# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 08:20:00 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 6-[(2S)-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
 2IK  2IK  6-[(2S)-2-amino-2-{3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]phenyl}ethyl]-4-methylpyridin-2-amine  ligand  54  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2IK
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
 2IK  C1    C  CR16  0  -0.391  -0.1480  -1.2108   0.5673
 2IK  C2    C  CR6   0   0.157  -1.3476  -1.8698   0.3019
 2IK  C3    C  CR16  0  -0.336  -1.2957  -3.1625  -0.2088
 2IK  C4    C  CR16  0  -0.223  -0.0723  -3.7750  -0.4488
 2IK  C5    C  CR16  0  -0.338   1.1108  -3.1021  -0.1838
 2IK  C6    C  CR6   0   0.214   1.0850  -1.8073   0.3320
 2IK  N11   N  N     0  -0.485  -5.4169  -0.3664  -0.4729
 2IK  C12   C  CR6   0   0.439  -6.6137   0.1699  -0.2640
 2IK  N12   N  NH2   0  -0.838  -7.6927  -0.6629  -0.3532
 2IK  C13   C  CR16  0  -0.448  -6.7883   1.5417  -0.0074
 2IK  C29   C  CH1   0  -0.207   2.3631  -1.0426   0.5871
 2IK  C14   C  CR6   0   0.206  -5.6813   2.3634   0.0263
 2IK  C15   C  CR16  0  -0.434  -4.4253   1.7866  -0.1979
 2IK  C16   C  CR6   0   0.277  -4.3439   0.4278  -0.4401
 2IK  C19   C  CH2   0  -0.510  -2.6629  -1.1772   0.5217
 2IK  N21   N  N     0  -0.480   3.9359   1.5140  -0.1166
 2IK  C22   C  CR6   0   0.441   4.9654   2.3212   0.1111
 2IK  N22   N  NH2   0  -0.839   4.6864   3.5600   0.6125
 2IK  C23   C  CR16  0  -0.446   6.2966   1.9215  -0.1067
 2IK  C24   C  CR6   0   0.203   6.5473   0.6452  -0.5639
 2IK  C25   C  CR16  0  -0.432   5.4536  -0.1998  -0.7910
 2IK  C26   C  CR6   0   0.268   4.1764   0.2774  -0.5615
 2IK  C28   C  CH2   0  -0.500   2.9711  -0.5944  -0.7594
 2IK  N29   N  NH2   0  -0.785   3.2670  -1.8078   1.4337
 2IK  H221  H  HNH2  0   0.388   5.3798   4.2791   0.4905
 2IK  H222  H  HNH2  0   0.379   3.7385   3.8809   0.5011
 2IK  H23   H  HCR6  0   0.255   7.1083   2.6140   0.0814
 2IK  H25   H  HCR6  0   0.243   5.6035  -1.2101  -1.1510
 2IK  H281  H  HCH2  0   0.244   3.2383  -1.4756  -1.3498
 2IK  H282  H  HCH2  0   0.248   2.2143  -0.0431  -1.3238
 2IK  H29   H  HCH1  0   0.249   2.1015  -0.1353   1.1394
 2IK  H291  H  HNH2  0   0.342   3.6029  -2.6264   0.9392
 2IK  H292  H  HNH2  0   0.352   4.0946  -1.2546   1.6242
 2IK  H1    H  HCR6  0   0.238  -0.1781  -0.2028   0.9700
 2IK  H5    H  HCR6  0   0.242   2.0542  -3.5946  -0.3893
 2IK  H4    H  HCR6  0   0.252  -0.0418  -4.7819  -0.8459
 2IK  H3    H  HCR6  0   0.244  -2.2171  -3.6933  -0.4189
 2IK  H191  H  HCH2  0   0.248  -3.4581  -1.9158   0.6403
 2IK  H192  H  HCH2  0   0.247  -2.6301  -0.5934   1.4455
 2IK  H15   H  HCR6  0   0.243  -3.5286   2.3932  -0.1757
 2IK  H121  H  HNH2  0   0.379  -7.4982  -1.6469  -0.2634
 2IK  H122  H  HNH2  0   0.387  -8.5422  -0.3715   0.1009
 2IK  H13   H  HCR6  0   0.255  -7.7813   1.9395   0.1643
 2IK  H171  H  HCH3  0   0.250  -5.1554   4.1434   1.1038
 2IK  H172  H  HCH3  0   0.253  -5.5119   4.4069  -0.5926
 2IK  H173  H  HCH3  0   0.247  -6.8290   4.1115   0.5426
 2IK  C27   C  CH3   0  -0.727   7.9432   0.1637  -0.8142
 2IK  C18   C  CH2   0  -0.488  -3.0171  -0.2460  -0.6461
 2IK  C17   C  CH3   0  -0.727  -5.8081   3.8329   0.2871
 2IK  H271  H  HCH3  0   0.252   8.1789  -0.6909  -0.1782
 2IK  H272  H  HCH3  0   0.251   8.0598  -0.1670  -1.8471
 2IK  H273  H  HCH3  0   0.247   8.6811   0.9407  -0.6218
 2IK  H181  H  HCH2  0   0.247  -3.0439  -0.8287  -1.5710
 2IK  H182  H  HCH2  0   0.246  -2.2340   0.5063  -0.7640

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
 2IK  N22  C22   single    1.365  0.020  1.365
 2IK  C22  C23   aromatic  1.407  0.020  1.407
 2IK  C22  N21   aromatic  1.328  0.020  1.328
 2IK  C23  C24   aromatic  1.379  0.020  1.379
 2IK  C24  C27   single    1.498  0.020  1.498
 2IK  C24  C25   aromatic  1.401  0.020  1.401
 2IK  C25  C26   aromatic  1.383  0.020  1.383
 2IK  N21  C26   aromatic  1.336  0.020  1.336
 2IK  C26  C28   single    1.501  0.020  1.501
 2IK  C28  C29   single    1.544  0.020  1.544
 2IK  C29  N29   single    1.456  0.020  1.456
 2IK  C29  C6    single    1.511  0.020  1.511
 2IK  C6   C1    aromatic  1.390  0.020  1.390
 2IK  C6   C5    aromatic  1.394  0.020  1.394
 2IK  C1   C2    aromatic  1.394  0.020  1.394
 2IK  C5   C4    aromatic  1.387  0.020  1.387
 2IK  C4   C3    aromatic  1.389  0.020  1.389
 2IK  C3   C2    aromatic  1.391  0.020  1.391
 2IK  C2   C19   single    1.503  0.020  1.503
 2IK  C19  C18   single    1.535  0.020  1.535
 2IK  C18  C16   single    1.502  0.020  1.502
 2IK  C16  C15   aromatic  1.383  0.020  1.383
 2IK  C16  N11   aromatic  1.335  0.020  1.335
 2IK  C15  C14   aromatic  1.400  0.020  1.400
 2IK  N11  C12   aromatic  1.328  0.020  1.328
 2IK  C12  N12   single    1.366  0.020  1.366
 2IK  C12  C13   aromatic  1.406  0.020  1.406
 2IK  C13  C14   aromatic  1.379  0.020  1.379
 2IK  C14  C17   single    1.498  0.020  1.498
 2IK  N22  H221  single    0.890  0.020  1.040
 2IK  N22  H222  single    0.890  0.020  1.040
 2IK  C23  H23   single    0.930  0.020  1.080
 2IK  C27  H271  single    0.970  0.020  1.090
 2IK  C27  H272  single    0.970  0.020  1.090
 2IK  C27  H273  single    0.970  0.020  1.090
 2IK  C25  H25   single    0.930  0.020  1.080
 2IK  C28  H281  single    0.970  0.020  1.090
 2IK  C28  H282  single    0.970  0.020  1.090
 2IK  C29  H29   single    0.970  0.020  1.090
 2IK  N29  H291  single    0.890  0.020  1.040
 2IK  N29  H292  single    0.890  0.020  1.040
 2IK  C1   H1    single    0.930  0.020  1.080
 2IK  C5   H5    single    0.930  0.020  1.080
 2IK  C4   H4    single    0.930  0.020  1.080
 2IK  C3   H3    single    0.930  0.020  1.080
 2IK  C19  H191  single    0.970  0.020  1.090
 2IK  C19  H192  single    0.970  0.020  1.090
 2IK  C18  H181  single    0.970  0.020  1.090
 2IK  C18  H182  single    0.970  0.020  1.090
 2IK  C15  H15   single    0.930  0.020  1.080
 2IK  N12  H121  single    0.890  0.020  1.040
 2IK  N12  H122  single    0.890  0.020  1.040
 2IK  C13  H13   single    0.930  0.020  1.080
 2IK  C17  H171  single    0.970  0.020  1.090
 2IK  C17  H172  single    0.970  0.020  1.090
 2IK  C17  H173  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
 2IK  H1    C1   C6    119.06  3.000
 2IK  H1    C1   C2    119.05  3.000
 2IK  C6    C1   C2    121.89  3.000
 2IK  C19   C2   C3    120.98  3.000
 2IK  C19   C2   C1    120.49  3.000
 2IK  C3    C2   C1    118.50  3.000
 2IK  H3    C3   C4    119.96  3.000
 2IK  H3    C3   C2    119.64  3.000
 2IK  C4    C3   C2    120.40  3.000
 2IK  H4    C4   C5    119.82  3.000
 2IK  H4    C4   C3    119.88  3.000
 2IK  C5    C4   C3    120.30  3.000
 2IK  H5    C5   C6    120.55  3.000
 2IK  H5    C5   C4    119.07  3.000
 2IK  C6    C5   C4    120.37  3.000
 2IK  C29   C6   C5    121.12  3.000
 2IK  C5    C6   C1    118.54  3.000
 2IK  C29   C6   C1    120.30  3.000
 2IK  C16   N11  C12   118.70  3.000
 2IK  C13   C12  N12   120.57  3.000
 2IK  C13   C12  N11   122.31  3.000
 2IK  N12   C12  N11   117.09  3.000
 2IK  H122  N12  H121  113.94  3.000
 2IK  H122  N12  C12   117.44  3.000
 2IK  H121  N12  C12   115.94  3.000
 2IK  H13   C13  C14   120.87  3.000
 2IK  H13   C13  C12   120.05  3.000
 2IK  C14   C13  C12   119.08  3.000
 2IK  H29   C29  N29   106.91  3.000
 2IK  H29   C29  C28   107.08  3.000
 2IK  N29   C29  C28   114.53  3.000
 2IK  H29   C29  C6    107.62  3.000
 2IK  N29   C29  C6    110.94  3.000
 2IK  C28   C29  C6    109.43  3.000
 2IK  C17   C14  C15   120.53  3.000
 2IK  C17   C14  C13   121.39  3.000
 2IK  C15   C14  C13   118.08  3.000
 2IK  H15   C15  C16   120.36  3.000
 2IK  H15   C15  C14   120.58  3.000
 2IK  C16   C15  C14   119.06  3.000
 2IK  C18   C16  C15   121.12  3.000
 2IK  C15   C16  N11   122.78  3.000
 2IK  C18   C16  N11   116.08  3.000
 2IK  H192  C19  H191  106.93  3.000
 2IK  H192  C19  C18   109.02  3.000
 2IK  H191  C19  C18   108.96  3.000
 2IK  H192  C19  C2    110.09  3.000
 2IK  H191  C19  C2    109.97  3.000
 2IK  C18   C19  C2    111.74  3.000
 2IK  C26   N21  C22   118.70  3.000
 2IK  C23   C22  N22   120.53  3.000
 2IK  C23   C22  N21   122.30  3.000
 2IK  N22   C22  N21   117.14  3.000
 2IK  H222  N22  H221  114.05  3.000
 2IK  H222  N22  C22   116.16  3.000
 2IK  H221  N22  C22   117.59  3.000
 2IK  H23   C23  C24   120.87  3.000
 2IK  H23   C23  C22   120.03  3.000
 2IK  C24   C23  C22   119.10  3.000
 2IK  C27   C24  C25   120.45  3.000
 2IK  C25   C24  C23   118.06  3.000
 2IK  C27   C24  C23   121.50  3.000
 2IK  H25   C25  C26   120.34  3.000
 2IK  H25   C25  C24   120.57  3.000
 2IK  C26   C25  C24   119.09  3.000
 2IK  C28   C26  C25   121.30  3.000
 2IK  C28   C26  N21   115.92  3.000
 2IK  C25   C26  N21   122.75  3.000
 2IK  H282  C28  H281  107.27  3.000
 2IK  H282  C28  C26   109.33  3.000
 2IK  H281  C28  C26   110.06  3.000
 2IK  H282  C28  C29   108.90  3.000
 2IK  H281  C28  C29   109.46  3.000
 2IK  C26   C28  C29   111.71  3.000
 2IK  H292  N29  H291  105.19  3.000
 2IK  H292  N29  C29   109.23  3.000
 2IK  H291  N29  C29   110.27  3.000
 2IK  H273  C27  H272  108.13  3.000
 2IK  H273  C27  H271  108.04  3.000
 2IK  H272  C27  H271  106.94  3.000
 2IK  H273  C27  C24   111.88  3.000
 2IK  H272  C27  C24   110.82  3.000
 2IK  H271  C27  C24   110.84  3.000
 2IK  H182  C18  H181  107.06  3.000
 2IK  H182  C18  C19   109.54  3.000
 2IK  H181  C18  C19   109.01  3.000
 2IK  H182  C18  C16   109.83  3.000
 2IK  H181  C18  C16   109.48  3.000
 2IK  C19   C18  C16   111.81  3.000
 2IK  H173  C17  H172  108.01  3.000
 2IK  H173  C17  H171  108.22  3.000
 2IK  H172  C17  H171  106.94  3.000
 2IK  H173  C17  C14   111.79  3.000
 2IK  H172  C17  C14   110.65  3.000
 2IK  H171  C17  C14   111.04  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
 2IK  CONST_01  C4    C5   C6   C1     0.00   0.0  0
 2IK  CONST_02  C4    C3   C2   C1     0.00   0.0  0
 2IK  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 2IK  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 2IK  CONST_05  C6    C5   C4   C3     0.00   0.0  0
 2IK  CONST_06  C6    C1   C2   C3     0.00   0.0  0
 2IK  CONST_07  C14   C15  C16  N11    0.00   0.0  0
 2IK  CONST_08  C14   C13  C12  N11    0.00   0.0  0
 2IK  CONST_09  C15   C16  N11  C12    0.00   0.0  0
 2IK  CONST_10  C15   C14  C13  C12    0.00   0.0  0
 2IK  CONST_11  C16   N11  C12  C13    0.00   0.0  0
 2IK  CONST_12  C16   C15  C14  C13    0.00   0.0  0
 2IK  CONST_13  C24   C23  C22  N21    0.00   0.0  0
 2IK  CONST_14  C24   C25  C26  N21    0.00   0.0  0
 2IK  CONST_15  C25   C24  C23  C22    0.00   0.0  0
 2IK  CONST_16  C25   C26  N21  C22    0.00   0.0  0
 2IK  CONST_17  C26   N21  C22  C23    0.00   0.0  0
 2IK  CONST_18  C26   C25  C24  C23    0.00   0.0  0
 2IK  CONST_19  C29   C6   C1   C2   180.00   0.0  0
 2IK  CONST_20  C29   C6   C5   C4   180.00   0.0  0
 2IK  CONST_21  C19   C2   C3   C4   180.00   0.0  0
 2IK  CONST_22  C19   C2   C1   C6   180.00   0.0  0
 2IK  CONST_23  C18   C16  N11  C12  180.00   0.0  0
 2IK  CONST_24  C17   C14  C13  C12  180.00   0.0  0
 2IK  CONST_25  C16   N11  C12  N12  180.00   0.0  0
 2IK  CONST_26  C14   C13  C12  N12  180.00   0.0  0
 2IK  CONST_27  C18   C16  C15  C14  180.00   0.0  0
 2IK  CONST_28  C17   C14  C15  C16  180.00   0.0  0
 2IK  CONST_29  C27   C24  C23  C22  180.00   0.0  0
 2IK  CONST_30  C28   C26  N21  C22  180.00   0.0  0
 2IK  CONST_31  C24   C23  C22  N22  180.00   0.0  0
 2IK  CONST_32  C26   N21  C22  N22  180.00   0.0  0
 2IK  CONST_33  C28   C26  C25  C24  180.00   0.0  0
 2IK  CONST_34  C27   C24  C25  C26  180.00   0.0  0
 2IK  CONST_35  H5    C5   C6   C1   180.00   0.0  0
 2IK  CONST_36  H3    C3   C2   C1   180.00   0.0  0
 2IK  CONST_37  H4    C4   C3   C2   180.00   0.0  0
 2IK  CONST_38  H1    C1   C2   C3   180.00   0.0  0
 2IK  CONST_39  H15   C15  C16  N11  180.00   0.0  0
 2IK  CONST_40  H13   C13  C12  N11  180.00   0.0  0
 2IK  CONST_41  H23   C23  C22  N21  180.00   0.0  0
 2IK  CONST_42  H25   C25  C26  N21  180.00   0.0  0
 2IK  Var_01    C18   C19  C2   C1    80.56  30.0  2
 2IK  Var_02    C16   C18  C19  C2   178.94  30.0  3
 2IK  Var_03    C19   C18  C16  N11  -67.43  30.0  1
 2IK  Var_04    C25   C26  C28  C29  105.80  30.0  1
 2IK  Var_05    H171  C17  C14  C13  127.17  30.0  2
 2IK  Var_06    H271  C27  C24  C23  118.91  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
 2IK  chir_01  C29  C28  N29  C6  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
 2IK  plan-1  C1    0.020
 2IK  plan-1  C2    0.020
 2IK  plan-1  C3    0.020
 2IK  plan-1  C4    0.020
 2IK  plan-1  C5    0.020
 2IK  plan-1  C6    0.020
 2IK  plan-1  C29   0.020
 2IK  plan-1  C19   0.020
 2IK  plan-1  H1    0.020
 2IK  plan-1  H5    0.020
 2IK  plan-1  H4    0.020
 2IK  plan-1  H3    0.020
 2IK  plan-2  N11   0.020
 2IK  plan-2  C12   0.020
 2IK  plan-2  N12   0.020
 2IK  plan-2  C13   0.020
 2IK  plan-2  C14   0.020
 2IK  plan-2  C15   0.020
 2IK  plan-2  C16   0.020
 2IK  plan-2  H15   0.020
 2IK  plan-2  H13   0.020
 2IK  plan-2  C18   0.020
 2IK  plan-2  C17   0.020
 2IK  plan-3  N21   0.020
 2IK  plan-3  C22   0.020
 2IK  plan-3  N22   0.020
 2IK  plan-3  C23   0.020
 2IK  plan-3  C24   0.020
 2IK  plan-3  C25   0.020
 2IK  plan-3  C26   0.020
 2IK  plan-3  C28   0.020
 2IK  plan-3  H23   0.020
 2IK  plan-3  H25   0.020
 2IK  plan-3  C27   0.020
 2IK  plan-4  C12   0.020
 2IK  plan-4  N12   0.020
 2IK  plan-4  H121  0.020
 2IK  plan-4  H122  0.020
 2IK  plan-5  C22   0.020
 2IK  plan-5  N22   0.020
 2IK  plan-5  H221  0.020
 2IK  plan-5  H222  0.020

