# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:01:42 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-5-{2-[4-methyl-6-(methylamino)pyridin-2-yl]ethyl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(C)cc(CCc2cc(CCc3cc(C)cc(N)n3)cc(c2)C#N)n1
#
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
 IVU  IVU  3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-5-{2-[4-methyl-6-(methylamino)pyridin-2-yl]ethyl}benzonitrile  ligand  56  29  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IVU
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
 IVU  C29   C  CH3   0  -0.726  -5.8994   4.2237  -0.4760
 IVU  C24   C  CR6   0   0.205  -5.8457   2.7332  -0.3369
 IVU  C25   C  CR16  0  -0.432  -4.6690   2.0330  -0.6302
 IVU  C23   C  CR16  0  -0.446  -6.9422   2.0112   0.0855
 IVU  C20   C  CR6   0   0.275  -4.6536   0.6581  -0.4858
 IVU  C22   C  CR6   0   0.440  -6.8378   0.6135   0.2020
 IVU  N28   N  NH2   0  -0.838  -7.8910  -0.1265   0.6584
 IVU  C19   C  CH2   0  -0.493  -3.4043  -0.1341  -0.7461
 IVU  N21   N  N     0  -0.483  -5.7166  -0.0402  -0.0801
 IVU  C14   C  CR6   0   0.171  -1.5176  -1.4139   0.3142
 IVU  C13   C  CR16  0  -0.344  -0.3236  -0.7531   0.0384
 IVU  C18   C  CH2   0  -0.515  -2.7772  -0.6346   0.5622
 IVU  C16   C  CR6   0   0.049  -0.3438  -3.4962   0.0447
 IVU  C12   C  CR6   0   0.171   0.8601  -1.4329  -0.2354
 IVU  C17   C  CR16  0  -0.335   0.8441  -2.8212  -0.2299
 IVU  C10   C  CH2   0  -0.493   2.7810  -0.2100   0.8261
 IVU  N01   N  N     0  -0.492   5.0561  -0.1140   0.0504
 IVU  C02   C  CR6   0   0.481   6.1906   0.5302  -0.2258
 IVU  C04   C  CR6   0   0.209   5.2910   2.6136   0.5655
 IVU  C03   C  CR16  0  -0.468   6.3457   1.9083   0.0193
 IVU  C06   C  CR6   0   0.277   4.0407   0.5695   0.5733
 IVU  C26   C  CSP   0   0.049  -0.3542  -4.9241   0.0490
 IVU  C05   C  CR16  0  -0.439   4.1074   1.9250   0.8489
 IVU  C11   C  CH2   0  -0.515   2.1312  -0.6730  -0.4848
 IVU  C15   C  CR16  0  -0.336  -1.5219  -2.8022   0.3153
 IVU  C08   C  CH3   0  -0.529   8.4321   0.3295  -1.2314
 IVU  H291  H  HCH3  0   0.252  -5.6737   4.5290  -1.4986
 IVU  H292  H  HCH3  0   0.247  -6.8783   4.6198  -0.2109
 IVU  H293  H  HCH3  0   0.251  -5.1575   4.6979   0.1683
 IVU  H25   H  HCR6  0   0.244  -3.7817   2.5558  -0.9650
 IVU  H23   H  HCR6  0   0.255  -7.8729   2.5090   0.3304
 IVU  H281  H  HNH2  0   0.388  -8.8119   0.2686   0.5658
 IVU  H282  H  HNH2  0   0.379  -7.8500  -1.1152   0.4723
 IVU  H191  H  HCH2  0   0.252  -3.6402  -0.9913  -1.3819
 IVU  H192  H  HCH2  0   0.250  -2.6811   0.4791  -1.2881
 IVU  H181  H  HCH2  0   0.256  -2.5582   0.2213   1.2057
 IVU  H182  H  HCH2  0   0.256  -3.5024  -1.2535   1.0938
 IVU  H13   H  HCR6  0   0.253  -0.3142   0.3321   0.0366
 IVU  H15   H  HCR6  0   0.272  -2.4339  -3.3461   0.5274
 IVU  H17   H  HCR6  0   0.271   1.7482  -3.3791  -0.4394
 IVU  H111  H  HCH2  0   0.256   2.8399  -1.2943  -1.0348
 IVU  H112  H  HCH2  0   0.255   1.9195   0.1991  -1.1086
 IVU  H101  H  HCH2  0   0.251   3.0112  -1.0850   1.4401
 IVU  H102  H  HCH2  0   0.250   2.0731   0.4004   1.3909
 IVU  H05   H  HCR6  0   0.242   3.2542   2.4388   1.2735
 IVU  H091  H  HCH3  0   0.250   4.6188   4.6392   0.3455
 IVU  H092  H  HCH3  0   0.252   5.2959   4.2734   1.9206
 IVU  H093  H  HCH3  0   0.246   6.3670   4.4804   0.5338
 IVU  H03   H  HCR6  0   0.260   7.2715   2.4143  -0.2215
 IVU  H07   H  HNH1  0   0.382   6.9475  -1.1525  -1.0195
 IVU  H081  H  HCH3  0   0.261   9.0322  -0.4809  -1.6365
 IVU  H082  H  HCH3  0   0.227   8.2857   1.0707  -2.0229
 IVU  H083  H  HCH3  0   0.233   9.0091   0.8010  -0.4330
 IVU  N07   N  NH1   0  -0.653   7.1950  -0.2175  -0.7434
 IVU  C09   C  CH3   0  -0.726   5.4060   4.0796   0.8526
 IVU  N27   N  NS    0  -0.254  -0.3621  -6.0765   0.0526

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
 IVU  C29  C24   single    1.498  0.020  1.498
 IVU  C24  C25   aromatic  1.400  0.020  1.400
 IVU  C24  C23   aromatic  1.379  0.020  1.379
 IVU  C25  C20   aromatic  1.383  0.020  1.383
 IVU  C23  C22   aromatic  1.406  0.020  1.406
 IVU  C22  N28   single    1.366  0.020  1.366
 IVU  C22  N21   aromatic  1.328  0.020  1.328
 IVU  N21  C20   aromatic  1.335  0.020  1.335
 IVU  C20  C19   single    1.502  0.020  1.502
 IVU  C19  C18   single    1.535  0.020  1.535
 IVU  C18  C14   single    1.502  0.020  1.502
 IVU  C14  C13   aromatic  1.392  0.020  1.392
 IVU  C14  C15   aromatic  1.388  0.020  1.388
 IVU  C13  C12   aromatic  1.392  0.020  1.392
 IVU  C15  C16   aromatic  1.394  0.020  1.394
 IVU  C16  C26   single    1.428  0.020  1.428
 IVU  C16  C17   aromatic  1.394  0.020  1.394
 IVU  C26  N27   triple    1.152  0.020  1.152
 IVU  C17  C12   aromatic  1.388  0.020  1.388
 IVU  C12  C11   single    1.502  0.020  1.502
 IVU  C11  C10   single    1.535  0.020  1.535
 IVU  C10  C06   single    1.503  0.020  1.503
 IVU  C06  N01   aromatic  1.331  0.020  1.331
 IVU  C06  C05   aromatic  1.385  0.020  1.385
 IVU  N01  C02   aromatic  1.334  0.020  1.334
 IVU  C05  C04   aromatic  1.398  0.020  1.398
 IVU  C04  C09   single    1.498  0.020  1.498
 IVU  C04  C03   aromatic  1.381  0.020  1.381
 IVU  C03  C02   aromatic  1.408  0.020  1.408
 IVU  C02  N07   single    1.355  0.020  1.355
 IVU  N07  C08   single    1.438  0.020  1.438
 IVU  C29  H291  single    0.970  0.020  1.090
 IVU  C29  H292  single    0.970  0.020  1.090
 IVU  C29  H293  single    0.970  0.020  1.090
 IVU  C25  H25   single    0.930  0.020  1.080
 IVU  C23  H23   single    0.930  0.020  1.080
 IVU  N28  H281  single    0.890  0.020  1.040
 IVU  N28  H282  single    0.890  0.020  1.040
 IVU  C19  H191  single    0.970  0.020  1.090
 IVU  C19  H192  single    0.970  0.020  1.090
 IVU  C18  H181  single    0.970  0.020  1.090
 IVU  C18  H182  single    0.970  0.020  1.090
 IVU  C13  H13   single    0.930  0.020  1.080
 IVU  C15  H15   single    0.930  0.020  1.080
 IVU  C17  H17   single    0.930  0.020  1.080
 IVU  C11  H111  single    0.970  0.020  1.090
 IVU  C11  H112  single    0.970  0.020  1.090
 IVU  C10  H101  single    0.970  0.020  1.090
 IVU  C10  H102  single    0.970  0.020  1.090
 IVU  C05  H05   single    0.930  0.020  1.080
 IVU  C09  H091  single    0.970  0.020  1.090
 IVU  C09  H092  single    0.970  0.020  1.090
 IVU  C09  H093  single    0.970  0.020  1.090
 IVU  C03  H03   single    0.930  0.020  1.080
 IVU  N07  H07   single    0.860  0.020  1.020
 IVU  C08  H081  single    0.970  0.020  1.090
 IVU  C08  H082  single    0.970  0.020  1.090
 IVU  C08  H083  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
 IVU  H293  C29  H292  108.03  3.000
 IVU  H293  C29  H291  106.94  3.000
 IVU  H292  C29  H291  108.21  3.000
 IVU  H293  C29  C24   110.69  3.000
 IVU  H292  C29  C24   111.81  3.000
 IVU  H291  C29  C24   110.98  3.000
 IVU  C23   C24  C25   118.06  3.000
 IVU  C23   C24  C29   121.39  3.000
 IVU  C25   C24  C29   120.55  3.000
 IVU  H25   C25  C20   120.21  3.000
 IVU  H25   C25  C24   120.79  3.000
 IVU  C20   C25  C24   119.00  3.000
 IVU  H23   C23  C22   120.10  3.000
 IVU  H23   C23  C24   120.78  3.000
 IVU  C22   C23  C24   119.12  3.000
 IVU  N21   C20  C19   116.05  3.000
 IVU  C19   C20  C25   121.04  3.000
 IVU  N21   C20  C25   122.89  3.000
 IVU  N21   C22  N28   117.09  3.000
 IVU  N21   C22  C23   122.29  3.000
 IVU  N28   C22  C23   120.59  3.000
 IVU  H282  N28  H281  113.95  3.000
 IVU  H282  N28  C22   116.03  3.000
 IVU  H281  N28  C22   117.53  3.000
 IVU  H192  C19  H191  107.13  3.000
 IVU  H192  C19  C18   109.60  3.000
 IVU  H191  C19  C18   109.16  3.000
 IVU  H192  C19  C20   109.92  3.000
 IVU  H191  C19  C20   109.57  3.000
 IVU  C18   C19  C20   111.36  3.000
 IVU  C22   N21  C20   118.64  3.000
 IVU  C15   C14  C18   121.08  3.000
 IVU  C15   C14  C13   118.51  3.000
 IVU  C18   C14  C13   120.38  3.000
 IVU  H13   C13  C12   118.72  3.000
 IVU  H13   C13  C14   118.84  3.000
 IVU  C12   C13  C14   122.44  3.000
 IVU  H182  C18  H181  106.88  3.000
 IVU  H182  C18  C14   110.08  3.000
 IVU  H181  C18  C14   109.60  3.000
 IVU  H182  C18  C19   109.19  3.000
 IVU  H181  C18  C19   109.17  3.000
 IVU  C14   C18  C19   111.79  3.000
 IVU  C15   C16  C26   119.42  3.000
 IVU  C26   C16  C17   119.41  3.000
 IVU  C15   C16  C17   121.17  3.000
 IVU  C11   C12  C17   121.09  3.000
 IVU  C11   C12  C13   120.35  3.000
 IVU  C17   C12  C13   118.53  3.000
 IVU  H17   C17  C12   120.31  3.000
 IVU  H17   C17  C16   120.02  3.000
 IVU  C12   C17  C16   119.66  3.000
 IVU  H102  C10  H101  107.06  3.000
 IVU  H102  C10  C11   109.63  3.000
 IVU  H101  C10  C11   109.11  3.000
 IVU  H102  C10  C06   109.90  3.000
 IVU  H101  C10  C06   109.45  3.000
 IVU  C11   C10  C06   111.58  3.000
 IVU  C06   N01  C02   118.84  3.000
 IVU  N07   C02  C03   121.66  3.000
 IVU  N07   C02  N01   116.31  3.000
 IVU  C03   C02  N01   122.03  3.000
 IVU  C05   C04  C03   118.36  3.000
 IVU  C03   C04  C09   121.12  3.000
 IVU  C05   C04  C09   120.53  3.000
 IVU  H03   C03  C04   120.16  3.000
 IVU  H03   C03  C02   120.86  3.000
 IVU  C04   C03  C02   118.97  3.000
 IVU  C05   C06  N01   122.96  3.000
 IVU  C05   C06  C10   120.97  3.000
 IVU  N01   C06  C10   116.05  3.000
 IVU  N27   C26  C16   180.00  3.000
 IVU  H05   C05  C06   120.30  3.000
 IVU  H05   C05  C04   120.85  3.000
 IVU  C06   C05  C04   118.85  3.000
 IVU  H112  C11  H111  107.01  3.000
 IVU  H112  C11  C10   109.20  3.000
 IVU  H111  C11  C10   109.10  3.000
 IVU  H112  C11  C12   109.55  3.000
 IVU  H111  C11  C12   110.20  3.000
 IVU  C10   C11  C12   111.66  3.000
 IVU  H15   C15  C16   119.99  3.000
 IVU  H15   C15  C14   120.33  3.000
 IVU  C16   C15  C14   119.68  3.000
 IVU  H083  C08  H082  107.88  3.000
 IVU  H083  C08  H081  107.62  3.000
 IVU  H082  C08  H081  108.03  3.000
 IVU  H083  C08  N07   111.76  3.000
 IVU  H082  C08  N07   112.83  3.000
 IVU  H081  C08  N07   108.54  3.000
 IVU  H07   N07  C08   118.17  3.000
 IVU  H07   N07  C02   115.82  3.000
 IVU  C08   N07  C02   123.88  3.000
 IVU  H093  C09  H092  108.08  3.000
 IVU  H093  C09  H091  108.18  3.000
 IVU  H092  C09  H091  106.92  3.000
 IVU  H093  C09  C04   111.82  3.000
 IVU  H092  C09  C04   110.71  3.000
 IVU  H091  C09  C04   110.95  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
 IVU  CONST_01  N21   C20  C25  C24     0.00   0.0  0
 IVU  CONST_02  N21   C22  C23  C24     0.00   0.0  0
 IVU  CONST_03  C22   C23  C24  C25     0.00   0.0  0
 IVU  CONST_04  C22   N21  C20  C25     0.00   0.0  0
 IVU  CONST_05  C20   C25  C24  C23     0.00   0.0  0
 IVU  CONST_06  C20   N21  C22  C23     0.00   0.0  0
 IVU  CONST_07  C17   C12  C13  C14     0.00   0.0  0
 IVU  CONST_08  C17   C16  C15  C14     0.00   0.0  0
 IVU  CONST_09  C16   C15  C14  C13     0.00   0.0  0
 IVU  CONST_10  C16   C17  C12  C13     0.00   0.0  0
 IVU  CONST_11  C15   C14  C13  C12     0.00   0.0  0
 IVU  CONST_12  C15   C16  C17  C12     0.00   0.0  0
 IVU  CONST_13  C04   C05  C06  N01     0.00   0.0  0
 IVU  CONST_14  C04   C03  C02  N01     0.00   0.0  0
 IVU  CONST_15  C05   C06  N01  C02     0.00   0.0  0
 IVU  CONST_16  C05   C04  C03  C02     0.00   0.0  0
 IVU  CONST_17  C06   C05  C04  C03     0.00   0.0  0
 IVU  CONST_18  C06   N01  C02  C03     0.00   0.0  0
 IVU  CONST_19  C20   C25  C24  C29   180.00   0.0  0
 IVU  CONST_20  C22   C23  C24  C29   180.00   0.0  0
 IVU  CONST_21  C19   C20  C25  C24   180.00   0.0  0
 IVU  CONST_22  N28   C22  C23  C24   180.00   0.0  0
 IVU  CONST_23  N28   C22  N21  C20   180.00   0.0  0
 IVU  CONST_24  C19   C20  N21  C22   180.00   0.0  0
 IVU  CONST_25  C11   C12  C13  C14   180.00   0.0  0
 IVU  CONST_26  C26   C16  C15  C14   180.00   0.0  0
 IVU  CONST_27  C12   C13  C14  C18   180.00   0.0  0
 IVU  CONST_28  C16   C15  C14  C18   180.00   0.0  0
 IVU  CONST_29  C11   C12  C17  C16   180.00   0.0  0
 IVU  CONST_30  C26   C16  C17  C12   180.00   0.0  0
 IVU  CONST_31  C02   N01  C06  C10   180.00   0.0  0
 IVU  CONST_32  C04   C05  C06  C10   180.00   0.0  0
 IVU  CONST_33  C09   C04  C03  C02   180.00   0.0  0
 IVU  CONST_34  C06   C05  C04  C09   180.00   0.0  0
 IVU  CONST_35  N07   C02  C03  C04   180.00   0.0  0
 IVU  CONST_36  N07   C02  N01  C06   180.00   0.0  0
 IVU  CONST_37  H23   C23  C24  C25   180.00   0.0  0
 IVU  CONST_38  H25   C25  C24  C23   180.00   0.0  0
 IVU  CONST_39  H15   C15  C14  C13   180.00   0.0  0
 IVU  CONST_40  H17   C17  C12  C13   180.00   0.0  0
 IVU  CONST_41  H13   C13  C12  C17   180.00   0.0  0
 IVU  CONST_42  H05   C05  C06  N01   180.00   0.0  0
 IVU  CONST_43  H03   C03  C02  N01   180.00   0.0  0
 IVU  CONST_44  C08   N07  C02  N01   180.00   0.0  0
 IVU  CONST_45  C08   N07  C02  C03     0.00   0.0  0
 IVU  CONST_48  H07   N07  C02  N01     0.00   0.0  0
 IVU  Var_01    C18   C19  C20  C25   106.76  30.0  2
 IVU  Var_02    C14   C18  C19  C20  -179.29  30.0  3
 IVU  Var_03    C13   C14  C18  C19    78.41  30.0  2
 IVU  Var_04    C10   C11  C12  C13    79.82  30.0  2
 IVU  Var_05    C06   C10  C11  C12  -179.07  30.0  3
 IVU  Var_06    C11   C10  C06  N01   -66.81  30.0  1
 IVU  Var_07    H291  C29  C24  C25    59.15  30.0  2
 IVU  Var_08    H091  C09  C04  C03   123.76  30.0  2
 IVU  Var_09    H081  C08  N07  C02  -177.02  30.0  3

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
 IVU  plan-1  C29   0.020
 IVU  plan-1  C24   0.020
 IVU  plan-1  C25   0.020
 IVU  plan-1  C23   0.020
 IVU  plan-1  C20   0.020
 IVU  plan-1  C22   0.020
 IVU  plan-1  N28   0.020
 IVU  plan-1  C19   0.020
 IVU  plan-1  N21   0.020
 IVU  plan-1  H25   0.020
 IVU  plan-1  H23   0.020
 IVU  plan-2  C14   0.020
 IVU  plan-2  C13   0.020
 IVU  plan-2  C18   0.020
 IVU  plan-2  C16   0.020
 IVU  plan-2  C12   0.020
 IVU  plan-2  C17   0.020
 IVU  plan-2  C26   0.020
 IVU  plan-2  C11   0.020
 IVU  plan-2  C15   0.020
 IVU  plan-2  H13   0.020
 IVU  plan-2  H15   0.020
 IVU  plan-2  H17   0.020
 IVU  plan-2  N27   0.020
 IVU  plan-3  C10   0.020
 IVU  plan-3  N01   0.020
 IVU  plan-3  C02   0.020
 IVU  plan-3  C04   0.020
 IVU  plan-3  C03   0.020
 IVU  plan-3  C06   0.020
 IVU  plan-3  C05   0.020
 IVU  plan-3  H05   0.020
 IVU  plan-3  H03   0.020
 IVU  plan-3  N07   0.020
 IVU  plan-3  C09   0.020
 IVU  plan-4  C22   0.020
 IVU  plan-4  N28   0.020
 IVU  plan-4  H281  0.020
 IVU  plan-4  H282  0.020
 IVU  plan-5  C02   0.020
 IVU  plan-5  C08   0.020
 IVU  plan-5  H07   0.020
 IVU  plan-5  N07   0.020

