# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 10:53:36 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 3-{[(3-{6-amino-8-[(6-iodo-2H-1,3-benzodioxol-5-yl)sulfanyl]-9H-purin-9-yl}propyl)amino]methyl}benzene-1-sulfinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCCNCc3cccc(c3)[S](O)=O)c(Sc4cc5OCOc5cc4I)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
 Q2J  Q2J  '3-{[(3-{6-amino-8-[(6-iodo-2H-1,3-benzodioxol-5-yl)sulfanyl]-9H-purin-9-yl}propyl)amino]methyl}benzene-1-sulfinic acid'  ligand  56  35  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Q2J
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
 Q2J  C8    C  CH2   0  -0.254  -2.8624   0.5033  -1.7108
 Q2J  C5    C  CR6   0  -0.123   2.9274  -1.4884   0.4335
 Q2J  C6    C  CH2   0  -0.329  -0.5352   1.3262  -1.2652
 Q2J  N1    N  N     0  -0.458   0.0756   3.9350   0.1802
 Q2J  C2    C  CR56  0   0.004   1.7580   2.5415   1.2338
 Q2J  N3    N  N     0  -0.428   2.1670   1.2346   1.1633
 Q2J  C4    C  CR5   0   0.303   1.3898   0.7118   0.2633
 Q2J  O2    O  OH1   0  -0.742  -7.0829  -1.4084   2.7539
 Q2J  N2    N  NR5   0  -0.530   0.4899   1.5913  -0.2755
 Q2J  C7    C  CH2   0  -0.459  -1.7774   0.6847  -0.6620
 Q2J  C     C  CR16  0   0.038   0.5620   4.8861   0.9602
 Q2J  C1    C  CR56  0   0.483   0.7123   2.7815   0.3579
 Q2J  C10   C  CR6   0   0.084  -6.3361  -0.8934  -1.4642
 Q2J  C11   C  CR16  0  -0.295  -7.1512  -1.7638  -2.1847
 Q2J  C12   C  CR16  0  -0.230  -8.3137  -2.2814  -1.6320
 Q2J  C13   C  CR16  0  -0.248  -8.6845  -1.9445  -0.3379
 Q2J  C14   C  CR6   0  -0.210  -7.8609  -1.0949   0.3815
 Q2J  C15   C  CR16  0  -0.269  -6.7020  -0.5623  -0.1642
 Q2J  C16   C  CR16  0  -0.294   2.8407  -2.2662   1.6002
 Q2J  C17   C  CR56  0   0.312   4.0115  -2.7298   2.1375
 Q2J  C18   C  CR56  0   0.321   5.2393  -2.4421   1.5615
 Q2J  C19   C  CR16  0  -0.316   5.3534  -1.6822   0.4239
 Q2J  C20   C  CR6   0  -0.196   4.1629  -1.2096  -0.1406
 Q2J  C21   C  CH2   0   0.071   5.6011  -3.6414   3.4014
 Q2J  C3    C  CR6   0   0.443   2.1866   3.6351   2.0056
 Q2J  I     I  I     0   0.095   4.3255  -0.0373  -1.8718
 Q2J  N     N  N     0  -0.472   1.5549   4.8038   1.8411
 Q2J  N5    N  NH1   0  -0.600  -4.0279  -0.1429  -1.1391
 Q2J  O     O  O     0  -0.478   4.1952  -3.4938   3.2332
 Q2J  O1    O  O     0  -0.475   6.2205  -3.0183   2.2784
 Q2J  O3    O  O     0  -0.714  -9.5904  -1.3152   2.3386
 Q2J  S     S  S2    0   0.079   1.4085  -0.9519  -0.2848
 Q2J  S1    S  S3    0   1.008  -8.3258  -0.6023   2.0364
 Q2J  H81   H  HCH2  0   0.228  -3.1665   1.4843  -2.0890
 Q2J  H82   H  HCH2  0   0.200  -2.4561  -0.0478  -2.5738
 Q2J  H62   H  HCH2  0   0.280  -0.7850   2.2819  -1.7258
 Q2J  H61   H  HCH2  0   0.272  -0.1071   0.6986  -2.0497
 Q2J  H1    H  HOH1  0   0.490  -6.8441  -0.9433   3.5698
 Q2J  HN41  H  HNH2  0   0.410   3.6627   2.6811   3.0488
 Q2J  HN42  H  HNH2  0   0.403   3.4364   4.3448   3.4481
 Q2J  H71   H  HCH2  0   0.247  -2.1541   1.3105   0.1506
 Q2J  H72   H  HCH2  0   0.235  -1.5188  -0.2860  -0.2274
 Q2J  H     H  HCR6  0   0.250   0.0936   5.8608   0.8742
 Q2J  H11   H  HCR6  0   0.260  -6.8738  -2.0391  -3.1951
 Q2J  H12   H  HCR6  0   0.267  -8.9319  -2.9551  -2.2103
 Q2J  H13   H  HCR6  0   0.277  -9.5913  -2.3409   0.0981
 Q2J  H15   H  HCR6  0   0.270  -6.0718   0.1054   0.4115
 Q2J  H16   H  HCR6  0   0.299   1.8815  -2.4817   2.0496
 Q2J  H19   H  HCR6  0   0.302   6.3196  -1.4695  -0.0115
 Q2J  H212  H  HCH2  0   0.247   5.9199  -3.1445   4.3206
 Q2J  H211  H  HCH2  0   0.251   5.8620  -4.7001   3.4245
 Q2J  H91   H  HCH2  0   0.220  -4.8217  -0.9028  -2.9711
 Q2J  H92   H  HCH2  0   0.248  -5.3557   0.6916  -2.4847
 Q2J  HN5   H  HNH1  0   0.346  -3.7603  -1.0580  -0.7943
 Q2J  N4    N  NH2   0  -0.819   3.1912   3.5521   2.8809
 Q2J  C9    C  CH2   0  -0.304  -5.1037  -0.3003  -2.0945

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
 Q2J  I    C20   single    2.097  0.020  2.097
 Q2J  S    C5    single    1.764  0.020  1.764
 Q2J  S    C4    single    1.752  0.020  1.752
 Q2J  C20  C5    aromatic  1.391  0.020  1.391
 Q2J  C20  C19   aromatic  1.400  0.020  1.400
 Q2J  N3   C4    aromatic  1.299  0.020  1.299
 Q2J  N3   C2    aromatic  1.371  0.020  1.371
 Q2J  C5   C16   aromatic  1.405  0.020  1.405
 Q2J  C4   N2    aromatic  1.369  0.020  1.369
 Q2J  C19  C18   aromatic  1.373  0.020  1.373
 Q2J  N4   C3    single    1.335  0.020  1.335
 Q2J  C16  C17   aromatic  1.369  0.020  1.369
 Q2J  C18  C17   aromatic  1.386  0.020  1.386
 Q2J  C18  O1    single    1.345  0.020  1.345
 Q2J  C2   C3    aromatic  1.405  0.020  1.405
 Q2J  C2   C1    aromatic  1.385  0.020  1.385
 Q2J  C17  O     single    1.348  0.020  1.348
 Q2J  C3   N     aromatic  1.339  0.020  1.339
 Q2J  O1   C21   single    1.426  0.020  1.426
 Q2J  N2   C1    aromatic  1.366  0.020  1.366
 Q2J  N2   C6    single    1.449  0.020  1.449
 Q2J  O    C21   single    1.424  0.020  1.424
 Q2J  C1   N1    aromatic  1.329  0.020  1.329
 Q2J  C7   C6    single    1.523  0.020  1.523
 Q2J  C7   C8    single    1.520  0.020  1.520
 Q2J  N    C     aromatic  1.330  0.020  1.330
 Q2J  C8   N5    single    1.450  0.020  1.450
 Q2J  N5   C9    single    1.447  0.020  1.447
 Q2J  N1   C     aromatic  1.323  0.020  1.323
 Q2J  C11  C12   aromatic  1.387  0.020  1.387
 Q2J  C11  C10   aromatic  1.393  0.020  1.393
 Q2J  C12  C13   aromatic  1.388  0.020  1.388
 Q2J  C9   C10   single    1.506  0.020  1.506
 Q2J  C10  C15   aromatic  1.390  0.020  1.390
 Q2J  C13  C14   aromatic  1.385  0.020  1.385
 Q2J  C15  C14   aromatic  1.387  0.020  1.387
 Q2J  C14  S1    single    1.788  0.020  1.788
 Q2J  S1   O3    double    1.483  0.020  1.483
 Q2J  S1   O2    single    1.646  0.020  1.646
 Q2J  C8   H81   single    0.970  0.020  1.090
 Q2J  C8   H82   single    0.970  0.020  1.090
 Q2J  C6   H62   single    0.970  0.020  1.090
 Q2J  C6   H61   single    0.970  0.020  1.090
 Q2J  O2   H1    single    0.850  0.020  0.980
 Q2J  N4   HN41  single    0.860  0.020  1.020
 Q2J  N4   HN42  single    0.860  0.020  1.020
 Q2J  C7   H71   single    0.970  0.020  1.090
 Q2J  C7   H72   single    0.970  0.020  1.090
 Q2J  C    H     single    0.930  0.020  1.080
 Q2J  C11  H11   single    0.930  0.020  1.080
 Q2J  C12  H12   single    0.930  0.020  1.080
 Q2J  C13  H13   single    0.930  0.020  1.080
 Q2J  C15  H15   single    0.930  0.020  1.080
 Q2J  C16  H16   single    0.930  0.020  1.080
 Q2J  C19  H19   single    0.930  0.020  1.080
 Q2J  C21  H212  single    0.970  0.020  1.090
 Q2J  C21  H211  single    0.970  0.020  1.090
 Q2J  C9   H91   single    0.970  0.020  1.090
 Q2J  C9   H92   single    0.970  0.020  1.090
 Q2J  N5   HN5   single    0.890  0.020  1.040

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
 Q2J  H82   C8   H81   106.27  3.000
 Q2J  H82   C8   N5    112.48  3.000
 Q2J  H81   C8   N5    108.20  3.000
 Q2J  H82   C8   C7    109.70  3.000
 Q2J  H81   C8   C7    109.26  3.000
 Q2J  N5    C8   C7    110.79  3.000
 Q2J  S     C5   C20   122.41  3.000
 Q2J  C20   C5   C16   120.57  3.000
 Q2J  S     C5   C16   116.97  3.000
 Q2J  H61   C6   H62   106.87  3.000
 Q2J  H61   C6   C7    111.24  3.000
 Q2J  H62   C6   C7    110.48  3.000
 Q2J  H61   C6   N2    108.57  3.000
 Q2J  H62   C6   N2    106.88  3.000
 Q2J  C7    C6   N2    112.55  3.000
 Q2J  C1    N1   C     111.65  3.000
 Q2J  C3    C2   C1    116.27  3.000
 Q2J  C1    C2   N3    110.97  3.000
 Q2J  C3    C2   N3    132.76  3.000
 Q2J  C4    N3   C2    103.93  3.000
 Q2J  S     C4   N2    119.61  3.000
 Q2J  N2    C4   N3    114.05  3.000
 Q2J  S     C4   N3    126.34  3.000
 Q2J  H1    O2   S1    108.54  3.000
 Q2J  C1    N2   C4    105.68  3.000
 Q2J  C1    N2   C6    126.23  3.000
 Q2J  C4    N2   C6    128.04  3.000
 Q2J  H72   C7   H71   107.10  3.000
 Q2J  H72   C7   C6    109.77  3.000
 Q2J  H71   C7   C6    109.55  3.000
 Q2J  H72   C7   C8    109.68  3.000
 Q2J  H71   C7   C8    109.60  3.000
 Q2J  C6    C7   C8    111.06  3.000
 Q2J  H     C    N     115.49  3.000
 Q2J  H     C    N1    116.14  3.000
 Q2J  N     C    N1    128.36  3.000
 Q2J  N2    C1   C2    105.37  3.000
 Q2J  N2    C1   N1    128.01  3.000
 Q2J  C2    C1   N1    126.62  3.000
 Q2J  C9    C10  C15   120.86  3.000
 Q2J  C15   C10  C11   118.57  3.000
 Q2J  C9    C10  C11   120.55  3.000
 Q2J  H11   C11  C12   119.42  3.000
 Q2J  H11   C11  C10   119.43  3.000
 Q2J  C12   C11  C10   121.15  3.000
 Q2J  H12   C12  C13   119.80  3.000
 Q2J  H12   C12  C11   119.88  3.000
 Q2J  C13   C12  C11   120.31  3.000
 Q2J  H13   C13  C14   120.94  3.000
 Q2J  H13   C13  C12   120.73  3.000
 Q2J  C14   C13  C12   118.33  3.000
 Q2J  S1    C14  C15   118.39  3.000
 Q2J  S1    C14  C13   119.68  3.000
 Q2J  C15   C14  C13   121.87  3.000
 Q2J  H15   C15  C14   120.89  3.000
 Q2J  H15   C15  C10   119.36  3.000
 Q2J  C14   C15  C10   119.75  3.000
 Q2J  H16   C16  C17   121.88  3.000
 Q2J  H16   C16  C5    120.69  3.000
 Q2J  C17   C16  C5    117.43  3.000
 Q2J  O     C17  C18   109.55  3.000
 Q2J  O     C17  C16   128.85  3.000
 Q2J  C18   C17  C16   121.60  3.000
 Q2J  O1    C18  C19   128.19  3.000
 Q2J  O1    C18  C17   109.62  3.000
 Q2J  C19   C18  C17   122.19  3.000
 Q2J  H19   C19  C20   122.09  3.000
 Q2J  H19   C19  C18   121.14  3.000
 Q2J  C20   C19  C18   116.77  3.000
 Q2J  I     C20  C19   117.11  3.000
 Q2J  C19   C20  C5    121.43  3.000
 Q2J  I     C20  C5    121.45  3.000
 Q2J  H211  C21  H212  110.72  3.000
 Q2J  H211  C21  O1    109.69  3.000
 Q2J  H212  C21  O1    109.70  3.000
 Q2J  H211  C21  O     109.84  3.000
 Q2J  H212  C21  O     109.91  3.000
 Q2J  O1    C21  O     106.90  3.000
 Q2J  N     C3   N4    119.34  3.000
 Q2J  N     C3   C2    117.90  3.000
 Q2J  N4    C3   C2    122.76  3.000
 Q2J  C3    N    C     119.19  3.000
 Q2J  HN5   N5   C9    108.81  3.000
 Q2J  HN5   N5   C8    108.92  3.000
 Q2J  C9    N5   C8    112.68  3.000
 Q2J  C21   O    C17   106.82  3.000
 Q2J  C21   O1   C18   106.86  3.000
 Q2J  C4    S    C5     99.83  3.000
 Q2J  O3    S1   C14   106.13  3.000
 Q2J  O3    S1   O2    108.64  3.000
 Q2J  C14   S1   O2     94.14  3.000
 Q2J  HN42  N4   HN41  118.36  3.000
 Q2J  HN42  N4   C3    120.30  3.000
 Q2J  HN41  N4   C3    121.11  3.000
 Q2J  H92   C9   H91   105.72  3.000
 Q2J  H92   C9   N5    107.92  3.000
 Q2J  H91   C9   N5    113.26  3.000
 Q2J  H92   C9   C10   108.51  3.000
 Q2J  H91   C9   C10   109.12  3.000
 Q2J  N5    C9   C10   112.01  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
 Q2J  CONST_01  C18   C19  C20  C5      0.00   0.0  0
 Q2J  CONST_02  C18   C17  C16  C5      0.00   0.0  0
 Q2J  CONST_03  N3    C2   C1   N1    180.00   0.0  0
 Q2J  CONST_04  C3    C2   C1   N1      0.00   0.0  0
 Q2J  CONST_05  C4    N2   C1   N1    180.00   0.0  0
 Q2J  CONST_06  C3    N    C    N1      0.00   0.0  0
 Q2J  CONST_07  N2    C4   N3   C2      0.00   0.0  0
 Q2J  CONST_08  C     N    C3   C2      0.00   0.0  0
 Q2J  CONST_09  C4    N2   C1   C2      0.00   0.0  0
 Q2J  CONST_10  C     N1   C1   C2      0.00   0.0  0
 Q2J  CONST_11  C1    N2   C4   N3      0.00   0.0  0
 Q2J  CONST_12  N     C3   C2   N3    180.00   0.0  0
 Q2J  CONST_13  N2    C1   C2   N3      0.00   0.0  0
 Q2J  CONST_14  C3    C2   N3   C4    180.00   0.0  0
 Q2J  CONST_15  C1    C2   N3   C4      0.00   0.0  0
 Q2J  CONST_16  C3    C2   C1   N2    180.00   0.0  0
 Q2J  CONST_17  C     N1   C1   N2    180.00   0.0  0
 Q2J  CONST_18  N     C3   C2   C1      0.00   0.0  0
 Q2J  CONST_19  N     C    N1   C1      0.00   0.0  0
 Q2J  CONST_20  C13   C12  C11  C10     0.00   0.0  0
 Q2J  CONST_21  C13   C14  C15  C10     0.00   0.0  0
 Q2J  CONST_22  C14   C13  C12  C11     0.00   0.0  0
 Q2J  CONST_23  C14   C15  C10  C11     0.00   0.0  0
 Q2J  CONST_24  C15   C10  C11  C12     0.00   0.0  0
 Q2J  CONST_25  C15   C14  C13  C12     0.00   0.0  0
 Q2J  CONST_26  C19   C20  C5   C16     0.00   0.0  0
 Q2J  CONST_27  C19   C18  C17  C16     0.00   0.0  0
 Q2J  CONST_28  C20   C5   C16  C17     0.00   0.0  0
 Q2J  CONST_29  C20   C19  C18  C17     0.00   0.0  0
 Q2J  CONST_30  N3    C4   N2   C6    180.00   0.0  0
 Q2J  CONST_31  C2    C1   N2   C6    180.00   0.0  0
 Q2J  CONST_32  N1    C1   N2   C6      0.00   0.0  0
 Q2J  CONST_33  S     C4   N3   C2    180.00   0.0  0
 Q2J  CONST_34  N4    C3   C2   N3      0.00   0.0  0
 Q2J  CONST_35  C1    C2   C3   N4    180.00   0.0  0
 Q2J  CONST_36  C     N    C3   N4    180.00   0.0  0
 Q2J  CONST_37  S     C4   N2   C1    180.00   0.0  0
 Q2J  CONST_38  S1    C14  C15  C10   180.00   0.0  0
 Q2J  CONST_39  C9    C10  C11  C12   180.00   0.0  0
 Q2J  CONST_40  S1    C14  C13  C12   180.00   0.0  0
 Q2J  CONST_41  C9    C10  C15  C14   180.00   0.0  0
 Q2J  CONST_42  I     C20  C5   C16   180.00   0.0  0
 Q2J  CONST_43  S     C5   C16  C17   180.00   0.0  0
 Q2J  CONST_44  I     C20  C19  C18   180.00   0.0  0
 Q2J  CONST_45  S     C5   C20  C19   180.00   0.0  0
 Q2J  CONST_46  H19   C19  C20  C5    180.00   0.0  0
 Q2J  CONST_47  H     C    N1   C1    180.00   0.0  0
 Q2J  CONST_48  H12   C12  C11  C10   180.00   0.0  0
 Q2J  CONST_49  H13   C13  C12  C11   180.00   0.0  0
 Q2J  CONST_50  H15   C15  C10  C11   180.00   0.0  0
 Q2J  CONST_51  H11   C11  C12  C13   180.00   0.0  0
 Q2J  CONST_52  H16   C16  C17  C18   180.00   0.0  0
 Q2J  CONST_53  HN41  N4   C3   C2      0.00   0.0  0
 Q2J  CONST_54  HN42  N4   C3   C2    180.00   0.0  0
 Q2J  Var_01    O1    C21  O    C17    -4.91  30.0  1
 Q2J  Var_02    O     C21  O1   C18     4.97  30.0  1
 Q2J  Var_03    N3    C4   S    C5    -12.06  30.0  2
 Q2J  Var_04    C20   C5   S    C4    -80.08  30.0  2
 Q2J  Var_05    C7    C6   N2   C4     79.98  30.0  2
 Q2J  Var_06    C13   C14  S1   O2    113.05  30.0  2
 Q2J  Var_07    N5    C9   C10  C11  -144.95  30.0  2
 Q2J  Var_08    N2    C6   C7   C8    176.37  30.0  3
 Q2J  Var_09    C10   C9   N5   C8   -176.41  30.0  3
 Q2J  Var_10    N5    C8   C7   C6    178.35  30.0  3
 Q2J  Var_11    C9    N5   C8   C7    178.27  30.0  3

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
 Q2J  plan-1  C10   0.020
 Q2J  plan-1  C11   0.020
 Q2J  plan-1  C12   0.020
 Q2J  plan-1  C13   0.020
 Q2J  plan-1  C14   0.020
 Q2J  plan-1  C15   0.020
 Q2J  plan-1  S1    0.020
 Q2J  plan-1  H11   0.020
 Q2J  plan-1  H12   0.020
 Q2J  plan-1  H13   0.020
 Q2J  plan-1  H15   0.020
 Q2J  plan-1  C9    0.020
 Q2J  plan-2  C6    0.020
 Q2J  plan-2  N1    0.020
 Q2J  plan-2  C2    0.020
 Q2J  plan-2  N3    0.020
 Q2J  plan-2  C4    0.020
 Q2J  plan-2  N2    0.020
 Q2J  plan-2  C     0.020
 Q2J  plan-2  C1    0.020
 Q2J  plan-2  C3    0.020
 Q2J  plan-2  N     0.020
 Q2J  plan-2  S     0.020
 Q2J  plan-2  H     0.020
 Q2J  plan-2  N4    0.020
 Q2J  plan-3  C5    0.020
 Q2J  plan-3  C16   0.020
 Q2J  plan-3  C17   0.020
 Q2J  plan-3  C18   0.020
 Q2J  plan-3  C19   0.020
 Q2J  plan-3  C20   0.020
 Q2J  plan-3  I     0.020
 Q2J  plan-3  O     0.020
 Q2J  plan-3  O1    0.020
 Q2J  plan-3  S     0.020
 Q2J  plan-3  H16   0.020
 Q2J  plan-3  H19   0.020
 Q2J  plan-4  C3    0.020
 Q2J  plan-4  HN41  0.020
 Q2J  plan-4  HN42  0.020
 Q2J  plan-4  N4    0.020
 Q2J  plan-5  O2    0.020
 Q2J  plan-5  C14   0.020
 Q2J  plan-5  O3    0.020
 Q2J  plan-5  S1    0.020

