# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:20:59 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(O)c(Cn2c(NC3CCN(CCN)CC3)nc4c(C)cccc24)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
 5NK  5NK  2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol  ligand  59  29  .  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_5NK
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
 5NK  C10  C  CH3   0  -0.724  -1.2508   4.7402   1.4116
 5NK  C15  C  CR16  0  -0.334  -2.6603  -4.0240   0.9146
 5NK  C17  C  CR6   0   0.288  -3.7061  -2.3150  -0.3941
 5NK  C20  C  CH2   0  -0.435   2.5780   1.1835  -0.8637
 5NK  C21  C  CH2   0  -0.286   3.9999   1.3913  -0.3667
 5NK  C24  C  CH2   0  -0.472   2.5805  -1.0315   0.2584
 5NK  C01  C  CR6   0  -0.002  -2.1779   3.7770   0.7368
 5NK  C02  C  CR16  0  -0.329  -3.5322   4.0434   0.5531
 5NK  C03  C  CR16  0  -0.277  -4.3943   3.1321  -0.0634
 5NK  C04  C  CR16  0  -0.331  -3.9371   1.9052  -0.5286
 5NK  C05  C  CR56  0   0.123  -1.7126   2.5480   0.2687
 5NK  C06  C  CR56  0   0.346  -2.5878   1.6445  -0.3537
 5NK  N07  N  NR5   0  -0.576  -1.8001   0.5644  -0.6942
 5NK  C08  C  CR5   0   0.693  -0.5336   0.8494  -0.2490
 5NK  N09  N  N     0  -0.521  -0.4418   2.0249   0.3239
 5NK  C11  C  CH2   0  -0.418  -2.1947  -0.5804  -1.4870
 5NK  C12  C  CR6   0   0.170  -2.4306  -1.8106  -0.6483
 5NK  N13  N  N     0  -0.457  -1.3415  -2.3826  -0.1490
 5NK  C14  C  CR6   0   0.242  -1.4221  -3.4590   0.6244
 5NK  C16  C  CR16  0  -0.262  -3.8086  -3.4496   0.4031
 5NK  N18  N  NH1   0  -0.737   0.4751  -0.0290  -0.4371
 5NK  C19  C  CH1   0  -0.043   1.8026   0.2631   0.0722
 5NK  N22  N  NT    0  -0.422   4.6926   0.1227  -0.2271
 5NK  C23  C  CH2   0  -0.287   3.9984  -0.7326   0.7182
 5NK  C25  C  CH2   0  -0.267   6.0936   0.2947   0.1077
 5NK  N27  N  NH2   0  -0.802   8.3344  -0.6631   0.0850
 5NK  H1   H  HCH3  0   0.239  -0.8788   4.3366   2.3556
 5NK  H2   H  HCH3  0   0.238  -0.3756   4.9533   0.7958
 5NK  H3   H  HCH3  0   0.239  -1.7487   5.6844   1.6277
 5NK  H4   H  HCR6  0   0.272  -2.7273  -4.9063   1.5370
 5NK  H5   H  HCH2  0   0.239   2.0739   2.1478  -0.9495
 5NK  H6   H  HCH2  0   0.217   2.6050   0.7347  -1.8607
 5NK  H7   H  HCH2  0   0.237   4.5444   2.0132  -1.0810
 5NK  H8   H  HCH2  0   0.186   3.9798   1.9526   0.5854
 5NK  H9   H  HCH2  0   0.243   2.0891  -1.6693   0.9981
 5NK  H10  H  HCH2  0   0.227   2.6096  -1.5862  -0.6851
 5NK  H11  H  HCH2  0   0.198   6.5384  -1.8260   0.1675
 5NK  H12  H  HCH2  0   0.217   6.8849  -1.0382  -1.3604
 5NK  H13  H  HCH3  0   0.253   0.2111  -3.4038   2.0102
 5NK  H14  H  HCH3  0   0.249  -0.2760  -5.0292   1.5465
 5NK  H15  H  HCH3  0   0.248   0.6391  -4.0210   0.4210
 5NK  H16  H  HCR6  0   0.236  -3.9323   4.9870   0.9058
 5NK  H17  H  HCR6  0   0.243  -5.4405   3.3854  -0.1761
 5NK  H18  H  HCR6  0   0.255  -4.6077   1.1929  -0.9918
 5NK  H19  H  HCH2  0   0.294  -3.0769  -0.3031  -2.0596
 5NK  H20  H  HCH2  0   0.292  -1.4024  -0.7866  -2.2099
 5NK  H21  H  HCR6  0   0.290  -4.7788  -3.8817   0.6201
 5NK  H22  H  HNH1  0   0.412   0.1862  -1.0046  -0.4368
 5NK  H23  H  HCH1  0   0.221   1.7212   0.7548   1.0503
 5NK  H25  H  HCH2  0   0.190   3.9617  -0.2692   1.7208
 5NK  H26  H  HCH2  0   0.242   4.5421  -1.6711   0.8309
 5NK  H27  H  HCH2  0   0.187   6.2330   0.5219   1.1798
 5NK  H28  H  HCH2  0   0.228   6.4769   1.1596  -0.4392
 5NK  H29  H  HNH2  0   0.339   8.4254  -0.6902   1.0934
 5NK  H30  H  HNH2  0   0.349   8.9094  -1.4220  -0.2569
 5NK  H32  H  HOH1  0   0.482  -5.5868  -2.1410  -0.6896
 5NK  O29  O  OH1   0  -0.624  -4.7691  -1.6914  -0.9320
 5NK  C26  C  CH2   0  -0.295   6.9453  -0.9081  -0.2776
 5NK  C28  C  CH3   0  -0.720  -0.1452  -4.0134   1.1773

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
 5NK  C04  C03  aromatic  1.390  0.020  1.390
 5NK  C04  C06  aromatic  1.385  0.020  1.385
 5NK  C28  C14  single    1.498  0.020  1.498
 5NK  C11  C12  single    1.507  0.020  1.507
 5NK  C11  N07  single    1.447  0.020  1.447
 5NK  N13  C14  aromatic  1.328  0.020  1.328
 5NK  N13  C12  aromatic  1.328  0.020  1.328
 5NK  C03  C02  aromatic  1.398  0.020  1.398
 5NK  C14  C15  aromatic  1.392  0.020  1.392
 5NK  C12  C17  aromatic  1.395  0.020  1.395
 5NK  C06  N07  aromatic  1.380  0.020  1.380
 5NK  C06  C05  aromatic  1.403  0.020  1.403
 5NK  N07  C08  aromatic  1.372  0.020  1.372
 5NK  C02  C01  aromatic  1.392  0.020  1.392
 5NK  C15  C16  aromatic  1.382  0.020  1.382
 5NK  C17  O29  single    1.345  0.020  1.345
 5NK  C17  C16  aromatic  1.390  0.020  1.390
 5NK  C19  C24  single    1.522  0.020  1.522
 5NK  C19  N18  single    1.452  0.020  1.452
 5NK  C19  C20  single    1.525  0.020  1.525
 5NK  C05  C01  aromatic  1.395  0.020  1.395
 5NK  C05  N09  aromatic  1.375  0.020  1.375
 5NK  C08  N18  single    1.351  0.020  1.351
 5NK  C08  N09  aromatic  1.311  0.020  1.311
 5NK  C24  C23  single    1.520  0.020  1.520
 5NK  C01  C10  single    1.498  0.020  1.498
 5NK  C20  C21  single    1.521  0.020  1.521
 5NK  C23  N22  single    1.452  0.020  1.452
 5NK  C21  N22  single    1.452  0.020  1.452
 5NK  C25  N22  single    1.451  0.020  1.451
 5NK  C25  C26  single    1.523  0.020  1.523
 5NK  C26  N27  single    1.456  0.020  1.456
 5NK  C10  H1   single    0.970  0.020  1.090
 5NK  C10  H2   single    0.970  0.020  1.090
 5NK  C10  H3   single    0.970  0.020  1.090
 5NK  C15  H4   single    0.930  0.020  1.080
 5NK  C20  H5   single    0.970  0.020  1.090
 5NK  C20  H6   single    0.970  0.020  1.090
 5NK  C21  H7   single    0.970  0.020  1.090
 5NK  C21  H8   single    0.970  0.020  1.090
 5NK  C24  H9   single    0.970  0.020  1.090
 5NK  C24  H10  single    0.970  0.020  1.090
 5NK  C26  H11  single    0.970  0.020  1.090
 5NK  C26  H12  single    0.970  0.020  1.090
 5NK  C28  H13  single    0.970  0.020  1.090
 5NK  C28  H14  single    0.970  0.020  1.090
 5NK  C28  H15  single    0.970  0.020  1.090
 5NK  C02  H16  single    0.930  0.020  1.080
 5NK  C03  H17  single    0.930  0.020  1.080
 5NK  C04  H18  single    0.930  0.020  1.080
 5NK  C11  H19  single    0.970  0.020  1.090
 5NK  C11  H20  single    0.970  0.020  1.090
 5NK  C16  H21  single    0.930  0.020  1.080
 5NK  N18  H22  single    0.890  0.020  1.040
 5NK  C19  H23  single    0.970  0.020  1.090
 5NK  C23  H25  single    0.970  0.020  1.090
 5NK  C23  H26  single    0.970  0.020  1.090
 5NK  C25  H27  single    0.970  0.020  1.090
 5NK  C25  H28  single    0.970  0.020  1.090
 5NK  N27  H29  single    0.890  0.020  1.040
 5NK  N27  H30  single    0.890  0.020  1.040
 5NK  O29  H32  single    0.850  0.020  0.980

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
 5NK  H3   C10  H2   108.02  3.000
 5NK  H3   C10  H1   107.74  3.000
 5NK  H2   C10  H1   106.67  3.000
 5NK  H3   C10  C01  111.35  3.000
 5NK  H2   C10  C01  111.58  3.000
 5NK  H1   C10  C01  111.27  3.000
 5NK  H4   C15  C16  120.02  3.000
 5NK  H4   C15  C14  120.42  3.000
 5NK  C16  C15  C14  119.56  3.000
 5NK  O29  C17  C16  123.33  3.000
 5NK  C16  C17  C12  117.84  3.000
 5NK  O29  C17  C12  118.83  3.000
 5NK  H6   C20  H5   107.59  3.000
 5NK  H6   C20  C19  108.94  3.000
 5NK  H5   C20  C19  110.29  3.000
 5NK  H6   C20  C21  109.32  3.000
 5NK  H5   C20  C21  109.68  3.000
 5NK  C19  C20  C21  110.95  3.000
 5NK  H8   C21  H7   106.44  3.000
 5NK  H8   C21  N22  111.68  3.000
 5NK  H7   C21  N22  108.81  3.000
 5NK  H8   C21  C20  109.50  3.000
 5NK  H7   C21  C20  109.28  3.000
 5NK  N22  C21  C20  110.99  3.000
 5NK  H10  C24  H9   107.42  3.000
 5NK  H10  C24  C23  109.60  3.000
 5NK  H9   C24  C23  109.23  3.000
 5NK  H10  C24  C19  109.82  3.000
 5NK  H9   C24  C19  110.44  3.000
 5NK  C23  C24  C19  110.28  3.000
 5NK  C05  C01  C02  116.66  3.000
 5NK  C05  C01  C10  120.75  3.000
 5NK  C02  C01  C10  122.58  3.000
 5NK  H16  C02  C03  118.91  3.000
 5NK  H16  C02  C01  118.86  3.000
 5NK  C03  C02  C01  122.23  3.000
 5NK  H17  C03  C04  119.33  3.000
 5NK  H17  C03  C02  119.31  3.000
 5NK  C04  C03  C02  121.36  3.000
 5NK  H18  C04  C06  122.25  3.000
 5NK  H18  C04  C03  121.37  3.000
 5NK  C06  C04  C03  116.38  3.000
 5NK  N09  C05  C06  110.44  3.000
 5NK  N09  C05  C01  129.03  3.000
 5NK  C06  C05  C01  120.52  3.000
 5NK  N07  C06  C05  104.91  3.000
 5NK  C05  C06  C04  122.84  3.000
 5NK  N07  C06  C04  132.25  3.000
 5NK  C11  N07  C08  126.41  3.000
 5NK  C08  N07  C06  106.52  3.000
 5NK  C11  N07  C06  126.79  3.000
 5NK  N18  C08  N09  126.28  3.000
 5NK  N09  C08  N07  113.12  3.000
 5NK  N18  C08  N07  120.59  3.000
 5NK  C08  N09  C05  105.00  3.000
 5NK  H20  C11  H19  106.75  3.000
 5NK  H20  C11  C12  109.13  3.000
 5NK  H19  C11  C12  111.96  3.000
 5NK  H20  C11  N07  108.31  3.000
 5NK  H19  C11  N07  107.93  3.000
 5NK  C12  C11  N07  112.54  3.000
 5NK  N13  C12  C11  115.63  3.000
 5NK  N13  C12  C17  121.72  3.000
 5NK  C11  C12  C17  122.65  3.000
 5NK  C14  N13  C12  121.23  3.000
 5NK  N13  C14  C28  117.60  3.000
 5NK  N13  C14  C15  120.31  3.000
 5NK  C28  C14  C15  122.08  3.000
 5NK  H21  C16  C17  120.40  3.000
 5NK  H21  C16  C15  120.26  3.000
 5NK  C17  C16  C15  119.35  3.000
 5NK  H22  N18  C19  116.91  3.000
 5NK  H22  N18  C08  114.29  3.000
 5NK  C19  N18  C08  120.21  3.000
 5NK  H23  C19  N18  109.57  3.000
 5NK  H23  C19  C24  108.06  3.000
 5NK  N18  C19  C24  109.83  3.000
 5NK  H23  C19  C20  108.32  3.000
 5NK  N18  C19  C20  111.79  3.000
 5NK  C24  C19  C20  109.19  3.000
 5NK  C25  N22  C23  112.42  3.000
 5NK  C25  N22  C21  112.30  3.000
 5NK  C23  N22  C21  110.44  3.000
 5NK  H26  C23  H25  106.48  3.000
 5NK  H26  C23  N22  109.63  3.000
 5NK  H25  C23  N22  111.08  3.000
 5NK  H26  C23  C24  109.09  3.000
 5NK  H25  C23  C24  109.01  3.000
 5NK  N22  C23  C24  111.40  3.000
 5NK  H28  C25  H27  106.18  3.000
 5NK  H28  C25  N22  108.48  3.000
 5NK  H27  C25  N22  111.73  3.000
 5NK  H28  C25  C26  107.60  3.000
 5NK  H27  C25  C26  109.72  3.000
 5NK  N22  C25  C26  112.83  3.000
 5NK  H30  N27  H29  105.39  3.000
 5NK  H30  N27  C26  109.37  3.000
 5NK  H29  N27  C26  109.21  3.000
 5NK  H32  O29  C17  110.71  3.000
 5NK  H12  C26  H11  106.37  3.000
 5NK  H12  C26  N27  108.63  3.000
 5NK  H11  C26  N27  113.15  3.000
 5NK  H12  C26  C25  108.29  3.000
 5NK  H11  C26  C25  110.51  3.000
 5NK  N27  C26  C25  109.72  3.000
 5NK  H15  C28  H14  108.39  3.000
 5NK  H15  C28  H13  107.36  3.000
 5NK  H14  C28  H13  107.54  3.000
 5NK  H15  C28  C14  111.10  3.000
 5NK  H14  C28  C14  111.60  3.000
 5NK  H13  C28  C14  110.67  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
 5NK  CONST_01  C12  N13  C14  C15     0.00   0.0  0
 5NK  CONST_02  C12  C17  C16  C15     0.00   0.0  0
 5NK  CONST_03  C14  N13  C12  C17     0.00   0.0  0
 5NK  CONST_04  C14  C15  C16  C17     0.00   0.0  0
 5NK  CONST_05  C04  C03  C02  C01     0.00   0.0  0
 5NK  CONST_06  C04  C06  C05  C01     0.00   0.0  0
 5NK  CONST_07  N07  C06  C05  C01   180.00   0.0  0
 5NK  CONST_08  C08  N09  C05  C01   180.00   0.0  0
 5NK  CONST_09  C06  C04  C03  C02     0.00   0.0  0
 5NK  CONST_10  C06  C05  C01  C02     0.00   0.0  0
 5NK  CONST_11  N09  C05  C01  C02   180.00   0.0  0
 5NK  CONST_12  N07  C06  C04  C03   180.00   0.0  0
 5NK  CONST_13  C05  C06  C04  C03     0.00   0.0  0
 5NK  CONST_14  C05  C01  C02  C03     0.00   0.0  0
 5NK  CONST_15  C08  N07  C06  C04   180.00   0.0  0
 5NK  CONST_16  N09  C05  C06  C04   180.00   0.0  0
 5NK  CONST_17  C08  N07  C06  C05     0.00   0.0  0
 5NK  CONST_18  N07  C08  N09  C05     0.00   0.0  0
 5NK  CONST_19  N09  C08  N07  C06     0.00   0.0  0
 5NK  CONST_20  C08  N09  C05  C06     0.00   0.0  0
 5NK  CONST_21  N09  C05  C06  N07     0.00   0.0  0
 5NK  CONST_22  C16  C15  C14  N13     0.00   0.0  0
 5NK  CONST_23  C16  C17  C12  N13     0.00   0.0  0
 5NK  CONST_24  C03  C02  C01  C10   180.00   0.0  0
 5NK  CONST_25  C06  C05  C01  C10   180.00   0.0  0
 5NK  CONST_26  N09  C05  C01  C10     0.00   0.0  0
 5NK  CONST_27  O29  C17  C16  C15   180.00   0.0  0
 5NK  CONST_28  C12  N13  C14  C28   180.00   0.0  0
 5NK  CONST_29  C16  C15  C14  C28   180.00   0.0  0
 5NK  CONST_30  C11  N07  C06  C04     0.00   0.0  0
 5NK  CONST_31  C11  N07  C06  C05   180.00   0.0  0
 5NK  CONST_32  N18  C08  N09  C05   180.00   0.0  0
 5NK  CONST_33  N18  C08  N07  C06   180.00   0.0  0
 5NK  CONST_34  C11  N07  C08  N09   180.00   0.0  0
 5NK  CONST_35  C14  N13  C12  C11   180.00   0.0  0
 5NK  CONST_36  C16  C17  C12  C11   180.00   0.0  0
 5NK  CONST_37  O29  C17  C12  N13   180.00   0.0  0
 5NK  CONST_38  C19  N18  C08  N07   180.00   0.0  0
 5NK  CONST_39  C19  N18  C08  N09     0.00   0.0  0
 5NK  CONST_40  H4   C15  C16  C17   180.00   0.0  0
 5NK  CONST_41  H17  C03  C02  C01   180.00   0.0  0
 5NK  CONST_42  H18  C04  C03  C02   180.00   0.0  0
 5NK  CONST_43  H16  C02  C03  C04   180.00   0.0  0
 5NK  CONST_44  H21  C16  C17  C12   180.00   0.0  0
 5NK  Var_01    C23  N22  C21  C20   -59.81  30.0  1
 5NK  Var_02    C24  C23  N22  C21    60.49  30.0  1
 5NK  Var_03    N22  C23  C24  C19   -57.99  30.0  1
 5NK  Var_04    N22  C21  C20  C19    57.24  30.0  1
 5NK  Var_05    N07  C11  C12  C17   107.10  30.0  3
 5NK  Var_06    C12  C11  N07  C06  -104.30  30.0  2
 5NK  Var_07    C26  C25  N22  C21  -157.00  30.0  1
 5NK  Var_08    H13  C28  C14  C15  -102.41  30.0  2
 5NK  Var_09    H1   C10  C01  C02   114.11  30.0  2
 5NK  Var_10    N27  C26  C25  N22   179.89  30.0  3
 5NK  Var_11    H29  N27  C26  C25    70.86  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
 5NK  chir_01  C19  C24  N18  C20  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
 5NK  plan-1  C15  0.020
 5NK  plan-1  C17  0.020
 5NK  plan-1  C11  0.020
 5NK  plan-1  C12  0.020
 5NK  plan-1  N13  0.020
 5NK  plan-1  C14  0.020
 5NK  plan-1  C16  0.020
 5NK  plan-1  H4   0.020
 5NK  plan-1  H21  0.020
 5NK  plan-1  O29  0.020
 5NK  plan-1  C28  0.020
 5NK  plan-2  C10  0.020
 5NK  plan-2  C01  0.020
 5NK  plan-2  C02  0.020
 5NK  plan-2  C03  0.020
 5NK  plan-2  C04  0.020
 5NK  plan-2  C05  0.020
 5NK  plan-2  C06  0.020
 5NK  plan-2  N07  0.020
 5NK  plan-2  C08  0.020
 5NK  plan-2  N09  0.020
 5NK  plan-2  C11  0.020
 5NK  plan-2  N18  0.020
 5NK  plan-2  H16  0.020
 5NK  plan-2  H17  0.020
 5NK  plan-2  H18  0.020
 5NK  plan-3  C08  0.020
 5NK  plan-3  N18  0.020
 5NK  plan-3  C19  0.020
 5NK  plan-3  H22  0.020

