# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 07:29:35 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 8-{[(2-chlorophenyl)methyl]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(NCc4ccccc4Cl)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
 HFY  HFY  8-{[(2-chlorophenyl)methyl]amino}adenosine  ligand  47  28  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HFY
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
 HFY  O3   O   OH1   0  -0.671  -0.5981  -2.9960   1.4397
 HFY  C4   C   CH2   0  -0.159  -4.1872  -2.3811  -1.2426
 HFY  C5   C   CR5   0   0.751   0.2344   0.9192  -0.5834
 HFY  C6   C   CR56  0   0.030  -1.1816   2.3291   0.1202
 HFY  N1   N   N     0  -0.533   0.0595   2.2074  -0.4530
 HFY  C7   C   CR6   0   0.420  -1.9385   3.4415   0.5057
 HFY  C8   C   CR16  0   0.032  -3.5903   1.9879   1.1659
 HFY  N2   N   N     0  -0.468  -3.1539   3.2331   1.0287
 HFY  C9   C   CR56  0   0.492  -1.7645   1.0922   0.3243
 HFY  C10  C   CH2   0  -0.361   2.4740   1.1135  -1.5311
 HFY  C11  C   CR6   0   0.185   3.7627   0.4671  -1.1034
 HFY  C12  C   CR16  0  -0.319   4.6079  -0.1072  -2.0472
 HFY  N3   N   N     0  -0.457  -2.9648   0.8659   0.8401
 HFY  C13  C   CR16  0  -0.231   5.7936  -0.7268  -1.6773
 HFY  C14  C   CR16  0  -0.276   6.1503  -0.7829  -0.3387
 HFY  C15  C   CR16  0  -0.200   5.3263  -0.2164   0.6244
 HFY  N4   N   NH2   0  -0.824  -1.4801   4.7011   0.3978
 HFY  C16  C   CR6   0  -0.103   4.1478   0.3986   0.2342
 HFY  N5   N   NH1   0  -0.703   1.3418   0.3355  -1.0803
 HFY  N    N   NR5   0  -0.613  -0.8353   0.1753  -0.1128
 HFY  C    C   CH1   0   0.168  -0.9767  -1.2572  -0.1297
 HFY  C1   C   CH1   0  -0.048  -1.4245  -1.8870   1.2016
 HFY  C2   C   CH1   0  -0.031  -2.8637  -2.3384   0.9076
 HFY  O2   O   OH1   0  -0.663  -3.2142  -3.5210   1.5787
 HFY  C3   C   CH1   0   0.017  -2.8367  -2.5740  -0.5997
 HFY  O    O   O2    0  -0.491  -1.9197  -1.6174  -1.1066
 HFY  H8   H   HOH1  0   0.448  -1.1381  -3.6614   1.8868
 HFY  H4   H   HCH2  0   0.206  -4.8999  -3.0298  -0.7170
 HFY  H5   H   HCH2  0   0.199  -4.5116  -1.3447  -1.0779
 HFY  H9   H   HCR6  0   0.247  -4.5799   1.8770   1.5960
 HFY  H14  H   HCH2  0   0.278   2.3842   2.1143  -1.1115
 HFY  H13  H   HCH2  0   0.267   2.4667   1.2223  -2.6188
 HFY  H15  H   HCR6  0   0.264   4.3251  -0.0654  -3.0922
 HFY  H16  H   HCR6  0   0.263   6.4333  -1.1646  -2.4319
 HFY  H17  H   HCR6  0   0.269   7.0705  -1.2638  -0.0351
 HFY  H18  H   HCR6  0   0.280   5.6010  -0.2533   1.6699
 HFY  H11  H   HNH2  0   0.402  -0.6636   4.8838  -0.1593
 HFY  H10  H   HNH2  0   0.395  -2.1231   5.4640   0.5242
 HFY  H12  H   HNH1  0   0.409   1.2837  -0.6055  -1.4325
 HFY  H    H   HCH1  0   0.256   0.0065  -1.6699  -0.3709
 HFY  H1   H   HCH1  0   0.249  -1.3744  -1.1696   2.0289
 HFY  H2   H   HCH1  0   0.258  -3.5495  -1.5202   1.1417
 HFY  H7   H   HOH1  0   0.468  -3.6231  -3.2908   2.4187
 HFY  H3   H   HCH1  0   0.232  -2.4744  -3.5925  -0.8024
 HFY  O1   O   OH1   0  -0.671  -4.1030  -2.6972  -2.6115
 HFY  CL   CL  CL    0  -0.123   3.1436   1.1124   1.4552
 HFY  H6   H   HOH1  0   0.457  -4.9761  -2.5835  -2.9971

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
 HFY  O2   C2   single    1.404  0.020  1.404
 HFY  O3   C1   single    1.403  0.020  1.403
 HFY  C2   C1   single    1.537  0.020  1.537
 HFY  C2   C3   single    1.526  0.020  1.526
 HFY  C1   C    single    1.539  0.020  1.539
 HFY  N3   C8   aromatic  1.325  0.020  1.325
 HFY  N3   C9   aromatic  1.326  0.020  1.326
 HFY  C8   N2   aromatic  1.327  0.020  1.327
 HFY  C    N    single    1.440  0.020  1.440
 HFY  C    O    single    1.405  0.020  1.405
 HFY  C3   O    single    1.419  0.020  1.419
 HFY  C3   C4   single    1.508  0.020  1.508
 HFY  N2   C7   aromatic  1.339  0.020  1.339
 HFY  C9   N    aromatic  1.377  0.020  1.377
 HFY  C9   C6   aromatic  1.383  0.020  1.383
 HFY  N    C5   aromatic  1.385  0.020  1.385
 HFY  CL   C16  single    1.735  0.020  1.735
 HFY  C4   O1   single    1.407  0.020  1.407
 HFY  C7   C6   aromatic  1.400  0.020  1.400
 HFY  C7   N4   single    1.345  0.020  1.345
 HFY  C6   N1   aromatic  1.372  0.020  1.372
 HFY  C5   N1   aromatic  1.307  0.020  1.307
 HFY  C5   N5   single    1.347  0.020  1.347
 HFY  C15  C16  aromatic  1.385  0.020  1.385
 HFY  C15  C14  aromatic  1.388  0.020  1.388
 HFY  C16  C11  aromatic  1.394  0.020  1.394
 HFY  N5   C10  single    1.446  0.020  1.446
 HFY  C14  C13  aromatic  1.386  0.020  1.386
 HFY  C11  C10  single    1.504  0.020  1.504
 HFY  C11  C12  aromatic  1.391  0.020  1.391
 HFY  C13  C12  aromatic  1.388  0.020  1.388
 HFY  O3   H8   single    0.850  0.020  0.980
 HFY  C4   H4   single    0.970  0.020  1.090
 HFY  C4   H5   single    0.970  0.020  1.090
 HFY  C8   H9   single    0.930  0.020  1.080
 HFY  C10  H14  single    0.970  0.020  1.090
 HFY  C10  H13  single    0.970  0.020  1.090
 HFY  C12  H15  single    0.930  0.020  1.080
 HFY  C13  H16  single    0.930  0.020  1.080
 HFY  C14  H17  single    0.930  0.020  1.080
 HFY  C15  H18  single    0.930  0.020  1.080
 HFY  N4   H11  single    0.890  0.020  1.040
 HFY  N4   H10  single    0.890  0.020  1.040
 HFY  N5   H12  single    0.890  0.020  1.040
 HFY  C    H    single    0.970  0.020  1.090
 HFY  C1   H1   single    0.970  0.020  1.090
 HFY  C2   H2   single    0.970  0.020  1.090
 HFY  O2   H7   single    0.850  0.020  0.980
 HFY  C3   H3   single    0.970  0.020  1.090
 HFY  O1   H6   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
 HFY  H8   O3   C1   107.07  3.000
 HFY  H5   C4   H4   107.10  3.000
 HFY  H5   C4   O1   112.05  3.000
 HFY  H4   C4   O1   111.83  3.000
 HFY  H5   C4   C3   108.74  3.000
 HFY  H4   C4   C3   107.56  3.000
 HFY  O1   C4   C3   109.41  3.000
 HFY  N    C5   N5   121.83  3.000
 HFY  N5   C5   N1   125.05  3.000
 HFY  N    C5   N1   113.09  3.000
 HFY  C9   C6   C7   116.26  3.000
 HFY  C7   C6   N1   132.42  3.000
 HFY  C9   C6   N1   111.32  3.000
 HFY  C6   N1   C5   104.48  3.000
 HFY  N4   C7   N2   119.11  3.000
 HFY  N4   C7   C6   122.55  3.000
 HFY  N2   C7   C6   118.33  3.000
 HFY  H9   C8   N3   116.20  3.000
 HFY  H9   C8   N2   115.92  3.000
 HFY  N3   C8   N2   127.88  3.000
 HFY  C8   N2   C7   119.01  3.000
 HFY  N    C9   N3   128.38  3.000
 HFY  N    C9   C6   105.33  3.000
 HFY  N3   C9   C6   126.28  3.000
 HFY  H13  C10  H14  106.94  3.000
 HFY  H13  C10  N5   111.02  3.000
 HFY  H14  C10  N5   108.05  3.000
 HFY  H13  C10  C11  109.36  3.000
 HFY  H14  C10  C11  110.86  3.000
 HFY  N5   C10  C11  110.55  3.000
 HFY  C16  C11  C12  117.58  3.000
 HFY  C12  C11  C10  120.34  3.000
 HFY  C16  C11  C10  122.07  3.000
 HFY  H15  C12  C13  119.82  3.000
 HFY  H15  C12  C11  118.68  3.000
 HFY  C13  C12  C11  121.50  3.000
 HFY  C9   N3   C8   112.24  3.000
 HFY  H16  C13  C14  120.33  3.000
 HFY  H16  C13  C12  119.99  3.000
 HFY  C14  C13  C12  119.68  3.000
 HFY  H17  C14  C15  119.45  3.000
 HFY  H17  C14  C13  120.52  3.000
 HFY  C15  C14  C13  120.04  3.000
 HFY  H18  C15  C16  120.23  3.000
 HFY  H18  C15  C14  120.38  3.000
 HFY  C16  C15  C14  119.38  3.000
 HFY  H10  N4   H11  116.81  3.000
 HFY  H10  N4   C7   118.85  3.000
 HFY  H11  N4   C7   119.45  3.000
 HFY  CL   C16  C15  118.48  3.000
 HFY  C15  C16  C11  121.82  3.000
 HFY  CL   C16  C11  119.70  3.000
 HFY  H12  N5   C10  116.05  3.000
 HFY  H12  N5   C5   119.13  3.000
 HFY  C10  N5   C5   121.71  3.000
 HFY  C    N    C9   126.88  3.000
 HFY  C9   N    C5   105.75  3.000
 HFY  C    N    C5   127.32  3.000
 HFY  H    C    O    110.70  3.000
 HFY  H    C    C1   107.34  3.000
 HFY  O    C    C1   107.53  3.000
 HFY  H    C    N    106.85  3.000
 HFY  O    C    N    109.23  3.000
 HFY  C1   C    N    115.19  3.000
 HFY  H1   C1   C2   112.30  3.000
 HFY  H1   C1   C    111.82  3.000
 HFY  C2   C1   C    103.13  3.000
 HFY  H1   C1   O3   111.24  3.000
 HFY  C    C1   O3   107.38  3.000
 HFY  C2   C1   O3   110.60  3.000
 HFY  H2   C2   C3   109.77  3.000
 HFY  H2   C2   O2   111.81  3.000
 HFY  C3   C2   O2   110.28  3.000
 HFY  H2   C2   C1   109.07  3.000
 HFY  C3   C2   C1   102.58  3.000
 HFY  O2   C2   C1   112.94  3.000
 HFY  H7   O2   C2   108.78  3.000
 HFY  H3   C3   O    110.22  3.000
 HFY  H3   C3   C2   109.32  3.000
 HFY  O    C3   C2   105.09  3.000
 HFY  H3   C3   C4   109.56  3.000
 HFY  O    C3   C4   109.90  3.000
 HFY  C2   C3   C4   112.67  3.000
 HFY  C3   O    C    111.00  3.000
 HFY  H6   O1   C4   108.01  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
 HFY  CONST_01  N3   C9   N    C5   180.00   0.0  0
 HFY  CONST_02  C6   C9   N    C5     0.00   0.0  0
 HFY  CONST_03  C9   C6   N1   C5     0.00   0.0  0
 HFY  CONST_04  C7   C6   N1   C5   180.00   0.0  0
 HFY  CONST_05  C8   N3   C9   C6     0.00   0.0  0
 HFY  CONST_06  C8   N2   C7   C6     0.00   0.0  0
 HFY  CONST_07  N    C5   N1   C6     0.00   0.0  0
 HFY  CONST_08  N3   C9   C6   N1   180.00   0.0  0
 HFY  CONST_09  N    C9   C6   N1     0.00   0.0  0
 HFY  CONST_10  N2   C7   C6   N1   180.00   0.0  0
 HFY  CONST_11  C9   N    C5   N1     0.00   0.0  0
 HFY  CONST_12  N3   C8   N2   C7     0.00   0.0  0
 HFY  CONST_13  N3   C9   C6   C7     0.00   0.0  0
 HFY  CONST_14  N    C9   C6   C7   180.00   0.0  0
 HFY  CONST_15  N    C9   N3   C8   180.00   0.0  0
 HFY  CONST_16  C9   N3   C8   N2     0.00   0.0  0
 HFY  CONST_17  C9   C6   C7   N2     0.00   0.0  0
 HFY  CONST_18  C14  C15  C16  C11    0.00   0.0  0
 HFY  CONST_19  C14  C13  C12  C11    0.00   0.0  0
 HFY  CONST_20  C15  C16  C11  C12    0.00   0.0  0
 HFY  CONST_21  C15  C14  C13  C12    0.00   0.0  0
 HFY  CONST_22  C16  C15  C14  C13    0.00   0.0  0
 HFY  CONST_23  C16  C11  C12  C13    0.00   0.0  0
 HFY  CONST_24  C    N    C9   C6   180.00   0.0  0
 HFY  CONST_25  C    N    C5   N1   180.00   0.0  0
 HFY  CONST_26  C    N    C9   N3     0.00   0.0  0
 HFY  CONST_27  N5   C5   N1   C6   180.00   0.0  0
 HFY  CONST_28  N4   C7   C6   N1     0.00   0.0  0
 HFY  CONST_29  N4   C7   N2   C8   180.00   0.0  0
 HFY  CONST_30  N5   C5   N    C9   180.00   0.0  0
 HFY  CONST_31  N4   C7   C6   C9   180.00   0.0  0
 HFY  CONST_32  C15  C16  C11  C10  180.00   0.0  0
 HFY  CONST_33  C13  C12  C11  C10  180.00   0.0  0
 HFY  CONST_34  CL   C16  C11  C12  180.00   0.0  0
 HFY  CONST_35  CL   C16  C15  C14  180.00   0.0  0
 HFY  CONST_36  C    N    C5   N5     0.00   0.0  0
 HFY  CONST_37  H9   C8   N2   C7   180.00   0.0  0
 HFY  CONST_38  H18  C15  C16  C11  180.00   0.0  0
 HFY  CONST_39  H16  C13  C12  C11  180.00   0.0  0
 HFY  CONST_40  H17  C14  C13  C12  180.00   0.0  0
 HFY  CONST_41  H15  C12  C13  C14  180.00   0.0  0
 HFY  CONST_42  C10  N5   C5   N1     0.00   0.0  0
 HFY  CONST_43  N    C5   N5   C10  180.00   0.0  0
 HFY  CONST_44  H11  N4   C7   C6     0.00   0.0  0
 HFY  CONST_45  H10  N4   C7   C6   180.00   0.0  0
 HFY  Var_01    C11  C10  N5   C5   139.03  30.0  3
 HFY  Var_02    N5   C10  C11  C12  110.87  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
 HFY  chir_01  C   C1  N   O   positiv
 HFY  chir_02  C1  O3  C2  C   positiv
 HFY  chir_03  C2  O2  C1  C3  negativ
 HFY  chir_04  C3  O   C2  C4  negativ

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
 HFY  plan-1  C10  0.020
 HFY  plan-1  C11  0.020
 HFY  plan-1  C12  0.020
 HFY  plan-1  C13  0.020
 HFY  plan-1  C14  0.020
 HFY  plan-1  C15  0.020
 HFY  plan-1  C16  0.020
 HFY  plan-1  H15  0.020
 HFY  plan-1  H16  0.020
 HFY  plan-1  H17  0.020
 HFY  plan-1  H18  0.020
 HFY  plan-1  CL   0.020
 HFY  plan-2  C5   0.020
 HFY  plan-2  C6   0.020
 HFY  plan-2  N1   0.020
 HFY  plan-2  C7   0.020
 HFY  plan-2  C8   0.020
 HFY  plan-2  N2   0.020
 HFY  plan-2  C9   0.020
 HFY  plan-2  N3   0.020
 HFY  plan-2  N4   0.020
 HFY  plan-2  N5   0.020
 HFY  plan-2  N    0.020
 HFY  plan-2  C    0.020
 HFY  plan-2  H9   0.020
 HFY  plan-3  C7   0.020
 HFY  plan-3  N4   0.020
 HFY  plan-3  H11  0.020
 HFY  plan-3  H10  0.020
 HFY  plan-4  C5   0.020
 HFY  plan-4  C10  0.020
 HFY  plan-4  N5   0.020
 HFY  plan-4  H12  0.020

