# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 06:48:39 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 6-[(2R)-3-amino-2-{5-[2-(6-amino-4-methylpyridin-2-yl)ethyl]pyridin-3-yl}propyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cncc(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
 S71  S71  6-[(2R)-3-amino-2-{5-[2-(6-amino-4-methylpyridin-2-yl)ethyl]pyridin-3-yl}propyl]-4-methylpyridin-2-amine  ligand  56  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_S71
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
 S71  N22   N  NH2   0  -0.841   7.5893  -0.0726   0.8386
 S71  C22   C  CR6   0   0.436   6.3800   0.5455   0.6925
 S71  C23   C  CR16  0  -0.448   6.3048   1.9011   0.3354
 S71  C24   C  CR6   0   0.194   5.0633   2.4779   0.1493
 S71  C27   C  CH3   0  -0.742   4.9257   3.9162  -0.2460
 S71  C25   C  CR16  0  -0.445   3.9328   1.6771   0.3285
 S71  N21   N  N     0  -0.479   5.2954  -0.2071   0.8641
 S71  C26   C  CR6   0   0.255   4.0973   0.3480   0.6822
 S71  C20   C  CH2   0  -0.522   2.8979  -0.5420   0.8577
 S71  C17   C  CH1   0  -0.347   2.2572  -0.9491  -0.4817
 S71  C18   C  CH2   0  -0.281   3.2220  -1.7443  -1.3605
 S71  N19   N  NH2   0  -0.788   2.6113  -2.0613  -2.6410
 S71  C15   C  CR6   0   0.067   0.9718  -1.6969  -0.2255
 S71  C16   C  CR16  0  -0.111   0.9654  -2.9836   0.3104
 S71  N11   N  N     0  -0.399  -0.1398  -3.6659   0.5755
 S71  C12   C  CR16  0  -0.121  -1.3081  -3.0886   0.3213
 S71  C14   C  CR16  0  -0.256  -0.2634  -1.1212  -0.4869
 S71  C13   C  CR6   0   0.053  -1.4390  -1.8120  -0.2121
 S71  C09   C  CH2   0  -0.511  -2.7848  -1.1912  -0.4412
 S71  C08   C  CH2   0  -0.491  -3.1498  -0.2049   0.6764
 S71  C06   C  CR6   0   0.286  -4.4814   0.4503   0.4417
 S71  C05   C  CR16  0  -0.417  -5.5439   0.2397   1.3026
 S71  C04   C  CR6   0   0.210  -6.7668   0.8670   1.0385
 S71  C07   C  CH3   0  -0.697  -7.9313   0.6965   1.9655
 S71  N01   N  N     0  -0.483  -4.5717   1.2239  -0.6412
 S71  C02   C  CR6   0   0.456  -5.7314   1.8156  -0.9091
 S71  N02   N  NH2   0  -0.817  -5.8013   2.5518  -2.0554
 S71  C03   C  CR16  0  -0.422  -6.8598   1.6635  -0.0846
 S71  H221  H  HNH2  0   0.384   8.3902   0.5100   1.0174
 S71  H222  H  HNH2  0   0.377   7.5861  -0.9349   1.3589
 S71  H23   H  HCR6  0   0.250   7.2111   2.4825   0.2123
 S71  H271  H  HCH3  0   0.246   4.6625   3.9995  -1.3021
 S71  H272  H  HCH3  0   0.259   4.1334   4.4059   0.3202
 S71  H273  H  HCH3  0   0.261   5.8507   4.4692  -0.0909
 S71  H25   H  HCR6  0   0.291   2.9388   2.0888   0.2006
 S71  H201  H  HCH2  0   0.266   3.1948  -1.4329   1.4162
 S71  H202  H  HCH2  0   0.293   2.1446  -0.0228   1.4556
 S71  H17   H  HCH1  0   0.284   1.9998  -0.0358  -1.0274
 S71  H181  H  HCH2  0   0.241   4.1056  -1.1320  -1.5501
 S71  H182  H  HCH2  0   0.194   3.5784  -2.6243  -0.8061
 S71  H191  H  HNH2  0   0.339   3.2967  -2.5101  -3.2347
 S71  H192  H  HNH2  0   0.334   1.8757  -2.7450  -2.5105
 S71  H16   H  HCR6  0   0.254   1.9012  -3.4882   0.5327
 S71  H14   H  HCR6  0   0.254  -0.3113  -0.1228  -0.9105
 S71  H12   H  HCR6  0   0.241  -2.1962  -3.6718   0.5475
 S71  H091  H  HCH2  0   0.258  -2.7933  -0.6631  -1.3969
 S71  H092  H  HCH2  0   0.247  -3.5483  -1.9704  -0.5004
 S71  H081  H  HCH2  0   0.247  -3.1562  -0.7260   1.6359
 S71  H082  H  HCH2  0   0.258  -2.3766   0.5667   0.7388
 S71  H05   H  HCR6  0   0.217  -5.4289  -0.4028   2.1667
 S71  H071  H  HCH3  0   0.246  -7.8778   1.4209   2.7806
 S71  H072  H  HCH3  0   0.235  -8.8802   0.8497   1.4535
 S71  H073  H  HCH3  0   0.238  -7.9392  -0.2954   2.4164
 S71  H03   H  HCR6  0   0.223  -7.7875   2.1643  -0.3358
 S71  H021  H  HNH2  0   0.361  -4.9246   2.8263  -2.4668
 S71  H022  H  HNH2  0   0.364  -6.5309   3.2399  -2.1318

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
 S71  N22  C22   single    1.366  0.020  1.366
 S71  C22  C23   aromatic  1.404  0.020  1.404
 S71  C22  N21   aromatic  1.331  0.020  1.331
 S71  C23  C24   aromatic  1.382  0.020  1.382
 S71  C24  C27   single    1.498  0.020  1.498
 S71  C24  C25   aromatic  1.397  0.020  1.397
 S71  C25  C26   aromatic  1.385  0.020  1.385
 S71  N21  C26   aromatic  1.333  0.020  1.333
 S71  C26  C20   single    1.504  0.020  1.504
 S71  C20  C17   single    1.540  0.020  1.540
 S71  C17  C18   single    1.528  0.020  1.528
 S71  C17  C15   single    1.509  0.020  1.509
 S71  C18  N19   single    1.454  0.020  1.454
 S71  C15  C16   aromatic  1.394  0.020  1.394
 S71  C15  C14   aromatic  1.388  0.020  1.388
 S71  C16  N11   aromatic  1.326  0.020  1.326
 S71  N11  C12   aromatic  1.328  0.020  1.328
 S71  C12  C13   aromatic  1.390  0.020  1.390
 S71  C14  C13   aromatic  1.391  0.020  1.391
 S71  C13  C09   single    1.500  0.020  1.500
 S71  C09  C08   single    1.535  0.020  1.535
 S71  C08  C06   single    1.503  0.020  1.503
 S71  C06  C05   aromatic  1.384  0.020  1.384
 S71  C06  N01   aromatic  1.334  0.020  1.334
 S71  C05  C04   aromatic  1.399  0.020  1.399
 S71  C04  C07   single    1.498  0.020  1.498
 S71  C04  C03   aromatic  1.380  0.020  1.380
 S71  N01  C02   aromatic  1.329  0.020  1.329
 S71  C02  N02   single    1.364  0.020  1.364
 S71  C02  C03   aromatic  1.406  0.020  1.406
 S71  N22  H221  single    0.890  0.020  1.040
 S71  N22  H222  single    0.890  0.020  1.040
 S71  C23  H23   single    0.930  0.020  1.080
 S71  C27  H271  single    0.970  0.020  1.090
 S71  C27  H272  single    0.970  0.020  1.090
 S71  C27  H273  single    0.970  0.020  1.090
 S71  C25  H25   single    0.930  0.020  1.080
 S71  C20  H201  single    0.970  0.020  1.090
 S71  C20  H202  single    0.970  0.020  1.090
 S71  C17  H17   single    0.970  0.020  1.090
 S71  C18  H181  single    0.970  0.020  1.090
 S71  C18  H182  single    0.970  0.020  1.090
 S71  N19  H191  single    0.890  0.020  1.040
 S71  N19  H192  single    0.890  0.020  1.040
 S71  C16  H16   single    0.930  0.020  1.080
 S71  C14  H14   single    0.930  0.020  1.080
 S71  C12  H12   single    0.930  0.020  1.080
 S71  C09  H091  single    0.970  0.020  1.090
 S71  C09  H092  single    0.970  0.020  1.090
 S71  C08  H081  single    0.970  0.020  1.090
 S71  C08  H082  single    0.970  0.020  1.090
 S71  C05  H05   single    0.930  0.020  1.080
 S71  C07  H071  single    0.970  0.020  1.090
 S71  C07  H072  single    0.970  0.020  1.090
 S71  C07  H073  single    0.970  0.020  1.090
 S71  C03  H03   single    0.930  0.020  1.080
 S71  N02  H021  single    0.890  0.020  1.040
 S71  N02  H022  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
 S71  H222  N22  H221  113.98  3.000
 S71  H222  N22  C22   116.09  3.000
 S71  H221  N22  C22   117.49  3.000
 S71  N21   C22  C23   122.35  3.000
 S71  N21   C22  N22   116.85  3.000
 S71  C23   C22  N22   120.77  3.000
 S71  H23   C23  C24   120.81  3.000
 S71  H23   C23  C22   120.14  3.000
 S71  C24   C23  C22   119.05  3.000
 S71  C25   C24  C27   120.66  3.000
 S71  C25   C24  C23   118.08  3.000
 S71  C27   C24  C23   121.26  3.000
 S71  H273  C27  H272  108.38  3.000
 S71  H273  C27  H271  107.69  3.000
 S71  H272  C27  H271  107.04  3.000
 S71  H273  C27  C24   111.84  3.000
 S71  H272  C27  C24   111.16  3.000
 S71  H271  C27  C24   110.53  3.000
 S71  H25   C25  C26   120.25  3.000
 S71  H25   C25  C24   120.63  3.000
 S71  C26   C25  C24   119.12  3.000
 S71  C26   N21  C22   118.64  3.000
 S71  C20   C26  N21   117.03  3.000
 S71  C20   C26  C25   120.19  3.000
 S71  N21   C26  C25   122.77  3.000
 S71  H202  C20  H201  107.16  3.000
 S71  H202  C20  C17   108.34  3.000
 S71  H201  C20  C17   110.01  3.000
 S71  H202  C20  C26   109.42  3.000
 S71  H201  C20  C26   109.00  3.000
 S71  C17   C20  C26   112.76  3.000
 S71  H17   C17  C15   107.32  3.000
 S71  H17   C17  C18   107.21  3.000
 S71  C15   C17  C18   112.18  3.000
 S71  H17   C17  C20   108.12  3.000
 S71  C15   C17  C20   109.74  3.000
 S71  C18   C17  C20   112.04  3.000
 S71  H182  C18  H181  105.90  3.000
 S71  H182  C18  N19   113.95  3.000
 S71  H181  C18  N19   108.03  3.000
 S71  H182  C18  C17   109.34  3.000
 S71  H181  C18  C17   108.60  3.000
 S71  N19   C18  C17   110.78  3.000
 S71  H192  N19  H191  105.55  3.000
 S71  H192  N19  C18   109.81  3.000
 S71  H191  N19  C18   109.21  3.000
 S71  C14   C15  C16   116.83  3.000
 S71  C14   C15  C17   121.38  3.000
 S71  C16   C15  C17   121.78  3.000
 S71  H16   C16  N11   116.00  3.000
 S71  H16   C16  C15   120.24  3.000
 S71  N11   C16  C15   123.77  3.000
 S71  C12   N11  C16   118.14  3.000
 S71  H12   C12  C13   119.74  3.000
 S71  H12   C12  N11   116.50  3.000
 S71  C13   C12  N11   123.76  3.000
 S71  H14   C14  C13   119.77  3.000
 S71  H14   C14  C15   119.62  3.000
 S71  C13   C14  C15   120.60  3.000
 S71  C09   C13  C14   121.51  3.000
 S71  C09   C13  C12   121.56  3.000
 S71  C14   C13  C12   116.90  3.000
 S71  H092  C09  H091  106.98  3.000
 S71  H092  C09  C08   109.37  3.000
 S71  H091  C09  C08   108.95  3.000
 S71  H092  C09  C13   109.89  3.000
 S71  H091  C09  C13   109.93  3.000
 S71  C08   C09  C13   111.61  3.000
 S71  H082  C08  H081  106.89  3.000
 S71  H082  C08  C06   109.13  3.000
 S71  H081  C08  C06   109.89  3.000
 S71  H082  C08  C09   109.07  3.000
 S71  H081  C08  C09   109.55  3.000
 S71  C06   C08  C09   112.17  3.000
 S71  N01   C06  C05   122.78  3.000
 S71  N01   C06  C08   116.08  3.000
 S71  C05   C06  C08   121.13  3.000
 S71  H05   C05  C04   120.62  3.000
 S71  H05   C05  C06   120.34  3.000
 S71  C04   C05  C06   119.04  3.000
 S71  C03   C04  C07   121.12  3.000
 S71  C03   C04  C05   118.11  3.000
 S71  C07   C04  C05   120.76  3.000
 S71  H073  C07  H072  108.44  3.000
 S71  H073  C07  H071  107.18  3.000
 S71  H072  C07  H071  107.48  3.000
 S71  H073  C07  C04   111.43  3.000
 S71  H072  C07  C04   111.74  3.000
 S71  H071  C07  C04   110.38  3.000
 S71  C02   N01  C06   118.74  3.000
 S71  C03   C02  N02   120.67  3.000
 S71  C03   C02  N01   122.28  3.000
 S71  N02   C02  N01   117.02  3.000
 S71  H022  N02  H021  114.46  3.000
 S71  H022  N02  C02   118.05  3.000
 S71  H021  N02  C02   116.49  3.000
 S71  H03   C03  C02   120.08  3.000
 S71  H03   C03  C04   120.86  3.000
 S71  C02   C03  C04   119.06  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
 S71  CONST_01  C25   C24  C23  C22    0.00   0.0  0
 S71  CONST_02  C25   C26  N21  C22    0.00   0.0  0
 S71  CONST_03  C26   N21  C22  C23    0.00   0.0  0
 S71  CONST_04  C26   C25  C24  C23    0.00   0.0  0
 S71  CONST_05  N21   C22  C23  C24    0.00   0.0  0
 S71  CONST_06  N21   C26  C25  C24    0.00   0.0  0
 S71  CONST_07  C12   N11  C16  C15    0.00   0.0  0
 S71  CONST_08  C12   C13  C14  C15    0.00   0.0  0
 S71  CONST_09  C13   C14  C15  C16    0.00   0.0  0
 S71  CONST_10  C13   C12  N11  C16    0.00   0.0  0
 S71  CONST_11  C14   C15  C16  N11    0.00   0.0  0
 S71  CONST_12  C14   C13  C12  N11    0.00   0.0  0
 S71  CONST_13  C03   C04  C05  C06    0.00   0.0  0
 S71  CONST_14  C03   C02  N01  C06    0.00   0.0  0
 S71  CONST_15  C02   N01  C06  C05    0.00   0.0  0
 S71  CONST_16  C02   C03  C04  C05    0.00   0.0  0
 S71  CONST_17  N01   C06  C05  C04    0.00   0.0  0
 S71  CONST_18  N01   C02  C03  C04    0.00   0.0  0
 S71  CONST_19  C24   C23  C22  N22  180.00   0.0  0
 S71  CONST_20  C26   N21  C22  N22  180.00   0.0  0
 S71  CONST_21  C27   C24  C23  C22  180.00   0.0  0
 S71  CONST_22  C20   C26  N21  C22  180.00   0.0  0
 S71  CONST_23  C20   C26  C25  C24  180.00   0.0  0
 S71  CONST_24  C26   C25  C24  C27  180.00   0.0  0
 S71  CONST_25  N11   C16  C15  C17  180.00   0.0  0
 S71  CONST_26  C13   C14  C15  C17  180.00   0.0  0
 S71  CONST_27  C09   C13  C14  C15  180.00   0.0  0
 S71  CONST_28  C09   C13  C12  N11  180.00   0.0  0
 S71  CONST_29  C04   C05  C06  C08  180.00   0.0  0
 S71  CONST_30  C02   N01  C06  C08  180.00   0.0  0
 S71  CONST_31  C07   C04  C05  C06  180.00   0.0  0
 S71  CONST_32  N02   C02  N01  C06  180.00   0.0  0
 S71  CONST_33  N02   C02  C03  C04  180.00   0.0  0
 S71  CONST_34  C02   C03  C04  C07  180.00   0.0  0
 S71  CONST_35  H25   C25  C24  C23  180.00   0.0  0
 S71  CONST_36  H23   C23  C24  C25  180.00   0.0  0
 S71  CONST_37  H14   C14  C15  C16  180.00   0.0  0
 S71  CONST_38  H12   C12  N11  C16  180.00   0.0  0
 S71  CONST_39  H16   C16  N11  C12  180.00   0.0  0
 S71  CONST_40  H03   C03  C04  C05  180.00   0.0  0
 S71  CONST_41  H05   C05  C06  N01  180.00   0.0  0
 S71  Var_01    C17   C20  C26  C25   74.54  30.0  2
 S71  Var_02    C08   C09  C13  C12  100.21  30.0  2
 S71  Var_03    C06   C08  C09  C13  178.58  30.0  3
 S71  Var_04    C05   C06  C08  C09  115.63  30.0  2
 S71  Var_05    H271  C27  C24  C23  104.23  30.0  2
 S71  Var_06    H071  C07  C04  C05   85.41  30.0  2
 S71  Var_07    H191  N19  C18  C17  174.75  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
 S71  chir_01  C17  C20  C18  C15  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
 S71  plan-1  N22   0.020
 S71  plan-1  C22   0.020
 S71  plan-1  C23   0.020
 S71  plan-1  C24   0.020
 S71  plan-1  C27   0.020
 S71  plan-1  C25   0.020
 S71  plan-1  N21   0.020
 S71  plan-1  C26   0.020
 S71  plan-1  C20   0.020
 S71  plan-1  H23   0.020
 S71  plan-1  H25   0.020
 S71  plan-2  C17   0.020
 S71  plan-2  C15   0.020
 S71  plan-2  C16   0.020
 S71  plan-2  N11   0.020
 S71  plan-2  C12   0.020
 S71  plan-2  C14   0.020
 S71  plan-2  C13   0.020
 S71  plan-2  C09   0.020
 S71  plan-2  H16   0.020
 S71  plan-2  H14   0.020
 S71  plan-2  H12   0.020
 S71  plan-3  C08   0.020
 S71  plan-3  C06   0.020
 S71  plan-3  C05   0.020
 S71  plan-3  C04   0.020
 S71  plan-3  C07   0.020
 S71  plan-3  N01   0.020
 S71  plan-3  C02   0.020
 S71  plan-3  N02   0.020
 S71  plan-3  C03   0.020
 S71  plan-3  H05   0.020
 S71  plan-3  H03   0.020
 S71  plan-4  N22   0.020
 S71  plan-4  C22   0.020
 S71  plan-4  H221  0.020
 S71  plan-4  H222  0.020
 S71  plan-5  C02   0.020
 S71  plan-5  N02   0.020
 S71  plan-5  H021  0.020
 S71  plan-5  H022  0.020

