# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 02:37:21 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 9-[(1~{S})-1-[4-[2,2-bis(fluoranyl)ethoxy]pyridin-2-yl]ethyl]-2-chloranyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](n1cnc2c(N)nc(Cl)nc12)c3cc(OCC(F)F)ccn3
#
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
 GJU  GJU  "9-[(1~{S})-1-[4-[2,2-bis(fluoranyl)ethoxy]pyridin-2-yl]ethyl]-2-chloranyl-purin-6-amine"
  ligand  37  24  .  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_GJU
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
 GJU  N1   N   N     0  -0.450   0.2581  154.2564  -11.6076
 GJU  C2   C   CR6   0   0.274   0.5623  153.0313  -11.9850
 GJU  N3   N   N     0  -0.426   1.1801  152.0766  -11.3362
 GJU  C4   C   CR56  0   0.502   1.5295  152.4845  -10.1146
 GJU  C5   C   CR56  0   0.006   1.2932  153.7310   -9.5606
 GJU  C6   C   CR6   0   0.475   0.6129  154.6544  -10.3778
 GJU  N7   N   NR5   0  -0.515   2.1920  151.7781   -9.1590
 GJU  C8   C   CR15  0   0.112   2.3186  152.6224   -8.0889
 GJU  N9   N   N     0  -0.445   1.7964  153.7974   -8.2895
 GJU  N10  N   NH2   0  -0.811   0.3094  155.8872   -9.9854
 GJU  CL1  CL  CL    0  -0.112   0.0633  152.6245  -13.5985
 GJU  C12  C   CH1   0  -0.151   2.6232  150.3972   -9.3060
 GJU  C13  C   CR6   0   0.261   1.4420  149.4504   -9.3514
 GJU  N14  N   N     0  -0.433   1.6310  148.3595  -10.0902
 GJU  C15  C   CR16  0  -0.074   0.6546  147.4662  -10.1221
 GJU  C16  C   CR16  0  -0.435  -0.5468  147.5942   -9.4426
 GJU  C17  C   CR6   0   0.489  -0.7344  148.7382   -8.6736
 GJU  C18  C   CR16  0  -0.419   0.2883  149.6853   -8.6276
 GJU  O19  O   O2    0  -0.462  -1.8335  149.0073   -7.9612
 GJU  C20  C   CH2   0  -0.293  -2.8823  148.0638   -7.9457
 GJU  C21  C   CH1   0   0.511  -3.9692  148.5961   -7.0518
 GJU  F22  F   F     0  -0.342  -3.4983  148.7959   -5.7906
 GJU  F23  F   F     0  -0.342  -4.4083  149.8032   -7.4996
 GJU  C24  C   CH3   0  -0.692   3.5985  149.9868   -8.2111
 GJU  H1   H   HCR5  0   0.298   2.8134  152.3180   -7.1797
 GJU  H2   H   HNH2  0   0.409  -0.1653  156.5191  -10.6078
 GJU  H3   H   HNH2  0   0.416   0.5726  156.2218   -9.0745
 GJU  H4   H   HCH1  0   0.291   3.1346  150.3249  -10.2682
 GJU  H5   H   HCR6  0   0.268   0.8245  146.5851  -10.7311
 GJU  H6   H   HCR6  0   0.294  -1.2896  146.8145   -9.5351
 GJU  H7   H   HCR6  0   0.280   0.1637  150.5809   -8.0321
 GJU  H8   H   HCH2  0   0.263  -3.2970  147.9012   -8.9458
 GJU  H9   H   HCH2  0   0.264  -2.5513  147.0949   -7.5578
 GJU  H10  H   HCH1  0   0.213  -4.8143  147.9078   -7.0068
 GJU  H11  H   HCH3  0   0.260   4.4708  150.6402   -8.1940
 GJU  H12  H   HCH3  0   0.247   3.1316  149.9906   -7.2260
 GJU  H13  H   HCH3  0   0.269   3.9428  148.9743   -8.4130

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
 GJU  CL1  C2   single    1.737  0.020  1.737
 GJU  C2   N1   aromatic  1.317  0.020  1.317
 GJU  C2   N3   aromatic  1.309  0.020  1.309
 GJU  N1   C6   aromatic  1.340  0.020  1.340
 GJU  N3   C4   aromatic  1.334  0.020  1.334
 GJU  C6   N10  single    1.329  0.020  1.329
 GJU  C6   C5   aromatic  1.408  0.020  1.408
 GJU  C15  N14  aromatic  1.324  0.020  1.324
 GJU  C15  C16  aromatic  1.386  0.020  1.386
 GJU  N14  C13  aromatic  1.331  0.020  1.331
 GJU  C4   C5   aromatic  1.384  0.020  1.384
 GJU  C4   N7   aromatic  1.361  0.020  1.361
 GJU  C16  C17  aromatic  1.391  0.020  1.391
 GJU  C5   N9   aromatic  1.369  0.020  1.369
 GJU  C13  C12  single    1.515  0.020  1.515
 GJU  C13  C18  aromatic  1.382  0.020  1.382
 GJU  C12  N7   single    1.454  0.020  1.454
 GJU  C12  C24  single    1.523  0.020  1.523
 GJU  N7   C8   aromatic  1.369  0.020  1.369
 GJU  C17  C18  aromatic  1.395  0.020  1.395
 GJU  C17  O19  single    1.337  0.020  1.337
 GJU  N9   C8   aromatic  1.301  0.020  1.301
 GJU  C20  O19  single    1.411  0.020  1.411
 GJU  C20  C21  single    1.505  0.020  1.505
 GJU  C21  F23  single    1.360  0.020  1.360
 GJU  C21  F22  single    1.361  0.020  1.361
 GJU  C8   H1   single    0.930  0.020  1.080
 GJU  N10  H2   single    0.860  0.020  1.020
 GJU  N10  H3   single    0.860  0.020  1.020
 GJU  C12  H4   single    0.970  0.020  1.090
 GJU  C15  H5   single    0.930  0.020  1.080
 GJU  C16  H6   single    0.930  0.020  1.080
 GJU  C18  H7   single    0.930  0.020  1.080
 GJU  C20  H8   single    0.970  0.020  1.090
 GJU  C20  H9   single    0.970  0.020  1.090
 GJU  C21  H10  single    0.970  0.020  1.090
 GJU  C24  H11  single    0.970  0.020  1.090
 GJU  C24  H12  single    0.970  0.020  1.090
 GJU  C24  H13  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
 GJU  C6   N1   C2   118.54  3.000
 GJU  CL1  C2   N3   115.16  3.000
 GJU  N3   C2   N1   130.17  3.000
 GJU  CL1  C2   N1   114.67  3.000
 GJU  C4   N3   C2   110.75  3.000
 GJU  N7   C4   C5   105.63  3.000
 GJU  N7   C4   N3   127.72  3.000
 GJU  C5   C4   N3   126.65  3.000
 GJU  N9   C5   C6   133.21  3.000
 GJU  N9   C5   C4   110.65  3.000
 GJU  C6   C5   C4   116.14  3.000
 GJU  N10  C6   C5   123.18  3.000
 GJU  C5   C6   N1   117.75  3.000
 GJU  N10  C6   N1   119.07  3.000
 GJU  C12  N7   C8   129.59  3.000
 GJU  C8   N7   C4   105.90  3.000
 GJU  C12  N7   C4   124.50  3.000
 GJU  H1   C8   N9   124.66  3.000
 GJU  H1   C8   N7   121.81  3.000
 GJU  N9   C8   N7   113.53  3.000
 GJU  C8   N9   C5   104.29  3.000
 GJU  H3   N10  H2   118.37  3.000
 GJU  H3   N10  C6   121.09  3.000
 GJU  H2   N10  C6   120.51  3.000
 GJU  H4   C12  C24  108.41  3.000
 GJU  H4   C12  C13  107.30  3.000
 GJU  C24  C12  C13  110.65  3.000
 GJU  H4   C12  N7   106.91  3.000
 GJU  C24  C12  N7   111.91  3.000
 GJU  C13  C12  N7   111.43  3.000
 GJU  C18  C13  N14  123.27  3.000
 GJU  C18  C13  C12  121.95  3.000
 GJU  N14  C13  C12  114.72  3.000
 GJU  C15  N14  C13  117.50  3.000
 GJU  H5   C15  C16  119.09  3.000
 GJU  H5   C15  N14  116.50  3.000
 GJU  C16  C15  N14  124.41  3.000
 GJU  H6   C16  C17  123.22  3.000
 GJU  H6   C16  C15  119.15  3.000
 GJU  C17  C16  C15  117.63  3.000
 GJU  O19  C17  C18  116.65  3.000
 GJU  O19  C17  C16  124.81  3.000
 GJU  C18  C17  C16  118.54  3.000
 GJU  H7   C18  C17  119.70  3.000
 GJU  H7   C18  C13  121.65  3.000
 GJU  C17  C18  C13  118.65  3.000
 GJU  C20  O19  C17  118.84  3.000
 GJU  H9   C20  H8   107.86  3.000
 GJU  H9   C20  C21  108.72  3.000
 GJU  H8   C20  C21  108.76  3.000
 GJU  H9   C20  O19  111.78  3.000
 GJU  H8   C20  O19  111.77  3.000
 GJU  C21  C20  O19  107.88  3.000
 GJU  H10  C21  F23  108.87  3.000
 GJU  H10  C21  F22  108.82  3.000
 GJU  F23  C21  F22  106.65  3.000
 GJU  H10  C21  C20  111.16  3.000
 GJU  F22  C21  C20  110.64  3.000
 GJU  F23  C21  C20  110.58  3.000
 GJU  H13  C24  H12  107.84  3.000
 GJU  H13  C24  H11  107.91  3.000
 GJU  H12  C24  H11  109.06  3.000
 GJU  H13  C24  C12  108.66  3.000
 GJU  H12  C24  C12  111.99  3.000
 GJU  H11  C24  C12  111.24  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
 GJU  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 GJU  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 GJU  CONST_03  N9   C5   C6   N1    180.00   0.0  0
 GJU  CONST_04  C5   C6   N1   C2      0.00   0.0  0
 GJU  CONST_05  C5   C4   N3   C2      0.00   0.0  0
 GJU  CONST_06  N7   C4   N3   C2    180.00   0.0  0
 GJU  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 GJU  CONST_08  C6   C5   C4   N3      0.00   0.0  0
 GJU  CONST_09  N9   C5   C4   N3    180.00   0.0  0
 GJU  CONST_10  C8   N7   C4   N3    180.00   0.0  0
 GJU  CONST_11  C8   N9   C5   C4      0.00   0.0  0
 GJU  CONST_12  N9   C8   N7   C4      0.00   0.0  0
 GJU  CONST_13  C8   N7   C4   C5      0.00   0.0  0
 GJU  CONST_14  N7   C8   N9   C5      0.00   0.0  0
 GJU  CONST_15  N7   C4   C5   C6    180.00   0.0  0
 GJU  CONST_16  C8   N9   C5   C6    180.00   0.0  0
 GJU  CONST_17  N9   C5   C4   N7      0.00   0.0  0
 GJU  CONST_18  C16  C15  N14  C13     0.00   0.0  0
 GJU  CONST_19  C16  C17  C18  C13     0.00   0.0  0
 GJU  CONST_20  C17  C16  C15  N14     0.00   0.0  0
 GJU  CONST_21  C17  C18  C13  N14     0.00   0.0  0
 GJU  CONST_22  C18  C13  N14  C15     0.00   0.0  0
 GJU  CONST_23  C18  C17  C16  C15     0.00   0.0  0
 GJU  CONST_24  N10  C6   N1   C2    180.00   0.0  0
 GJU  CONST_25  C12  N7   C4   N3      0.00   0.0  0
 GJU  CONST_26  CL1  C2   N3   C4    180.00   0.0  0
 GJU  CONST_27  N10  C6   C5   C4    180.00   0.0  0
 GJU  CONST_28  C12  N7   C4   C5    180.00   0.0  0
 GJU  CONST_29  CL1  C2   N1   C6    180.00   0.0  0
 GJU  CONST_30  N10  C6   C5   N9      0.00   0.0  0
 GJU  CONST_31  C12  N7   C8   N9    180.00   0.0  0
 GJU  CONST_32  C15  N14  C13  C12   180.00   0.0  0
 GJU  CONST_33  C17  C18  C13  C12   180.00   0.0  0
 GJU  CONST_34  O19  C17  C18  C13   180.00   0.0  0
 GJU  CONST_35  O19  C17  C16  C15   180.00   0.0  0
 GJU  CONST_36  H1   C8   N7   C4    180.00   0.0  0
 GJU  CONST_37  H1   C8   N9   C5    180.00   0.0  0
 GJU  CONST_38  H5   C15  N14  C13   180.00   0.0  0
 GJU  CONST_39  H6   C16  C15  N14   180.00   0.0  0
 GJU  CONST_40  H7   C18  C13  N14   180.00   0.0  0
 GJU  CONST_41  H7   C18  C17  C16   180.00   0.0  0
 GJU  CONST_42  H5   C15  C16  C17   180.00   0.0  0
 GJU  CONST_43  H6   C16  C17  C18   180.00   0.0  0
 GJU  CONST_44  H2   N10  C6   N1      0.00   0.0  0
 GJU  CONST_45  H3   N10  C6   N1    180.00   0.0  0
 GJU  CONST_46  H2   N10  C6   C5    180.00   0.0  0
 GJU  CONST_47  H3   N10  C6   C5      0.00   0.0  0
 GJU  Var_01    C20  O19  C17  C16     1.58  30.0  2
 GJU  Var_02    C20  O19  C17  C18  -178.30  30.0  2
 GJU  Var_03    C21  C20  O19  C17   178.66  30.0  1
 GJU  Var_04    H8   C20  O19  C17   -61.83  30.0  1
 GJU  Var_05    H9   C20  O19  C17    59.18  30.0  1
 GJU  Var_06    F23  C21  C20  O19    58.54  30.0  3
 GJU  Var_07    F22  C21  C20  O19   -59.39  30.0  3
 GJU  Var_08    H10  C21  C20  O19   179.59  30.0  3
 GJU  Var_09    H8   C20  C21  F22   179.20  30.0  1
 GJU  Var_10    H9   C20  C21  F22    62.00  30.0  1
 GJU  Var_11    H8   C20  C21  F23   -62.87  30.0  1
 GJU  Var_12    H9   C20  C21  F23   179.93  30.0  1

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
 GJU  chir_01  C12  C13  N7  C24  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
 GJU  plan-1  C12  0.020
 GJU  plan-1  C13  0.020
 GJU  plan-1  N14  0.020
 GJU  plan-1  C15  0.020
 GJU  plan-1  C16  0.020
 GJU  plan-1  C17  0.020
 GJU  plan-1  C18  0.020
 GJU  plan-1  O19  0.020
 GJU  plan-1  H5   0.020
 GJU  plan-1  H6   0.020
 GJU  plan-1  H7   0.020
 GJU  plan-2  N1   0.020
 GJU  plan-2  C2   0.020
 GJU  plan-2  N3   0.020
 GJU  plan-2  C4   0.020
 GJU  plan-2  C5   0.020
 GJU  plan-2  C6   0.020
 GJU  plan-2  N7   0.020
 GJU  plan-2  C8   0.020
 GJU  plan-2  N9   0.020
 GJU  plan-2  N10  0.020
 GJU  plan-2  CL1  0.020
 GJU  plan-2  C12  0.020
 GJU  plan-2  H1   0.020
 GJU  plan-3  C6   0.020
 GJU  plan-3  N10  0.020
 GJU  plan-3  H2   0.020
 GJU  plan-3  H3   0.020

