# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 04:48:43 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 6-[(2S)-2-amino-2-{3-[2-(4-methylpyridin-2-yl)ethyl]phenyl}ethyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccnc(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
 S7K  S7K  6-[(2S)-2-amino-2-{3-[2-(4-methylpyridin-2-yl)ethyl]phenyl}ethyl]-4-methylpyridin-2-amine  ligand  52  26  .  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_S7K
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
 S7K  C1    C  CR16  0  -0.381  -0.4601   1.2708  -0.6180
 S7K  C2    C  CR6   0   0.157  -1.6558   1.9424  -0.3715
 S7K  C3    C  CR16  0  -0.338  -1.5991   3.2755   0.0234
 S7K  C4    C  CR16  0  -0.221  -0.3740   3.9151   0.1615
 S7K  C5    C  CR16  0  -0.345   0.8060   3.2310  -0.0902
 S7K  C6    C  CR6   0   0.177   0.7750   1.8946  -0.4822
 S7K  N11   N  N     0  -0.430  -5.6699   0.4052   0.8444
 S7K  C12   C  CR16  0  -0.076  -6.8640  -0.1577   0.7053
 S7K  C13   C  CR16  0  -0.372  -7.0548  -1.4718   0.3129
 S7K  C14   C  CR6   0   0.194  -5.9423  -2.2642   0.0454
 S7K  C15   C  CR16  0  -0.392  -4.6940  -1.6704   0.1969
 S7K  C16   C  CR6   0   0.261  -4.5953  -0.3407   0.5937
 S7K  C19   C  CH2   0  -0.511  -2.9720   1.2278  -0.4978
 S7K  N21   N  N     0  -0.489   3.5466  -1.4780  -0.1463
 S7K  C22   C  CR6   0   0.434   4.5660  -2.3118  -0.3170
 S7K  N22   N  NH2   0  -0.838   4.3151  -3.4714  -0.9969
 S7K  C23   C  CR16  0  -0.449   5.8631  -2.0160   0.1370
 S7K  C24   C  CR6   0   0.203   6.0914  -0.8152   0.7772
 S7K  C25   C  CR16  0  -0.436   5.0104   0.0572   0.9439
 S7K  C26   C  CR6   0   0.310   3.7665  -0.3145   0.4692
 S7K  C28   C  CH2   0  -0.503   2.5733   0.5826   0.6271
 S7K  C29   C  CH1   0  -0.174   2.0509   1.1072  -0.7164
 S7K  N29   N  NH2   0  -0.781   3.1143   1.8161  -1.4034
 S7K  H1    H  HCR6  0   0.237  -0.4925   0.2309  -0.9302
 S7K  H3    H  HCR6  0   0.244  -2.5176   3.8175   0.2163
 S7K  H4    H  HCR6  0   0.251  -0.3400   4.9544   0.4632
 S7K  H5    H  HCR6  0   0.237   1.7519   3.7488   0.0189
 S7K  H12   H  HCR6  0   0.257  -7.7213   0.4707   0.9227
 S7K  H13   H  HCR6  0   0.259  -8.0578  -1.8681   0.2199
 S7K  H15   H  HCR6  0   0.255  -3.7913  -2.2407   0.0109
 S7K  H17   H  HCH3  0   0.258  -6.2265  -3.7287  -1.4868
 S7K  H17A  H  HCH3  0   0.249  -5.1968  -4.2704  -0.1687
 S7K  H17B  H  HCH3  0   0.251  -6.9471  -4.1649   0.0550
 S7K  H19   H  HCH2  0   0.250  -3.7805   1.9548  -0.6033
 S7K  H19A  H  HCH2  0   0.249  -2.9781   0.6132  -1.4021
 S7K  H23   H  HCR6  0   0.254   6.6661  -2.7275  -0.0145
 S7K  H25   H  HCR6  0   0.240   5.1412   1.0096   1.4425
 S7K  H28   H  HCH2  0   0.256   1.7701   0.0332   1.1246
 S7K  H28A  H  HCH2  0   0.245   2.8231   1.4288   1.2739
 S7K  H29   H  HCH1  0   0.244   1.7919   0.2364  -1.3273
 S7K  HN29  H  HNH2  0   0.348   2.7645   2.2175  -2.2645
 S7K  HN2B  H  HNH2  0   0.343   3.4484   2.5916  -0.8434
 S7K  HN22  H  HNH2  0   0.378   3.3483  -3.7496  -1.0433
 S7K  HN23  H  HNH2  0   0.386   4.9480  -4.2391  -0.8449
 S7K  C27   C  CH3   0  -0.727   7.4555  -0.4382   1.2687
 S7K  C18   C  CH2   0  -0.490  -3.2597   0.3340   0.7171
 S7K  C17   C  CH3   0  -0.722  -6.0840  -3.6849  -0.4051
 S7K  H18   H  HCH2  0   0.251  -3.2435   0.9441   1.6234
 S7K  H18A  H  HCH2  0   0.249  -2.4693  -0.4136   0.8153
 S7K  H27   H  HCH3  0   0.253   7.8565   0.3904   0.6826
 S7K  H27A  H  HCH3  0   0.249   7.4204  -0.1064   2.3068
 S7K  H27B  H  HCH3  0   0.246   8.1565  -1.2679   1.1980

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
 S7K  C1   C2    aromatic  1.393  0.020  1.393
 S7K  C1   C6    aromatic  1.390  0.020  1.390
 S7K  C2   C3    aromatic  1.391  0.020  1.391
 S7K  C2   C19   single    1.503  0.020  1.503
 S7K  C3   C4    aromatic  1.389  0.020  1.389
 S7K  C4   C5    aromatic  1.387  0.020  1.387
 S7K  C5   C6    aromatic  1.393  0.020  1.393
 S7K  C6   C29   single    1.518  0.020  1.518
 S7K  N11  C12   aromatic  1.327  0.020  1.327
 S7K  N11  C16   aromatic  1.332  0.020  1.332
 S7K  C12  C13   aromatic  1.385  0.020  1.385
 S7K  C13  C14   aromatic  1.392  0.020  1.392
 S7K  C14  C15   aromatic  1.391  0.020  1.391
 S7K  C14  C17   single    1.497  0.020  1.497
 S7K  C15  C16   aromatic  1.391  0.020  1.391
 S7K  C16  C18   single    1.501  0.020  1.501
 S7K  C18  C19   single    1.536  0.020  1.536
 S7K  N21  C22   aromatic  1.328  0.020  1.328
 S7K  N21  C26   aromatic  1.335  0.020  1.335
 S7K  C22  N22   single    1.367  0.020  1.367
 S7K  C22  C23   aromatic  1.406  0.020  1.406
 S7K  C23  C24   aromatic  1.380  0.020  1.380
 S7K  C24  C25   aromatic  1.399  0.020  1.399
 S7K  C24  C27   single    1.498  0.020  1.498
 S7K  C25  C26   aromatic  1.382  0.020  1.382
 S7K  C26  C28   single    1.501  0.020  1.501
 S7K  C28  C29   single    1.534  0.020  1.534
 S7K  C29  N29   single    1.451  0.020  1.451
 S7K  C1   H1    single    0.930  0.020  1.080
 S7K  C3   H3    single    0.930  0.020  1.080
 S7K  C4   H4    single    0.930  0.020  1.080
 S7K  C5   H5    single    0.930  0.020  1.080
 S7K  C12  H12   single    0.930  0.020  1.080
 S7K  C13  H13   single    0.930  0.020  1.080
 S7K  C15  H15   single    0.930  0.020  1.080
 S7K  C17  H17   single    0.970  0.020  1.090
 S7K  C17  H17A  single    0.970  0.020  1.090
 S7K  C17  H17B  single    0.970  0.020  1.090
 S7K  C18  H18   single    0.970  0.020  1.090
 S7K  C18  H18A  single    0.970  0.020  1.090
 S7K  C19  H19   single    0.970  0.020  1.090
 S7K  C19  H19A  single    0.970  0.020  1.090
 S7K  C23  H23   single    0.930  0.020  1.080
 S7K  C25  H25   single    0.930  0.020  1.080
 S7K  C27  H27   single    0.970  0.020  1.090
 S7K  C27  H27A  single    0.970  0.020  1.090
 S7K  C27  H27B  single    0.970  0.020  1.090
 S7K  C28  H28   single    0.970  0.020  1.090
 S7K  C28  H28A  single    0.970  0.020  1.090
 S7K  C29  H29   single    0.970  0.020  1.090
 S7K  N29  HN29  single    0.890  0.020  1.040
 S7K  N29  HN2B  single    0.890  0.020  1.040
 S7K  N22  HN22  single    0.890  0.020  1.040
 S7K  N22  HN23  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
 S7K  H1    C1   C6    118.95  3.000
 S7K  H1    C1   C2    119.12  3.000
 S7K  C6    C1   C2    121.92  3.000
 S7K  C19   C2   C3    121.00  3.000
 S7K  C19   C2   C1    120.49  3.000
 S7K  C3    C2   C1    118.49  3.000
 S7K  H3    C3   C4    119.97  3.000
 S7K  H3    C3   C2    119.67  3.000
 S7K  C4    C3   C2    120.35  3.000
 S7K  H4    C4   C5    119.82  3.000
 S7K  H4    C4   C3    119.83  3.000
 S7K  C5    C4   C3    120.35  3.000
 S7K  H5    C5   C6    120.40  3.000
 S7K  H5    C5   C4    119.25  3.000
 S7K  C6    C5   C4    120.35  3.000
 S7K  C29   C6   C5    121.50  3.000
 S7K  C29   C6   C1    119.94  3.000
 S7K  C5    C6   C1    118.53  3.000
 S7K  C16   N11  C12   117.94  3.000
 S7K  H12   C12  C13   119.84  3.000
 S7K  H12   C12  N11   116.37  3.000
 S7K  C13   C12  N11   123.79  3.000
 S7K  H13   C13  C14   121.05  3.000
 S7K  H13   C13  C12   119.97  3.000
 S7K  C14   C13  C12   118.99  3.000
 S7K  C17   C14  C15   121.53  3.000
 S7K  C17   C14  C13   121.49  3.000
 S7K  C15   C14  C13   116.97  3.000
 S7K  H15   C15  C16   119.52  3.000
 S7K  H15   C15  C14   120.29  3.000
 S7K  C16   C15  C14   120.19  3.000
 S7K  C18   C16  C15   121.07  3.000
 S7K  C18   C16  N11   116.78  3.000
 S7K  C15   C16  N11   122.12  3.000
 S7K  H19A  C19  H19   106.86  3.000
 S7K  H19A  C19  C18   109.04  3.000
 S7K  H19   C19  C18   108.97  3.000
 S7K  H19A  C19  C2    109.98  3.000
 S7K  H19   C19  C2    109.87  3.000
 S7K  C18   C19  C2    111.98  3.000
 S7K  C26   N21  C22   118.70  3.000
 S7K  C23   C22  N22   120.55  3.000
 S7K  C23   C22  N21   122.32  3.000
 S7K  N22   C22  N21   117.10  3.000
 S7K  HN23  N22  HN22  113.57  3.000
 S7K  HN23  N22  C22   117.15  3.000
 S7K  HN22  N22  C22   115.68  3.000
 S7K  H23   C23  C24   120.91  3.000
 S7K  H23   C23  C22   120.03  3.000
 S7K  C24   C23  C22   119.06  3.000
 S7K  C27   C24  C25   120.49  3.000
 S7K  C27   C24  C23   121.46  3.000
 S7K  C25   C24  C23   118.04  3.000
 S7K  H25   C25  C26   120.22  3.000
 S7K  H25   C25  C24   120.66  3.000
 S7K  C26   C25  C24   119.12  3.000
 S7K  C28   C26  C25   121.23  3.000
 S7K  C28   C26  N21   116.01  3.000
 S7K  C25   C26  N21   122.76  3.000
 S7K  H28A  C28  H28   106.71  3.000
 S7K  H28A  C28  C29   109.33  3.000
 S7K  H28   C28  C29   108.69  3.000
 S7K  H28A  C28  C26   110.05  3.000
 S7K  H28   C28  C26   109.37  3.000
 S7K  C29   C28  C26   112.51  3.000
 S7K  H29   C29  N29   107.32  3.000
 S7K  H29   C29  C28   107.29  3.000
 S7K  N29   C29  C28   109.40  3.000
 S7K  H29   C29  C6    107.45  3.000
 S7K  N29   C29  C6    115.84  3.000
 S7K  C28   C29  C6    109.18  3.000
 S7K  HN2B  N29  HN29  106.29  3.000
 S7K  HN2B  N29  C29   110.73  3.000
 S7K  HN29  N29  C29   110.07  3.000
 S7K  H27B  C27  H27A  108.33  3.000
 S7K  H27B  C27  H27   107.88  3.000
 S7K  H27A  C27  H27   106.99  3.000
 S7K  H27B  C27  C24   111.91  3.000
 S7K  H27A  C27  C24   111.08  3.000
 S7K  H27   C27  C24   110.46  3.000
 S7K  H18A  C18  H18   107.28  3.000
 S7K  H18A  C18  C19   109.51  3.000
 S7K  H18   C18  C19   109.18  3.000
 S7K  H18A  C18  C16   110.09  3.000
 S7K  H18   C18  C16   109.41  3.000
 S7K  C19   C18  C16   111.29  3.000
 S7K  H17B  C17  H17A  108.47  3.000
 S7K  H17B  C17  H17   107.29  3.000
 S7K  H17A  C17  H17   107.45  3.000
 S7K  H17B  C17  C14   111.47  3.000
 S7K  H17A  C17  C14   111.57  3.000
 S7K  H17   C17  C14   110.40  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
 S7K  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 S7K  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 S7K  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 S7K  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 S7K  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 S7K  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 S7K  CONST_07  C14  C13  C12  N11    0.00   0.0  0
 S7K  CONST_08  C14  C15  C16  N11    0.00   0.0  0
 S7K  CONST_09  C15  C16  N11  C12    0.00   0.0  0
 S7K  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 S7K  CONST_11  C16  N11  C12  C13    0.00   0.0  0
 S7K  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 S7K  CONST_13  C24  C23  C22  N21    0.00   0.0  0
 S7K  CONST_14  C24  C25  C26  N21    0.00   0.0  0
 S7K  CONST_15  C25  C26  N21  C22    0.00   0.0  0
 S7K  CONST_16  C25  C24  C23  C22    0.00   0.0  0
 S7K  CONST_17  C26  N21  C22  C23    0.00   0.0  0
 S7K  CONST_18  C26  C25  C24  C23    0.00   0.0  0
 S7K  CONST_19  C29  C6   C1   C2   180.00   0.0  0
 S7K  CONST_20  C19  C2   C3   C4   180.00   0.0  0
 S7K  CONST_21  C29  C6   C5   C4   180.00   0.0  0
 S7K  CONST_22  C19  C2   C1   C6   180.00   0.0  0
 S7K  CONST_23  C18  C16  N11  C12  180.00   0.0  0
 S7K  CONST_24  C17  C14  C13  C12  180.00   0.0  0
 S7K  CONST_25  C18  C16  C15  C14  180.00   0.0  0
 S7K  CONST_26  C17  C14  C15  C16  180.00   0.0  0
 S7K  CONST_27  C28  C26  N21  C22  180.00   0.0  0
 S7K  CONST_28  C27  C24  C23  C22  180.00   0.0  0
 S7K  CONST_29  C26  N21  C22  N22  180.00   0.0  0
 S7K  CONST_30  C24  C23  C22  N22  180.00   0.0  0
 S7K  CONST_31  C28  C26  C25  C24  180.00   0.0  0
 S7K  CONST_32  C27  C24  C25  C26  180.00   0.0  0
 S7K  CONST_33  H3   C3   C2   C1   180.00   0.0  0
 S7K  CONST_34  H5   C5   C6   C1   180.00   0.0  0
 S7K  CONST_35  H4   C4   C3   C2   180.00   0.0  0
 S7K  CONST_36  H1   C1   C2   C3   180.00   0.0  0
 S7K  CONST_37  H13  C13  C12  N11  180.00   0.0  0
 S7K  CONST_38  H15  C15  C16  N11  180.00   0.0  0
 S7K  CONST_39  H12  C12  C13  C14  180.00   0.0  0
 S7K  CONST_40  H23  C23  C22  N21  180.00   0.0  0
 S7K  CONST_41  H25  C25  C26  N21  180.00   0.0  0
 S7K  Var_01    C18  C19  C2   C1    77.74  30.0  2
 S7K  Var_02    C16  C18  C19  C2   178.33  30.0  2
 S7K  Var_03    C19  C18  C16  N11  -76.83  30.0  2
 S7K  Var_04    C29  C28  C26  N21  -66.60  30.0  2
 S7K  Var_05    H17  C17  C14  C13   84.75  30.0  2
 S7K  Var_06    H27  C27  C24  C23  111.27  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
 S7K  chir_01  C29  C6  C28  N29  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
 S7K  plan-1  C1    0.020
 S7K  plan-1  C2    0.020
 S7K  plan-1  C3    0.020
 S7K  plan-1  C4    0.020
 S7K  plan-1  C5    0.020
 S7K  plan-1  C6    0.020
 S7K  plan-1  C19   0.020
 S7K  plan-1  C29   0.020
 S7K  plan-1  H1    0.020
 S7K  plan-1  H3    0.020
 S7K  plan-1  H4    0.020
 S7K  plan-1  H5    0.020
 S7K  plan-2  N11   0.020
 S7K  plan-2  C12   0.020
 S7K  plan-2  C13   0.020
 S7K  plan-2  C14   0.020
 S7K  plan-2  C15   0.020
 S7K  plan-2  C16   0.020
 S7K  plan-2  H12   0.020
 S7K  plan-2  H13   0.020
 S7K  plan-2  H15   0.020
 S7K  plan-2  C18   0.020
 S7K  plan-2  C17   0.020
 S7K  plan-3  N21   0.020
 S7K  plan-3  C22   0.020
 S7K  plan-3  N22   0.020
 S7K  plan-3  C23   0.020
 S7K  plan-3  C24   0.020
 S7K  plan-3  C25   0.020
 S7K  plan-3  C26   0.020
 S7K  plan-3  C28   0.020
 S7K  plan-3  H23   0.020
 S7K  plan-3  H25   0.020
 S7K  plan-3  C27   0.020
 S7K  plan-4  C22   0.020
 S7K  plan-4  N22   0.020
 S7K  plan-4  HN22  0.020
 S7K  plan-4  HN23  0.020

