# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 12:45:37 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-[2-(pyridin-3-ylmethylamino)pyrimidin-4-yl]pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccnc(c1)c2ccnc(NCc3cccnc3)n2
#
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
 5YQ  5YQ  '2-[2-(pyridin-3-ylmethylamino)pyrimidin-4-yl]pyridine-4-carboxylic acid'  ligand  36  23  .  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_5YQ
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
 5YQ  C01   C  CR16  0  -0.311  -2.7206   0.4989  -0.3483
 5YQ  C02   C  CR6   0   0.033  -4.0154   0.9816  -0.2229
 5YQ  C03   C  CR16  0  -0.328  -4.8784   0.3566   0.6674
 5YQ  C04   C  CR16  0  -0.059  -4.3983  -0.7277   1.3895
 5YQ  N05   N  N     0  -0.415  -3.1663  -1.1925   1.2707
 5YQ  C06   C  CR6   0   0.202  -2.3375  -0.5942   0.4204
 5YQ  C07   C  C     0   0.543  -4.4231   2.1505  -1.0554
 5YQ  O08   O  OH1   0  -0.586  -5.6734   2.5165  -0.8388
 5YQ  O09   O  O     0  -0.421  -3.6843   2.6931  -1.8374
 5YQ  C10   C  CR6   0   0.264  -0.9669  -1.1519   0.3170
 5YQ  N11   N  N     0  -0.498  -0.1239  -0.5162  -0.4795
 5YQ  C12   C  CR6   0   0.609   1.1137  -1.0099  -0.5899
 5YQ  N13   N  N     0  -0.458   1.5731  -2.0911   0.0468
 5YQ  C14   C  CR16  0  -0.007   0.7125  -2.7112   0.8376
 5YQ  C15   C  CR16  0  -0.369  -0.5925  -2.2909   1.0240
 5YQ  N16   N  NH1   0  -0.649   1.9420  -0.3619  -1.4325
 5YQ  C17   C  CH2   0  -0.397   3.3511  -0.6488  -1.5724
 5YQ  C18   C  CR6   0   0.027   4.1927  -0.0291  -0.4854
 5YQ  C19   C  CR16  0  -0.095   4.6491   1.2797  -0.6075
 5YQ  N20   N  N     0  -0.403   5.3679   1.9073   0.3142
 5YQ  C21   C  CR16  0  -0.071   5.6721   1.2394   1.4214
 5YQ  C22   C  CR16  0  -0.319   5.2800  -0.0714   1.6471
 5YQ  C23   C  CR16  0  -0.178   4.5277  -0.7148   0.6763
 5YQ  H01   H  HCR6  0   0.283  -2.0165   0.9554  -1.0287
 5YQ  H03   H  HCR6  0   0.287  -5.8980   0.6831   0.8110
 5YQ  H04   H  HCR6  0   0.278  -5.0449  -1.2379   2.0934
 5YQ  HO08  H  HOH1  0   0.494  -5.9056   3.2717  -1.4003
 5YQ  H14   H  HCR6  0   0.272   1.0822  -3.5903   1.3542
 5YQ  H15   H  HCR6  0   0.270  -1.2715  -2.8135   1.6782
 5YQ  HN16  H  HNH1  0   0.395   1.5999   0.5091  -1.8044
 5YQ  H17   H  HCH2  0   0.269   3.4996  -1.7275  -1.5939
 5YQ  H17A  H  HCH2  0   0.278   3.6598  -0.2636  -2.5442
 5YQ  H19   H  HCR6  0   0.258   4.4214   1.8457  -1.5067
 5YQ  H21   H  HCR6  0   0.264   6.2605   1.7693   2.1622
 5YQ  H22   H  HCR6  0   0.270   5.5630  -0.5743   2.5618
 5YQ  H23   H  HCR6  0   0.270   4.2061  -1.7384   0.8161

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
 5YQ  C02  C01   aromatic  1.388  0.020  1.388
 5YQ  C01  C06   aromatic  1.390  0.020  1.390
 5YQ  C01  H01   single    0.930  0.020  1.080
 5YQ  C07  C02   single    1.492  0.020  1.492
 5YQ  C03  C02   aromatic  1.389  0.020  1.389
 5YQ  C03  C04   aromatic  1.388  0.020  1.388
 5YQ  C03  H03   single    0.930  0.020  1.080
 5YQ  C04  N05   aromatic  1.322  0.020  1.322
 5YQ  C04  H04   single    0.930  0.020  1.080
 5YQ  N05  C06   aromatic  1.330  0.020  1.330
 5YQ  C06  C10   single    1.483  0.020  1.483
 5YQ  O09  C07   double    1.205  0.020  1.205
 5YQ  C07  O08   single    1.321  0.020  1.321
 5YQ  O08  HO08  single    0.850  0.020  0.980
 5YQ  C10  N11   aromatic  1.323  0.020  1.323
 5YQ  C10  C15   aromatic  1.392  0.020  1.392
 5YQ  N11  C12   aromatic  1.337  0.020  1.337
 5YQ  C12  N16   single    1.348  0.020  1.348
 5YQ  C12  N13   aromatic  1.336  0.020  1.336
 5YQ  C14  N13   aromatic  1.323  0.020  1.323
 5YQ  C15  C14   aromatic  1.384  0.020  1.384
 5YQ  C14  H14   single    0.930  0.020  1.080
 5YQ  C15  H15   single    0.930  0.020  1.080
 5YQ  N16  C17   single    1.445  0.020  1.445
 5YQ  N16  HN16  single    0.860  0.020  1.020
 5YQ  C18  C17   single    1.508  0.020  1.508
 5YQ  C17  H17   single    0.970  0.020  1.090
 5YQ  C17  H17A  single    0.970  0.020  1.090
 5YQ  C19  C18   aromatic  1.392  0.020  1.392
 5YQ  C18  C23   aromatic  1.390  0.020  1.390
 5YQ  N20  C19   aromatic  1.327  0.020  1.327
 5YQ  C19  H19   single    0.930  0.020  1.080
 5YQ  N20  C21   aromatic  1.328  0.020  1.328
 5YQ  C21  C22   aromatic  1.387  0.020  1.387
 5YQ  C21  H21   single    0.930  0.020  1.080
 5YQ  C22  C23   aromatic  1.386  0.020  1.386
 5YQ  C22  H22   single    0.930  0.020  1.080
 5YQ  C23  H23   single    0.930  0.020  1.080

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
 5YQ  H01   C01  C06  120.06  3.000
 5YQ  H01   C01  C02  121.20  3.000
 5YQ  C06   C01  C02  118.73  3.000
 5YQ  C07   C02  C03  122.72  3.000
 5YQ  C03   C02  C01  118.78  3.000
 5YQ  C07   C02  C01  118.50  3.000
 5YQ  H03   C03  C04  119.56  3.000
 5YQ  H03   C03  C02  122.40  3.000
 5YQ  C04   C03  C02  118.04  3.000
 5YQ  H04   C04  N05  116.68  3.000
 5YQ  H04   C04  C03  119.96  3.000
 5YQ  N05   C04  C03  123.37  3.000
 5YQ  C06   N05  C04  118.70  3.000
 5YQ  C10   C06  N05  116.84  3.000
 5YQ  C10   C06  C01  120.78  3.000
 5YQ  N05   C06  C01  122.38  3.000
 5YQ  O09   C07  O08  124.20  3.000
 5YQ  O08   C07  C02  112.60  3.000
 5YQ  O09   C07  C02  123.20  3.000
 5YQ  HO08  O08  C07  110.35  3.000
 5YQ  C15   C10  N11  121.86  3.000
 5YQ  C15   C10  C06  121.38  3.000
 5YQ  N11   C10  C06  116.76  3.000
 5YQ  C12   N11  C10  117.53  3.000
 5YQ  N16   C12  N13  118.41  3.000
 5YQ  N13   C12  N11  125.29  3.000
 5YQ  N16   C12  N11  116.29  3.000
 5YQ  C14   N13  C12  116.13  3.000
 5YQ  H14   C14  C15  120.24  3.000
 5YQ  H14   C14  N13  116.28  3.000
 5YQ  C15   C14  N13  123.48  3.000
 5YQ  H15   C15  C14  121.91  3.000
 5YQ  H15   C15  C10  122.38  3.000
 5YQ  C14   C15  C10  115.71  3.000
 5YQ  HN16  N16  C17  117.87  3.000
 5YQ  HN16  N16  C12  115.98  3.000
 5YQ  C17   N16  C12  124.36  3.000
 5YQ  H17A  C17  H17  107.08  3.000
 5YQ  H17A  C17  C18  109.84  3.000
 5YQ  H17   C17  C18  110.19  3.000
 5YQ  H17A  C17  N16  107.00  3.000
 5YQ  H17   C17  N16  109.37  3.000
 5YQ  C18   C17  N16  113.14  3.000
 5YQ  C23   C18  C19  117.28  3.000
 5YQ  C23   C18  C17  122.29  3.000
 5YQ  C19   C18  C17  120.42  3.000
 5YQ  H19   C19  N20  116.23  3.000
 5YQ  H19   C19  C18  119.60  3.000
 5YQ  N20   C19  C18  124.17  3.000
 5YQ  C21   N20  C19  117.73  3.000
 5YQ  H21   C21  C22  120.28  3.000
 5YQ  H21   C21  N20  116.61  3.000
 5YQ  C22   C21  N20  123.11  3.000
 5YQ  H22   C22  C23  121.22  3.000
 5YQ  H22   C22  C21  120.21  3.000
 5YQ  C23   C22  C21  118.56  3.000
 5YQ  H23   C23  C22  120.65  3.000
 5YQ  H23   C23  C18  120.20  3.000
 5YQ  C22   C23  C18  119.15  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
 5YQ  CONST_01  C04   C03  C02  C01    0.00   0.0  0
 5YQ  CONST_02  C04   N05  C06  C01    0.00   0.0  0
 5YQ  CONST_03  N11   C10  C06  C01    0.00   0.0  0
 5YQ  CONST_04  C15   C10  C06  C01  180.00   0.0  0
 5YQ  CONST_05  N05   C06  C01  C02    0.00   0.0  0
 5YQ  CONST_06  C10   C06  C01  C02  180.00   0.0  0
 5YQ  CONST_07  N05   C04  C03  C02    0.00   0.0  0
 5YQ  CONST_08  C06   C01  C02  C03    0.00   0.0  0
 5YQ  CONST_09  C06   N05  C04  C03    0.00   0.0  0
 5YQ  CONST_10  C10   C06  N05  C04  180.00   0.0  0
 5YQ  CONST_11  N11   C10  C06  N05  180.00   0.0  0
 5YQ  CONST_12  C15   C10  C06  N05    0.00   0.0  0
 5YQ  CONST_13  C12   N11  C10  C06  180.00   0.0  0
 5YQ  CONST_14  C14   C15  C10  C06  180.00   0.0  0
 5YQ  CONST_15  N13   C12  N11  C10    0.00   0.0  0
 5YQ  CONST_16  N13   C14  C15  C10    0.00   0.0  0
 5YQ  CONST_17  C14   C15  C10  N11    0.00   0.0  0
 5YQ  CONST_18  C14   N13  C12  N11    0.00   0.0  0
 5YQ  CONST_19  C15   C10  N11  C12    0.00   0.0  0
 5YQ  CONST_20  C15   C14  N13  C12    0.00   0.0  0
 5YQ  CONST_21  C21   N20  C19  C18    0.00   0.0  0
 5YQ  CONST_22  C21   C22  C23  C18    0.00   0.0  0
 5YQ  CONST_23  C22   C23  C18  C19    0.00   0.0  0
 5YQ  CONST_24  C22   C21  N20  C19    0.00   0.0  0
 5YQ  CONST_25  C23   C18  C19  N20    0.00   0.0  0
 5YQ  CONST_26  C23   C22  C21  N20    0.00   0.0  0
 5YQ  CONST_27  C07   C02  C03  C04  180.00   0.0  0
 5YQ  CONST_28  C07   C02  C01  C06  180.00   0.0  0
 5YQ  CONST_29  N16   C12  N11  C10  180.00   0.0  0
 5YQ  CONST_30  N16   C12  N13  C14  180.00   0.0  0
 5YQ  CONST_31  N20   C19  C18  C17  180.00   0.0  0
 5YQ  CONST_32  C22   C23  C18  C17  180.00   0.0  0
 5YQ  CONST_33  H03   C03  C02  C01  180.00   0.0  0
 5YQ  CONST_34  H04   C04  C03  C02  180.00   0.0  0
 5YQ  CONST_35  H01   C01  C02  C03  180.00   0.0  0
 5YQ  CONST_36  H15   C15  C10  C06    0.00   0.0  0
 5YQ  CONST_37  H14   C14  C15  C10  180.00   0.0  0
 5YQ  CONST_38  H22   C22  C23  C18  180.00   0.0  0
 5YQ  CONST_39  H23   C23  C18  C19  180.00   0.0  0
 5YQ  CONST_40  H21   C21  N20  C19  180.00   0.0  0
 5YQ  CONST_41  H19   C19  N20  C21  180.00   0.0  0
 5YQ  CONST_42  C17   N16  C12  N11  180.00   0.0  0
 5YQ  CONST_43  C17   N16  C12  N13    0.00   0.0  0
 5YQ  CONST_44  HN16  N16  C12  N11    0.00   0.0  0
 5YQ  CONST_45  HO08  O08  C07  C02  180.00   0.0  0
 5YQ  Var_01    O09   C07  C02  C01    0.37  30.0  3
 5YQ  Var_02    C18   C17  N16  C12  -80.00  30.0  3
 5YQ  Var_03    C19   C18  C17  N16  -85.85  30.0  2

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
 5YQ  plan-1  C01   0.020
 5YQ  plan-1  C02   0.020
 5YQ  plan-1  C03   0.020
 5YQ  plan-1  C04   0.020
 5YQ  plan-1  N05   0.020
 5YQ  plan-1  C06   0.020
 5YQ  plan-1  C07   0.020
 5YQ  plan-1  C10   0.020
 5YQ  plan-1  H01   0.020
 5YQ  plan-1  H03   0.020
 5YQ  plan-1  H04   0.020
 5YQ  plan-2  C06   0.020
 5YQ  plan-2  C10   0.020
 5YQ  plan-2  N11   0.020
 5YQ  plan-2  C12   0.020
 5YQ  plan-2  N13   0.020
 5YQ  plan-2  C14   0.020
 5YQ  plan-2  C15   0.020
 5YQ  plan-2  N16   0.020
 5YQ  plan-2  H14   0.020
 5YQ  plan-2  H15   0.020
 5YQ  plan-3  C17   0.020
 5YQ  plan-3  C18   0.020
 5YQ  plan-3  C19   0.020
 5YQ  plan-3  N20   0.020
 5YQ  plan-3  C21   0.020
 5YQ  plan-3  C22   0.020
 5YQ  plan-3  C23   0.020
 5YQ  plan-3  H19   0.020
 5YQ  plan-3  H21   0.020
 5YQ  plan-3  H22   0.020
 5YQ  plan-3  H23   0.020
 5YQ  plan-4  C12   0.020
 5YQ  plan-4  N16   0.020
 5YQ  plan-4  C17   0.020
 5YQ  plan-4  HN16  0.020
 5YQ  plan-5  C02   0.020
 5YQ  plan-5  C07   0.020
 5YQ  plan-5  O08   0.020
 5YQ  plan-5  O09   0.020
 5YQ  plan-5  HO08  0.020

