# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:27:16 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 8-[(3,4-dichlorobenzyl)amino]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c(NCc4ccc(Cl)c(Cl)c4)nc12
#
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
 3BK  3BK  8-[(3,4-dichlorobenzyl)amino]adenosine  ligand  47  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_3BK
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
 3BK  C18   C   CR16  0  -0.247  -3.2023  -0.2663  -0.4935
 3BK  C19   C   CR6   0   0.023  -4.4812   0.2536  -0.6042
 3BK  CL28  CL  CL    0  -0.097  -4.7977   1.4720  -1.7812
 3BK  C20   C   CR6   0  -0.017  -5.4985  -0.2060   0.2267
 3BK  CL29  CL  CL    0  -0.098  -7.0934   0.4320   0.1027
 3BK  C21   C   CR16  0  -0.198  -5.2231  -1.1847   1.1675
 3BK  C22   C   CR16  0  -0.308  -3.9406  -1.6982   1.2776
 3BK  C17   C   CR6   0   0.074  -2.9202  -1.2493   0.4488
 3BK  C16   C   CH2   0  -0.319  -1.5387  -1.8363   0.5484
 3BK  N15   N   NH1   0  -0.708  -0.5407  -0.7856   0.5457
 3BK  C6    C   CR5   0   0.725   0.7626  -1.1413   0.3846
 3BK  N7    N   N     0  -0.518   1.1889  -2.3575   0.1914
 3BK  C8    C   CR56  0   0.025   2.5458  -2.2201   0.0279
 3BK  C4    C   CR6   0   0.427   3.5656  -3.1511  -0.2050
 3BK  N27   N   NH2   0  -0.822   3.3325  -4.4698  -0.3085
 3BK  N1    N   N     0  -0.468   4.8238  -2.7031  -0.2965
 3BK  C2    C   CR16  0   0.035   5.0542  -1.4033  -0.1612
 3BK  N3    N   N     0  -0.454   4.1755  -0.4376   0.0601
 3BK  C9    C   CR56  0   0.499   2.9332  -0.8967   0.1430
 3BK  N5    N   NR5   0  -0.607   1.7706  -0.1959   0.3672
 3BK  C10   C   CH1   0   0.168   1.6017   1.2405   0.3896
 3BK  O11   O   O2    0  -0.491   2.1170   1.7831  -0.7951
 3BK  C12   C   CH1   0   0.023   3.0214   2.8445  -0.5232
 3BK  C23   C   CH2   0  -0.163   4.1285   2.8546  -1.5462
 3BK  O26   O   OH1   0  -0.672   3.5911   3.1823  -2.8062
 3BK  C13   C   CH1   0  -0.042   3.5196   2.5925   0.8977
 3BK  O25   O   OH1   0  -0.662   3.9004   3.8029   1.4979
 3BK  C14   C   CH1   0  -0.043   2.2910   1.9530   1.5621
 3BK  O24   O   OH1   0  -0.671   1.4121   2.9407   2.0320
 3BK  H18   H   HCR6  0   0.283  -2.4217   0.1015  -1.1467
 3BK  H21   H   HCR6  0   0.290  -6.0098  -1.5397   1.8188
 3BK  H22   H   HCR6  0   0.272  -3.7402  -2.4563   2.0239
 3BK  H16   H   HCH2  0   0.255  -1.4696  -2.4695   1.4390
 3BK  H16A  H   HCH2  0   0.274  -1.3539  -2.4845  -0.3100
 3BK  HN15  H   HNH1  0   0.403  -0.7148  -0.0629   1.2292
 3BK  HN27  H   HNH2  0   0.404   2.3905  -4.8003  -0.4280
 3BK  HN2A  H   HNH2  0   0.397   4.0701  -5.0688  -0.6386
 3BK  H2    H   HCR6  0   0.248   6.0911  -1.0964  -0.2428
 3BK  H10   H   HCH1  0   0.258   0.5248   1.4211   0.4472
 3BK  H12   H   HCH1  0   0.231   2.4872   3.8056  -0.5516
 3BK  H23   H   HCH2  0   0.203   4.8760   3.5900  -1.2202
 3BK  H23A  H   HCH2  0   0.207   4.6161   1.8717  -1.5483
 3BK  HO26  H   HOH1  0   0.457   4.3073   3.1745  -3.4472
 3BK  H13   H   HCH1  0   0.259   4.3390   1.8686   0.8819
 3BK  HO25  H   HOH1  0   0.468   4.5322   3.6163   2.1995
 3BK  H14   H   HCH1  0   0.250   2.5599   1.2474   2.3573
 3BK  HO24  H   HOH1  0   0.449   1.9507   3.6902   2.3185

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
 3BK  C18  C19   aromatic  1.385  0.020  1.385
 3BK  C18  C17   aromatic  1.391  0.020  1.391
 3BK  C19  CL28  single    1.723  0.020  1.723
 3BK  C19  C20   aromatic  1.392  0.020  1.392
 3BK  C20  CL29  single    1.722  0.020  1.722
 3BK  C20  C21   aromatic  1.385  0.020  1.385
 3BK  C21  C22   aromatic  1.386  0.020  1.386
 3BK  C22  C17   aromatic  1.389  0.020  1.389
 3BK  C17  C16   single    1.504  0.020  1.504
 3BK  C16  N15   single    1.449  0.020  1.449
 3BK  N15  C6    single    1.360  0.020  1.360
 3BK  C6   N7    aromatic  1.303  0.020  1.303
 3BK  C6   N5    aromatic  1.382  0.020  1.382
 3BK  N7   C8    aromatic  1.374  0.020  1.374
 3BK  C8   C4    aromatic  1.400  0.020  1.400
 3BK  C8   C9    aromatic  1.384  0.020  1.384
 3BK  C4   N27   single    1.343  0.020  1.343
 3BK  C4   N1    aromatic  1.339  0.020  1.339
 3BK  N1   C2    aromatic  1.327  0.020  1.327
 3BK  C2   N3    aromatic  1.324  0.020  1.324
 3BK  N3   C9    aromatic  1.327  0.020  1.327
 3BK  C9   N5    aromatic  1.376  0.020  1.376
 3BK  N5   C10   single    1.446  0.020  1.446
 3BK  C10  O11   single    1.401  0.020  1.401
 3BK  C10  C14   single    1.535  0.020  1.535
 3BK  O11  C12   single    1.421  0.020  1.421
 3BK  C12  C23   single    1.507  0.020  1.507
 3BK  C12  C13   single    1.527  0.020  1.527
 3BK  C23  O26   single    1.408  0.020  1.408
 3BK  C13  O25   single    1.404  0.020  1.404
 3BK  C13  C14   single    1.536  0.020  1.536
 3BK  C14  O24   single    1.403  0.020  1.403
 3BK  C18  H18   single    0.930  0.020  1.080
 3BK  C21  H21   single    0.930  0.020  1.080
 3BK  C22  H22   single    0.930  0.020  1.080
 3BK  C16  H16   single    0.970  0.020  1.090
 3BK  C16  H16A  single    0.970  0.020  1.090
 3BK  N15  HN15  single    0.890  0.020  1.040
 3BK  N27  HN27  single    0.890  0.020  1.040
 3BK  N27  HN2A  single    0.890  0.020  1.040
 3BK  C2   H2    single    0.930  0.020  1.080
 3BK  C10  H10   single    0.970  0.020  1.090
 3BK  C12  H12   single    0.970  0.020  1.090
 3BK  C23  H23   single    0.970  0.020  1.090
 3BK  C23  H23A  single    0.970  0.020  1.090
 3BK  O26  HO26  single    0.850  0.020  0.980
 3BK  C13  H13   single    0.970  0.020  1.090
 3BK  O25  HO25  single    0.850  0.020  0.980
 3BK  C14  H14   single    0.970  0.020  1.090
 3BK  O24  HO24  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
 3BK  H18   C18  C17   120.19  3.000
 3BK  H18   C18  C19   119.35  3.000
 3BK  C17   C18  C19   120.45  3.000
 3BK  C20   C19  CL28  120.47  3.000
 3BK  C20   C19  C18   120.22  3.000
 3BK  CL28  C19  C18   119.31  3.000
 3BK  C21   C20  CL29  119.65  3.000
 3BK  C21   C20  C19   119.57  3.000
 3BK  CL29  C20  C19   120.77  3.000
 3BK  H21   C21  C22   120.25  3.000
 3BK  H21   C21  C20   119.77  3.000
 3BK  C22   C21  C20   119.98  3.000
 3BK  H22   C22  C17   120.11  3.000
 3BK  H22   C22  C21   119.05  3.000
 3BK  C17   C22  C21   120.84  3.000
 3BK  C16   C17  C22   120.59  3.000
 3BK  C16   C17  C18   120.47  3.000
 3BK  C22   C17  C18   118.93  3.000
 3BK  H16A  C16  H16   106.60  3.000
 3BK  H16A  C16  N15   108.21  3.000
 3BK  H16   C16  N15   112.17  3.000
 3BK  H16A  C16  C17   109.58  3.000
 3BK  H16   C16  C17   109.73  3.000
 3BK  N15   C16  C17   110.45  3.000
 3BK  HN15  N15  C6    115.63  3.000
 3BK  HN15  N15  C16   113.50  3.000
 3BK  C6    N15  C16   118.06  3.000
 3BK  N5    C6   N7    113.45  3.000
 3BK  N5    C6   N15   121.42  3.000
 3BK  N7    C6   N15   125.10  3.000
 3BK  C8    N7   C6    104.33  3.000
 3BK  C9    C8   C4    116.48  3.000
 3BK  C9    C8   N7    111.25  3.000
 3BK  C4    C8   N7    132.27  3.000
 3BK  N1    C4   N27   119.11  3.000
 3BK  N1    C4   C8    118.25  3.000
 3BK  N27   C4   C8    122.63  3.000
 3BK  HN2A  N27  HN27  116.89  3.000
 3BK  HN2A  N27  C4    118.86  3.000
 3BK  HN27  N27  C4    119.64  3.000
 3BK  C2    N1   C4    118.95  3.000
 3BK  H2    C2   N3    116.14  3.000
 3BK  H2    C2   N1    115.82  3.000
 3BK  N3    C2   N1    128.04  3.000
 3BK  C9    N3   C2    112.29  3.000
 3BK  N5    C9   N3    128.68  3.000
 3BK  N5    C9   C8    105.31  3.000
 3BK  N3    C9   C8    126.00  3.000
 3BK  C10   N5   C9    127.37  3.000
 3BK  C10   N5   C6    126.43  3.000
 3BK  C9    N5   C6    105.66  3.000
 3BK  H10   C10  C14   108.98  3.000
 3BK  H10   C10  O11   110.04  3.000
 3BK  C14   C10  O11   107.51  3.000
 3BK  H10   C10  N5    106.25  3.000
 3BK  C14   C10  N5    114.84  3.000
 3BK  O11   C10  N5    109.18  3.000
 3BK  C12   O11  C10   111.20  3.000
 3BK  H12   C12  C13   109.07  3.000
 3BK  H12   C12  C23   109.47  3.000
 3BK  C13   C12  C23   113.14  3.000
 3BK  H12   C12  O11   109.80  3.000
 3BK  C13   C12  O11   105.22  3.000
 3BK  C23   C12  O11   110.04  3.000
 3BK  H23A  C23  H23   107.33  3.000
 3BK  H23A  C23  O26   112.10  3.000
 3BK  H23   C23  O26   111.69  3.000
 3BK  H23A  C23  C12   108.76  3.000
 3BK  H23   C23  C12   107.64  3.000
 3BK  O26   C23  C12   109.17  3.000
 3BK  HO26  O26  C23   108.08  3.000
 3BK  H13   C13  C14   109.27  3.000
 3BK  H13   C13  O25   111.95  3.000
 3BK  C14   C13  O25   113.02  3.000
 3BK  H13   C13  C12   109.90  3.000
 3BK  C14   C13  C12   102.14  3.000
 3BK  O25   C13  C12   110.13  3.000
 3BK  HO25  O25  C13   108.82  3.000
 3BK  H14   C14  O24   111.33  3.000
 3BK  H14   C14  C13   112.66  3.000
 3BK  O24   C14  C13   110.65  3.000
 3BK  H14   C14  C10   111.43  3.000
 3BK  O24   C14  C10   107.53  3.000
 3BK  C13   C14  C10   102.82  3.000
 3BK  HO24  O24  C14   107.22  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
 3BK  CONST_01  C21   C20  C19  C18      0.00   0.0  0
 3BK  CONST_02  C21   C22  C17  C18      0.00   0.0  0
 3BK  CONST_03  C22   C17  C18  C19      0.00   0.0  0
 3BK  CONST_04  C22   C21  C20  C19      0.00   0.0  0
 3BK  CONST_05  C17   C18  C19  C20      0.00   0.0  0
 3BK  CONST_06  C17   C22  C21  C20      0.00   0.0  0
 3BK  CONST_07  C4    C8   N7   C6     180.00   0.0  0
 3BK  CONST_08  C9    C8   N7   C6       0.00   0.0  0
 3BK  CONST_09  C8    C9   N5   C6       0.00   0.0  0
 3BK  CONST_10  N3    C9   N5   C6     180.00   0.0  0
 3BK  CONST_11  C9    N5   C6   N7       0.00   0.0  0
 3BK  CONST_12  N1    C4   C8   N7     180.00   0.0  0
 3BK  CONST_13  N3    C9   C8   N7     180.00   0.0  0
 3BK  CONST_14  N5    C9   C8   N7       0.00   0.0  0
 3BK  CONST_15  N5    C6   N7   C8       0.00   0.0  0
 3BK  CONST_16  C2    N1   C4   C8       0.00   0.0  0
 3BK  CONST_17  C2    N3   C9   C8       0.00   0.0  0
 3BK  CONST_18  N3    C9   C8   C4       0.00   0.0  0
 3BK  CONST_19  N5    C9   C8   C4     180.00   0.0  0
 3BK  CONST_20  N3    C2   N1   C4       0.00   0.0  0
 3BK  CONST_21  C9    C8   C4   N1       0.00   0.0  0
 3BK  CONST_22  C9    N3   C2   N1       0.00   0.0  0
 3BK  CONST_23  N5    C9   N3   C2     180.00   0.0  0
 3BK  CONST_24  C10   N5   C6   N7     180.00   0.0  0
 3BK  CONST_25  C10   N5   C9   C8     180.00   0.0  0
 3BK  CONST_26  C10   N5   C9   N3       0.00   0.0  0
 3BK  CONST_27  CL29  C20  C19  C18    180.00   0.0  0
 3BK  CONST_28  C16   C17  C18  C19    180.00   0.0  0
 3BK  CONST_29  C17   C18  C19  CL28   180.00   0.0  0
 3BK  CONST_30  C21   C20  C19  CL28   180.00   0.0  0
 3BK  CONST_31  C22   C21  C20  CL29   180.00   0.0  0
 3BK  CONST_32  C16   C17  C22  C21    180.00   0.0  0
 3BK  CONST_33  C8    N7   C6   N15    180.00   0.0  0
 3BK  CONST_34  C9    N5   C6   N15    180.00   0.0  0
 3BK  CONST_35  C10   N5   C6   N15      0.00   0.0  0
 3BK  CONST_36  N27   C4   C8   N7       0.00   0.0  0
 3BK  CONST_37  C9    C8   C4   N27    180.00   0.0  0
 3BK  CONST_38  C2    N1   C4   N27    180.00   0.0  0
 3BK  CONST_39  H22   C22  C17  C18    180.00   0.0  0
 3BK  CONST_40  H21   C21  C20  C19    180.00   0.0  0
 3BK  CONST_41  H18   C18  C19  C20    180.00   0.0  0
 3BK  CONST_42  H2    C2   N1   C4     180.00   0.0  0
 3BK  CONST_43  N7    C6   N15  C16      0.00   0.0  0
 3BK  CONST_44  N5    C6   N15  C16    180.00   0.0  0
 3BK  CONST_46  HN27  N27  C4   C8       0.00   0.0  0
 3BK  CONST_47  HN2A  N27  C4   C8     180.00   0.0  0
 3BK  Var_01    N15   C16  C17  C18     46.95  30.0  2
 3BK  Var_02    C6    N15  C16  C17   -168.25  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
 3BK  chir_01  C10  N5   O11  C14  positiv
 3BK  chir_02  C12  O11  C23  C13  positiv
 3BK  chir_03  C13  O25  C12  C14  positiv
 3BK  chir_04  C14  O24  C13  C10  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
 3BK  plan-1  C18   0.020
 3BK  plan-1  C19   0.020
 3BK  plan-1  CL28  0.020
 3BK  plan-1  C20   0.020
 3BK  plan-1  CL29  0.020
 3BK  plan-1  C21   0.020
 3BK  plan-1  C22   0.020
 3BK  plan-1  C17   0.020
 3BK  plan-1  C16   0.020
 3BK  plan-1  H18   0.020
 3BK  plan-1  H21   0.020
 3BK  plan-1  H22   0.020
 3BK  plan-2  N15   0.020
 3BK  plan-2  C6    0.020
 3BK  plan-2  N7    0.020
 3BK  plan-2  C8    0.020
 3BK  plan-2  C4    0.020
 3BK  plan-2  N27   0.020
 3BK  plan-2  N1    0.020
 3BK  plan-2  C2    0.020
 3BK  plan-2  N3    0.020
 3BK  plan-2  C9    0.020
 3BK  plan-2  N5    0.020
 3BK  plan-2  C10   0.020
 3BK  plan-2  H2    0.020
 3BK  plan-3  C16   0.020
 3BK  plan-3  N15   0.020
 3BK  plan-3  C6    0.020
 3BK  plan-3  HN15  0.020
 3BK  plan-4  C4    0.020
 3BK  plan-4  N27   0.020
 3BK  plan-4  HN27  0.020
 3BK  plan-4  HN2A  0.020

