# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 02:13:49 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 6-[(2R)-3-amino-2-{6-[2-(6-amino-4-methylpyridin-2-yl)ethyl]pyridin-2-yl}propyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cccc(n2)[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
 7S7  7S7  6-[(2R)-3-amino-2-{6-[2-(6-amino-4-methylpyridin-2-yl)ethyl]pyridin-2-yl}propyl]-4-methylpyridin-2-amine  ligand  56  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7S7
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
 7S7  N22   N  NH2   0  -0.841   4.6060   3.3989  -0.8504
 7S7  C22   C  CR6   0   0.437   4.9873   2.1150  -0.5720
 7S7  C23   C  CR16  0  -0.456   6.3117   1.8202  -0.2138
 7S7  C24   C  CR6   0   0.202   6.6668   0.5022   0.0039
 7S7  C27   C  CH3   0  -0.727   8.0609   0.1298   0.4086
 7S7  C25   C  CR16  0  -0.432   5.6830  -0.4776  -0.1397
 7S7  N21   N  N     0  -0.497   4.0611   1.1714  -0.7078
 7S7  C26   C  CR6   0   0.340   4.3976  -0.0984  -0.4875
 7S7  C20   C  CH2   0  -0.512   3.3257  -1.1306  -0.7131
 7S7  C17   C  CH1   0  -0.320   1.9639  -0.7852  -0.1045
 7S7  C18   C  CH2   0  -0.251   1.9154  -1.0191   1.4103
 7S7  N19   N  NH2   0  -0.783   2.9681  -0.3027   2.1038
 7S7  C16   C  CR6   0   0.253   0.8222  -1.5531  -0.7240
 7S7  N11   N  N     0  -0.432  -0.3633  -0.9495  -0.7038
 7S7  C15   C  CR16  0  -0.350   0.9768  -2.8409  -1.2313
 7S7  C14   C  CR16  0  -0.147  -0.1357  -3.4996  -1.7285
 7S7  C13   C  CR16  0  -0.356  -1.3664  -2.8641  -1.6993
 7S7  C12   C  CR6   0   0.239  -1.4380  -1.5786  -1.1732
 7S7  C09   C  CH2   0  -0.489  -2.7435  -0.8444  -1.0718
 7S7  C08   C  CH2   0  -0.491  -3.2064  -0.7264   0.3856
 7S7  C06   C  CR6   0   0.276  -4.4843   0.0525   0.5092
 7S7  N01   N  N     0  -0.485  -4.4188   1.3442   0.1773
 7S7  C02   C  CR6   0   0.440  -5.5231   2.0778   0.2482
 7S7  N02   N  NH2   0  -0.839  -5.4085   3.4053  -0.0523
 7S7  C03   C  CR16  0  -0.448  -6.7567   1.5409   0.6579
 7S7  C04   C  CR6   0   0.206  -6.8270   0.2067   0.9999
 7S7  C05   C  CR16  0  -0.434  -5.6552  -0.5560   0.9225
 7S7  C07   C  CH3   0  -0.728  -8.1140  -0.4162   1.4461
 7S7  H221  H  HNH2  0   0.385   5.1712   4.1410  -0.4732
 7S7  H222  H  HNH2  0   0.377   3.6162   3.5802  -0.8131
 7S7  H23   H  HCR6  0   0.251   7.0403   2.6161  -0.1166
 7S7  H271  H  HCH3  0   0.252   8.0914  -0.1550   1.4618
 7S7  H272  H  HCH3  0   0.248   8.4219  -0.7249  -0.1638
 7S7  H273  H  HCH3  0   0.245   8.7580   0.9543   0.2678
 7S7  H25   H  HCR6  0   0.235   5.9144  -1.5214   0.0318
 7S7  H201  H  HCH2  0   0.253   3.2061  -1.2359  -1.7973
 7S7  H202  H  HCH2  0   0.242   3.6786  -2.1001  -0.3518
 7S7  H17   H  HCH1  0   0.246   1.7692   0.2750  -0.2919
 7S7  H181  H  HCH2  0   0.203   0.9030  -0.7653   1.7571
 7S7  H182  H  HCH2  0   0.211   2.0461  -2.0898   1.6004
 7S7  H191  H  HNH2  0   0.337   2.8689   0.6918   1.9427
 7S7  H192  H  HNH2  0   0.346   2.8623  -0.4370   3.1014
 7S7  H15   H  HCR6  0   0.263   1.9445  -3.3235  -1.2427
 7S7  H14   H  HCR6  0   0.266  -0.0429  -4.4994  -2.1329
 7S7  H13   H  HCR6  0   0.260  -2.2558  -3.3521  -2.0758
 7S7  H091  H  HCH2  0   0.249  -2.6318   0.1579  -1.4911
 7S7  H092  H  HCH2  0   0.247  -3.5072  -1.3583  -1.6592
 7S7  H081  H  HCH2  0   0.246  -3.3399  -1.7238   0.8096
 7S7  H082  H  HCH2  0   0.248  -2.4216  -0.2329   0.9647
 7S7  H05   H  HCR6  0   0.243  -5.6636  -1.6086   1.1769
 7S7  H021  H  HNH2  0   0.379  -4.6040   3.6658  -0.5991
 7S7  H022  H  HNH2  0   0.387  -6.2496   3.8980  -0.3016
 7S7  H03   H  HCR6  0   0.255  -7.6363   2.1722   0.6992
 7S7  H071  H  HCH3  0   0.251  -8.3724  -1.2715   0.8203
 7S7  H072  H  HCH3  0   0.252  -8.0307  -0.7856   2.4694
 7S7  H073  H  HCH3  0   0.247  -8.9398   0.2925   1.4091

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
 7S7  N22  C22   single    1.368  0.020  1.368
 7S7  C22  C23   aromatic  1.403  0.020  1.403
 7S7  C22  N21   aromatic  1.329  0.020  1.329
 7S7  C23  C24   aromatic  1.382  0.020  1.382
 7S7  C24  C27   single    1.499  0.020  1.499
 7S7  C24  C25   aromatic  1.396  0.020  1.396
 7S7  C25  C26   aromatic  1.385  0.020  1.385
 7S7  N21  C26   aromatic  1.332  0.020  1.332
 7S7  C26  C20   single    1.505  0.020  1.505
 7S7  C20  C17   single    1.531  0.020  1.531
 7S7  C17  C18   single    1.533  0.020  1.533
 7S7  C17  C16   single    1.509  0.020  1.509
 7S7  C18  N19   single    1.450  0.020  1.450
 7S7  C16  N11   aromatic  1.330  0.020  1.330
 7S7  C16  C15   aromatic  1.393  0.020  1.393
 7S7  N11  C12   aromatic  1.331  0.020  1.331
 7S7  C15  C14   aromatic  1.385  0.020  1.385
 7S7  C14  C13   aromatic  1.385  0.020  1.385
 7S7  C13  C12   aromatic  1.391  0.020  1.391
 7S7  C12  C09   single    1.501  0.020  1.501
 7S7  C09  C08   single    1.534  0.020  1.534
 7S7  C08  C06   single    1.502  0.020  1.502
 7S7  C06  N01   aromatic  1.335  0.020  1.335
 7S7  C06  C05   aromatic  1.383  0.020  1.383
 7S7  N01  C02   aromatic  1.328  0.020  1.328
 7S7  C02  N02   single    1.366  0.020  1.366
 7S7  C02  C03   aromatic  1.406  0.020  1.406
 7S7  C03  C04   aromatic  1.379  0.020  1.379
 7S7  C04  C05   aromatic  1.400  0.020  1.400
 7S7  C04  C07   single    1.498  0.020  1.498
 7S7  N22  H221  single    0.890  0.020  1.040
 7S7  N22  H222  single    0.890  0.020  1.040
 7S7  C23  H23   single    0.930  0.020  1.080
 7S7  C27  H271  single    0.970  0.020  1.090
 7S7  C27  H272  single    0.970  0.020  1.090
 7S7  C27  H273  single    0.970  0.020  1.090
 7S7  C25  H25   single    0.930  0.020  1.080
 7S7  C20  H201  single    0.970  0.020  1.090
 7S7  C20  H202  single    0.970  0.020  1.090
 7S7  C17  H17   single    0.970  0.020  1.090
 7S7  C18  H181  single    0.970  0.020  1.090
 7S7  C18  H182  single    0.970  0.020  1.090
 7S7  N19  H191  single    0.890  0.020  1.040
 7S7  N19  H192  single    0.890  0.020  1.040
 7S7  C15  H15   single    0.930  0.020  1.080
 7S7  C14  H14   single    0.930  0.020  1.080
 7S7  C13  H13   single    0.930  0.020  1.080
 7S7  C09  H091  single    0.970  0.020  1.090
 7S7  C09  H092  single    0.970  0.020  1.090
 7S7  C08  H081  single    0.970  0.020  1.090
 7S7  C08  H082  single    0.970  0.020  1.090
 7S7  C05  H05   single    0.930  0.020  1.080
 7S7  N02  H021  single    0.890  0.020  1.040
 7S7  N02  H022  single    0.890  0.020  1.040
 7S7  C03  H03   single    0.930  0.020  1.080
 7S7  C07  H071  single    0.970  0.020  1.090
 7S7  C07  H072  single    0.970  0.020  1.090
 7S7  C07  H073  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
 7S7  H222  N22  H221  113.92  3.000
 7S7  H222  N22  C22   115.82  3.000
 7S7  H221  N22  C22   117.34  3.000
 7S7  N21   C22  C23   122.32  3.000
 7S7  N21   C22  N22   116.82  3.000
 7S7  C23   C22  N22   120.81  3.000
 7S7  H23   C23  C24   120.90  3.000
 7S7  H23   C23  C22   120.22  3.000
 7S7  C24   C23  C22   118.88  3.000
 7S7  C25   C24  C27   120.59  3.000
 7S7  C25   C24  C23   118.17  3.000
 7S7  C27   C24  C23   121.23  3.000
 7S7  H273  C27  H272  108.29  3.000
 7S7  H273  C27  H271  107.73  3.000
 7S7  H272  C27  H271  107.03  3.000
 7S7  H273  C27  C24   111.87  3.000
 7S7  H272  C27  C24   111.17  3.000
 7S7  H271  C27  C24   110.57  3.000
 7S7  H25   C25  C26   120.15  3.000
 7S7  H25   C25  C24   120.65  3.000
 7S7  C26   C25  C24   119.20  3.000
 7S7  C26   N21  C22   118.93  3.000
 7S7  C20   C26  N21   116.68  3.000
 7S7  C20   C26  C25   120.73  3.000
 7S7  N21   C26  C25   122.50  3.000
 7S7  H202  C20  H201  106.08  3.000
 7S7  H202  C20  C17   110.85  3.000
 7S7  H201  C20  C17   108.54  3.000
 7S7  H202  C20  C26   109.20  3.000
 7S7  H201  C20  C26   106.97  3.000
 7S7  C17   C20  C26   114.78  3.000
 7S7  H17   C17  C16   106.75  3.000
 7S7  H17   C17  C18   108.14  3.000
 7S7  C16   C17  C18   107.70  3.000
 7S7  H17   C17  C20   107.99  3.000
 7S7  C16   C17  C20   113.26  3.000
 7S7  C18   C17  C20   112.73  3.000
 7S7  H182  C18  H181  106.31  3.000
 7S7  H182  C18  N19   108.26  3.000
 7S7  H181  C18  N19   113.79  3.000
 7S7  H182  C18  C17   108.47  3.000
 7S7  H181  C18  C17   107.79  3.000
 7S7  N19   C18  C17   111.97  3.000
 7S7  H192  N19  H191  106.08  3.000
 7S7  H192  N19  C18   109.27  3.000
 7S7  H191  N19  C18   109.77  3.000
 7S7  C15   C16  N11   121.60  3.000
 7S7  C15   C16  C17   122.42  3.000
 7S7  N11   C16  C17   115.92  3.000
 7S7  C12   N11  C16   119.98  3.000
 7S7  H15   C15  C14   120.18  3.000
 7S7  H15   C15  C16   121.05  3.000
 7S7  C14   C15  C16   118.77  3.000
 7S7  H14   C14  C13   120.51  3.000
 7S7  H14   C14  C15   120.29  3.000
 7S7  C13   C14  C15   119.19  3.000
 7S7  H13   C13  C12   120.41  3.000
 7S7  H13   C13  C14   121.06  3.000
 7S7  C12   C13  C14   118.53  3.000
 7S7  C09   C12  C13   121.49  3.000
 7S7  C09   C12  N11   116.57  3.000
 7S7  C13   C12  N11   121.92  3.000
 7S7  H092  C09  H091  107.27  3.000
 7S7  H092  C09  C08   109.66  3.000
 7S7  H091  C09  C08   108.97  3.000
 7S7  H092  C09  C12   109.98  3.000
 7S7  H091  C09  C12   109.51  3.000
 7S7  C08   C09  C12   111.36  3.000
 7S7  H082  C08  H081  107.13  3.000
 7S7  H082  C08  C06   109.46  3.000
 7S7  H081  C08  C06   109.74  3.000
 7S7  H082  C08  C09   108.75  3.000
 7S7  H081  C08  C09   109.61  3.000
 7S7  C06   C08  C09   112.02  3.000
 7S7  C05   C06  N01   122.79  3.000
 7S7  C05   C06  C08   121.13  3.000
 7S7  N01   C06  C08   116.08  3.000
 7S7  C02   N01  C06   118.71  3.000
 7S7  C03   C02  N02   120.58  3.000
 7S7  C03   C02  N01   122.29  3.000
 7S7  N02   C02  N01   117.09  3.000
 7S7  H022  N02  H021  114.00  3.000
 7S7  H022  N02  C02   117.40  3.000
 7S7  H021  N02  C02   115.97  3.000
 7S7  H03   C03  C04   120.86  3.000
 7S7  H03   C03  C02   120.05  3.000
 7S7  C04   C03  C02   119.10  3.000
 7S7  C07   C04  C05   120.60  3.000
 7S7  C07   C04  C03   121.33  3.000
 7S7  C05   C04  C03   118.07  3.000
 7S7  H05   C05  C04   120.65  3.000
 7S7  H05   C05  C06   120.30  3.000
 7S7  C04   C05  C06   119.04  3.000
 7S7  H073  C07  H072  108.06  3.000
 7S7  H073  C07  H071  108.13  3.000
 7S7  H072  C07  H071  106.90  3.000
 7S7  H073  C07  C04   111.77  3.000
 7S7  H072  C07  C04   110.76  3.000
 7S7  H071  C07  C04   111.02  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
 7S7  CONST_01  C25   C24  C23  C22    0.00   0.0  0
 7S7  CONST_02  C25   C26  N21  C22    0.00   0.0  0
 7S7  CONST_03  C26   N21  C22  C23    0.00   0.0  0
 7S7  CONST_04  C26   C25  C24  C23    0.00   0.0  0
 7S7  CONST_05  N21   C22  C23  C24    0.00   0.0  0
 7S7  CONST_06  N21   C26  C25  C24    0.00   0.0  0
 7S7  CONST_07  C13   C12  N11  C16    0.00   0.0  0
 7S7  CONST_08  C13   C14  C15  C16    0.00   0.0  0
 7S7  CONST_09  C14   C15  C16  N11    0.00   0.0  0
 7S7  CONST_10  C14   C13  C12  N11    0.00   0.0  0
 7S7  CONST_11  C12   N11  C16  C15    0.00   0.0  0
 7S7  CONST_12  C12   C13  C14  C15    0.00   0.0  0
 7S7  CONST_13  C03   C02  N01  C06    0.00   0.0  0
 7S7  CONST_14  C03   C04  C05  C06    0.00   0.0  0
 7S7  CONST_15  C04   C05  C06  N01    0.00   0.0  0
 7S7  CONST_16  C04   C03  C02  N01    0.00   0.0  0
 7S7  CONST_17  C05   C06  N01  C02    0.00   0.0  0
 7S7  CONST_18  C05   C04  C03  C02    0.00   0.0  0
 7S7  CONST_19  C24   C23  C22  N22  180.00   0.0  0
 7S7  CONST_20  C26   N21  C22  N22  180.00   0.0  0
 7S7  CONST_21  C27   C24  C23  C22  180.00   0.0  0
 7S7  CONST_22  C20   C26  N21  C22  180.00   0.0  0
 7S7  CONST_23  C20   C26  C25  C24  180.00   0.0  0
 7S7  CONST_24  C26   C25  C24  C27  180.00   0.0  0
 7S7  CONST_25  C12   N11  C16  C17  180.00   0.0  0
 7S7  CONST_26  C14   C15  C16  C17  180.00   0.0  0
 7S7  CONST_27  C09   C12  N11  C16  180.00   0.0  0
 7S7  CONST_28  C09   C12  C13  C14  180.00   0.0  0
 7S7  CONST_29  C02   N01  C06  C08  180.00   0.0  0
 7S7  CONST_30  C04   C05  C06  C08  180.00   0.0  0
 7S7  CONST_31  N02   C02  N01  C06  180.00   0.0  0
 7S7  CONST_32  C07   C04  C05  C06  180.00   0.0  0
 7S7  CONST_33  C07   C04  C03  C02  180.00   0.0  0
 7S7  CONST_34  C04   C03  C02  N02  180.00   0.0  0
 7S7  CONST_35  H25   C25  C24  C23  180.00   0.0  0
 7S7  CONST_36  H23   C23  C24  C25  180.00   0.0  0
 7S7  CONST_37  H14   C14  C15  C16  180.00   0.0  0
 7S7  CONST_38  H15   C15  C16  N11  180.00   0.0  0
 7S7  CONST_39  H13   C13  C12  N11  180.00   0.0  0
 7S7  CONST_40  H05   C05  C06  N01  180.00   0.0  0
 7S7  CONST_41  H03   C03  C02  N01  180.00   0.0  0
 7S7  Var_01    C17   C20  C26  C25  137.29  30.0  2
 7S7  Var_02    C08   C09  C12  N11  -69.57  30.0  2
 7S7  Var_03    C06   C08  C09  C12  177.76  30.0  3
 7S7  Var_04    N01   C06  C08  C09  -65.79  30.0  2
 7S7  Var_05    H271  C27  C24  C23  106.38  30.0  2
 7S7  Var_06    H071  C07  C04  C03  123.65  30.0  2
 7S7  Var_07    H191  N19  C18  C17   60.45  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
 7S7  chir_01  C17  C20  C18  C16  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
 7S7  plan-1  N22   0.020
 7S7  plan-1  C22   0.020
 7S7  plan-1  C23   0.020
 7S7  plan-1  C24   0.020
 7S7  plan-1  C27   0.020
 7S7  plan-1  C25   0.020
 7S7  plan-1  N21   0.020
 7S7  plan-1  C26   0.020
 7S7  plan-1  C20   0.020
 7S7  plan-1  H23   0.020
 7S7  plan-1  H25   0.020
 7S7  plan-2  C17   0.020
 7S7  plan-2  C16   0.020
 7S7  plan-2  N11   0.020
 7S7  plan-2  C15   0.020
 7S7  plan-2  C14   0.020
 7S7  plan-2  C13   0.020
 7S7  plan-2  C12   0.020
 7S7  plan-2  C09   0.020
 7S7  plan-2  H15   0.020
 7S7  plan-2  H14   0.020
 7S7  plan-2  H13   0.020
 7S7  plan-3  C08   0.020
 7S7  plan-3  C06   0.020
 7S7  plan-3  N01   0.020
 7S7  plan-3  C02   0.020
 7S7  plan-3  N02   0.020
 7S7  plan-3  C03   0.020
 7S7  plan-3  C04   0.020
 7S7  plan-3  C05   0.020
 7S7  plan-3  C07   0.020
 7S7  plan-3  H05   0.020
 7S7  plan-3  H03   0.020
 7S7  plan-4  N22   0.020
 7S7  plan-4  C22   0.020
 7S7  plan-4  H221  0.020
 7S7  plan-4  H222  0.020
 7S7  plan-5  C02   0.020
 7S7  plan-5  N02   0.020
 7S7  plan-5  H021  0.020
 7S7  plan-5  H022  0.020

