# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 03:10:15 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 9-[[4-[2,2-bis(fluoranyl)ethoxy]pyridin-2-yl]methyl]-2-chloranyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Cl)nc2n(Cc3cc(OCC(F)F)ccn3)cnc12
#
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
 GJR  GJR  "9-[[4-[2,2-bis(fluoranyl)ethoxy]pyridin-2-yl]methyl]-2-chloranyl-purin-6-amine"
  ligand  34  23  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GJR
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
 GJR  N1   N   N     0  -0.450  -0.2745  -22.6871  -11.5401
 GJR  C8   C   CR15  0   0.112  -2.6756  -21.3215   -8.1259
 GJR  C5   C   CR56  0   0.004  -1.5370  -22.3250   -9.5873
 GJR  C6   C   CR6   0   0.476  -0.8182  -23.1981  -10.4263
 GJR  N3   N   N     0  -0.424  -1.0933  -20.4898  -11.1175
 GJR  C4   C   CR56  0   0.505  -1.6246  -21.0085  -10.0090
 GJR  C2   C   CR6   0   0.275  -0.4477  -21.4058  -11.7941
 GJR  C13  C   CR6   0   0.242  -1.6013  -18.0248   -9.0236
 GJR  C15  C   CR16  0  -0.073  -0.7887  -16.0120   -9.6841
 GJR  N7   N   NR5   0  -0.508  -2.3601  -20.3726   -9.0586
 GJR  N9   N   N     0  -0.445  -2.2043  -22.5010   -8.4043
 GJR  N10  N   NH2   0  -0.811  -0.6581  -24.4910  -10.1634
 GJR  CL1  CL  CL    0  -0.112   0.3024  -20.8491  -13.2593
 GJR  N14  N   N     0  -0.438  -1.7643  -16.9068   -9.7262
 GJR  C16  C   CR16  0  -0.434   0.3861  -16.1684   -8.9669
 GJR  C17  C   CR6   0   0.487   0.5462  -17.3411   -8.2347
 GJR  C18  C   CR16  0  -0.405  -0.4769  -18.2876   -8.2628
 GJR  O19  O   O2    0  -0.462   1.6199  -17.6353   -7.4936
 GJR  C20  C   CH2   0  -0.294   2.6757  -16.7013   -7.4297
 GJR  C21  C   CH1   0   0.511   3.7413  -17.2627   -6.5281
 GJR  F22  F   F     0  -0.342   3.2486  -17.4796   -5.2782
 GJR  F23  F   F     0  -0.341   4.1752  -18.4664   -6.9895
 GJR  H1   H   HCR5  0   0.299  -3.2668  -21.0689   -7.2574
 GJR  H2   H   HCH2  0   0.302  -3.4236  -18.8234   -8.2261
 GJR  H3   H   HCH2  0   0.292  -3.3435  -18.7878   -9.9797
 GJR  H4   H   HCR6  0   0.268  -0.9370  -15.1073  -10.2631
 GJR  H5   H   HNH2  0   0.409  -0.1492  -25.0828  -10.7980
 GJR  H6   H   HNH2  0   0.417  -1.0664  -24.9076   -9.3446
 GJR  H7   H   HCR6  0   0.294   1.1318  -15.3869   -9.0017
 GJR  H8   H   HCR6  0   0.280  -0.3805  -19.2069   -7.6987
 GJR  H9   H   HCH2  0   0.264   3.1121  -16.5157   -8.4166
 GJR  H10  H   HCH2  0   0.264   2.3441  -15.7403   -7.0230
 GJR  H11  H   HCH1  0   0.213   4.5924  -16.5839   -6.4576
 GJR  C11  C   CH2   0  -0.373  -2.7622  -18.9865   -9.0791

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
 GJR  CL1  C2   single    1.738  0.020  1.738
 GJR  C2   N1   aromatic  1.318  0.020  1.318
 GJR  C2   N3   aromatic  1.309  0.020  1.309
 GJR  N1   C6   aromatic  1.341  0.020  1.341
 GJR  N3   C4   aromatic  1.334  0.020  1.334
 GJR  C6   N10  single    1.329  0.020  1.329
 GJR  C6   C5   aromatic  1.408  0.020  1.408
 GJR  C15  N14  aromatic  1.325  0.020  1.325
 GJR  C15  C16  aromatic  1.385  0.020  1.385
 GJR  N14  C13  aromatic  1.330  0.020  1.330
 GJR  C4   C5   aromatic  1.385  0.020  1.385
 GJR  C4   N7   aromatic  1.360  0.020  1.360
 GJR  C5   N9   aromatic  1.370  0.020  1.370
 GJR  C16  C17  aromatic  1.392  0.020  1.392
 GJR  C13  C11  single    1.509  0.020  1.509
 GJR  C13  C18  aromatic  1.383  0.020  1.383
 GJR  N7   C11  single    1.443  0.020  1.443
 GJR  N7   C8   aromatic  1.367  0.020  1.367
 GJR  N9   C8   aromatic  1.300  0.020  1.300
 GJR  C17  C18  aromatic  1.394  0.020  1.394
 GJR  C17  O19  single    1.337  0.020  1.337
 GJR  C20  O19  single    1.411  0.020  1.411
 GJR  C20  C21  single    1.505  0.020  1.505
 GJR  F23  C21  single    1.360  0.020  1.360
 GJR  C21  F22  single    1.361  0.020  1.361
 GJR  C8   H1   single    0.930  0.020  1.080
 GJR  C11  H2   single    0.970  0.020  1.090
 GJR  C11  H3   single    0.970  0.020  1.090
 GJR  C15  H4   single    0.930  0.020  1.080
 GJR  N10  H5   single    0.860  0.020  1.020
 GJR  N10  H6   single    0.860  0.020  1.020
 GJR  C16  H7   single    0.930  0.020  1.080
 GJR  C18  H8   single    0.930  0.020  1.080
 GJR  C20  H9   single    0.970  0.020  1.090
 GJR  C20  H10  single    0.970  0.020  1.090
 GJR  C21  H11  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
 GJR  C2   N1   C6   118.52  3.000
 GJR  H1   C8   N9   125.62  3.000
 GJR  H1   C8   N7   120.81  3.000
 GJR  N9   C8   N7   113.56  3.000
 GJR  N9   C5   C4   110.75  3.000
 GJR  N9   C5   C6   133.13  3.000
 GJR  C4   C5   C6   116.12  3.000
 GJR  N10  C6   C5   123.15  3.000
 GJR  C5   C6   N1   117.75  3.000
 GJR  N10  C6   N1   119.10  3.000
 GJR  C2   N3   C4   110.72  3.000
 GJR  N7   C4   N3   127.91  3.000
 GJR  N7   C4   C5   105.42  3.000
 GJR  N3   C4   C5   126.67  3.000
 GJR  CL1  C2   N3   115.12  3.000
 GJR  N3   C2   N1   130.21  3.000
 GJR  CL1  C2   N1   114.67  3.000
 GJR  C18  C13  N14  123.36  3.000
 GJR  C18  C13  C11  121.65  3.000
 GJR  N14  C13  C11  114.96  3.000
 GJR  H4   C15  C16  119.12  3.000
 GJR  H4   C15  N14  116.49  3.000
 GJR  C16  C15  N14  124.40  3.000
 GJR  C11  N7   C4   126.15  3.000
 GJR  C11  N7   C8   127.72  3.000
 GJR  C4   N7   C8   106.08  3.000
 GJR  C5   N9   C8   104.18  3.000
 GJR  H6   N10  H5   118.39  3.000
 GJR  H6   N10  C6   121.02  3.000
 GJR  H5   N10  C6   120.56  3.000
 GJR  C15  N14  C13  117.43  3.000
 GJR  H7   C16  C17  123.15  3.000
 GJR  H7   C16  C15  119.14  3.000
 GJR  C17  C16  C15  117.71  3.000
 GJR  O19  C17  C18  116.81  3.000
 GJR  O19  C17  C16  124.70  3.000
 GJR  C18  C17  C16  118.50  3.000
 GJR  H8   C18  C17  120.04  3.000
 GJR  H8   C18  C13  121.35  3.000
 GJR  C17  C18  C13  118.61  3.000
 GJR  C20  O19  C17  118.70  3.000
 GJR  H10  C20  H9   107.86  3.000
 GJR  H10  C20  C21  108.62  3.000
 GJR  H9   C20  C21  108.73  3.000
 GJR  H10  C20  O19  111.78  3.000
 GJR  H9   C20  O19  111.70  3.000
 GJR  C21  C20  O19  108.06  3.000
 GJR  H11  C21  F23  108.89  3.000
 GJR  H11  C21  F22  108.80  3.000
 GJR  F23  C21  F22  106.62  3.000
 GJR  H11  C21  C20  111.04  3.000
 GJR  F22  C21  C20  110.69  3.000
 GJR  F23  C21  C20  110.66  3.000
 GJR  H3   C11  H2   107.17  3.000
 GJR  H3   C11  N7   109.60  3.000
 GJR  H2   C11  N7   107.53  3.000
 GJR  H3   C11  C13  108.93  3.000
 GJR  H2   C11  C13  110.01  3.000
 GJR  N7   C11  C13  113.41  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
 GJR  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 GJR  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 GJR  CONST_03  N9   C5   C6   N1    180.00   0.0  0
 GJR  CONST_04  N3   C4   N7   C8    180.00   0.0  0
 GJR  CONST_05  C5   C4   N7   C8      0.00   0.0  0
 GJR  CONST_06  C6   C5   N9   C8    180.00   0.0  0
 GJR  CONST_07  C4   C5   N9   C8      0.00   0.0  0
 GJR  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 GJR  CONST_09  C2   N3   C4   C5      0.00   0.0  0
 GJR  CONST_10  N7   C8   N9   C5      0.00   0.0  0
 GJR  CONST_11  N3   C2   N1   C6      0.00   0.0  0
 GJR  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 GJR  CONST_13  N7   C4   C5   C6    180.00   0.0  0
 GJR  CONST_14  N9   C5   C4   N3    180.00   0.0  0
 GJR  CONST_15  N9   C8   N7   C4      0.00   0.0  0
 GJR  CONST_16  N7   C4   N3   C2    180.00   0.0  0
 GJR  CONST_17  C16  C15  N14  C13     0.00   0.0  0
 GJR  CONST_18  C16  C17  C18  C13     0.00   0.0  0
 GJR  CONST_19  C18  C13  N14  C15     0.00   0.0  0
 GJR  CONST_20  C18  C17  C16  C15     0.00   0.0  0
 GJR  CONST_21  N9   C5   C4   N7      0.00   0.0  0
 GJR  CONST_22  C17  C16  C15  N14     0.00   0.0  0
 GJR  CONST_23  C17  C18  C13  N14     0.00   0.0  0
 GJR  CONST_24  C11  N7   C4   C5    180.00   0.0  0
 GJR  CONST_25  CL1  C2   N1   C6    180.00   0.0  0
 GJR  CONST_26  C11  N7   C4   N3      0.00   0.0  0
 GJR  CONST_27  CL1  C2   N3   C4    180.00   0.0  0
 GJR  CONST_28  N10  C6   C5   C4    180.00   0.0  0
 GJR  CONST_29  N10  C6   N1   C2    180.00   0.0  0
 GJR  CONST_30  C15  N14  C13  C11   180.00   0.0  0
 GJR  CONST_31  C17  C18  C13  C11   180.00   0.0  0
 GJR  CONST_32  N9   C8   N7   C11   180.00   0.0  0
 GJR  CONST_33  O19  C17  C18  C13   180.00   0.0  0
 GJR  CONST_34  O19  C17  C16  C15   180.00   0.0  0
 GJR  CONST_35  N10  C6   C5   N9      0.00   0.0  0
 GJR  CONST_36  H1   C8   N9   C5    180.00   0.0  0
 GJR  CONST_37  H1   C8   N7   C4    180.00   0.0  0
 GJR  CONST_38  H4   C15  N14  C13   180.00   0.0  0
 GJR  CONST_39  H7   C16  C15  N14   180.00   0.0  0
 GJR  CONST_40  H8   C18  C13  N14   180.00   0.0  0
 GJR  CONST_41  H8   C18  C17  C16   180.00   0.0  0
 GJR  CONST_42  H4   C15  C16  C17   180.00   0.0  0
 GJR  CONST_43  H7   C16  C17  C18   180.00   0.0  0
 GJR  CONST_44  H5   N10  C6   N1      0.00   0.0  0
 GJR  CONST_45  H6   N10  C6   N1    180.00   0.0  0
 GJR  CONST_46  H5   N10  C6   C5    180.00   0.0  0
 GJR  CONST_47  H6   N10  C6   C5      0.00   0.0  0
 GJR  Var_01    C13  C11  N7   C8    118.99  30.0  2
 GJR  Var_02    C13  C11  N7   C4    -63.83  30.0  2
 GJR  Var_03    N14  C13  C11  N7    144.93  30.0  2
 GJR  Var_04    C18  C13  C11  N7    -36.81  30.0  2
 GJR  Var_05    C20  O19  C17  C16     0.33  30.0  2
 GJR  Var_06    C20  O19  C17  C18  -179.59  30.0  2
 GJR  Var_07    H2   C11  N7   C8     -2.87  30.0  2
 GJR  Var_08    H3   C11  N7   C8   -119.05  30.0  2
 GJR  Var_09    H2   C11  N7   C4    174.31  30.0  2
 GJR  Var_10    H3   C11  N7   C4     58.14  30.0  2
 GJR  Var_11    H2   C11  C13  N14   -94.61  30.0  2
 GJR  Var_12    H3   C11  C13  N14    22.59  30.0  2
 GJR  Var_13    H2   C11  C13  C18    83.65  30.0  2
 GJR  Var_14    H3   C11  C13  C18  -159.15  30.0  2
 GJR  Var_15    C21  C20  O19  C17   179.37  30.0  1
 GJR  Var_16    H9   C20  O19  C17   -61.07  30.0  1
 GJR  Var_17    H10  C20  O19  C17    59.90  30.0  1
 GJR  Var_18    F23  C21  C20  O19    57.97  30.0  3
 GJR  Var_19    F22  C21  C20  O19   -60.02  30.0  3
 GJR  Var_20    H11  C21  C20  O19   179.02  30.0  3
 GJR  Var_21    H9   C20  C21  F22   178.57  30.0  2
 GJR  Var_22    H10  C20  C21  F22    61.44  30.0  2
 GJR  Var_23    H9   C20  C21  F23   -63.45  30.0  2
 GJR  Var_24    H10  C20  C21  F23   179.42  30.0  2

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
 GJR  plan-1  C13  0.020
 GJR  plan-1  C15  0.020
 GJR  plan-1  N14  0.020
 GJR  plan-1  C16  0.020
 GJR  plan-1  C17  0.020
 GJR  plan-1  C18  0.020
 GJR  plan-1  O19  0.020
 GJR  plan-1  H4   0.020
 GJR  plan-1  H7   0.020
 GJR  plan-1  H8   0.020
 GJR  plan-1  C11  0.020
 GJR  plan-2  N1   0.020
 GJR  plan-2  C8   0.020
 GJR  plan-2  C5   0.020
 GJR  plan-2  C6   0.020
 GJR  plan-2  N3   0.020
 GJR  plan-2  C4   0.020
 GJR  plan-2  C2   0.020
 GJR  plan-2  N7   0.020
 GJR  plan-2  N9   0.020
 GJR  plan-2  N10  0.020
 GJR  plan-2  CL1  0.020
 GJR  plan-2  H1   0.020
 GJR  plan-2  C11  0.020
 GJR  plan-3  C6   0.020
 GJR  plan-3  N10  0.020
 GJR  plan-3  H5   0.020
 GJR  plan-3  H6   0.020

