# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 13:40:27 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: 3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-8-yl)sulfanyl]-N-{[2-(morpholin-4-yl)ethyl]sulfonyl}propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2[nH]c(SCCC(=O)N[S](=O)(=O)CCN3CCOCC3)nc2C1=O
#
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
 XYJ  XYJ  3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-8-yl)sulfanyl]-N-{[2-(morpholin-4-yl)ethyl]sulfonyl}propanamide  ligand  54  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XYJ
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
 XYJ  C10  C  C     0   0.583  35.6012  -38.0993   8.2164
 XYJ  C13  C  CH2   0  -0.627  37.6624  -39.6493   6.1114
 XYJ  C17  C  CH2   0  -0.183  41.2031  -39.6034   3.5308
 XYJ  C20  C  CH2   0  -0.306  38.6053  -40.0011   2.5643
 XYJ  C02  C  CR6   0   0.545  34.3078  -31.9803   7.7630
 XYJ  C03  C  CR56  0  -0.060  33.7656  -33.1218   8.4343
 XYJ  C04  C  CR56  0   0.664  33.2272  -32.9861   9.6877
 XYJ  C06  C  CR5   0   0.205  33.0900  -35.0513   8.9916
 XYJ  C08  C  CH2   0  -0.573  33.9890  -37.4281  10.0431
 XYJ  C09  C  CH2   0  -0.558  35.3973  -37.2872   9.4720
 XYJ  C14  C  CH2   0  -0.270  37.7740  -40.4104   4.7910
 XYJ  C16  C  CH2   0  -0.312  40.1444  -40.3104   4.3548
 XYJ  C19  C  CH2   0  -0.186  39.7007  -39.2959   1.7872
 XYJ  C27  C  CR6   0   0.729  33.6694  -30.6774   9.7978
 XYJ  N05  N  NR15  0  -0.644  32.7941  -34.2086  10.0432
 XYJ  N11  N  NC1   0  -0.801  36.2248  -39.3109   8.4148
 XYJ  N15  N  NT    0  -0.429  38.8254  -39.8241   3.9893
 XYJ  N24  N  N     0  -0.390  33.6728  -34.4177   8.0172
 XYJ  N25  N  NR6   0  -0.590  33.1623  -31.8244  10.3804
 XYJ  N28  N  NR6   0  -0.605  34.2330  -30.8110   8.5337
 XYJ  O01  O  O     0  -0.451  34.7915  -31.9654   6.6492
 XYJ  O18  O  O2    0  -0.479  40.9796  -39.7664   2.1490
 XYJ  O21  O  OS    0  -0.649  37.1468  -41.5538   7.8840
 XYJ  O22  O  OS    0  -0.637  35.2635  -40.6846   6.4815
 XYJ  O23  O  O     0  -0.423  35.2464  -37.7349   7.1195
 XYJ  O30  O  O     0  -0.468  33.6202  -29.6101  10.3717
 XYJ  S07  S  S2    0   0.056  32.6585  -36.7403   8.9997
 XYJ  S12  S  S     0   1.370  36.4982  -40.4474   7.2030
 XYJ  H1   H  HCH2  0   0.309  38.6041  -39.6074   6.6599
 XYJ  H2   H  HCH2  0   0.310  37.3147  -38.6334   5.9290
 XYJ  H3   H  HCH2  0   0.236  42.1874  -40.0172   3.7547
 XYJ  H4   H  HCH2  0   0.200  41.2157  -38.5366   3.7960
 XYJ  H5   H  HCH2  0   0.246  37.6419  -39.5650   2.2896
 XYJ  H6   H  HCH2  0   0.203  38.5768  -41.0660   2.2789
 XYJ  H7   H  HCH3  0   0.287  32.6316  -30.7927  12.1088
 XYJ  H8   H  HCH3  0   0.269  31.4903  -32.0536  11.6274
 XYJ  H9   H  HCH3  0   0.268  33.0499  -32.4891  12.3637
 XYJ  H10  H  HCH2  0   0.308  33.9468  -36.9531  11.0220
 XYJ  H11  H  HCH2  0   0.304  33.7169  -38.4759  10.1802
 XYJ  H12  H  HCH2  0   0.291  36.0997  -37.5870  10.2523
 XYJ  H13  H  HCH2  0   0.294  35.6059  -36.2422   9.2387
 XYJ  H14  H  HCH2  0   0.265  36.8303  -40.3121   4.2536
 XYJ  H15  H  HCH2  0   0.229  37.9347  -41.4850   4.9651
 XYJ  H16  H  HCH2  0   0.206  40.2252  -41.4010   4.2087
 XYJ  H17  H  HCH2  0   0.245  40.3398  -40.1124   5.4111
 XYJ  H18  H  HCH2  0   0.200  39.6255  -38.2128   1.9603
 XYJ  H19  H  HCH2  0   0.236  39.5759  -39.4746   0.7182
 XYJ  H20  H  HCH3  0   0.270  34.7776  -28.7966   8.6201
 XYJ  H21  H  HCH3  0   0.256  35.8124  -29.7947   7.5984
 XYJ  H22  H  HCH3  0   0.255  34.1995  -29.3278   7.0383
 XYJ  H23  H  HNR5  0   0.444  32.3211  -34.4748  10.8961
 XYJ  H24  H  HNC1  0   0.447  36.5764  -39.5655   9.3306
 XYJ  C29  C  CH3   0  -0.530  34.7865  -29.6128   7.9096
 XYJ  C26  C  CH3   0  -0.558  32.5452  -31.7907  11.6975

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
 XYJ  C19  O18  single    1.410  0.020  1.410
 XYJ  C19  C20  single    1.517  0.020  1.517
 XYJ  O18  C17  single    1.409  0.020  1.409
 XYJ  C20  N15  single    1.453  0.020  1.453
 XYJ  C17  C16  single    1.517  0.020  1.517
 XYJ  N15  C16  single    1.453  0.020  1.453
 XYJ  N15  C14  single    1.446  0.020  1.446
 XYJ  C14  C13  single    1.528  0.020  1.528
 XYJ  C13  S12  single    1.784  0.020  1.784
 XYJ  O22  S12  double    1.450  0.020  1.450
 XYJ  O01  C02  double    1.214  0.020  1.214
 XYJ  O23  C10  double    1.209  0.020  1.209
 XYJ  S12  O21  double    1.452  0.020  1.452
 XYJ  S12  N11  single    1.684  0.020  1.684
 XYJ  N24  C03  aromatic  1.364  0.020  1.364
 XYJ  N24  C06  aromatic  1.300  0.020  1.300
 XYJ  C02  C03  single    1.431  0.020  1.431
 XYJ  C02  N28  single    1.402  0.020  1.402
 XYJ  C29  N28  single    1.460  0.020  1.460
 XYJ  C10  N11  single    1.377  0.020  1.377
 XYJ  C10  C09  single    1.509  0.020  1.509
 XYJ  C03  C04  aromatic  1.371  0.020  1.371
 XYJ  S07  C06  single    1.743  0.020  1.743
 XYJ  S07  C08  single    1.825  0.020  1.825
 XYJ  N28  C27  single    1.391  0.020  1.391
 XYJ  C06  N05  aromatic  1.380  0.020  1.380
 XYJ  C09  C08  single    1.526  0.020  1.526
 XYJ  C04  N05  aromatic  1.345  0.020  1.345
 XYJ  C04  N25  single    1.354  0.020  1.354
 XYJ  C27  N25  single    1.383  0.020  1.383
 XYJ  C27  O30  double    1.213  0.020  1.213
 XYJ  N25  C26  single    1.455  0.020  1.455
 XYJ  C13  H1   single    0.970  0.020  1.090
 XYJ  C13  H2   single    0.970  0.020  1.090
 XYJ  C17  H3   single    0.970  0.020  1.090
 XYJ  C17  H4   single    0.970  0.020  1.090
 XYJ  C20  H5   single    0.970  0.020  1.090
 XYJ  C20  H6   single    0.970  0.020  1.090
 XYJ  C26  H7   single    0.970  0.020  1.090
 XYJ  C26  H8   single    0.970  0.020  1.090
 XYJ  C26  H9   single    0.970  0.020  1.090
 XYJ  C08  H10  single    0.970  0.020  1.090
 XYJ  C08  H11  single    0.970  0.020  1.090
 XYJ  C09  H12  single    0.970  0.020  1.090
 XYJ  C09  H13  single    0.970  0.020  1.090
 XYJ  C14  H14  single    0.970  0.020  1.090
 XYJ  C14  H15  single    0.970  0.020  1.090
 XYJ  C16  H16  single    0.970  0.020  1.090
 XYJ  C16  H17  single    0.970  0.020  1.090
 XYJ  C19  H18  single    0.970  0.020  1.090
 XYJ  C19  H19  single    0.970  0.020  1.090
 XYJ  C29  H20  single    0.970  0.020  1.090
 XYJ  C29  H21  single    0.970  0.020  1.090
 XYJ  C29  H22  single    0.970  0.020  1.090
 XYJ  N05  H23  single    0.860  0.020  1.020
 XYJ  N11  H24  single    0.860  0.020  1.020

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
 XYJ  O23  C10  N11  121.92  3.000
 XYJ  N11  C10  C09  114.51  3.000
 XYJ  O23  C10  C09  123.58  3.000
 XYJ  H2   C13  H1   108.91  3.000
 XYJ  H2   C13  S12  108.13  3.000
 XYJ  H1   C13  S12  105.83  3.000
 XYJ  H2   C13  C14  110.08  3.000
 XYJ  H1   C13  C14  113.00  3.000
 XYJ  S12  C13  C14  110.70  3.000
 XYJ  H4   C17  H3   107.95  3.000
 XYJ  H4   C17  O18  110.53  3.000
 XYJ  H3   C17  O18  107.49  3.000
 XYJ  H4   C17  C16  109.23  3.000
 XYJ  H3   C17  C16  109.97  3.000
 XYJ  O18  C17  C16  111.60  3.000
 XYJ  H6   C20  H5   107.32  3.000
 XYJ  H6   C20  N15  112.04  3.000
 XYJ  H5   C20  N15  109.37  3.000
 XYJ  H6   C20  C19  109.57  3.000
 XYJ  H5   C20  C19  108.81  3.000
 XYJ  N15  C20  C19  109.66  3.000
 XYJ  O01  C02  N28  121.00  3.000
 XYJ  N28  C02  C03  112.78  3.000
 XYJ  O01  C02  C03  126.23  3.000
 XYJ  N24  C03  C04  110.29  3.000
 XYJ  C04  C03  C02  119.92  3.000
 XYJ  N24  C03  C02  129.79  3.000
 XYJ  N25  C04  N05  128.99  3.000
 XYJ  N25  C04  C03  124.86  3.000
 XYJ  N05  C04  C03  106.15  3.000
 XYJ  S07  C06  N24  125.91  3.000
 XYJ  S07  C06  N05  122.36  3.000
 XYJ  N24  C06  N05  111.69  3.000
 XYJ  H11  C08  H10  107.23  3.000
 XYJ  H11  C08  S07  104.59  3.000
 XYJ  H10  C08  S07  108.74  3.000
 XYJ  H11  C08  C09  111.45  3.000
 XYJ  H10  C08  C09  109.39  3.000
 XYJ  S07  C08  C09  115.08  3.000
 XYJ  H13  C09  H12  107.02  3.000
 XYJ  H13  C09  C08  110.18  3.000
 XYJ  H12  C09  C08  107.51  3.000
 XYJ  H13  C09  C10  108.16  3.000
 XYJ  H12  C09  C10  111.10  3.000
 XYJ  C08  C09  C10  112.73  3.000
 XYJ  H15  C14  H14  107.00  3.000
 XYJ  H15  C14  N15  112.17  3.000
 XYJ  H14  C14  N15  108.63  3.000
 XYJ  H15  C14  C13  111.12  3.000
 XYJ  H14  C14  C13  108.53  3.000
 XYJ  N15  C14  C13  109.28  3.000
 XYJ  H17  C16  H16  107.11  3.000
 XYJ  H17  C16  N15  110.19  3.000
 XYJ  H16  C16  N15  111.35  3.000
 XYJ  H17  C16  C17  108.42  3.000
 XYJ  H16  C16  C17  109.74  3.000
 XYJ  N15  C16  C17  109.95  3.000
 XYJ  H19  C19  H18  107.93  3.000
 XYJ  H19  C19  O18  107.49  3.000
 XYJ  H18  C19  O18  110.51  3.000
 XYJ  H19  C19  C20  110.07  3.000
 XYJ  H18  C19  C20  109.14  3.000
 XYJ  O18  C19  C20  111.62  3.000
 XYJ  O30  C27  N28  122.09  3.000
 XYJ  O30  C27  N25  121.05  3.000
 XYJ  N28  C27  N25  116.87  3.000
 XYJ  H23  N05  C06  125.63  3.000
 XYJ  H23  N05  C04  127.81  3.000
 XYJ  C06  N05  C04  106.54  3.000
 XYJ  H24  N11  S12  115.11  3.000
 XYJ  H24  N11  C10  120.55  3.000
 XYJ  S12  N11  C10  124.32  3.000
 XYJ  C16  N15  C14  112.64  3.000
 XYJ  C14  N15  C20  112.60  3.000
 XYJ  C16  N15  C20  110.10  3.000
 XYJ  C06  N24  C03  105.32  3.000
 XYJ  C27  N25  C04  118.59  3.000
 XYJ  C27  N25  C26  121.18  3.000
 XYJ  C04  N25  C26  120.23  3.000
 XYJ  C29  N28  C27  117.60  3.000
 XYJ  C27  N28  C02  126.97  3.000
 XYJ  C29  N28  C02  115.42  3.000
 XYJ  C19  O18  C17  110.91  3.000
 XYJ  C08  S07  C06  100.80  3.000
 XYJ  O22  S12  O21  119.29  3.000
 XYJ  O21  S12  N11  104.44  3.000
 XYJ  O22  S12  N11  109.29  3.000
 XYJ  N11  S12  C13  104.15  3.000
 XYJ  O21  S12  C13  109.65  3.000
 XYJ  O22  S12  C13  108.93  3.000
 XYJ  H22  C29  H21  108.87  3.000
 XYJ  H22  C29  H20  108.88  3.000
 XYJ  H21  C29  H20  108.77  3.000
 XYJ  H22  C29  N28  110.65  3.000
 XYJ  H21  C29  N28  110.04  3.000
 XYJ  H20  C29  N28  109.59  3.000
 XYJ  H9   C26  H8   109.47  3.000
 XYJ  H9   C26  H7   108.77  3.000
 XYJ  H8   C26  H7   108.92  3.000
 XYJ  H9   C26  N25  110.01  3.000
 XYJ  H8   C26  N25  110.29  3.000
 XYJ  H7   C26  N25  109.35  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
 XYJ  CONST_01  N05  C06  N24  C03     0.00   0.0  0
 XYJ  CONST_02  C06  N05  C04  C03     0.00   0.0  0
 XYJ  CONST_03  C06  N24  C03  C04     0.00   0.0  0
 XYJ  CONST_04  N24  C06  N05  C04     0.00   0.0  0
 XYJ  CONST_05  N24  C03  C04  N05     0.00   0.0  0
 XYJ  CONST_06  N25  C27  N28  C02     0.00   0.0  0
 XYJ  CONST_07  C27  N28  C02  C03     0.00   0.0  0
 XYJ  CONST_08  N28  C27  N25  C04     0.00   0.0  0
 XYJ  CONST_09  S07  C06  N24  C03   180.00   0.0  0
 XYJ  CONST_10  S07  C06  N05  C04   180.00   0.0  0
 XYJ  CONST_11  N28  C27  N25  C26   180.00   0.0  0
 XYJ  CONST_12  O30  C27  N28  C02   180.00   0.0  0
 XYJ  CONST_13  C29  N28  C02  C03   180.00   0.0  0
 XYJ  CONST_14  O30  C27  N25  C04   180.00   0.0  0
 XYJ  CONST_15  O01  C02  N28  C27   180.00   0.0  0
 XYJ  CONST_16  N25  C27  N28  C29   180.00   0.0  0
 XYJ  CONST_17  H23  N05  C04  C03   180.00   0.0  0
 XYJ  CONST_18  O30  C27  N25  C26     0.00   0.0  0
 XYJ  CONST_19  O01  C02  N28  C29     0.00   0.0  0
 XYJ  CONST_20  O30  C27  N28  C29     0.00   0.0  0
 XYJ  CONST_21  S12  N11  C10  C09   180.00   0.0  0
 XYJ  CONST_22  S12  N11  C10  O23     0.00   0.0  0
 XYJ  CONST_23  H24  N11  C10  C09     0.00   0.0  0
 XYJ  Var_01    C20  C19  O18  C17   -57.59  30.0  1
 XYJ  Var_02    C20  N15  C16  C17    56.46  30.0  1
 XYJ  Var_03    C19  C20  N15  C16   -56.60  30.0  1
 XYJ  Var_04    O18  C19  C20  N15    57.34  30.0  1
 XYJ  Var_05    O18  C17  C16  N15   -56.87  30.0  1
 XYJ  Var_06    H3   C17  O18  C19   177.92  30.0  1
 XYJ  Var_07    N24  C06  S07  C08   102.74  30.0  2
 XYJ  Var_08    H20  C29  N28  C02  -173.95  30.0  3
 XYJ  Var_09    H7   C26  N25  C04   177.27  30.0  3
 XYJ  Var_10    C09  C08  S07  C06   -63.36  30.0  3
 XYJ  Var_11    S12  C13  C14  N15  -173.90  30.0  3
 XYJ  Var_12    C13  S12  N11  C10    66.14  30.0  2
 XYJ  Var_13    S07  C08  C09  C10   -66.12  30.0  3
 XYJ  Var_14    O23  C10  C09  C08    81.24  30.0  1

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
 XYJ  plan-1  C02  0.020
 XYJ  plan-1  C03  0.020
 XYJ  plan-1  C04  0.020
 XYJ  plan-1  C06  0.020
 XYJ  plan-1  C27  0.020
 XYJ  plan-1  N05  0.020
 XYJ  plan-1  N24  0.020
 XYJ  plan-1  N25  0.020
 XYJ  plan-1  N28  0.020
 XYJ  plan-1  O01  0.020
 XYJ  plan-1  O30  0.020
 XYJ  plan-1  S07  0.020
 XYJ  plan-1  H23  0.020
 XYJ  plan-1  C29  0.020
 XYJ  plan-1  C26  0.020
 XYJ  plan-2  C10  0.020
 XYJ  plan-2  C09  0.020
 XYJ  plan-2  N11  0.020
 XYJ  plan-2  O23  0.020
 XYJ  plan-2  S12  0.020
 XYJ  plan-2  H24  0.020

