# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 11:26:59 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 1-{2-[1-(aminomethyl)cyclohexyl]ethyl}-3-isoquinolin-6-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1(CCCCC1)CCNC(=O)Nc2ccc3cnccc3c2
#
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
 3BQ  3BQ  1-{2-[1-(aminomethyl)cyclohexyl]ethyl}-3-isoquinolin-6-ylurea  ligand  50  24  .  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_3BQ
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
 3BQ  O    O  O     0  -0.520  -0.3582  -1.5351   0.0050
 3BQ  C4   C  C     0   0.748  -0.3518  -0.3414  -0.2583
 3BQ  N2   N  NH1   0  -0.794  -1.4964   0.4186  -0.3945
 3BQ  C5   C  CR6   0   0.408  -2.8180   0.0369  -0.2297
 3BQ  C13  C  CR16  0  -0.442  -3.7649   1.0403  -0.1606
 3BQ  C12  C  CR66  0   0.233  -5.1301   0.7390  -0.0221
 3BQ  C11  C  CR16  0  -0.385  -6.1445   1.7223   0.0562
 3BQ  C10  C  CR16  0  -0.084  -7.4451   1.3295   0.1961
 3BQ  N3   N  N     0  -0.416  -7.8422   0.0371   0.2667
 3BQ  C9   C  CR16  0  -0.090  -6.9183  -0.8839   0.1964
 3BQ  C8   C  CR66  0  -0.019  -5.5405  -0.6119   0.0526
 3BQ  C7   C  CR16  0  -0.291  -4.5612  -1.6238  -0.0248
 3BQ  C6   C  CR16  0  -0.315  -3.2369  -1.3209  -0.1649
 3BQ  N1   N  NH1   0  -0.691   0.7847   0.3622  -0.4358
 3BQ  C3   C  CH2   0  -0.235   2.0877  -0.2689  -0.3751
 3BQ  C2   C  CH2   0  -0.469   3.1720   0.8001  -0.3605
 3BQ  C1   C  CT    0  -0.085   4.6109   0.3049  -0.1260
 3BQ  C    C  CH2   0  -0.271   5.5447   1.5131  -0.3302
 3BQ  N    N  NH2   0  -0.801   5.2812   2.6059   0.5940
 3BQ  C18  C  CH2   0  -0.424   4.9867  -0.7783  -1.1508
 3BQ  C17  C  CH2   0  -0.438   6.3545  -1.4107  -0.8988
 3BQ  C16  C  CH2   0  -0.426   6.4429  -1.9704   0.5172
 3BQ  C15  C  CH2   0  -0.440   6.1212  -0.9012   1.5560
 3BQ  C14  C  CH2   0  -0.407   4.7593  -0.2632   1.2938
 3BQ  H1   H  HNH1  0   0.412  -1.3639   1.4098  -0.5272
 3BQ  H2   H  HCR6  0   0.267  -3.4587   2.0792  -0.2143
 3BQ  H3   H  HCR6  0   0.264  -5.8949   2.7744   0.0053
 3BQ  H4   H  HCR6  0   0.261  -8.2336   2.0702   0.2570
 3BQ  H5   H  HCR6  0   0.264  -7.2452  -1.9191   0.2548
 3BQ  H6   H  HCR6  0   0.262  -4.8662  -2.6621   0.0241
 3BQ  H7   H  HCR6  0   0.288  -2.5131  -2.1150  -0.2284
 3BQ  H8   H  HNH1  0   0.399   0.7436   1.3247  -0.7309
 3BQ  H9   H  HCH2  0   0.234   2.1442  -0.8826   0.5250
 3BQ  H10  H  HCH2  0   0.230   2.2192  -0.9428  -1.2259
 3BQ  H11  H  HCH2  0   0.232   3.1416   1.3453  -1.3122
 3BQ  H12  H  HCH2  0   0.235   2.9242   1.5236   0.4231
 3BQ  H13  H  HCH2  0   0.227   6.5805   1.2055  -0.1813
 3BQ  H14  H  HCH2  0   0.198   5.4686   1.8161  -1.3862
 3BQ  H15  H  HNH2  0   0.348   6.0528   3.2586   0.5631
 3BQ  H16  H  HNH2  0   0.343   4.4718   3.1308   0.2901
 3BQ  H18  H  HCH2  0   0.224   4.2443  -1.5818  -1.1211
 3BQ  H19  H  HCH2  0   0.220   4.9403  -0.3589  -2.1620
 3BQ  H20  H  HCH2  0   0.227   6.5238  -2.2054  -1.6298
 3BQ  H21  H  HCH2  0   0.214   7.1539  -0.6809  -1.0575
 3BQ  H22  H  HCH2  0   0.205   5.7273  -2.7943   0.6205
 3BQ  H23  H  HCH2  0   0.224   7.4339  -2.3945   0.6981
 3BQ  H24  H  HCH2  0   0.225   6.1264  -1.3394   2.5576
 3BQ  H25  H  HCH2  0   0.212   6.9068  -0.1393   1.5597
 3BQ  H26  H  HCH2  0   0.223   4.5694   0.5300   2.0202
 3BQ  H27  H  HCH2  0   0.213   3.9928  -1.0280   1.4598

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
 3BQ  N3   C10  aromatic  1.354  0.020  1.354
 3BQ  N3   C9   aromatic  1.306  0.020  1.306
 3BQ  C10  C11  aromatic  1.366  0.020  1.366
 3BQ  C9   C8   aromatic  1.412  0.020  1.412
 3BQ  C11  C12  aromatic  1.415  0.020  1.415
 3BQ  C8   C12  aromatic  1.414  0.020  1.414
 3BQ  C8   C7   aromatic  1.410  0.020  1.410
 3BQ  C12  C13  aromatic  1.405  0.020  1.405
 3BQ  C7   C6   aromatic  1.366  0.020  1.366
 3BQ  C13  C5   aromatic  1.381  0.020  1.381
 3BQ  C6   C5   aromatic  1.422  0.020  1.422
 3BQ  C5   N2   single    1.385  0.020  1.385
 3BQ  O    C4   double    1.222  0.020  1.222
 3BQ  N2   C4   single    1.381  0.020  1.381
 3BQ  C4   N1   single    1.348  0.020  1.348
 3BQ  N1   C3   single    1.449  0.020  1.449
 3BQ  C3   C2   single    1.523  0.020  1.523
 3BQ  C2   C1   single    1.540  0.020  1.540
 3BQ  C14  C1   single    1.536  0.020  1.536
 3BQ  C14  C15  single    1.527  0.020  1.527
 3BQ  C1   C18  single    1.538  0.020  1.538
 3BQ  C1   C    single    1.541  0.020  1.541
 3BQ  C15  C16  single    1.525  0.020  1.525
 3BQ  C18  C17  single    1.528  0.020  1.528
 3BQ  C16  C17  single    1.525  0.020  1.525
 3BQ  N    C    single    1.455  0.020  1.455
 3BQ  N2   H1   single    0.860  0.020  1.020
 3BQ  C13  H2   single    0.930  0.020  1.080
 3BQ  C11  H3   single    0.930  0.020  1.080
 3BQ  C10  H4   single    0.930  0.020  1.080
 3BQ  C9   H5   single    0.930  0.020  1.080
 3BQ  C7   H6   single    0.930  0.020  1.080
 3BQ  C6   H7   single    0.930  0.020  1.080
 3BQ  N1   H8   single    0.860  0.020  1.020
 3BQ  C3   H9   single    0.970  0.020  1.090
 3BQ  C3   H10  single    0.970  0.020  1.090
 3BQ  C2   H11  single    0.970  0.020  1.090
 3BQ  C2   H12  single    0.970  0.020  1.090
 3BQ  C    H13  single    0.970  0.020  1.090
 3BQ  C    H14  single    0.970  0.020  1.090
 3BQ  N    H15  single    0.890  0.020  1.040
 3BQ  N    H16  single    0.890  0.020  1.040
 3BQ  C18  H18  single    0.970  0.020  1.090
 3BQ  C18  H19  single    0.970  0.020  1.090
 3BQ  C17  H20  single    0.970  0.020  1.090
 3BQ  C17  H21  single    0.970  0.020  1.090
 3BQ  C16  H22  single    0.970  0.020  1.090
 3BQ  C16  H23  single    0.970  0.020  1.090
 3BQ  C15  H24  single    0.970  0.020  1.090
 3BQ  C15  H25  single    0.970  0.020  1.090
 3BQ  C14  H26  single    0.970  0.020  1.090
 3BQ  C14  H27  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
 3BQ  N1   C4   N2   113.49  3.000
 3BQ  N1   C4   O    122.84  3.000
 3BQ  N2   C4   O    123.68  3.000
 3BQ  H1   N2   C5   114.31  3.000
 3BQ  H1   N2   C4   116.42  3.000
 3BQ  C5   N2   C4   128.86  3.000
 3BQ  C6   C5   C13  119.28  3.000
 3BQ  C6   C5   N2   123.33  3.000
 3BQ  C13  C5   N2   117.37  3.000
 3BQ  H2   C13  C12  118.99  3.000
 3BQ  H2   C13  C5   119.99  3.000
 3BQ  C12  C13  C5   121.02  3.000
 3BQ  C8   C12  C11  116.94  3.000
 3BQ  C8   C12  C13  119.48  3.000
 3BQ  C11  C12  C13  123.58  3.000
 3BQ  H3   C11  C10  120.26  3.000
 3BQ  H3   C11  C12  120.50  3.000
 3BQ  C10  C11  C12  119.24  3.000
 3BQ  H4   C10  N3   115.86  3.000
 3BQ  H4   C10  C11  120.14  3.000
 3BQ  N3   C10  C11  124.00  3.000
 3BQ  C9   N3   C10  117.56  3.000
 3BQ  H5   C9   C8   118.84  3.000
 3BQ  H5   C9   N3   117.11  3.000
 3BQ  C8   C9   N3   124.05  3.000
 3BQ  C7   C8   C9   123.03  3.000
 3BQ  C7   C8   C12  118.75  3.000
 3BQ  C9   C8   C12  118.21  3.000
 3BQ  H6   C7   C6   119.35  3.000
 3BQ  H6   C7   C8   119.32  3.000
 3BQ  C6   C7   C8   121.33  3.000
 3BQ  H7   C6   C7   119.64  3.000
 3BQ  H7   C6   C5   120.23  3.000
 3BQ  C7   C6   C5   120.13  3.000
 3BQ  H8   N1   C3   117.71  3.000
 3BQ  H8   N1   C4   120.17  3.000
 3BQ  C3   N1   C4   121.68  3.000
 3BQ  H10  C3   H9   106.80  3.000
 3BQ  H10  C3   C2   110.76  3.000
 3BQ  H9   C3   C2   110.50  3.000
 3BQ  H10  C3   N1   110.12  3.000
 3BQ  H9   C3   N1   109.04  3.000
 3BQ  C2   C3   N1   109.57  3.000
 3BQ  H12  C2   H11  106.63  3.000
 3BQ  H12  C2   C1   108.36  3.000
 3BQ  H11  C2   C1   108.53  3.000
 3BQ  H12  C2   C3   108.03  3.000
 3BQ  H11  C2   C3   108.71  3.000
 3BQ  C1   C2   C3   116.18  3.000
 3BQ  C14  C1   C18  109.38  3.000
 3BQ  C18  C1   C    108.42  3.000
 3BQ  C14  C1   C    110.73  3.000
 3BQ  C    C1   C2   107.10  3.000
 3BQ  C18  C1   C2   110.70  3.000
 3BQ  C14  C1   C2   110.48  3.000
 3BQ  H14  C    H13  105.91  3.000
 3BQ  H14  C    N    112.94  3.000
 3BQ  H13  C    N    107.28  3.000
 3BQ  H14  C    C1   107.52  3.000
 3BQ  H13  C    C1   109.65  3.000
 3BQ  N    C    C1   113.27  3.000
 3BQ  H16  N    H15  105.46  3.000
 3BQ  H16  N    C    110.11  3.000
 3BQ  H15  N    C    109.09  3.000
 3BQ  H19  C18  H18  106.10  3.000
 3BQ  H19  C18  C17  110.40  3.000
 3BQ  H18  C18  C17  107.39  3.000
 3BQ  H19  C18  C1   109.58  3.000
 3BQ  H18  C18  C1   109.47  3.000
 3BQ  C17  C18  C1   113.60  3.000
 3BQ  H21  C17  H20  105.95  3.000
 3BQ  H21  C17  C16  109.70  3.000
 3BQ  H20  C17  C16  110.19  3.000
 3BQ  H21  C17  C18  110.74  3.000
 3BQ  H20  C17  C18  109.23  3.000
 3BQ  C16  C17  C18  110.92  3.000
 3BQ  H23  C16  H22  106.55  3.000
 3BQ  H23  C16  C15  110.52  3.000
 3BQ  H22  C16  C15  108.97  3.000
 3BQ  H23  C16  C17  110.40  3.000
 3BQ  H22  C16  C17  108.99  3.000
 3BQ  C15  C16  C17  111.28  3.000
 3BQ  H25  C15  H24  105.82  3.000
 3BQ  H25  C15  C14  110.49  3.000
 3BQ  H24  C15  C14  109.21  3.000
 3BQ  H25  C15  C16  109.82  3.000
 3BQ  H24  C15  C16  110.00  3.000
 3BQ  C14  C15  C16  111.36  3.000
 3BQ  H27  C14  H26  106.54  3.000
 3BQ  H27  C14  C15  107.85  3.000
 3BQ  H26  C14  C15  110.14  3.000
 3BQ  H27  C14  C1   109.31  3.000
 3BQ  H26  C14  C1   109.22  3.000
 3BQ  C15  C14  C1   113.54  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
 3BQ  CONST_01  C11  C12  C13  C5    180.00   0.0  0
 3BQ  CONST_02  C8   C12  C13  C5      0.00   0.0  0
 3BQ  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 3BQ  CONST_04  C10  C11  C12  C13   180.00   0.0  0
 3BQ  CONST_05  C9   C8   C12  C13   180.00   0.0  0
 3BQ  CONST_06  C7   C8   C12  C13     0.00   0.0  0
 3BQ  CONST_07  C7   C6   C5   C13     0.00   0.0  0
 3BQ  CONST_08  N3   C10  C11  C12     0.00   0.0  0
 3BQ  CONST_09  N3   C9   C8   C12     0.00   0.0  0
 3BQ  CONST_10  C6   C7   C8   C12     0.00   0.0  0
 3BQ  CONST_11  C6   C5   C13  C12     0.00   0.0  0
 3BQ  CONST_12  C9   N3   C10  C11     0.00   0.0  0
 3BQ  CONST_13  C9   C8   C12  C11     0.00   0.0  0
 3BQ  CONST_14  C7   C8   C12  C11   180.00   0.0  0
 3BQ  CONST_15  C8   C9   N3   C10     0.00   0.0  0
 3BQ  CONST_16  C8   C12  C11  C10     0.00   0.0  0
 3BQ  CONST_17  C7   C8   C9   N3    180.00   0.0  0
 3BQ  CONST_18  C6   C7   C8   C9    180.00   0.0  0
 3BQ  CONST_19  C12  C13  C5   N2    180.00   0.0  0
 3BQ  CONST_20  C7   C6   C5   N2    180.00   0.0  0
 3BQ  CONST_21  H6   C7   C6   C5    180.00   0.0  0
 3BQ  CONST_22  H3   C11  C12  C13     0.00   0.0  0
 3BQ  CONST_23  H7   C6   C5   C13   180.00   0.0  0
 3BQ  CONST_24  H4   C10  C11  C12   180.00   0.0  0
 3BQ  CONST_25  H5   C9   C8   C12   180.00   0.0  0
 3BQ  CONST_26  H2   C13  C12  C11     0.00   0.0  0
 3BQ  CONST_27  C13  C5   N2   C4    180.00   0.0  0
 3BQ  CONST_28  C6   C5   N2   C4      0.00   0.0  0
 3BQ  CONST_29  H1   N2   C5   C13     0.00   0.0  0
 3BQ  CONST_30  C5   N2   C4   O       0.00   0.0  0
 3BQ  CONST_31  N1   C4   N2   C5    180.00   0.0  0
 3BQ  CONST_32  C3   N1   C4   O       0.00   0.0  0
 3BQ  CONST_33  C3   N1   C4   N2    180.00   0.0  0
 3BQ  CONST_34  H8   N1   C4   O     180.00   0.0  0
 3BQ  Var_01    C16  C15  C14  C1    -54.54  30.0  1
 3BQ  Var_02    C16  C17  C18  C1     55.16  30.0  1
 3BQ  Var_03    C15  C16  C17  C18   -55.24  30.0  1
 3BQ  Var_04    C14  C15  C16  C17    55.09  30.0  1
 3BQ  Var_05    C1   C2   C3   N1    172.86  30.0  3
 3BQ  Var_06    H15  N    C    C1    166.36  30.0  3
 3BQ  Var_07    C2   C3   N1   C4   -169.86  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
 3BQ  chir_01  C1  C14  C18  C  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
 3BQ  plan-1  N2   0.020
 3BQ  plan-1  C5   0.020
 3BQ  plan-1  C13  0.020
 3BQ  plan-1  C12  0.020
 3BQ  plan-1  C11  0.020
 3BQ  plan-1  C10  0.020
 3BQ  plan-1  N3   0.020
 3BQ  plan-1  C9   0.020
 3BQ  plan-1  C8   0.020
 3BQ  plan-1  C7   0.020
 3BQ  plan-1  C6   0.020
 3BQ  plan-1  H2   0.020
 3BQ  plan-1  H3   0.020
 3BQ  plan-1  H4   0.020
 3BQ  plan-1  H5   0.020
 3BQ  plan-1  H6   0.020
 3BQ  plan-1  H7   0.020
 3BQ  plan-2  O    0.020
 3BQ  plan-2  C4   0.020
 3BQ  plan-2  N2   0.020
 3BQ  plan-2  C5   0.020
 3BQ  plan-2  N1   0.020
 3BQ  plan-2  C3   0.020
 3BQ  plan-2  H1   0.020
 3BQ  plan-2  H8   0.020

