# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:20:03 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 6-[(2R)-3-amino-2-{3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]phenyl}propyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cccc(c2)[C@H](CN)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
 S42  S42  6-[(2R)-3-amino-2-{3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]phenyl}propyl]-4-methylpyridin-2-amine  ligand  57  28  .  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_S42
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
 S42  N01   N  N     0  -0.482  -4.4670   1.5447  -0.2802
 S42  C02   C  CR6   0   0.438  -5.5963   2.1632  -0.6086
 S42  N02   N  NH2   0  -0.838  -5.4949   3.2281  -1.4592
 S42  C03   C  CR16  0  -0.444  -6.8412   1.7860  -0.0773
 S42  C04   C  CR6   0   0.202  -6.8989   0.7333   0.8140
 S42  C05   C  CR16  0  -0.432  -5.7022   0.0954   1.1578
 S42  C06   C  CR6   0   0.271  -4.5193   0.5331   0.5885
 S42  C07   C  CH3   0  -0.725  -8.2049   0.2652   1.3800
 S42  C08   C  CH2   0  -0.489  -3.2140  -0.1448   0.8911
 S42  C09   C  CH2   0  -0.510  -2.7766  -1.0733  -0.2520
 S42  C11   C  CR6   0   0.152  -1.4585  -1.7299   0.0469
 S42  C12   C  CR16  0  -0.331  -1.4055  -2.9559   0.7021
 S42  C13   C  CR16  0  -0.225  -0.1813  -3.5299   1.0196
 S42  C14   C  CR16  0  -0.326   1.0010  -2.8844   0.6893
 S42  C15   C  CR6   0   0.176   0.9750  -1.6540   0.0332
 S42  C16   C  CR16  0  -0.391  -0.2604  -1.0975  -0.2804
 S42  N21   N  N     0  -0.481   5.4170  -0.2388   0.7255
 S42  C22   C  CR6   0   0.439   6.4884   0.5083   0.4680
 S42  N22   N  NH2   0  -0.839   7.7069  -0.1005   0.5824
 S42  C23   C  CR16  0  -0.443   6.3946   1.8698   0.1423
 S42  C24   C  CR6   0   0.202   5.1469   2.4618   0.0856
 S42  C25   C  CR16  0  -0.418   4.0312   1.6693   0.3629
 S42  C26   C  CR6   0   0.268   4.2134   0.3309   0.6733
 S42  C28   C  CH2   0  -0.494   3.0256  -0.5484   0.9493
 S42  C29   C  CH1   0  -0.329   2.2546  -0.9346  -0.3254
 S42  C30   C  CH2   0  -0.268   3.1138  -1.7629  -1.2812
 S42  N31   N  NH2   0  -0.797   2.3911  -2.0457  -2.5101
 S42  HN02  H  HNH2  0   0.379  -4.6501   3.2736  -2.0056
 S42  HN0A  H  HNH2  0   0.387  -6.3218   3.4936  -1.9678
 S42  H03   H  HCR6  0   0.254  -7.7390   2.3193  -0.3667
 S42  H05   H  HCR6  0   0.243  -5.6982  -0.7301   1.8585
 S42  H07   H  HCH3  0   0.255  -8.5493  -0.6243   0.8491
 S42  H07A  H  HCH3  0   0.248  -8.1081  -0.0060   2.4312
 S42  H07B  H  HCH3  0   0.247  -8.9805   1.0240   1.2901
 S42  H08   H  HCH2  0   0.247  -2.4419   0.6121   1.0502
 S42  H08A  H  HCH2  0   0.246  -3.2946  -0.7239   1.8133
 S42  H09   H  HCH2  0   0.248  -3.5455  -1.8340  -0.4079
 S42  H09A  H  HCH2  0   0.248  -2.7101  -0.4934  -1.1753
 S42  H12   H  HCR6  0   0.243  -2.3264  -3.4650   0.9626
 S42  H13   H  HCR6  0   0.250  -0.1492  -4.4863   1.5264
 S42  H14   H  HCR6  0   0.247   1.9478  -3.3465   0.9430
 S42  H16   H  HCR6  0   0.237  -0.2913  -0.1420  -0.7950
 S42  HN22  H  HNH2  0   0.378   7.7024  -1.1064   0.5330
 S42  HN2A  H  HNH2  0   0.386   8.4813   0.3255   0.1011
 S42  H23   H  HCR6  0   0.254   7.2920   2.4439  -0.0569
 S42  H25   H  HCR6  0   0.241   3.0334   2.0906   0.3385
 S42  H27   H  HCH3  0   0.255   4.7287   4.0070  -1.3353
 S42  H27A  H  HCH3  0   0.248   4.1884   4.3733   0.2937
 S42  H27B  H  HCH3  0   0.247   5.9058   4.4685  -0.1117
 S42  H28   H  HCH2  0   0.243   3.3632  -1.4485   1.4685
 S42  H28A  H  HCH2  0   0.254   2.3386  -0.0278   1.6210
 S42  H29   H  HCH1  0   0.245   1.9804  -0.0137  -0.8507
 S42  H30   H  HCH2  0   0.232   4.0087  -1.1922  -1.5386
 S42  H30A  H  HCH2  0   0.190   3.4684  -2.6622  -0.7558
 S42  HN31  H  HNH2  0   0.348   2.9974  -2.5464  -3.1469
 S42  HN3A  H  HNH2  0   0.341   1.6211  -2.6742  -2.3152
 S42  C27   C  CH3   0  -0.726   4.9886   3.9060  -0.2797

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
 S42  N01  C02   aromatic  1.329  0.020  1.329
 S42  N01  C06   aromatic  1.334  0.020  1.334
 S42  C02  N02   single    1.367  0.020  1.367
 S42  C02  C03   aromatic  1.405  0.020  1.405
 S42  C03  C04   aromatic  1.380  0.020  1.380
 S42  C04  C05   aromatic  1.399  0.020  1.399
 S42  C04  C07   single    1.498  0.020  1.498
 S42  C05  C06   aromatic  1.384  0.020  1.384
 S42  C06  C08   single    1.502  0.020  1.502
 S42  C08  C09   single    1.536  0.020  1.536
 S42  C09  C11   single    1.503  0.020  1.503
 S42  C11  C12   aromatic  1.391  0.020  1.391
 S42  C11  C16   aromatic  1.394  0.020  1.394
 S42  C12  C13   aromatic  1.389  0.020  1.389
 S42  C13  C14   aromatic  1.387  0.020  1.387
 S42  C14  C15   aromatic  1.395  0.020  1.395
 S42  C15  C16   aromatic  1.391  0.020  1.391
 S42  C15  C29   single    1.511  0.020  1.511
 S42  N21  C22   aromatic  1.331  0.020  1.331
 S42  N21  C26   aromatic  1.333  0.020  1.333
 S42  C22  N22   single    1.367  0.020  1.367
 S42  C22  C23   aromatic  1.403  0.020  1.403
 S42  C23  C24   aromatic  1.382  0.020  1.382
 S42  C24  C25   aromatic  1.396  0.020  1.396
 S42  C24  C27   single    1.498  0.020  1.498
 S42  C25  C26   aromatic  1.386  0.020  1.386
 S42  C26  C28   single    1.504  0.020  1.504
 S42  C28  C29   single    1.539  0.020  1.539
 S42  C29  C30   single    1.529  0.020  1.529
 S42  C30  N31   single    1.453  0.020  1.453
 S42  N02  HN02  single    0.890  0.020  1.040
 S42  N02  HN0A  single    0.890  0.020  1.040
 S42  C03  H03   single    0.930  0.020  1.080
 S42  C05  H05   single    0.930  0.020  1.080
 S42  C07  H07   single    0.970  0.020  1.090
 S42  C07  H07A  single    0.970  0.020  1.090
 S42  C07  H07B  single    0.970  0.020  1.090
 S42  C08  H08   single    0.970  0.020  1.090
 S42  C08  H08A  single    0.970  0.020  1.090
 S42  C09  H09   single    0.970  0.020  1.090
 S42  C09  H09A  single    0.970  0.020  1.090
 S42  C12  H12   single    0.930  0.020  1.080
 S42  C13  H13   single    0.930  0.020  1.080
 S42  C14  H14   single    0.930  0.020  1.080
 S42  C16  H16   single    0.930  0.020  1.080
 S42  N22  HN22  single    0.890  0.020  1.040
 S42  N22  HN2A  single    0.890  0.020  1.040
 S42  C23  H23   single    0.930  0.020  1.080
 S42  C25  H25   single    0.930  0.020  1.080
 S42  C27  H27   single    0.970  0.020  1.090
 S42  C27  H27A  single    0.970  0.020  1.090
 S42  C27  H27B  single    0.970  0.020  1.090
 S42  C28  H28   single    0.970  0.020  1.090
 S42  C28  H28A  single    0.970  0.020  1.090
 S42  C29  H29   single    0.970  0.020  1.090
 S42  C30  H30   single    0.970  0.020  1.090
 S42  C30  H30A  single    0.970  0.020  1.090
 S42  N31  HN31  single    0.890  0.020  1.040
 S42  N31  HN3A  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
 S42  C06   N01  C02   118.71  3.000
 S42  C03   C02  N02   120.68  3.000
 S42  C03   C02  N01   122.31  3.000
 S42  N02   C02  N01   116.97  3.000
 S42  HN0A  N02  HN02  113.77  3.000
 S42  HN0A  N02  C02   117.33  3.000
 S42  HN02  N02  C02   115.79  3.000
 S42  H03   C03  C04   120.87  3.000
 S42  H03   C03  C02   120.06  3.000
 S42  C04   C03  C02   119.07  3.000
 S42  C07   C04  C05   120.68  3.000
 S42  C07   C04  C03   121.24  3.000
 S42  C05   C04  C03   118.07  3.000
 S42  H05   C05  C06   120.28  3.000
 S42  H05   C05  C04   120.65  3.000
 S42  C06   C05  C04   119.07  3.000
 S42  C08   C06  C05   121.15  3.000
 S42  C08   C06  N01   116.06  3.000
 S42  C05   C06  N01   122.76  3.000
 S42  H07B  C07  H07A  108.45  3.000
 S42  H07B  C07  H07   107.63  3.000
 S42  H07A  C07  H07   107.11  3.000
 S42  H07B  C07  C04   111.83  3.000
 S42  H07A  C07  C04   111.39  3.000
 S42  H07   C07  C04   110.23  3.000
 S42  H08A  C08  H08   107.25  3.000
 S42  H08A  C08  C09   109.20  3.000
 S42  H08   C08  C09   109.01  3.000
 S42  H08A  C08  C06   110.21  3.000
 S42  H08   C08  C06   109.32  3.000
 S42  C09   C08  C06   111.74  3.000
 S42  H09A  C09  H09   106.97  3.000
 S42  H09A  C09  C11   110.29  3.000
 S42  H09   C09  C11   109.97  3.000
 S42  H09A  C09  C08   108.99  3.000
 S42  H09   C09  C08   109.06  3.000
 S42  C11   C09  C08   111.46  3.000
 S42  C16   C11  C12   118.54  3.000
 S42  C16   C11  C09   120.61  3.000
 S42  C12   C11  C09   120.81  3.000
 S42  H12   C12  C13   119.99  3.000
 S42  H12   C12  C11   119.65  3.000
 S42  C13   C12  C11   120.36  3.000
 S42  H13   C13  C14   119.82  3.000
 S42  H13   C13  C12   119.87  3.000
 S42  C14   C13  C12   120.30  3.000
 S42  H14   C14  C15   120.17  3.000
 S42  H14   C14  C13   119.38  3.000
 S42  C15   C14  C13   120.45  3.000
 S42  C29   C15  C16   120.54  3.000
 S42  C29   C15  C14   121.06  3.000
 S42  C16   C15  C14   118.40  3.000
 S42  H16   C16  C15   118.97  3.000
 S42  H16   C16  C11   119.09  3.000
 S42  C15   C16  C11   121.94  3.000
 S42  C26   N21  C22   118.64  3.000
 S42  C23   C22  N22   120.74  3.000
 S42  C23   C22  N21   122.39  3.000
 S42  N22   C22  N21   116.82  3.000
 S42  HN2A  N22  HN22  113.76  3.000
 S42  HN2A  N22  C22   117.22  3.000
 S42  HN22  N22  C22   115.89  3.000
 S42  H23   C23  C24   120.87  3.000
 S42  H23   C23  C22   120.09  3.000
 S42  C24   C23  C22   119.04  3.000
 S42  C27   C24  C25   120.74  3.000
 S42  C27   C24  C23   121.22  3.000
 S42  C25   C24  C23   118.04  3.000
 S42  H25   C25  C26   120.12  3.000
 S42  H25   C25  C24   120.71  3.000
 S42  C26   C25  C24   119.17  3.000
 S42  C28   C26  C25   120.13  3.000
 S42  C28   C26  N21   117.15  3.000
 S42  C25   C26  N21   122.72  3.000
 S42  H28A  C28  H28   107.14  3.000
 S42  H28A  C28  C29   108.29  3.000
 S42  H28   C28  C29   109.98  3.000
 S42  H28A  C28  C26   109.32  3.000
 S42  H28   C28  C26   108.96  3.000
 S42  C29   C28  C26   112.98  3.000
 S42  H29   C29  C30   107.25  3.000
 S42  H29   C29  C28   108.17  3.000
 S42  C30   C29  C28   111.85  3.000
 S42  H29   C29  C15   107.58  3.000
 S42  C30   C29  C15   111.49  3.000
 S42  C28   C29  C15   110.31  3.000
 S42  H30A  C30  H30   105.99  3.000
 S42  H30A  C30  N31   113.89  3.000
 S42  H30   C30  N31   108.05  3.000
 S42  H30A  C30  C29   108.99  3.000
 S42  H30   C30  C29   108.95  3.000
 S42  N31   C30  C29   110.76  3.000
 S42  HN3A  N31  HN31  105.64  3.000
 S42  HN3A  N31  C30   109.63  3.000
 S42  HN31  N31  C30   109.29  3.000
 S42  H27B  C27  H27A  108.41  3.000
 S42  H27B  C27  H27   107.57  3.000
 S42  H27A  C27  H27   107.12  3.000
 S42  H27B  C27  C24   111.80  3.000
 S42  H27A  C27  C24   111.26  3.000
 S42  H27   C27  C24   110.49  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
 S42  CONST_01  C04   C03  C02  N01     0.00   0.0  0
 S42  CONST_02  C04   C05  C06  N01     0.00   0.0  0
 S42  CONST_03  C05   C06  N01  C02     0.00   0.0  0
 S42  CONST_04  C05   C04  C03  C02     0.00   0.0  0
 S42  CONST_05  C06   N01  C02  C03     0.00   0.0  0
 S42  CONST_06  C06   C05  C04  C03     0.00   0.0  0
 S42  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 S42  CONST_08  C14   C15  C16  C11     0.00   0.0  0
 S42  CONST_09  C15   C16  C11  C12     0.00   0.0  0
 S42  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 S42  CONST_11  C16   C11  C12  C13     0.00   0.0  0
 S42  CONST_12  C16   C15  C14  C13     0.00   0.0  0
 S42  CONST_13  C24   C23  C22  N21     0.00   0.0  0
 S42  CONST_14  C24   C25  C26  N21     0.00   0.0  0
 S42  CONST_15  C25   C26  N21  C22     0.00   0.0  0
 S42  CONST_16  C25   C24  C23  C22     0.00   0.0  0
 S42  CONST_17  C26   N21  C22  C23     0.00   0.0  0
 S42  CONST_18  C26   C25  C24  C23     0.00   0.0  0
 S42  CONST_19  C08   C06  N01  C02   180.00   0.0  0
 S42  CONST_20  C07   C04  C03  C02   180.00   0.0  0
 S42  CONST_21  C06   N01  C02  N02   180.00   0.0  0
 S42  CONST_22  C04   C03  C02  N02   180.00   0.0  0
 S42  CONST_23  C08   C06  C05  C04   180.00   0.0  0
 S42  CONST_24  C07   C04  C05  C06   180.00   0.0  0
 S42  CONST_25  C13   C12  C11  C09   180.00   0.0  0
 S42  CONST_26  C15   C16  C11  C09   180.00   0.0  0
 S42  CONST_27  C29   C15  C16  C11   180.00   0.0  0
 S42  CONST_28  C29   C15  C14  C13   180.00   0.0  0
 S42  CONST_29  C28   C26  N21  C22   180.00   0.0  0
 S42  CONST_30  C27   C24  C23  C22   180.00   0.0  0
 S42  CONST_31  C26   N21  C22  N22   180.00   0.0  0
 S42  CONST_32  C24   C23  C22  N22   180.00   0.0  0
 S42  CONST_33  C28   C26  C25  C24   180.00   0.0  0
 S42  CONST_34  C27   C24  C25  C26   180.00   0.0  0
 S42  CONST_35  H03   C03  C02  N01   180.00   0.0  0
 S42  CONST_36  H05   C05  C06  N01   180.00   0.0  0
 S42  CONST_37  H13   C13  C12  C11   180.00   0.0  0
 S42  CONST_38  H16   C16  C11  C12   180.00   0.0  0
 S42  CONST_39  H14   C14  C13  C12   180.00   0.0  0
 S42  CONST_40  H12   C12  C13  C14   180.00   0.0  0
 S42  CONST_41  H23   C23  C22  N21   180.00   0.0  0
 S42  CONST_42  H25   C25  C26  N21   180.00   0.0  0
 S42  Var_01    C09   C08  C06  N01   -76.12  30.0  2
 S42  Var_02    C11   C09  C08  C06   179.01  30.0  3
 S42  Var_03    C12   C11  C09  C08    90.41  30.0  2
 S42  Var_04    C29   C28  C26  N21  -104.09  30.0  2
 S42  Var_05    H07   C07  C04  C03   100.13  30.0  2
 S42  Var_06    H27   C27  C24  C23    98.09  30.0  2
 S42  Var_07    HN31  N31  C30  C29   176.69  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
 S42  chir_01  C29  C15  C28  C30  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
 S42  plan-1  N01   0.020
 S42  plan-1  C02   0.020
 S42  plan-1  N02   0.020
 S42  plan-1  C03   0.020
 S42  plan-1  C04   0.020
 S42  plan-1  C05   0.020
 S42  plan-1  C06   0.020
 S42  plan-1  C07   0.020
 S42  plan-1  C08   0.020
 S42  plan-1  H03   0.020
 S42  plan-1  H05   0.020
 S42  plan-2  C09   0.020
 S42  plan-2  C11   0.020
 S42  plan-2  C12   0.020
 S42  plan-2  C13   0.020
 S42  plan-2  C14   0.020
 S42  plan-2  C15   0.020
 S42  plan-2  C16   0.020
 S42  plan-2  C29   0.020
 S42  plan-2  H12   0.020
 S42  plan-2  H13   0.020
 S42  plan-2  H14   0.020
 S42  plan-2  H16   0.020
 S42  plan-3  N21   0.020
 S42  plan-3  C22   0.020
 S42  plan-3  N22   0.020
 S42  plan-3  C23   0.020
 S42  plan-3  C24   0.020
 S42  plan-3  C25   0.020
 S42  plan-3  C26   0.020
 S42  plan-3  C28   0.020
 S42  plan-3  H23   0.020
 S42  plan-3  H25   0.020
 S42  plan-3  C27   0.020
 S42  plan-4  C02   0.020
 S42  plan-4  N02   0.020
 S42  plan-4  HN02  0.020
 S42  plan-4  HN0A  0.020
 S42  plan-5  C22   0.020
 S42  plan-5  N22   0.020
 S42  plan-5  HN22  0.020
 S42  plan-5  HN2A  0.020

