# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 07:09:01 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 6-[(2R)-2-amino-2-{3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]phenyl}ethyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cccc(c2)[C@H](N)Cc3cc(C)cc(N)n3)c1
#
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
 S5D  S5D  6-[(2R)-2-amino-2-{3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]phenyl}ethyl]-4-methylpyridin-2-amine  ligand  54  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S5D
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
 S5D  C1    C  CR16  0  -0.394  -0.1212   0.9599  -0.1594
 S5D  C2    C  CR6   0   0.158  -1.2942   1.6031  -0.5516
 S5D  C3    C  CR16  0  -0.337  -1.2636   2.9801  -0.7438
 S5D  C4    C  CR16  0  -0.223  -0.0843   3.6893  -0.5535
 S5D  C5    C  CR16  0  -0.338   1.0739   3.0326  -0.1659
 S5D  C6    C  CR6   0   0.210   1.0660   1.6536   0.0409
 S5D  N11   N  N     0  -0.485  -5.5406   0.4672  -0.0772
 S5D  C12   C  CR6   0   0.440  -6.6957  -0.1609  -0.2631
 S5D  N12   N  NH2   0  -0.839  -7.7216   0.5687  -0.7922
 S5D  C13   C  CR16  0  -0.448  -6.8896  -1.5039   0.1077
 S5D  C14   C  CR6   0   0.205  -5.8469  -2.1962   0.6870
 S5D  C15   C  CR16  0  -0.434  -4.6352  -1.5214   0.8813
 S5D  C16   C  CR6   0   0.277  -4.5309  -0.2009   0.4861
 S5D  C19   C  CH2   0  -0.510  -2.5700   0.8249  -0.7105
 S5D  N21   N  N     0  -0.493   5.4062   0.3504   0.3679
 S5D  C22   C  CR6   0   0.446   6.4155  -0.4663   0.6553
 S5D  N22   N  NH2   0  -0.839   7.3839   0.0151   1.4876
 S5D  C23   C  CR16  0  -0.445   6.5225  -1.7525   0.0995
 S5D  C24   C  CR6   0   0.205   5.5509  -2.1864  -0.7789
 S5D  C25   C  CR16  0  -0.430   4.4934  -1.3190  -1.0731
 S5D  C26   C  CR6   0   0.278   4.4619  -0.0682  -0.4805
 S5D  C28   C  CH2   0  -0.496   3.3132   0.8653  -0.7342
 S5D  C29   C  CH1   0  -0.209   2.3212   0.9188   0.4533
 S5D  N29   N  NH2   0  -0.784   2.8571   1.4923   1.6792
 S5D  H1    H  HCR6  0   0.238  -0.1372  -0.1144  -0.0035
 S5D  H3    H  HCR6  0   0.245  -2.1654   3.5005  -1.0453
 S5D  H4    H  HCR6  0   0.252  -0.0681   4.7605  -0.7090
 S5D  H5    H  HCR6  0   0.244   1.9824   3.6082  -0.0281
 S5D  HN12  H  HNH2  0   0.379  -7.4615   1.4104  -1.2798
 S5D  HN1A  H  HNH2  0   0.388  -8.4781   0.0641  -1.2227
 S5D  H13   H  HCR6  0   0.255  -7.8474  -1.9811  -0.0621
 S5D  H15   H  HCR6  0   0.243  -3.7896  -2.0249   1.3332
 S5D  H17   H  HCH3  0   0.251  -5.2754  -4.2601   0.5823
 S5D  H17A  H  HCH3  0   0.251  -5.8045  -3.7416   2.1711
 S5D  H17B  H  HCH3  0   0.246  -6.9943  -4.0080   0.8954
 S5D  H19   H  HCH2  0   0.248  -3.2646   1.3718  -1.3511
 S5D  H19A  H  HCH2  0   0.247  -2.3656  -0.1303  -1.2015
 S5D  HN22  H  HNH2  0   0.379   7.1300   0.8067   2.0554
 S5D  HN2A  H  HNH2  0   0.388   7.9756  -0.6534   1.9517
 S5D  H23   H  HCR6  0   0.255   7.3576  -2.3909   0.3626
 S5D  H25   H  HCR6  0   0.243   3.7056  -1.6189  -1.7533
 S5D  H28   H  HCH2  0   0.242   3.6876   1.8735  -0.9344
 S5D  H28A  H  HCH2  0   0.247   2.7778   0.5369  -1.6273
 S5D  H29   H  HCH1  0   0.248   2.0369  -0.1138   0.6802
 S5D  HN29  H  HNH2  0   0.352   3.7255   1.0208   1.9063
 S5D  HN2B  H  HNH2  0   0.338   3.1288   2.4548   1.5118
 S5D  C27   C  CH3   0  -0.726   5.6266  -3.5401  -1.4153
 S5D  C18   C  CH2   0  -0.489  -3.2444   0.5581   0.6430
 S5D  C17   C  CH3   0  -0.726  -5.9954  -3.6273   1.1032
 S5D  H18   H  HCH2  0   0.247  -3.4452   1.5133   1.1355
 S5D  H18A  H  HCH2  0   0.246  -2.5601   0.0015   1.2869
 S5D  H27   H  HCH3  0   0.250   4.6830  -4.0770  -1.3138
 S5D  H27A  H  HCH3  0   0.253   5.8287  -3.4500  -2.4840
 S5D  H27B  H  HCH3  0   0.246   6.4151  -4.1492  -0.9761

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
 S5D  C1   C2    aromatic  1.394  0.020  1.394
 S5D  C1   C6    aromatic  1.390  0.020  1.390
 S5D  C2   C3    aromatic  1.391  0.020  1.391
 S5D  C2   C19   single    1.503  0.020  1.503
 S5D  C3   C4    aromatic  1.389  0.020  1.389
 S5D  C4   C5    aromatic  1.387  0.020  1.387
 S5D  C5   C6    aromatic  1.394  0.020  1.394
 S5D  C6   C29   single    1.512  0.020  1.512
 S5D  N11  C12   aromatic  1.328  0.020  1.328
 S5D  N11  C16   aromatic  1.335  0.020  1.335
 S5D  C12  N12   single    1.366  0.020  1.366
 S5D  C12  C13   aromatic  1.407  0.020  1.407
 S5D  C13  C14   aromatic  1.379  0.020  1.379
 S5D  C14  C15   aromatic  1.400  0.020  1.400
 S5D  C14  C17   single    1.498  0.020  1.498
 S5D  C15  C16   aromatic  1.382  0.020  1.382
 S5D  C16  C18   single    1.502  0.020  1.502
 S5D  C18  C19   single    1.536  0.020  1.536
 S5D  N21  C22   aromatic  1.330  0.020  1.330
 S5D  N21  C26   aromatic  1.337  0.020  1.337
 S5D  C22  N22   single    1.365  0.020  1.365
 S5D  C22  C23   aromatic  1.405  0.020  1.405
 S5D  C23  C24   aromatic  1.380  0.020  1.380
 S5D  C24  C25   aromatic  1.399  0.020  1.399
 S5D  C24  C27   single    1.498  0.020  1.498
 S5D  C25  C26   aromatic  1.384  0.020  1.384
 S5D  C26  C28   single    1.502  0.020  1.502
 S5D  C28  C29   single    1.548  0.020  1.548
 S5D  C29  N29   single    1.456  0.020  1.456
 S5D  C1   H1    single    0.930  0.020  1.080
 S5D  C3   H3    single    0.930  0.020  1.080
 S5D  C4   H4    single    0.930  0.020  1.080
 S5D  C5   H5    single    0.930  0.020  1.080
 S5D  N12  HN12  single    0.890  0.020  1.040
 S5D  N12  HN1A  single    0.890  0.020  1.040
 S5D  C13  H13   single    0.930  0.020  1.080
 S5D  C15  H15   single    0.930  0.020  1.080
 S5D  C17  H17   single    0.970  0.020  1.090
 S5D  C17  H17A  single    0.970  0.020  1.090
 S5D  C17  H17B  single    0.970  0.020  1.090
 S5D  C18  H18   single    0.970  0.020  1.090
 S5D  C18  H18A  single    0.970  0.020  1.090
 S5D  C19  H19   single    0.970  0.020  1.090
 S5D  C19  H19A  single    0.970  0.020  1.090
 S5D  N22  HN22  single    0.890  0.020  1.040
 S5D  N22  HN2A  single    0.890  0.020  1.040
 S5D  C23  H23   single    0.930  0.020  1.080
 S5D  C25  H25   single    0.930  0.020  1.080
 S5D  C27  H27   single    0.970  0.020  1.090
 S5D  C27  H27A  single    0.970  0.020  1.090
 S5D  C27  H27B  single    0.970  0.020  1.090
 S5D  C28  H28   single    0.970  0.020  1.090
 S5D  C28  H28A  single    0.970  0.020  1.090
 S5D  C29  H29   single    0.970  0.020  1.090
 S5D  N29  HN29  single    0.890  0.020  1.040
 S5D  N29  HN2B  single    0.890  0.020  1.040

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
 S5D  H1    C1   C6    119.07  3.000
 S5D  H1    C1   C2    118.98  3.000
 S5D  C6    C1   C2    121.95  3.000
 S5D  C19   C2   C3    121.12  3.000
 S5D  C19   C2   C1    120.34  3.000
 S5D  C3    C2   C1    118.50  3.000
 S5D  H3    C3   C4    119.95  3.000
 S5D  H3    C3   C2    119.71  3.000
 S5D  C4    C3   C2    120.34  3.000
 S5D  H4    C4   C5    119.75  3.000
 S5D  H4    C4   C3    119.88  3.000
 S5D  C5    C4   C3    120.37  3.000
 S5D  H5    C5   C6    120.72  3.000
 S5D  H5    C5   C4    118.94  3.000
 S5D  C6    C5   C4    120.34  3.000
 S5D  C29   C6   C5    121.10  3.000
 S5D  C29   C6   C1    120.40  3.000
 S5D  C5    C6   C1    118.50  3.000
 S5D  C16   N11  C12   118.70  3.000
 S5D  C13   C12  N12   120.58  3.000
 S5D  C13   C12  N11   122.31  3.000
 S5D  N12   C12  N11   117.07  3.000
 S5D  HN1A  N12  HN12  113.98  3.000
 S5D  HN1A  N12  C12   117.55  3.000
 S5D  HN12  N12  C12   116.11  3.000
 S5D  H13   C13  C14   120.87  3.000
 S5D  H13   C13  C12   120.07  3.000
 S5D  C14   C13  C12   119.06  3.000
 S5D  C17   C14  C15   120.50  3.000
 S5D  C17   C14  C13   121.43  3.000
 S5D  C15   C14  C13   118.07  3.000
 S5D  H15   C15  C16   120.30  3.000
 S5D  H15   C15  C14   120.63  3.000
 S5D  C16   C15  C14   119.07  3.000
 S5D  C18   C16  C15   121.17  3.000
 S5D  C18   C16  N11   116.04  3.000
 S5D  C15   C16  N11   122.78  3.000
 S5D  H19A  C19  H19   107.04  3.000
 S5D  H19A  C19  C18   109.03  3.000
 S5D  H19   C19  C18   108.96  3.000
 S5D  H19A  C19  C2    109.95  3.000
 S5D  H19   C19  C2    110.04  3.000
 S5D  C18   C19  C2    111.70  3.000
 S5D  C26   N21  C22   118.76  3.000
 S5D  C23   C22  N22   120.67  3.000
 S5D  C23   C22  N21   122.31  3.000
 S5D  N22   C22  N21   116.98  3.000
 S5D  HN2A  N22  HN22  114.24  3.000
 S5D  HN2A  N22  C22   117.66  3.000
 S5D  HN22  N22  C22   116.26  3.000
 S5D  H23   C23  C24   120.80  3.000
 S5D  H23   C23  C22   120.12  3.000
 S5D  C24   C23  C22   119.08  3.000
 S5D  C27   C24  C25   120.62  3.000
 S5D  C27   C24  C23   121.27  3.000
 S5D  C25   C24  C23   118.11  3.000
 S5D  H25   C25  C26   120.16  3.000
 S5D  H25   C25  C24   120.67  3.000
 S5D  C26   C25  C24   119.17  3.000
 S5D  C28   C26  C25   120.44  3.000
 S5D  C28   C26  N21   116.94  3.000
 S5D  C25   C26  N21   122.58  3.000
 S5D  H28A  C28  H28   107.18  3.000
 S5D  H28A  C28  C29   108.88  3.000
 S5D  H28   C28  C29   109.14  3.000
 S5D  H28A  C28  C26   109.05  3.000
 S5D  H28   C28  C26   110.00  3.000
 S5D  C29   C28  C26   112.46  3.000
 S5D  H29   C29  N29   107.02  3.000
 S5D  H29   C29  C28   107.02  3.000
 S5D  N29   C29  C28   115.06  3.000
 S5D  H29   C29  C6    107.42  3.000
 S5D  N29   C29  C6    110.11  3.000
 S5D  C28   C29  C6    109.85  3.000
 S5D  HN2B  N29  HN29  104.42  3.000
 S5D  HN2B  N29  C29   109.49  3.000
 S5D  HN29  N29  C29   108.71  3.000
 S5D  H27B  C27  H27A  107.88  3.000
 S5D  H27B  C27  H27   108.28  3.000
 S5D  H27A  C27  H27   106.98  3.000
 S5D  H27B  C27  C24   111.77  3.000
 S5D  H27A  C27  C24   110.54  3.000
 S5D  H27   C27  C24   111.21  3.000
 S5D  H18A  C18  H18   107.14  3.000
 S5D  H18A  C18  C19   109.46  3.000
 S5D  H18   C18  C19   109.02  3.000
 S5D  H18A  C18  C16   109.93  3.000
 S5D  H18   C18  C16   109.34  3.000
 S5D  C19   C18  C16   111.84  3.000
 S5D  H17B  C17  H17A  108.10  3.000
 S5D  H17B  C17  H17   108.15  3.000
 S5D  H17A  C17  H17   106.92  3.000
 S5D  H17B  C17  C14   111.84  3.000
 S5D  H17A  C17  C14   110.78  3.000
 S5D  H17   C17  C14   110.86  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
 S5D  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 S5D  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 S5D  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 S5D  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 S5D  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 S5D  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 S5D  CONST_07  C14  C13  C12  N11    0.00   0.0  0
 S5D  CONST_08  C14  C15  C16  N11    0.00   0.0  0
 S5D  CONST_09  C15  C16  N11  C12    0.00   0.0  0
 S5D  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 S5D  CONST_11  C16  N11  C12  C13    0.00   0.0  0
 S5D  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 S5D  CONST_13  C24  C23  C22  N21    0.00   0.0  0
 S5D  CONST_14  C24  C25  C26  N21    0.00   0.0  0
 S5D  CONST_15  C25  C26  N21  C22    0.00   0.0  0
 S5D  CONST_16  C25  C24  C23  C22    0.00   0.0  0
 S5D  CONST_17  C26  N21  C22  C23    0.00   0.0  0
 S5D  CONST_18  C26  C25  C24  C23    0.00   0.0  0
 S5D  CONST_19  C29  C6   C1   C2   180.00   0.0  0
 S5D  CONST_20  C19  C2   C3   C4   180.00   0.0  0
 S5D  CONST_21  C29  C6   C5   C4   180.00   0.0  0
 S5D  CONST_22  C19  C2   C1   C6   180.00   0.0  0
 S5D  CONST_23  C18  C16  N11  C12  180.00   0.0  0
 S5D  CONST_24  C17  C14  C13  C12  180.00   0.0  0
 S5D  CONST_25  C16  N11  C12  N12  180.00   0.0  0
 S5D  CONST_26  C14  C13  C12  N12  180.00   0.0  0
 S5D  CONST_27  C18  C16  C15  C14  180.00   0.0  0
 S5D  CONST_28  C17  C14  C15  C16  180.00   0.0  0
 S5D  CONST_29  C28  C26  N21  C22  180.00   0.0  0
 S5D  CONST_30  C27  C24  C23  C22  180.00   0.0  0
 S5D  CONST_31  C26  N21  C22  N22  180.00   0.0  0
 S5D  CONST_32  C24  C23  C22  N22  180.00   0.0  0
 S5D  CONST_33  C28  C26  C25  C24  180.00   0.0  0
 S5D  CONST_34  C27  C24  C25  C26  180.00   0.0  0
 S5D  CONST_35  H3   C3   C2   C1   180.00   0.0  0
 S5D  CONST_36  H5   C5   C6   C1   180.00   0.0  0
 S5D  CONST_37  H4   C4   C3   C2   180.00   0.0  0
 S5D  CONST_38  H1   C1   C2   C3   180.00   0.0  0
 S5D  CONST_39  H13  C13  C12  N11  180.00   0.0  0
 S5D  CONST_40  H15  C15  C16  N11  180.00   0.0  0
 S5D  CONST_41  H23  C23  C22  N21  180.00   0.0  0
 S5D  CONST_42  H25  C25  C26  N21  180.00   0.0  0
 S5D  Var_01    C18  C19  C2   C1    79.55  30.0  2
 S5D  Var_02    C16  C18  C19  C2   179.11  30.0  1
 S5D  Var_03    C19  C18  C16  N11  -69.66  30.0  2
 S5D  Var_04    C29  C28  C26  N21  -74.66  30.0  2
 S5D  Var_05    H17  C17  C14  C13  120.44  30.0  2
 S5D  Var_06    H27  C27  C24  C23  130.47  30.0  2

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
 S5D  chir_01  C29  C6  C28  N29  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
 S5D  plan-1  C1    0.020
 S5D  plan-1  C2    0.020
 S5D  plan-1  C3    0.020
 S5D  plan-1  C4    0.020
 S5D  plan-1  C5    0.020
 S5D  plan-1  C6    0.020
 S5D  plan-1  C19   0.020
 S5D  plan-1  C29   0.020
 S5D  plan-1  H1    0.020
 S5D  plan-1  H3    0.020
 S5D  plan-1  H4    0.020
 S5D  plan-1  H5    0.020
 S5D  plan-2  N11   0.020
 S5D  plan-2  C12   0.020
 S5D  plan-2  N12   0.020
 S5D  plan-2  C13   0.020
 S5D  plan-2  C14   0.020
 S5D  plan-2  C15   0.020
 S5D  plan-2  C16   0.020
 S5D  plan-2  H13   0.020
 S5D  plan-2  H15   0.020
 S5D  plan-2  C18   0.020
 S5D  plan-2  C17   0.020
 S5D  plan-3  N21   0.020
 S5D  plan-3  C22   0.020
 S5D  plan-3  N22   0.020
 S5D  plan-3  C23   0.020
 S5D  plan-3  C24   0.020
 S5D  plan-3  C25   0.020
 S5D  plan-3  C26   0.020
 S5D  plan-3  C28   0.020
 S5D  plan-3  H23   0.020
 S5D  plan-3  H25   0.020
 S5D  plan-3  C27   0.020
 S5D  plan-4  C12   0.020
 S5D  plan-4  N12   0.020
 S5D  plan-4  HN12  0.020
 S5D  plan-4  HN1A  0.020
 S5D  plan-5  C22   0.020
 S5D  plan-5  N22   0.020
 S5D  plan-5  HN22  0.020
 S5D  plan-5  HN2A  0.020

