
 J0G  C18  H23  single    0.930  0.020  1.080
 J0G  C19  H24  single    0.930  0.020  1.080
 J0G  C23  H25  single    0.970  0.020  1.090
 J0G  C23  H26  single    0.970  0.020  1.090
 J0G  C23  H27  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
 J0G  H1   N1   C8   117.31  3.000
 J0G  H1   N1   C7   118.71  3.000
 J0G  C8   N1   C7   122.96  3.000
 J0G  C19  N3   C20  117.12  3.000
 J0G  C3   C4   N2   120.48  3.000
 J0G  C3   C4   C5   117.80  3.000
 J0G  N2   C4   C5   121.70  3.000
 J0G  C7   C5   C6   120.21  3.000
 J0G  C6   C5   C4   119.05  3.000
 J0G  C7   C5   C4   120.72  3.000
 J0G  H2   C6   C1   117.98  3.000
 J0G  H2   C6   C5   119.64  3.000
 J0G  C1   C6   C5   122.36  3.000
 J0G  O1   C7   C5   121.99  3.000
 J0G  C5   C7   N1   116.11  3.000
 J0G  O1   C7   N1   121.90  3.000
 J0G  H3   C8   C23  108.35  3.000
 J0G  H3   C8   C9   108.28  3.000
 J0G  C23  C8   C9   112.04  3.000
 J0G  H3   C8   N1   106.91  3.000
 J0G  C9   C8   N1   109.46  3.000
 J0G  C23  C8   N1   111.60  3.000
 J0G  H4   C10  C11  118.98  3.000
 J0G  H4   C10  C9   120.08  3.000
 J0G  C11  C10  C9   120.94  3.000
 J0G  H5   C13  C14  119.79  3.000
 J0G  H5   C13  C12  118.91  3.000
 J0G  C14  C13  C12  121.30  3.000
 J0G  H8   C15  H7   108.79  3.000
 J0G  H8   C15  H6   108.80  3.000
 J0G  H7   C15  H6   108.71  3.000
 J0G  H8   C15  O2   111.93  3.000
 J0G  H7   C15  O2   112.00  3.000
 J0G  H6   C15  O2   106.51  3.000
 J0G  C18  C17  C2   121.43  3.000
 J0G  C18  C17  C21  116.96  3.000
 J0G  C2   C17  C21  121.60  3.000
 J0G  H9   C20  C21  119.72  3.000
 J0G  H9   C20  N3   116.58  3.000
 J0G  C21  C20  N3   123.70  3.000
 J0G  H10  C21  C20  119.57  3.000
 J0G  H10  C21  C17  121.16  3.000
 J0G  C20  C21  C17  119.26  3.000
 J0G  H12  C22  H11  106.57  3.000
 J0G  H12  C22  C16  109.20  3.000
 J0G  H11  C22  C16  108.77  3.000
 J0G  H12  C22  N4   113.83  3.000
 J0G  H11  C22  N4   108.59  3.000
 J0G  C16  C22  N4   109.74  3.000
 J0G  H13  C1   C2   121.05  3.000
 J0G  H13  C1   C6   119.86  3.000
 J0G  C2   C1   C6   119.08  3.000
 J0G  C3   C2   C1   119.63  3.000
 J0G  C1   C2   C17  120.41  3.000
 J0G  C3   C2   C17  119.95  3.000
 J0G  H15  C3   C2   118.83  3.000
 J0G  H15  C3   C4   119.08  3.000
 J0G  C2   C3   C4   122.05  3.000
 J0G  H17  N4   H16  105.78  3.000
 J0G  H17  N4   C22  109.54  3.000
 J0G  H16  N4   C22  109.70  3.000
 J0G  C14  C9   C10  119.37  3.000
 J0G  C14  C9   C8   120.84  3.000
 J0G  C10  C9   C8   119.78  3.000
 J0G  C12  C11  O2   124.46  3.000
 J0G  C12  C11  C10  119.57  3.000
 J0G  O2   C11  C10  115.97  3.000
 J0G  H19  C12  C11  121.78  3.000
 J0G  H19  C12  C13  119.05  3.000
 J0G  C11  C12  C13  119.17  3.000
 J0G  H20  C14  C9   121.07  3.000
 J0G  H20  C14  C13  119.30  3.000
 J0G  C9   C14  C13  119.64  3.000
 J0G  H22  C16  H21  106.80  3.000
 J0G  H22  C16  N2   110.39  3.000
 J0G  H21  C16  N2   111.36  3.000
 J0G  H22  C16  C22  108.38  3.000
 J0G  H21  C16  C22  109.72  3.000
 J0G  N2   C16  C22  110.10  3.000
 J0G  H23  C18  C19  119.47  3.000
 J0G  H23  C18  C17  121.27  3.000
 J0G  C19  C18  C17  119.24  3.000
 J0G  H24  C19  C18  119.67  3.000
 J0G  H24  C19  N3   116.62  3.000
 J0G  C18  C19  N3   123.71  3.000
 J0G  H27  C23  H26  108.14  3.000
 J0G  H27  C23  H25  108.02  3.000
 J0G  H26  C23  H25  108.26  3.000
 J0G  H27  C23  C8   110.35  3.000
 J0G  H26  C23  C8   110.52  3.000
 J0G  H25  C23  C8   111.45  3.000
 J0G  C11  O2   C15  118.54  3.000
 J0G  H14  N2   C16  116.89  3.000
 J0G  H14  N2   C4   114.98  3.000
 J0G  C16  N2   C4   123.09  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
 J0G  CONST_01  C17  C18  C19  N3      0.00   0.0  0
 J0G  CONST_02  C17  C21  C20  N3      0.00   0.0  0
 J0G  CONST_03  C17  C2   C3   C4    180.00   0.0  0
 J0G  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 J0G  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 J0G  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 J0G  CONST_07  C2   C1   C6   C5      0.00   0.0  0
 J0G  CONST_08  C3   C4   C5   C6      0.00   0.0  0
 J0G  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 J0G  CONST_10  C17  C2   C1   C6    180.00   0.0  0
 J0G  CONST_11  C13  C14  C9   C10     0.00   0.0  0
 J0G  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 J0G  CONST_13  C2   C17  C21  C20   180.00   0.0  0
 J0G  CONST_14  C18  C17  C21  C20     0.00   0.0  0
 J0G  CONST_15  C18  C19  N3   C20     0.00   0.0  0
 J0G  CONST_18  C19  C18  C17  C21     0.00   0.0  0
 J0G  CONST_19  C19  N3   C20  C21     0.00   0.0  0
 J0G  CONST_21  C19  C18  C17  C2    180.00   0.0  0
 J0G  CONST_23  C12  C11  C10  C9      0.00   0.0  0
 J0G  CONST_24  C12  C13  C14  C9      0.00   0.0  0
 J0G  CONST_25  C14  C9   C10  C11     0.00   0.0  0
 J0G  CONST_26  C14  C13  C12  C11     0.00   0.0  0
 J0G  CONST_27  N2   C4   C5   C6    180.00   0.0  0
 J0G  CONST_28  C3   C4   C5   C7    180.00   0.0  0
 J0G  CONST_29  C1   C6   C5   C7    180.00   0.0  0
 J0G  CONST_30  C11  C10  C9   C8    180.00   0.0  0
 J0G  CONST_31  C13  C14  C9   C8    180.00   0.0  0
 J0G  CONST_32  O2   C11  C12  C13   180.00   0.0  0
 J0G  CONST_33  N2   C4   C3   C2    180.00   0.0  0
 J0G  CONST_34  C9   C10  C11  O2    180.00   0.0  0
 J0G  CONST_35  H23  C18  C19  N3    180.00   0.0  0
 J0G  CONST_36  H10  C21  C20  N3    180.00   0.0  0
 J0G  CONST_37  H2   C6   C5   C4    180.00   0.0  0
 J0G  CONST_38  H15  C3   C4   C5    180.00   0.0  0
 J0G  CONST_39  H13  C1   C6   C5    180.00   0.0  0
 J0G  CONST_40  H20  C14  C9   C10   180.00   0.0  0
 J0G  CONST_41  H19  C12  C11  C10   180.00   0.0  0
 J0G  CONST_42  H24  C19  C18  C17   180.00   0.0  0
 J0G  CONST_43  H9   C20  C21  C17   180.00   0.0  0
 J0G  CONST_44  H5   C13  C14  C9    180.00   0.0  0
 J0G  CONST_45  H4   C10  C11  C12   180.00   0.0  0
 J0G  CONST_46  C16  N2   C4   C5    180.00   0.0  0
 J0G  CONST_47  C16  N2   C4   C3      0.00   0.0  0
 J0G  CONST_49  C8   N1   C7   C5    180.00   0.0  0
 J0G  CONST_50  H1   N1   C7   C5      0.00   0.0  0
 J0G  CONST_51  O1   C7   N1   C8      0.00   0.0  0
 J0G  Var_01    C4   C5   C7   N1   -151.04  30.0  2
 J0G  Var_02    C12  C11  O2   C15     1.02  30.0  2
 J0G  Var_03    C22  C16  N2   C4   -179.68  30.0  1
 J0G  Var_04    H6   C15  O2   C11   178.65  30.0  3
 J0G  Var_05    N4   C22  C16  N2   -178.57  30.0  2
 J0G  Var_06    H16  N4   C22  C16    73.63  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
 J0G  chir_01  C8  C23  N1  C9  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
 J0G  plan-1  C4   0.020
 J0G  plan-1  C5   0.020
 J0G  plan-1  C6   0.020
 J0G  plan-1  C7   0.020
 J0G  plan-1  C17  0.020
 J0G  plan-1  C1   0.020
 J0G  plan-1  C2   0.020
 J0G  plan-1  C3   0.020
 J0G  plan-1  H2   0.020
 J0G  plan-1  H13  0.020
 J0G  plan-1  H15  0.020
 J0G  plan-1  N2   0.020
 J0G  plan-2  N3   0.020
 J0G  plan-2  C17  0.020
 J0G  plan-2  C20  0.020
 J0G  plan-2  C21  0.020
 J0G  plan-2  C2   0.020
 J0G  plan-2  C18  0.020
 J0G  plan-2  C19  0.020
 J0G  plan-2  H9   0.020
 J0G  plan-2  H10  0.020
 J0G  plan-2  H23  0.020
 J0G  plan-2  H24  0.020
 J0G  plan-3  C8   0.020
 J0G  plan-3  C10  0.020
 J0G  plan-3  C13  0.020
 J0G  plan-3  C9   0.020
 J0G  plan-3  C11  0.020
 J0G  plan-3  C12  0.020
 J0G  plan-3  C14  0.020
 J0G  plan-3  H4   0.020
 J0G  plan-3  H5   0.020
 J0G  plan-3  H19  0.020
 J0G  plan-3  H20  0.020
 J0G  plan-3  O2   0.020
 J0G  plan-4  N1   0.020
 J0G  plan-4  C5   0.020
 J0G  plan-4  C7   0.020
 J0G  plan-4  C8   0.020
 J0G  plan-4  O1   0.020
 J0G  plan-4  H1   0.020
 J0G  plan-5  C4   0.020
 J0G  plan-5  C16  0.020
 J0G  plan-5  H14  0.020
 J0G  plan-5  N2   0.020

