# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 00:12:43 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (1S)-2-(6-amino-4-methylpyridin-2-yl)-1-{3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]phenyl}ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cccc(c2)[C@@H](O)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
 S20  S20  (1S)-2-(6-amino-4-methylpyridin-2-yl)-1-{3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]phenyl}ethanol  ligand  53  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_S20
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
 S20  C1    C  CR16  0  -0.368  -0.1163   1.2697  -0.6496
 S20  C2    C  CR6   0   0.157  -1.3331   1.9164  -0.4494
 S20  C3    C  CR16  0  -0.335  -1.3172   3.2599  -0.0848
 S20  C4    C  CR16  0  -0.222  -0.1129   3.9330   0.0669
 S20  C5    C  CR16  0  -0.345   1.0913   3.2747  -0.1387
 S20  C6    C  CR6   0   0.144   1.0979   1.9297  -0.4965
 S20  N11   N  N     0  -0.484  -5.3419   0.3217   0.5504
 S20  C12   C  CR6   0   0.441  -6.5265  -0.2511   0.3686
 S20  N12   N  NH2   0  -0.839  -7.6240   0.5594   0.4257
 S20  C13   C  CR16  0  -0.448  -6.6627  -1.6215   0.0840
 S20  C14   C  CR6   0   0.205  -5.5298  -2.4029  -0.0082
 S20  C15   C  CR16  0  -0.432  -4.2871  -1.7867   0.1805
 S20  C16   C  CR6   0   0.273  -4.2441  -0.4318   0.4542
 S20  C19   C  CH2   0  -0.510  -2.6291   1.1708  -0.6007
 S20  N21   N  N     0  -0.485   3.8565  -1.4882  -0.2206
 S20  C22   C  CR6   0   0.439   4.9147  -2.2691  -0.4063
 S20  N22   N  NH2   0  -0.838   4.7395  -3.3817  -1.1789
 S20  C23   C  CR16  0  -0.446   6.1790  -1.9604   0.1272
 S20  C24   C  CR6   0   0.204   6.3321  -0.8069   0.8675
 S20  C25   C  CR16  0  -0.439   5.2094   0.0090   1.0536
 S20  C26   C  CR6   0   0.296   4.0042  -0.3717   0.4948
 S20  C28   C  CH2   0  -0.558   2.7764   0.4789   0.6442
 S20  C29   C  CH1   0  -0.026   2.3882   1.1599  -0.6748
 S20  O29   O  OH1   0  -0.660   3.4385   1.9520  -1.1741
 S20  H1    H  HCR6  0   0.238  -0.1154   0.2230  -0.9408
 S20  H3    H  HCR6  0   0.245  -2.2526   3.7841   0.0727
 S20  H4    H  HCR6  0   0.252  -0.1124   4.9804   0.3411
 S20  H5    H  HCR6  0   0.239   2.0180   3.8231  -0.0224
 S20  HN12  H  HNH2  0   0.379  -7.5019   1.4397   0.8992
 S20  HN1A  H  HNH2  0   0.388  -8.5157   0.1241   0.5933
 S20  H13   H  HCR6  0   0.255  -7.6468  -2.0509  -0.0617
 S20  H15   H  HCR6  0   0.243  -3.3711  -2.3601   0.1111
 S20  H17   H  HCH3  0   0.249  -4.9469  -4.1555  -1.1017
 S20  H17A  H  HCH3  0   0.253  -5.3158  -4.4489   0.5871
 S20  H17B  H  HCH3  0   0.247  -6.6272  -4.1731  -0.5587
 S20  H19   H  HCH2  0   0.248  -3.4491   1.8787  -0.7386
 S20  H19A  H  HCH2  0   0.248  -2.5964   0.5445  -1.4962
 S20  HN22  H  HNH2  0   0.379   3.7893  -3.6964  -1.2895
 S20  HN2A  H  HNH2  0   0.388   5.4045  -4.1291  -1.0703
 S20  H23   H  HCR6  0   0.255   7.0160  -2.6271  -0.0428
 S20  H25   H  HCR6  0   0.244   5.2788   0.9190   1.6368
 S20  H28   H  HCH2  0   0.265   1.9381  -0.1348   0.9814
 S20  H28A  H  HCH2  0   0.257   2.9335   1.2446   1.4102
 S20  H29   H  HCH1  0   0.251   2.2219   0.3777  -1.4225
 S20  HO29  H  HOH1  0   0.448   3.8411   2.4403  -0.4485
 S20  C27   C  CH3   0  -0.726   7.6592  -0.4178   1.4428
 S20  C18   C  CH2   0  -0.488  -2.9340   0.2852   0.6153
 S20  C17   C  CH3   0  -0.727  -5.6164  -3.8717  -0.2891
 S20  H18   H  HCH2  0   0.247  -2.9645   0.9072   1.5137
 S20  H18A  H  HCH2  0   0.245  -2.1282  -0.4397   0.7515
 S20  H27   H  HCH3  0   0.254   8.0671   0.4422   0.9087
 S20  H27A  H  HCH3  0   0.249   7.5647  -0.1281   2.4896
 S20  H27B  H  HCH3  0   0.247   8.3839  -1.2272   1.3747

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
 S20  C1   C2    aromatic  1.392  0.020  1.392
 S20  C1   C6    aromatic  1.390  0.020  1.390
 S20  C2   C3    aromatic  1.392  0.020  1.392
 S20  C2   C19   single    1.503  0.020  1.503
 S20  C3   C4    aromatic  1.388  0.020  1.388
 S20  C4   C5    aromatic  1.388  0.020  1.388
 S20  C5   C6    aromatic  1.392  0.020  1.392
 S20  C6   C29   single    1.513  0.020  1.513
 S20  N11  C12   aromatic  1.328  0.020  1.328
 S20  N11  C16   aromatic  1.335  0.020  1.335
 S20  C12  N12   single    1.366  0.020  1.366
 S20  C12  C13   aromatic  1.406  0.020  1.406
 S20  C13  C14   aromatic  1.379  0.020  1.379
 S20  C14  C15   aromatic  1.400  0.020  1.400
 S20  C14  C17   single    1.498  0.020  1.498
 S20  C15  C16   aromatic  1.383  0.020  1.383
 S20  C16  C18   single    1.502  0.020  1.502
 S20  C18  C19   single    1.535  0.020  1.535
 S20  N21  C22   aromatic  1.328  0.020  1.328
 S20  N21  C26   aromatic  1.334  0.020  1.334
 S20  C22  N22   single    1.366  0.020  1.366
 S20  C22  C23   aromatic  1.407  0.020  1.407
 S20  C23  C24   aromatic  1.379  0.020  1.379
 S20  C24  C25   aromatic  1.400  0.020  1.400
 S20  C24  C27   single    1.498  0.020  1.498
 S20  C25  C26   aromatic  1.382  0.020  1.382
 S20  C26  C28   single    1.501  0.020  1.501
 S20  C28  C29   single    1.534  0.020  1.534
 S20  C29  O29   single    1.407  0.020  1.407
 S20  C1   H1    single    0.930  0.020  1.080
 S20  C3   H3    single    0.930  0.020  1.080
 S20  C4   H4    single    0.930  0.020  1.080
 S20  C5   H5    single    0.930  0.020  1.080
 S20  N12  HN12  single    0.890  0.020  1.040
 S20  N12  HN1A  single    0.890  0.020  1.040
 S20  C13  H13   single    0.930  0.020  1.080
 S20  C15  H15   single    0.930  0.020  1.080
 S20  C17  H17   single    0.970  0.020  1.090
 S20  C17  H17A  single    0.970  0.020  1.090
 S20  C17  H17B  single    0.970  0.020  1.090
 S20  C18  H18   single    0.970  0.020  1.090
 S20  C18  H18A  single    0.970  0.020  1.090
 S20  C19  H19   single    0.970  0.020  1.090
 S20  C19  H19A  single    0.970  0.020  1.090
 S20  N22  HN22  single    0.890  0.020  1.040
 S20  N22  HN2A  single    0.890  0.020  1.040
 S20  C23  H23   single    0.930  0.020  1.080
 S20  C25  H25   single    0.930  0.020  1.080
 S20  C27  H27   single    0.970  0.020  1.090
 S20  C27  H27A  single    0.970  0.020  1.090
 S20  C27  H27B  single    0.970  0.020  1.090
 S20  C28  H28   single    0.970  0.020  1.090
 S20  C28  H28A  single    0.970  0.020  1.090
 S20  C29  H29   single    0.970  0.020  1.090
 S20  O29  HO29  single    0.850  0.020  0.980

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
 S20  H1    C1   C6    119.08  3.000
 S20  H1    C1   C2    119.13  3.000
 S20  C6    C1   C2    121.79  3.000
 S20  C19   C2   C3    121.00  3.000
 S20  C19   C2   C1    120.58  3.000
 S20  C3    C2   C1    118.41  3.000
 S20  H3    C3   C4    119.89  3.000
 S20  H3    C3   C2    119.67  3.000
 S20  C4    C3   C2    120.43  3.000
 S20  H4    C4   C5    119.74  3.000
 S20  H4    C4   C3    119.81  3.000
 S20  C5    C4   C3    120.44  3.000
 S20  H5    C5   C6    120.86  3.000
 S20  H5    C5   C4    119.10  3.000
 S20  C6    C5   C4    120.04  3.000
 S20  C29   C6   C5    121.74  3.000
 S20  C29   C6   C1    119.36  3.000
 S20  C5    C6   C1    118.87  3.000
 S20  C16   N11  C12   118.69  3.000
 S20  C13   C12  N12   120.60  3.000
 S20  C13   C12  N11   122.29  3.000
 S20  N12   C12  N11   117.07  3.000
 S20  HN1A  N12  HN12  114.03  3.000
 S20  HN1A  N12  C12   117.54  3.000
 S20  HN12  N12  C12   116.17  3.000
 S20  H13   C13  C14   120.83  3.000
 S20  H13   C13  C12   120.09  3.000
 S20  C14   C13  C12   119.08  3.000
 S20  C17   C14  C15   120.54  3.000
 S20  C17   C14  C13   121.37  3.000
 S20  C15   C14  C13   118.09  3.000
 S20  H15   C15  C16   120.34  3.000
 S20  H15   C15  C14   120.62  3.000
 S20  C16   C15  C14   119.05  3.000
 S20  C18   C16  C15   121.07  3.000
 S20  C18   C16  N11   116.10  3.000
 S20  C15   C16  N11   122.80  3.000
 S20  H19A  C19  H19   106.88  3.000
 S20  H19A  C19  C18   108.93  3.000
 S20  H19   C19  C18   108.96  3.000
 S20  H19A  C19  C2    109.93  3.000
 S20  H19   C19  C2    109.79  3.000
 S20  C18   C19  C2    112.20  3.000
 S20  C26   N21  C22   118.60  3.000
 S20  C23   C22  N22   120.58  3.000
 S20  C23   C22  N21   122.28  3.000
 S20  N22   C22  N21   117.12  3.000
 S20  HN2A  N22  HN22  113.78  3.000
 S20  HN2A  N22  C22   117.33  3.000
 S20  HN22  N22  C22   115.96  3.000
 S20  H23   C23  C24   120.88  3.000
 S20  H23   C23  C22   119.98  3.000
 S20  C24   C23  C22   119.14  3.000
 S20  C27   C24  C25   120.53  3.000
 S20  C27   C24  C23   121.45  3.000
 S20  C25   C24  C23   118.02  3.000
 S20  H25   C25  C26   120.33  3.000
 S20  H25   C25  C24   120.65  3.000
 S20  C26   C25  C24   119.01  3.000
 S20  C28   C26  C25   121.13  3.000
 S20  C28   C26  N21   115.91  3.000
 S20  C25   C26  N21   122.95  3.000
 S20  H28A  C28  H28   106.69  3.000
 S20  H28A  C28  C29   109.11  3.000
 S20  H28   C28  C29   108.70  3.000
 S20  H28A  C28  C26   110.41  3.000
 S20  H28   C28  C26   109.89  3.000
 S20  C29   C28  C26   111.89  3.000
 S20  H29   C29  O29   105.86  3.000
 S20  H29   C29  C28   107.97  3.000
 S20  O29   C29  C28   111.48  3.000
 S20  H29   C29  C6    108.32  3.000
 S20  O29   C29  C6    113.07  3.000
 S20  C28   C29  C6    109.89  3.000
 S20  HO29  O29  C29   109.29  3.000
 S20  H27B  C27  H27A  108.38  3.000
 S20  H27B  C27  H27   107.84  3.000
 S20  H27A  C27  H27   107.03  3.000
 S20  H27B  C27  C24   111.89  3.000
 S20  H27A  C27  C24   111.16  3.000
 S20  H27   C27  C24   110.36  3.000
 S20  H18A  C18  H18   107.20  3.000
 S20  H18A  C18  C19   109.58  3.000
 S20  H18   C18  C19   109.17  3.000
 S20  H18A  C18  C16   109.87  3.000
 S20  H18   C18  C16   109.60  3.000
 S20  C19   C18  C16   111.32  3.000
 S20  H17B  C17  H17A  107.95  3.000
 S20  H17B  C17  H17   108.27  3.000
 S20  H17A  C17  H17   106.94  3.000
 S20  H17B  C17  C14   111.81  3.000
 S20  H17A  C17  C14   110.62  3.000
 S20  H17   C17  C14   111.07  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
 S20  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 S20  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 S20  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 S20  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 S20  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 S20  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 S20  CONST_07  C14  C13  C12  N11    0.00   0.0  0
 S20  CONST_08  C14  C15  C16  N11    0.00   0.0  0
 S20  CONST_09  C15  C16  N11  C12    0.00   0.0  0
 S20  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 S20  CONST_11  C16  N11  C12  C13    0.00   0.0  0
 S20  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 S20  CONST_13  C24  C23  C22  N21    0.00   0.0  0
 S20  CONST_14  C24  C25  C26  N21    0.00   0.0  0
 S20  CONST_15  C25  C26  N21  C22    0.00   0.0  0
 S20  CONST_16  C25  C24  C23  C22    0.00   0.0  0
 S20  CONST_17  C26  N21  C22  C23    0.00   0.0  0
 S20  CONST_18  C26  C25  C24  C23    0.00   0.0  0
 S20  CONST_19  C29  C6   C1   C2   180.00   0.0  0
 S20  CONST_20  C19  C2   C3   C4   180.00   0.0  0
 S20  CONST_21  C29  C6   C5   C4   180.00   0.0  0
 S20  CONST_22  C19  C2   C1   C6   180.00   0.0  0
 S20  CONST_23  C18  C16  N11  C12  180.00   0.0  0
 S20  CONST_24  C17  C14  C13  C12  180.00   0.0  0
 S20  CONST_25  C16  N11  C12  N12  180.00   0.0  0
 S20  CONST_26  C14  C13  C12  N12  180.00   0.0  0
 S20  CONST_27  C18  C16  C15  C14  180.00   0.0  0
 S20  CONST_28  C17  C14  C15  C16  180.00   0.0  0
 S20  CONST_29  C28  C26  N21  C22  180.00   0.0  0
 S20  CONST_30  C27  C24  C23  C22  180.00   0.0  0
 S20  CONST_31  C26  N21  C22  N22  180.00   0.0  0
 S20  CONST_32  C24  C23  C22  N22  180.00   0.0  0
 S20  CONST_33  C28  C26  C25  C24  180.00   0.0  0
 S20  CONST_34  C27  C24  C25  C26  180.00   0.0  0
 S20  CONST_35  H3   C3   C2   C1   180.00   0.0  0
 S20  CONST_36  H5   C5   C6   C1   180.00   0.0  0
 S20  CONST_37  H4   C4   C3   C2   180.00   0.0  0
 S20  CONST_38  H1   C1   C2   C3   180.00   0.0  0
 S20  CONST_39  H13  C13  C12  N11  180.00   0.0  0
 S20  CONST_40  H15  C15  C16  N11  180.00   0.0  0
 S20  CONST_41  H23  C23  C22  N21  180.00   0.0  0
 S20  CONST_42  H25  C25  C26  N21  180.00   0.0  0
 S20  Var_01    C18  C19  C2   C1    77.49  30.0  2
 S20  Var_02    C16  C18  C19  C2   179.01  30.0  1
 S20  Var_03    C19  C18  C16  N11  -71.52  30.0  2
 S20  Var_04    C29  C28  C26  N21  -70.37  30.0  2
 S20  Var_05    H17  C17  C14  C13  130.21  30.0  2
 S20  Var_06    H27  C27  C24  C23  108.69  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
 S20  chir_01  C29  C6  C28  O29  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
 S20  plan-1  C1    0.020
 S20  plan-1  C2    0.020
 S20  plan-1  C3    0.020
 S20  plan-1  C4    0.020
 S20  plan-1  C5    0.020
 S20  plan-1  C6    0.020
 S20  plan-1  C19   0.020
 S20  plan-1  C29   0.020
 S20  plan-1  H1    0.020
 S20  plan-1  H3    0.020
 S20  plan-1  H4    0.020
 S20  plan-1  H5    0.020
 S20  plan-2  N11   0.020
 S20  plan-2  C12   0.020
 S20  plan-2  N12   0.020
 S20  plan-2  C13   0.020
 S20  plan-2  C14   0.020
 S20  plan-2  C15   0.020
 S20  plan-2  C16   0.020
 S20  plan-2  H13   0.020
 S20  plan-2  H15   0.020
 S20  plan-2  C18   0.020
 S20  plan-2  C17   0.020
 S20  plan-3  N21   0.020
 S20  plan-3  C22   0.020
 S20  plan-3  N22   0.020
 S20  plan-3  C23   0.020
 S20  plan-3  C24   0.020
 S20  plan-3  C25   0.020
 S20  plan-3  C26   0.020
 S20  plan-3  C28   0.020
 S20  plan-3  H23   0.020
 S20  plan-3  H25   0.020
 S20  plan-3  C27   0.020
 S20  plan-4  C12   0.020
 S20  plan-4  N12   0.020
 S20  plan-4  HN12  0.020
 S20  plan-4  HN1A  0.020
 S20  plan-5  C22   0.020
 S20  plan-5  N22   0.020
 S20  plan-5  HN22  0.020
 S20  plan-5  HN2A  0.020

