# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 05:53:20 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: 1-[(3,4-dichlorophenyl)methyl]-3,7-dimethyl-8-[(4-oxidanylcyclohexyl)amino]purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(Cc2ccc(Cl)c(Cl)c2)C(=O)c3n(C)c(N[C@@H]4CC[C@@H](O)CC4)nc13
#
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
 J4L  J4L  1-[(3,4-dichlorophenyl)methyl]-3,7-dimethyl-8-[(4-oxidanylcyclohexyl)amino]purine-2,6-dione  ligand  53  30  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J4L
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
 J4L  C2   C   CR6   0   0.757  -52.7347  16.8901  -3.4968
 J4L  C4   C   CR56  0   0.457  -53.2630  18.8603  -2.3013
 J4L  C8   C   CR5   0   0.778  -54.1228  20.3362  -1.0615
 J4L  C5   C   CR56  0   0.112  -54.3208  18.2436  -1.6824
 J4L  C6   C   CR6   0   0.563  -54.6722  16.9002  -1.9194
 J4L  CAA  C   CH1   0  -0.052  -53.6719  22.7452  -0.6310
 J4L  CAB  C   CH2   0  -0.451  -53.8237  23.2999  -2.0478
 J4L  CAC  C   CH2   0  -0.462  -53.1604  24.6681  -2.1658
 J4L  CAD  C   CH1   0   0.085  -51.6947  24.6031  -1.7668
 J4L  CAE  C   CH2   0  -0.479  -51.5575  24.0599  -0.3480
 J4L  CAF  C   CH2   0  -0.450  -52.2030  22.6847  -0.2167
 J4L  CAH  C   CR6   0  -0.020  -51.3409  12.0900  -1.5765
 J4L  CAI  C   CR6   0   0.025  -52.1042  12.9062  -0.7485
 J4L  CAJ  C   CR16  0  -0.261  -52.9912  13.8197  -1.2953
 J4L  CAK  C   CR6   0   0.142  -53.1205  13.9368  -2.6743
 J4L  CAL  C   CR16  0  -0.303  -52.3531  13.1180  -3.4929
 J4L  CAM  C   CR16  0  -0.203  -51.4728  12.1959  -2.9519
 J4L  N1   N   NR6   0  -0.609  -53.8240  16.2990  -2.8742
 J4L  N3   N   NR6   0  -0.595  -52.4622  18.1975  -3.1839
 J4L  N7   N   NR5   0  -0.562  -54.8707  19.2292  -0.8652
 J4L  N9   N   N     0  -0.531  -53.1291  20.1390  -1.9323
 J4L  NBD  N   NH1   0  -0.734  -54.3748  21.4864  -0.4248
 J4L  O2   O   O     0  -0.484  -52.0497  16.2754  -4.2923
 J4L  O6   O   O     0  -0.489  -55.5853  16.2692  -1.4019
 J4L  OAG  O   OH1   0  -0.672  -51.1463  25.8984  -1.8999
 J4L  CL2  CL  CL    0  -0.099  -51.9642  12.7873   0.9655
 J4L  H1   H   HCH1  0   0.248  -54.1728  23.4416   0.0476
 J4L  H2   H   HCH2  0   0.239  -54.8838  23.3761  -2.2994
 J4L  H3   H   HCH2  0   0.231  -53.3739  22.6085  -2.7638
 J4L  H4   H   HCH2  0   0.238  -53.2553  25.0364  -3.1903
 J4L  H5   H   HCH2  0   0.218  -53.6754  25.3868  -1.5184
 J4L  H6   H   HCH1  0   0.185  -51.1888  23.8998  -2.4484
 J4L  H7   H   HCH2  0   0.235  -50.5013  23.9985  -0.0696
 J4L  H8   H   HCH2  0   0.218  -52.0298  24.7618   0.3485
 J4L  H9   H   HCH2  0   0.238  -52.1254  22.3300   0.8132
 J4L  H10  H   HCH2  0   0.233  -51.6721  21.9656  -0.8441
 J4L  H11  H   HCR6  0   0.283  -53.5880  14.4338  -0.6331
 J4L  H12  H   HCR6  0   0.267  -52.4389  13.1973  -4.5688
 J4L  H13  H   HCR6  0   0.286  -50.8791  11.5634  -3.5978
 J4L  H22  H   HNH1  0   0.414  -55.1961  21.5259   0.1555
 J4L  H23  H   HOH1  0   0.443  -50.2175  25.8573  -1.6516
 J4L  CAP  C   CH2   0  -0.408  -54.0960  14.9197  -3.2649
 J4L  CAW  C   CH3   0  -0.533  -51.3217  18.8407  -3.8140
 J4L  CBC  C   CH3   0  -0.571  -56.0025  19.1200   0.0269
 J4L  CL1  CL  CL    0  -0.098  -50.2340  10.9495  -0.9136
 J4L  H14  H   HCH2  0   0.293  -55.1043  14.6856  -2.9323
 J4L  H15  H   HCH2  0   0.287  -54.0902  14.8481  -4.3511
 J4L  H16  H   HCH3  0   0.267  -51.2352  19.8479  -3.4210
 J4L  H17  H   HCH3  0   0.257  -50.4054  18.2973  -3.5939
 J4L  H18  H   HCH3  0   0.256  -51.4533  18.8937  -4.8931
 J4L  H19  H   HCH3  0   0.260  -55.7117  19.3682   1.0480
 J4L  H20  H   HCH3  0   0.260  -56.8102  19.7829  -0.2849
 J4L  H21  H   HCH3  0   0.286  -56.3687  18.1005   0.0126

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
 J4L  CAW  N3   single    1.453  0.020  1.453
 J4L  O2   C2   double    1.217  0.020  1.217
 J4L  C2   N3   single    1.372  0.020  1.372
 J4L  C2   N1   single    1.387  0.020  1.387
 J4L  N3   C4   single    1.364  0.020  1.364
 J4L  CAL  CAM  aromatic  1.385  0.020  1.385
 J4L  CAL  CAK  aromatic  1.389  0.020  1.389
 J4L  CAP  N1   single    1.459  0.020  1.459
 J4L  CAP  CAK  single    1.506  0.020  1.506
 J4L  N1   C6   single    1.412  0.020  1.412
 J4L  C4   N9   aromatic  1.338  0.020  1.338
 J4L  C4   C5   aromatic  1.372  0.020  1.372
 J4L  CAM  CAH  aromatic  1.386  0.020  1.386
 J4L  N9   C8   aromatic  1.336  0.020  1.336
 J4L  CAK  CAJ  aromatic  1.390  0.020  1.390
 J4L  C6   C5   single    1.409  0.020  1.409
 J4L  C6   O6   double    1.225  0.020  1.225
 J4L  C5   N7   aromatic  1.393  0.020  1.393
 J4L  C8   N7   aromatic  1.350  0.020  1.350
 J4L  C8   NBD  single    1.339  0.020  1.339
 J4L  CAB  CAC  single    1.525  0.020  1.525
 J4L  CAB  CAA  single    1.529  0.020  1.529
 J4L  CAH  CL1  single    1.722  0.020  1.722
 J4L  CAH  CAI  aromatic  1.391  0.020  1.391
 J4L  N7   CBC  single    1.445  0.020  1.445
 J4L  CAD  CAC  single    1.520  0.020  1.520
 J4L  CAD  CAE  single    1.525  0.020  1.525
 J4L  CAD  OAG  single    1.413  0.020  1.413
 J4L  NBD  CAA  single    1.456  0.020  1.456
 J4L  CAF  CAA  single    1.527  0.020  1.527
 J4L  CAF  CAE  single    1.525  0.020  1.525
 J4L  CAJ  CAI  aromatic  1.386  0.020  1.386
 J4L  CAI  CL2  single    1.724  0.020  1.724
 J4L  CAA  H1   single    0.970  0.020  1.090
 J4L  CAB  H2   single    0.970  0.020  1.090
 J4L  CAB  H3   single    0.970  0.020  1.090
 J4L  CAC  H4   single    0.970  0.020  1.090
 J4L  CAC  H5   single    0.970  0.020  1.090
 J4L  CAD  H6   single    0.970  0.020  1.090
 J4L  CAE  H7   single    0.970  0.020  1.090
 J4L  CAE  H8   single    0.970  0.020  1.090
 J4L  CAF  H9   single    0.970  0.020  1.090
 J4L  CAF  H10  single    0.970  0.020  1.090
 J4L  CAJ  H11  single    0.930  0.020  1.080
 J4L  CAL  H12  single    0.930  0.020  1.080
 J4L  CAM  H13  single    0.930  0.020  1.080
 J4L  CAP  H14  single    0.970  0.020  1.090
 J4L  CAP  H15  single    0.970  0.020  1.090
 J4L  CAW  H16  single    0.970  0.020  1.090
 J4L  CAW  H17  single    0.970  0.020  1.090
 J4L  CAW  H18  single    0.970  0.020  1.090
 J4L  CBC  H19  single    0.970  0.020  1.090
 J4L  CBC  H20  single    0.970  0.020  1.090
 J4L  CBC  H21  single    0.970  0.020  1.090
 J4L  NBD  H22  single    0.860  0.020  1.020
 J4L  OAG  H23  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
 J4L  O2   C2   N3   121.26  3.000
 J4L  N3   C2   N1   117.37  3.000
 J4L  O2   C2   N1   121.36  3.000
 J4L  N9   C4   N3   125.76  3.000
 J4L  N9   C4   C5   112.49  3.000
 J4L  N3   C4   C5   121.75  3.000
 J4L  NBD  C8   N9   125.23  3.000
 J4L  NBD  C8   N7   122.07  3.000
 J4L  N9   C8   N7   112.69  3.000
 J4L  N7   C5   C6   132.44  3.000
 J4L  N7   C5   C4   104.53  3.000
 J4L  C6   C5   C4   123.03  3.000
 J4L  O6   C6   N1   120.96  3.000
 J4L  O6   C6   C5   127.32  3.000
 J4L  N1   C6   C5   111.72  3.000
 J4L  H1   CAA  NBD  103.97  3.000
 J4L  H1   CAA  CAF  107.30  3.000
 J4L  NBD  CAA  CAF  113.05  3.000
 J4L  H1   CAA  CAB  107.36  3.000
 J4L  CAF  CAA  CAB  111.17  3.000
 J4L  NBD  CAA  CAB  113.38  3.000
 J4L  H3   CAB  H2   107.03  3.000
 J4L  H3   CAB  CAC  109.76  3.000
 J4L  H2   CAB  CAC  109.98  3.000
 J4L  H3   CAB  CAA  109.69  3.000
 J4L  H2   CAB  CAA  109.58  3.000
 J4L  CAC  CAB  CAA  110.73  3.000
 J4L  H5   CAC  H4   106.98  3.000
 J4L  H5   CAC  CAD  109.03  3.000
 J4L  H4   CAC  CAD  110.13  3.000
 J4L  H5   CAC  CAB  109.77  3.000
 J4L  H4   CAC  CAB  109.70  3.000
 J4L  CAD  CAC  CAB  111.14  3.000
 J4L  H6   CAD  OAG  110.40  3.000
 J4L  H6   CAD  CAE  107.86  3.000
 J4L  OAG  CAD  CAE  112.28  3.000
 J4L  H6   CAD  CAC  107.90  3.000
 J4L  OAG  CAD  CAC  108.07  3.000
 J4L  CAE  CAD  CAC  110.24  3.000
 J4L  H8   CAE  H7   106.88  3.000
 J4L  H8   CAE  CAF  109.91  3.000
 J4L  H7   CAE  CAF  109.64  3.000
 J4L  H8   CAE  CAD  108.93  3.000
 J4L  H7   CAE  CAD  110.09  3.000
 J4L  CAF  CAE  CAD  111.29  3.000
 J4L  H10  CAF  H9   107.06  3.000
 J4L  H10  CAF  CAE  109.79  3.000
 J4L  H9   CAF  CAE  110.12  3.000
 J4L  H10  CAF  CAA  109.74  3.000
 J4L  H9   CAF  CAA  109.69  3.000
 J4L  CAE  CAF  CAA  110.37  3.000
 J4L  CL1  CAH  CAM  119.60  3.000
 J4L  CL1  CAH  CAI  120.81  3.000
 J4L  CAM  CAH  CAI  119.59  3.000
 J4L  CL2  CAI  CAJ  119.33  3.000
 J4L  CL2  CAI  CAH  120.46  3.000
 J4L  CAJ  CAI  CAH  120.21  3.000
 J4L  H11  CAJ  CAK  120.52  3.000
 J4L  H11  CAJ  CAI  119.04  3.000
 J4L  CAK  CAJ  CAI  120.44  3.000
 J4L  CAP  CAK  CAL  120.77  3.000
 J4L  CAP  CAK  CAJ  120.30  3.000
 J4L  CAL  CAK  CAJ  118.92  3.000
 J4L  H12  CAL  CAM  119.18  3.000
 J4L  H12  CAL  CAK  119.93  3.000
 J4L  CAM  CAL  CAK  120.89  3.000
 J4L  H13  CAM  CAL  120.34  3.000
 J4L  H13  CAM  CAH  119.72  3.000
 J4L  CAL  CAM  CAH  119.94  3.000
 J4L  CAP  N1   C6   118.14  3.000
 J4L  C6   N1   C2   126.45  3.000
 J4L  CAP  N1   C2   115.41  3.000
 J4L  CAW  N3   C4   121.76  3.000
 J4L  C4   N3   C2   119.62  3.000
 J4L  CAW  N3   C2   118.61  3.000
 J4L  CBC  N7   C5   128.14  3.000
 J4L  CBC  N7   C8   125.83  3.000
 J4L  C5   N7   C8   106.03  3.000
 J4L  C8   N9   C4   104.27  3.000
 J4L  H22  NBD  CAA  116.21  3.000
 J4L  H22  NBD  C8   117.49  3.000
 J4L  CAA  NBD  C8   125.76  3.000
 J4L  H23  OAG  CAD  108.13  3.000
 J4L  H15  CAP  H14  107.22  3.000
 J4L  H15  CAP  N1   109.17  3.000
 J4L  H14  CAP  N1   107.13  3.000
 J4L  H15  CAP  CAK  110.19  3.000
 J4L  H14  CAP  CAK  109.90  3.000
 J4L  N1   CAP  CAK  113.03  3.000
 J4L  H18  CAW  H17  109.08  3.000
 J4L  H18  CAW  H16  108.89  3.000
 J4L  H17  CAW  H16  108.87  3.000
 J4L  H18  CAW  N3   110.89  3.000
 J4L  H17  CAW  N3   110.62  3.000
 J4L  H16  CAW  N3   108.45  3.000
 J4L  H21  CBC  H20  108.54  3.000
 J4L  H21  CBC  H19  108.46  3.000
 J4L  H20  CBC  H19  109.08  3.000
 J4L  H21  CBC  N7   109.13  3.000
 J4L  H20  CBC  N7   110.96  3.000
 J4L  H19  CBC  N7   110.61  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
 J4L  CONST_01  N7   C8   N9   C4      0.00   0.0  0
 J4L  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 J4L  CONST_03  C5   C4   N9   C8      0.00   0.0  0
 J4L  CONST_04  N9   C8   N7   C5      0.00   0.0  0
 J4L  CONST_05  CAK  CAL  CAM  CAH     0.00   0.0  0
 J4L  CONST_06  CAK  CAJ  CAI  CAH     0.00   0.0  0
 J4L  CONST_07  CAL  CAM  CAH  CAI     0.00   0.0  0
 J4L  CONST_08  CAL  CAK  CAJ  CAI     0.00   0.0  0
 J4L  CONST_09  CAM  CAL  CAK  CAJ     0.00   0.0  0
 J4L  CONST_10  CAM  CAH  CAI  CAJ     0.00   0.0  0
 J4L  CONST_11  N9   C4   C5   N7      0.00   0.0  0
 J4L  CONST_12  N1   C2   N3   C4      0.00   0.0  0
 J4L  CONST_13  N3   C2   N1   C6      0.00   0.0  0
 J4L  CONST_14  NBD  C8   N9   C4    180.00   0.0  0
 J4L  CONST_15  CBC  N7   C5   C4    180.00   0.0  0
 J4L  CONST_16  NBD  C8   N7   C5    180.00   0.0  0
 J4L  CONST_17  CBC  N7   C5   C6      0.00   0.0  0
 J4L  CONST_18  CAP  CAK  CAJ  CAI   180.00   0.0  0
 J4L  CONST_19  CL1  CAH  CAI  CAJ   180.00   0.0  0
 J4L  CONST_20  CL2  CAI  CAJ  CAK   180.00   0.0  0
 J4L  CONST_21  CL1  CAH  CAM  CAL   180.00   0.0  0
 J4L  CONST_22  CAP  CAK  CAL  CAM   180.00   0.0  0
 J4L  CONST_23  CL2  CAI  CAH  CAM   180.00   0.0  0
 J4L  CONST_24  N9   C8   N7   CBC   180.00   0.0  0
 J4L  CONST_25  N9   C8   NBD  CAA     0.00   0.0  0
 J4L  CONST_26  N7   C8   NBD  CAA   180.00   0.0  0
 J4L  CONST_27  O2   C2   N3   C4    180.00   0.0  0
 J4L  CONST_28  O2   C2   N1   C6    180.00   0.0  0
 J4L  CONST_29  N3   C2   N1   CAP   180.00   0.0  0
 J4L  CONST_30  N1   C2   N3   CAW   180.00   0.0  0
 J4L  CONST_31  H12  CAL  CAM  CAH   180.00   0.0  0
 J4L  CONST_32  H11  CAJ  CAI  CAH   180.00   0.0  0
 J4L  CONST_33  H13  CAM  CAH  CAI   180.00   0.0  0
 J4L  CONST_34  O2   C2   N1   CAP     0.00   0.0  0
 J4L  CONST_35  O2   C2   N3   CAW     0.00   0.0  0
 J4L  CONST_36  H22  NBD  C8   N7      0.00   0.0  0
 J4L  Var_01    CAD  CAC  CAB  CAA    56.46  30.0  1
 J4L  Var_02    CAD  CAE  CAF  CAA   -56.72  30.0  1
 J4L  Var_03    CAK  CAP  N1   C2     74.48  30.0  2
 J4L  Var_04    N1   CAP  CAK  CAJ    59.71  30.0  3
 J4L  Var_05    H16  CAW  N3   C2   -177.67  30.0  3
 J4L  Var_06    H19  CBC  N7   C8    -57.81  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
 J4L  chir_01  CAA  CAB  NBD  CAF  negativ
 J4L  chir_02  CAD  OAG  CAE  CAC  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
 J4L  plan-1  CAH  0.020
 J4L  plan-1  CAI  0.020
 J4L  plan-1  CAJ  0.020
 J4L  plan-1  CAK  0.020
 J4L  plan-1  CAL  0.020
 J4L  plan-1  CAM  0.020
 J4L  plan-1  CL2  0.020
 J4L  plan-1  H11  0.020
 J4L  plan-1  H12  0.020
 J4L  plan-1  H13  0.020
 J4L  plan-1  CAP  0.020
 J4L  plan-1  CL1  0.020
 J4L  plan-2  C2   0.020
 J4L  plan-2  C4   0.020
 J4L  plan-2  C8   0.020
 J4L  plan-2  C5   0.020
 J4L  plan-2  C6   0.020
 J4L  plan-2  N1   0.020
 J4L  plan-2  N3   0.020
 J4L  plan-2  N7   0.020
 J4L  plan-2  N9   0.020
 J4L  plan-2  NBD  0.020
 J4L  plan-2  O2   0.020
 J4L  plan-2  O6   0.020
 J4L  plan-2  CAP  0.020
 J4L  plan-2  CAW  0.020
 J4L  plan-2  CBC  0.020
 J4L  plan-3  C8   0.020
 J4L  plan-3  CAA  0.020
 J4L  plan-3  NBD  0.020
 J4L  plan-3  H22  0.020

