# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 14:08:24 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (1-{3-[4-(1H-benzimidazol-2-ylamino)phenoxy]pyridin-2-yl}piperidin-4-yl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1CCN(CC1)c2ncccc2Oc3ccc(Nc4[nH]c5ccccc5n4)cc3
#
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
 15J  15J  (1-{3-[4-(1H-benzimidazol-2-ylamino)phenoxy]pyridin-2-yl}piperidin-4-yl)methanol  ligand  56  31  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_15J
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
 15J  O2   O  OH1   0  -0.674  -8.3356  -2.5296  -1.1990
 15J  C24  C  CH2   0  -0.127  -7.0035  -2.7731  -0.8030
 15J  C21  C  CH1   0  -0.281  -6.4177  -1.5173  -0.1859
 15J  C22  C  CH2   0  -0.432  -5.0035  -1.7802   0.3212
 15J  C23  C  CH2   0  -0.301  -4.3937  -0.5237   0.9158
 15J  C20  C  CH2   0  -0.421  -6.3832  -0.3387  -1.1543
 15J  C19  C  CH2   0  -0.285  -5.7375   0.8842  -0.5206
 15J  N2   N  NT    0  -0.486  -4.3938   0.5688  -0.0581
 15J  C4   C  CR6   0   0.406  -3.5925   1.6609   0.2646
 15J  N1   N  N     0  -0.437  -4.1595   2.8365   0.4708
 15J  C3   C  CR16  0  -0.089  -3.4118   3.8981   0.7651
 15J  C2   C  CR16  0  -0.335  -2.0417   3.8337   0.8915
 15J  C1   C  CR16  0  -0.245  -1.4157   2.6119   0.6560
 15J  C5   C  CR6   0   0.256  -2.1858   1.5192   0.3149
 15J  O1   O  O2    0  -0.510  -1.6748   0.3061  -0.0240
 15J  C6   C  CR6   0   0.285  -0.3523   0.0500   0.2550
 15J  C11  C  CR16  0  -0.292   0.0275  -0.3299   1.5345
 15J  C10  C  CR16  0  -0.354   1.3537  -0.6124   1.7989
 15J  C7   C  CR16  0  -0.297   0.5934   0.1428  -0.7494
 15J  C8   C  CR16  0  -0.317   1.9274  -0.1430  -0.4905
 15J  C9   C  CR6   0   0.365   2.3231  -0.5184   0.7941
 15J  N3   N  NH1   0  -0.808   3.6310  -0.8241   1.1509
 15J  C12  C  CR5   0   0.706   4.7657  -0.6875   0.4200
 15J  N5   N  NR15  0  -0.746   5.9642  -1.0306   0.9724
 15J  C14  C  CR56  0   0.324   6.9285  -0.7835   0.0247
 15J  C18  C  CR16  0  -0.310   8.3054  -0.9340   0.0267
 15J  C17  C  CR16  0  -0.286   8.9765  -0.5696  -1.1340
 15J  C16  C  CR16  0  -0.271   8.2880  -0.0760  -2.2463
 15J  C15  C  CR16  0  -0.346   6.9074   0.0698  -2.2368
 15J  C13  C  CR56  0   0.193   6.2188  -0.2894  -1.0830
 15J  N4   N  N     0  -0.535   4.8710  -0.2428  -0.8048
 15J  H1   H  HOH1  0   0.453  -8.6914  -3.3408  -1.5722
 15J  H2   H  HCH2  0   0.198  -6.9508  -3.5893  -0.0695
 15J  H3   H  HCH2  0   0.182  -6.3798  -3.0741  -1.6575
 15J  H4   H  HCH1  0   0.218  -7.0353  -1.2372   0.6782
 15J  H5   H  HCH2  0   0.236  -5.0065  -2.5628   1.0841
 15J  H6   H  HCH2  0   0.220  -4.3719  -2.1329  -0.5014
 15J  H7   H  HCH2  0   0.212  -4.9652  -0.2289   1.8091
 15J  H8   H  HCH2  0   0.257  -3.3789  -0.7328   1.2452
 15J  H9   H  HCH2  0   0.212  -5.8239  -0.6243  -2.0522
 15J  H10  H  HCH2  0   0.236  -7.3901  -0.0683  -1.4768
 15J  H11  H  HCH2  0   0.242  -5.6773   1.6906  -1.2512
 15J  H12  H  HCH2  0   0.202  -6.3713   1.2481   0.3009
 15J  H13  H  HCR6  0   0.255  -3.9397   4.8332   0.9143
 15J  H14  H  HCR6  0   0.267  -1.4643   4.7094   1.1527
 15J  H15  H  HCR6  0   0.288  -0.3374   2.5392   0.7096
 15J  H16  H  HCR6  0   0.277  -0.7075  -0.4061   2.3262
 15J  H17  H  HCR6  0   0.276   1.6426  -0.9078   2.8006
 15J  H18  H  HCR6  0   0.273   0.2952   0.4361  -1.7480
 15J  H19  H  HCR6  0   0.293   2.6535  -0.0662  -1.2840
 15J  H20  H  HNH1  0   0.419   3.7571  -1.1300   2.1029
 15J  H21  H  HNR5  0   0.420   6.1135  -1.4110   1.8937
 15J  H22  H  HCR6  0   0.263   8.8366  -1.3150   0.8892
 15J  H23  H  HCR6  0   0.251  10.0532  -0.6692  -1.1762
 15J  H24  H  HCR6  0   0.249   8.8446   0.2003  -3.1325
 15J  H25  H  HCR6  0   0.250   6.3801   0.4541  -3.1005

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
 15J  C24  O2   single    1.411  0.020  1.411
 15J  C24  C21  single    1.517  0.020  1.517
 15J  C20  C21  single    1.526  0.020  1.526
 15J  C20  C19  single    1.521  0.020  1.521
 15J  C21  C22  single    1.525  0.020  1.525
 15J  C19  N2   single    1.456  0.020  1.456
 15J  C22  C23  single    1.518  0.020  1.518
 15J  N2   C23  single    1.464  0.020  1.464
 15J  N2   C4   single    1.392  0.020  1.392
 15J  N1   C4   aromatic  1.321  0.020  1.321
 15J  N1   C3   aromatic  1.331  0.020  1.331
 15J  C4   C5   aromatic  1.415  0.020  1.415
 15J  C3   C2   aromatic  1.377  0.020  1.377
 15J  C5   O1   single    1.359  0.020  1.359
 15J  C5   C1   aromatic  1.380  0.020  1.380
 15J  O1   C6   single    1.376  0.020  1.376
 15J  C2   C1   aromatic  1.393  0.020  1.393
 15J  C6   C11  aromatic  1.388  0.020  1.388
 15J  C6   C7   aromatic  1.383  0.020  1.383
 15J  C11  C10  aromatic  1.381  0.020  1.381
 15J  C7   C8   aromatic  1.389  0.020  1.389
 15J  C10  C9   aromatic  1.399  0.020  1.399
 15J  C8   C9   aromatic  1.396  0.020  1.396
 15J  C9   N3   single    1.390  0.020  1.390
 15J  N5   C12  aromatic  1.364  0.020  1.364
 15J  N5   C14  aromatic  1.374  0.020  1.374
 15J  N3   C12  single    1.357  0.020  1.357
 15J  C12  N4   aromatic  1.307  0.020  1.307
 15J  C18  C14  aromatic  1.385  0.020  1.385
 15J  C18  C17  aromatic  1.389  0.020  1.389
 15J  C14  C13  aromatic  1.405  0.020  1.405
 15J  C17  C16  aromatic  1.398  0.020  1.398
 15J  N4   C13  aromatic  1.377  0.020  1.377
 15J  C13  C15  aromatic  1.391  0.020  1.391
 15J  C16  C15  aromatic  1.388  0.020  1.388
 15J  O2   H1   single    0.850  0.020  0.980
 15J  C24  H2   single    0.970  0.020  1.090
 15J  C24  H3   single    0.970  0.020  1.090
 15J  C21  H4   single    0.970  0.020  1.090
 15J  C22  H5   single    0.970  0.020  1.090
 15J  C22  H6   single    0.970  0.020  1.090
 15J  C23  H7   single    0.970  0.020  1.090
 15J  C23  H8   single    0.970  0.020  1.090
 15J  C20  H9   single    0.970  0.020  1.090
 15J  C20  H10  single    0.970  0.020  1.090
 15J  C19  H11  single    0.970  0.020  1.090
 15J  C19  H12  single    0.970  0.020  1.090
 15J  C3   H13  single    0.930  0.020  1.080
 15J  C2   H14  single    0.930  0.020  1.080
 15J  C1   H15  single    0.930  0.020  1.080
 15J  C11  H16  single    0.930  0.020  1.080
 15J  C10  H17  single    0.930  0.020  1.080
 15J  C7   H18  single    0.930  0.020  1.080
 15J  C8   H19  single    0.930  0.020  1.080
 15J  N3   H20  single    0.860  0.020  1.020
 15J  N5   H21  single    0.860  0.020  1.020
 15J  C18  H22  single    0.930  0.020  1.080
 15J  C17  H23  single    0.930  0.020  1.080
 15J  C16  H24  single    0.930  0.020  1.080
 15J  C15  H25  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
 15J  H1   O2   C24  108.23  3.000
 15J  H3   C24  H2   106.75  3.000
 15J  H3   C24  C21  108.88  3.000
 15J  H2   C24  C21  108.96  3.000
 15J  H3   C24  O2   111.38  3.000
 15J  H2   C24  O2   111.16  3.000
 15J  C21  C24  O2   109.63  3.000
 15J  H4   C21  C20  108.36  3.000
 15J  H4   C21  C22  107.69  3.000
 15J  C20  C21  C22  108.86  3.000
 15J  H4   C21  C24  108.30  3.000
 15J  C22  C21  C24  110.53  3.000
 15J  C20  C21  C24  112.96  3.000
 15J  H6   C22  H5   107.17  3.000
 15J  H6   C22  C23  109.21  3.000
 15J  H5   C22  C23  108.68  3.000
 15J  H6   C22  C21  109.90  3.000
 15J  H5   C22  C21  110.67  3.000
 15J  C23  C22  C21  111.10  3.000
 15J  H8   C23  H7   106.87  3.000
 15J  H8   C23  N2   110.20  3.000
 15J  H7   C23  N2   109.88  3.000
 15J  H8   C23  C22  109.54  3.000
 15J  H7   C23  C22  109.33  3.000
 15J  N2   C23  C22  110.93  3.000
 15J  H10  C20  H9   107.06  3.000
 15J  H10  C20  C19  108.39  3.000
 15J  H9   C20  C19  109.53  3.000
 15J  H10  C20  C21  110.98  3.000
 15J  H9   C20  C21  109.29  3.000
 15J  C19  C20  C21  111.48  3.000
 15J  H12  C19  H11  106.73  3.000
 15J  H12  C19  N2   111.49  3.000
 15J  H11  C19  N2   108.80  3.000
 15J  H12  C19  C20  109.43  3.000
 15J  H11  C19  C20  109.82  3.000
 15J  N2   C19  C20  110.49  3.000
 15J  C4   N2   C19  115.78  3.000
 15J  C4   N2   C23  115.54  3.000
 15J  C19  N2   C23  111.92  3.000
 15J  C5   C4   N1   120.68  3.000
 15J  C5   C4   N2   120.13  3.000
 15J  N1   C4   N2   119.15  3.000
 15J  C3   N1   C4   120.20  3.000
 15J  H13  C3   C2   120.80  3.000
 15J  H13  C3   N1   116.40  3.000
 15J  C2   C3   N1   122.79  3.000
 15J  H14  C2   C1   120.75  3.000
 15J  H14  C2   C3   121.04  3.000
 15J  C1   C2   C3   118.20  3.000
 15J  H15  C1   C5   121.02  3.000
 15J  H15  C1   C2   119.90  3.000
 15J  C5   C1   C2   119.05  3.000
 15J  O1   C5   C1   123.96  3.000
 15J  C1   C5   C4   118.98  3.000
 15J  O1   C5   C4   117.02  3.000
 15J  C6   O1   C5   118.49  3.000
 15J  C7   C6   C11  120.07  3.000
 15J  C7   C6   O1   119.85  3.000
 15J  C11  C6   O1   120.07  3.000
 15J  H16  C11  C10  119.82  3.000
 15J  H16  C11  C6   120.50  3.000
 15J  C10  C11  C6   119.68  3.000
 15J  H17  C10  C9   119.83  3.000
 15J  H17  C10  C11  119.25  3.000
 15J  C9   C10  C11  120.92  3.000
 15J  H18  C7   C8   119.49  3.000
 15J  H18  C7   C6   119.99  3.000
 15J  C8   C7   C6   120.52  3.000
 15J  H19  C8   C9   120.37  3.000
 15J  H19  C8   C7   119.67  3.000
 15J  C9   C8   C7   119.96  3.000
 15J  N3   C9   C8   124.22  3.000
 15J  N3   C9   C10  116.93  3.000
 15J  C8   C9   C10  118.85  3.000
 15J  H20  N3   C12  115.77  3.000
 15J  H20  N3   C9   115.28  3.000
 15J  C12  N3   C9   128.81  3.000
 15J  N4   C12  N5   113.22  3.000
 15J  N4   C12  N3   127.33  3.000
 15J  N5   C12  N3   119.44  3.000
 15J  H21  N5   C14  126.45  3.000
 15J  H21  N5   C12  126.55  3.000
 15J  C14  N5   C12  106.98  3.000
 15J  C13  C14  C18  122.78  3.000
 15J  C13  C14  N5   104.62  3.000
 15J  C18  C14  N5   132.60  3.000
 15J  H22  C18  C17  121.40  3.000
 15J  H22  C18  C14  121.83  3.000
 15J  C17  C18  C14  116.77  3.000
 15J  H23  C17  C16  119.43  3.000
 15J  H23  C17  C18  119.28  3.000
 15J  C16  C17  C18  121.29  3.000
 15J  H24  C16  C15  119.36  3.000
 15J  H24  C16  C17  119.23  3.000
 15J  C15  C16  C17  121.42  3.000
 15J  H25  C15  C13  120.82  3.000
 15J  H25  C15  C16  121.08  3.000
 15J  C13  C15  C16  118.10  3.000
 15J  N4   C13  C15  130.05  3.000
 15J  C15  C13  C14  119.65  3.000
 15J  N4   C13  C14  110.30  3.000
 15J  C13  N4   C12  104.87  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
 15J  CONST_01  C2   C3   N1   C4      0.00   0.0  0
 15J  CONST_02  C2   C1   C5   C4      0.00   0.0  0
 15J  CONST_03  C1   C5   C4   N1      0.00   0.0  0
 15J  CONST_04  C1   C2   C3   N1      0.00   0.0  0
 15J  CONST_05  C5   C4   N1   C3      0.00   0.0  0
 15J  CONST_06  C5   C1   C2   C3      0.00   0.0  0
 15J  CONST_07  C9   C10  C11  C6      0.00   0.0  0
 15J  CONST_08  C9   C8   C7   C6      0.00   0.0  0
 15J  CONST_09  C8   C7   C6   C11     0.00   0.0  0
 15J  CONST_10  C8   C9   C10  C11     0.00   0.0  0
 15J  CONST_11  C7   C6   C11  C10     0.00   0.0  0
 15J  CONST_12  C7   C8   C9   C10     0.00   0.0  0
 15J  CONST_13  C18  C14  N5   C12   180.00   0.0  0
 15J  CONST_14  C13  C14  N5   C12     0.00   0.0  0
 15J  CONST_15  C14  C13  N4   C12     0.00   0.0  0
 15J  CONST_16  C15  C13  N4   C12   180.00   0.0  0
 15J  CONST_17  C13  N4   C12  N5      0.00   0.0  0
 15J  CONST_18  C17  C18  C14  N5    180.00   0.0  0
 15J  CONST_19  N4   C13  C14  N5      0.00   0.0  0
 15J  CONST_20  C15  C13  C14  N5    180.00   0.0  0
 15J  CONST_21  N4   C12  N5   C14     0.00   0.0  0
 15J  CONST_22  C16  C17  C18  C14     0.00   0.0  0
 15J  CONST_23  C16  C15  C13  C14     0.00   0.0  0
 15J  CONST_24  N4   C13  C14  C18   180.00   0.0  0
 15J  CONST_25  C15  C13  C14  C18     0.00   0.0  0
 15J  CONST_26  C15  C16  C17  C18     0.00   0.0  0
 15J  CONST_27  C13  C14  C18  C17     0.00   0.0  0
 15J  CONST_28  C13  C15  C16  C17     0.00   0.0  0
 15J  CONST_29  N4   C13  C15  C16   180.00   0.0  0
 15J  CONST_30  C3   N1   C4   N2    180.00   0.0  0
 15J  CONST_31  C1   C5   C4   N2    180.00   0.0  0
 15J  CONST_32  O1   C5   C4   N2      0.00   0.0  0
 15J  CONST_33  O1   C5   C4   N1    180.00   0.0  0
 15J  CONST_34  O1   C5   C1   C2    180.00   0.0  0
 15J  CONST_35  C10  C11  C6   O1    180.00   0.0  0
 15J  CONST_36  C8   C7   C6   O1    180.00   0.0  0
 15J  CONST_37  N3   C9   C10  C11   180.00   0.0  0
 15J  CONST_38  N3   C9   C8   C7    180.00   0.0  0
 15J  CONST_39  C14  N5   C12  N3    180.00   0.0  0
 15J  CONST_40  C13  N4   C12  N3    180.00   0.0  0
 15J  CONST_41  H13  C3   N1   C4    180.00   0.0  0
 15J  CONST_42  H15  C1   C5   C4    180.00   0.0  0
 15J  CONST_43  H14  C2   C3   N1    180.00   0.0  0
 15J  CONST_44  H17  C10  C11  C6    180.00   0.0  0
 15J  CONST_45  H19  C8   C7   C6    180.00   0.0  0
 15J  CONST_46  H18  C7   C6   C11   180.00   0.0  0
 15J  CONST_47  H16  C11  C6   C7    180.00   0.0  0
 15J  CONST_48  H22  C18  C14  N5      0.00   0.0  0
 15J  CONST_49  H23  C17  C18  C14   180.00   0.0  0
 15J  CONST_50  H25  C15  C13  C14   180.00   0.0  0
 15J  CONST_51  H21  N5   C14  C18     0.00   0.0  0
 15J  CONST_52  H24  C16  C17  C18   180.00   0.0  0
 15J  Var_01    N2   C19  C20  C21    56.88  30.0  1
 15J  Var_02    N2   C23  C22  C21   -56.69  30.0  1
 15J  Var_03    C19  N2   C23  C22    58.77  30.0  1
 15J  Var_04    C20  C19  N2   C23   -58.54  30.0  1
 15J  Var_05    N1   C4   N2   C23  -116.39  30.0  2
 15J  Var_06    C11  C6   O1   C5     80.79  30.0  2
 15J  Var_07    C12  N3   C9   C10  -172.77  30.0  2
 15J  Var_08    N5   C12  N3   C9    178.93  30.0  2

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
 15J  chir_01  C21  C24  C20  C22  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
 15J  plan-1  N2   0.020
 15J  plan-1  C4   0.020
 15J  plan-1  N1   0.020
 15J  plan-1  C3   0.020
 15J  plan-1  C2   0.020
 15J  plan-1  C1   0.020
 15J  plan-1  C5   0.020
 15J  plan-1  O1   0.020
 15J  plan-1  H13  0.020
 15J  plan-1  H14  0.020
 15J  plan-1  H15  0.020
 15J  plan-2  O1   0.020
 15J  plan-2  C6   0.020
 15J  plan-2  C11  0.020
 15J  plan-2  C10  0.020
 15J  plan-2  C7   0.020
 15J  plan-2  C8   0.020
 15J  plan-2  C9   0.020
 15J  plan-2  N3   0.020
 15J  plan-2  H16  0.020
 15J  plan-2  H17  0.020
 15J  plan-2  H18  0.020
 15J  plan-2  H19  0.020
 15J  plan-3  N3   0.020
 15J  plan-3  C12  0.020
 15J  plan-3  N5   0.020
 15J  plan-3  C14  0.020
 15J  plan-3  C18  0.020
 15J  plan-3  C17  0.020
 15J  plan-3  C16  0.020
 15J  plan-3  C15  0.020
 15J  plan-3  C13  0.020
 15J  plan-3  N4   0.020
 15J  plan-3  H21  0.020
 15J  plan-3  H22  0.020
 15J  plan-3  H23  0.020
 15J  plan-3  H24  0.020
 15J  plan-3  H25  0.020

