# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:40:27 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 5'-deoxy-5'-[(L-isoleucylsulfamoyl)amino]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](N)C(=O)N[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 ILA  ILA  5'-deoxy-5'-[(L-isoleucylsulfamoyl)amino]adenosine  ligand  57  31  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ILA
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
 ILA  N     N  NH2   0  -0.790  -1.7876   1.5539   1.7638
 ILA  CA    C  CH1   0  -0.190  -1.4348   0.9136   3.0184
 ILA  CB    C  CH1   0  -0.243  -2.5741   0.2174   3.7895
 ILA  CG2   C  CH3   0  -0.682  -2.0352  -0.4384   5.0587
 ILA  CG1   C  CH2   0  -0.418  -3.6927   1.2147   4.0970
 ILA  CD    C  CH3   0  -0.669  -4.9191   0.5863   4.7461
 ILA  C     C  C     0   0.601  -0.3555  -0.1003   2.6793
 ILA  O     O  O     0  -0.442  -0.5394  -1.0202   1.9104
 ILA  SA    S  S     0   1.540   2.1640  -0.9417   3.0417
 ILA  O1A   O  OS    0  -0.646   3.2571  -0.2795   3.7154
 ILA  O2A   O  OS    0  -0.629   1.7595  -2.2761   3.4098
 ILA  N3A   N  NC1   0  -0.819   0.8579   0.0996   3.2780
 ILA  N5'   N  NC1   0  -0.742   2.4676  -0.9465   1.4406
 ILA  C5'   C  CH2   0  -0.293   2.8505   0.3048   0.7974
 ILA  C4'   C  CH1   0  -0.031   3.2114   0.0241  -0.6521
 ILA  O4'   O  O2    0  -0.495   2.1125  -0.6005  -1.3197
 ILA  C1'   C  CH1   0   0.215   1.5385   0.2737  -2.2596
 ILA  N9    N  NR5   0  -0.546   0.1053   0.1912  -2.1964
 ILA  C4    C  CR56  0   0.491  -0.7141  -0.3512  -3.1483
 ILA  N3    N  N     0  -0.457  -0.3799  -0.8619  -4.3299
 ILA  C2    C  CR16  0   0.046  -1.4403  -1.2848  -4.9968
 ILA  N1    N  N     0  -0.474  -2.7176  -1.2491  -4.6275
 ILA  C6    C  CR6   0   0.461  -3.0371  -0.7342  -3.4345
 ILA  N6    N  NH2   0  -0.816  -4.3158  -0.7007  -3.0582
 ILA  C5    C  CR56  0  -0.004  -1.9923  -0.2525  -2.6250
 ILA  N7    N  N     0  -0.458  -1.9660   0.3250  -1.3805
 ILA  C8    C  CR15  0   0.123  -0.7103   0.5705  -1.1623
 ILA  C2'   C  CH1   0  -0.062   2.0961   1.6591  -1.9317
 ILA  O2'   O  OH1   0  -0.651   2.0664   2.4606  -3.0727
 ILA  C3'   C  CH1   0  -0.021   3.4971   1.3027  -1.4287
 ILA  O3'   O  OH1   0  -0.666   4.3470   0.9930  -2.5000
 ILA  HN1   H  HNH2  0   0.358  -2.3451   0.9348   1.1864
 ILA  HN2   H  HNH2  0   0.367  -2.3463   2.3782   1.9379
 ILA  HA1   H  HCH1  0   0.260  -1.0135   1.6873   3.6686
 ILA  HB    H  HCH1  0   0.227  -2.9856  -0.5647   3.1393
 ILA  HG21  H  HCH3  0   0.223  -1.5674   0.3010   5.7137
 ILA  HG22  H  HCH3  0   0.247  -2.8300  -0.9230   5.6238
 ILA  HG23  H  HCH3  0   0.236  -1.2922  -1.2091   4.8472
 ILA  HG11  H  HCH2  0   0.220  -4.0097   1.6964   3.1686
 ILA  HG12  H  HCH2  0   0.216  -3.3006   2.0122   4.7379
 ILA  HD1   H  HCH3  0   0.233  -5.7285   1.3124   4.8248
 ILA  HD2   H  HCH3  0   0.219  -5.2866  -0.2542   4.1542
 ILA  HD3   H  HCH3  0   0.223  -4.7167   0.2187   5.7518
 ILA  HNA   H  HNC1  0   0.447   1.0225   0.9028   3.8722
 ILA  HN5   H  HNC1  0   0.420   1.7746  -1.4852   0.9282
 ILA  H51   H  HCH2  0   0.243   2.0558   1.0584   0.8642
 ILA  H52   H  HCH2  0   0.289   3.7297   0.7073   1.2993
 ILA  H4    H  HCH1  0   0.281   4.0673  -0.6555  -0.6804
 ILA  H1    H  HCH1  0   0.269   1.8157  -0.0148  -3.2785
 ILA  H2    H  HCR6  0   0.253  -1.2492  -1.7175  -5.9729
 ILA  H61   H  HNH2  0   0.404  -5.0374  -1.0101  -3.6861
 ILA  H62   H  HNH2  0   0.412  -4.5898  -0.2836  -2.1864
 ILA  H8    H  HCR5  0   0.284  -0.3359   1.0337  -0.2609
 ILA  H2'   H  HCH1  0   0.254   1.5271   2.1093  -1.1085
 ILA  HO2   H  HOH1  0   0.472   2.1233   3.3841  -2.8068
 ILA  H3    H  HCH1  0   0.260   3.9179   2.0880  -0.7873
 ILA  HO3   H  HOH1  0   0.452   4.2255   1.6666  -3.1797

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
 ILA  N    CA    single    1.452  0.020  1.452
 ILA  N    HN1   single    0.890  0.020  1.040
 ILA  N    HN2   single    0.890  0.020  1.040
 ILA  CA   CB    single    1.542  0.020  1.542
 ILA  CA   C     single    1.519  0.020  1.519
 ILA  CA   HA1   single    0.970  0.020  1.090
 ILA  CB   CG2   single    1.527  0.020  1.527
 ILA  CB   CG1   single    1.530  0.020  1.530
 ILA  CB   HB    single    0.970  0.020  1.090
 ILA  CG2  HG21  single    0.970  0.020  1.090
 ILA  CG2  HG22  single    0.970  0.020  1.090
 ILA  CG2  HG23  single    0.970  0.020  1.090
 ILA  CG1  CD    single    1.523  0.020  1.523
 ILA  CG1  HG11  single    0.970  0.020  1.090
 ILA  CG1  HG12  single    0.970  0.020  1.090
 ILA  CD   HD1   single    0.970  0.020  1.090
 ILA  CD   HD2   single    0.970  0.020  1.090
 ILA  CD   HD3   single    0.970  0.020  1.090
 ILA  C    O     double    1.213  0.020  1.213
 ILA  C    N3A   single    1.368  0.020  1.368
 ILA  SA   O1A   double    1.445  0.020  1.445
 ILA  SA   O2A   double    1.442  0.020  1.442
 ILA  SA   N3A   single    1.687  0.020  1.687
 ILA  SA   N5'   single    1.630  0.020  1.630
 ILA  N3A  HNA   single    0.860  0.020  1.020
 ILA  N5'  C5'   single    1.458  0.020  1.458
 ILA  N5'  HN5   single    0.890  0.020  1.040
 ILA  C5'  C4'   single    1.520  0.020  1.520
 ILA  C5'  H51   single    0.970  0.020  1.090
 ILA  C5'  H52   single    0.970  0.020  1.090
 ILA  C4'  O4'   single    1.429  0.020  1.429
 ILA  C4'  C3'   single    1.523  0.020  1.523
 ILA  C4'  H4    single    0.970  0.020  1.090
 ILA  O4'  C1'   single    1.406  0.020  1.406
 ILA  C1'  N9    single    1.437  0.020  1.437
 ILA  C1'  C2'   single    1.529  0.020  1.529
 ILA  C1'  H1    single    0.970  0.020  1.090
 ILA  N9   C4    aromatic  1.368  0.020  1.368
 ILA  N9   C8    aromatic  1.371  0.020  1.371
 ILA  C4   N3    aromatic  1.330  0.020  1.330
 ILA  C4   C5    aromatic  1.385  0.020  1.385
 ILA  N3   C2    aromatic  1.322  0.020  1.322
 ILA  C2   N1    aromatic  1.330  0.020  1.330
 ILA  C2   H2    single    0.930  0.020  1.080
 ILA  N1   C6    aromatic  1.338  0.020  1.338
 ILA  C6   N6    single    1.333  0.020  1.333
 ILA  C6   C5    aromatic  1.407  0.020  1.407
 ILA  N6   H61   single    0.860  0.020  1.020
 ILA  N6   H62   single    0.860  0.020  1.020
 ILA  C5   N7    aromatic  1.372  0.020  1.372
 ILA  N7   C8    aromatic  1.298  0.020  1.298
 ILA  C8   H8    single    0.930  0.020  1.080
 ILA  C2'  O2'   single    1.395  0.020  1.395
 ILA  C2'  C3'   single    1.531  0.020  1.531
 ILA  C2'  H2'   single    0.970  0.020  1.090
 ILA  O2'  HO2   single    0.850  0.020  0.980
 ILA  C3'  O3'   single    1.402  0.020  1.402
 ILA  C3'  H3    single    0.970  0.020  1.090
 ILA  O3'  HO3   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
 ILA  HN2   N    HN1   106.98  3.000
 ILA  HN2   N    CA    110.18  3.000
 ILA  HN1   N    CA    110.88  3.000
 ILA  HA1   CA   C     109.32  3.000
 ILA  HA1   CA   CB    107.84  3.000
 ILA  C     CA   CB    109.59  3.000
 ILA  HA1   CA   N     107.16  3.000
 ILA  C     CA   N     105.91  3.000
 ILA  CB    CA   N     116.85  3.000
 ILA  HB    CB   CG1   108.03  3.000
 ILA  HB    CB   CG2   108.59  3.000
 ILA  CG1   CB   CG2   111.78  3.000
 ILA  HB    CB   CA    107.61  3.000
 ILA  CG1   CB   CA    110.27  3.000
 ILA  CG2   CB   CA    110.42  3.000
 ILA  HG23  CG2  HG22  106.46  3.000
 ILA  HG23  CG2  HG21  107.61  3.000
 ILA  HG22  CG2  HG21  107.61  3.000
 ILA  HG23  CG2  CB    112.49  3.000
 ILA  HG22  CG2  CB    111.40  3.000
 ILA  HG21  CG2  CB    111.02  3.000
 ILA  HG12  CG1  HG11  106.25  3.000
 ILA  HG12  CG1  CD    109.83  3.000
 ILA  HG11  CG1  CD    108.08  3.000
 ILA  HG12  CG1  CB    109.29  3.000
 ILA  HG11  CG1  CB    109.19  3.000
 ILA  CD    CG1  CB    113.92  3.000
 ILA  HD3   CD   HD2   107.65  3.000
 ILA  HD3   CD   HD1   107.21  3.000
 ILA  HD2   CD   HD1   107.58  3.000
 ILA  HD3   CD   CG1   112.51  3.000
 ILA  HD2   CD   CG1   110.95  3.000
 ILA  HD1   CD   CG1   110.71  3.000
 ILA  N3A   C    O     121.52  3.000
 ILA  N3A   C    CA    115.79  3.000
 ILA  O     C    CA    122.68  3.000
 ILA  N5'   SA   N3A   106.48  3.000
 ILA  N5'   SA   O2A   107.47  3.000
 ILA  N3A   SA   O2A   108.56  3.000
 ILA  N5'   SA   O1A   108.58  3.000
 ILA  N3A   SA   O1A   103.74  3.000
 ILA  O2A   SA   O1A   121.15  3.000
 ILA  HNA   N3A  SA    116.49  3.000
 ILA  HNA   N3A  C     121.13  3.000
 ILA  SA    N3A  C     122.36  3.000
 ILA  HN5   N5'  C5'   114.30  3.000
 ILA  HN5   N5'  SA    111.71  3.000
 ILA  C5'   N5'  SA    118.67  3.000
 ILA  H52   C5'  H51   107.62  3.000
 ILA  H52   C5'  C4'   108.42  3.000
 ILA  H51   C5'  C4'   110.91  3.000
 ILA  H52   C5'  N5'   109.01  3.000
 ILA  H51   C5'  N5'   111.86  3.000
 ILA  C4'   C5'  N5'   108.94  3.000
 ILA  H4    C4'  C3'   111.21  3.000
 ILA  H4    C4'  O4'   108.55  3.000
 ILA  C3'   C4'  O4'   105.84  3.000
 ILA  H4    C4'  C5'   108.99  3.000
 ILA  C3'   C4'  C5'   112.07  3.000
 ILA  O4'   C4'  C5'   110.09  3.000
 ILA  C1'   O4'  C4'   110.75  3.000
 ILA  H1    C1'  C2'   110.25  3.000
 ILA  H1    C1'  N9    106.16  3.000
 ILA  C2'   C1'  N9    113.97  3.000
 ILA  H1    C1'  O4'   110.79  3.000
 ILA  C2'   C1'  O4'   105.73  3.000
 ILA  N9    C1'  O4'   110.00  3.000
 ILA  C8    N9   C4    106.16  3.000
 ILA  C8    N9   C1'   127.65  3.000
 ILA  C4    N9   C1'   126.12  3.000
 ILA  C5    C4   N3    126.52  3.000
 ILA  C5    C4   N9    105.17  3.000
 ILA  N3    C4   N9    128.31  3.000
 ILA  C2    N3   C4    111.68  3.000
 ILA  H2    C2   N1    115.45  3.000
 ILA  H2    C2   N3    116.12  3.000
 ILA  N1    C2   N3    128.43  3.000
 ILA  C6    N1   C2    119.16  3.000
 ILA  C5    C6   N6    122.77  3.000
 ILA  C5    C6   N1    117.87  3.000
 ILA  N6    C6   N1    119.36  3.000
 ILA  H62   N6   H61   118.29  3.000
 ILA  H62   N6   C6    121.13  3.000
 ILA  H61   N6   C6    120.29  3.000
 ILA  N7    C5   C6    132.86  3.000
 ILA  N7    C5   C4    110.79  3.000
 ILA  C6    C5   C4    116.34  3.000
 ILA  C8    N7   C5    104.52  3.000
 ILA  H8    C8   N7    123.83  3.000
 ILA  H8    C8   N9    122.81  3.000
 ILA  N7    C8   N9    113.36  3.000
 ILA  H2'   C2'  C3'   108.89  3.000
 ILA  H2'   C2'  O2'   111.52  3.000
 ILA  C3'   C2'  O2'   114.97  3.000
 ILA  H2'   C2'  C1'   110.09  3.000
 ILA  C3'   C2'  C1'   101.15  3.000
 ILA  O2'   C2'  C1'   109.73  3.000
 ILA  HO2   O2'  C2'   108.91  3.000
 ILA  H3    C3'  O3'   111.85  3.000
 ILA  H3    C3'  C2'   112.11  3.000
 ILA  O3'   C3'  C2'   110.81  3.000
 ILA  H3    C3'  C4'   111.99  3.000
 ILA  O3'   C3'  C4'   108.53  3.000
 ILA  C2'   C3'  C4'   101.03  3.000
 ILA  HO3   O3'  C3'   107.92  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
 ILA  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 ILA  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 ILA  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 ILA  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 ILA  CONST_05  N7   C8   N9   C4      0.00   0.0  0
 ILA  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 ILA  CONST_07  N1   C6   C5   C4      0.00   0.0  0
 ILA  CONST_08  C8   N7   C5   C4      0.00   0.0  0
 ILA  CONST_09  C8   N9   C4   N3    180.00   0.0  0
 ILA  CONST_10  C6   C5   C4   N3      0.00   0.0  0
 ILA  CONST_11  N7   C5   C4   N3    180.00   0.0  0
 ILA  CONST_12  C6   N1   C2   N3      0.00   0.0  0
 ILA  CONST_13  C5   C4   N3   C2      0.00   0.0  0
 ILA  CONST_14  C5   C6   N1   C2      0.00   0.0  0
 ILA  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 ILA  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 ILA  CONST_17  C8   N9   C4   C5      0.00   0.0  0
 ILA  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 ILA  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 ILA  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 ILA  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 ILA  CONST_22  N6   C6   N1   C2    180.00   0.0  0
 ILA  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 ILA  CONST_24  H8   C8   N9   C1'     0.00   0.0  0
 ILA  CONST_25  H2   C2   N3   C4    180.00   0.0  0
 ILA  CONST_26  H61  N6   C6   N1      0.00   0.0  0
 ILA  CONST_27  H62  N6   C6   N1    180.00   0.0  0
 ILA  CONST_28  SA   N3A  C    CA    180.00   0.0  0
 ILA  CONST_29  SA   N3A  C    O       0.00   0.0  0
 ILA  CONST_30  HNA  N3A  C    CA      0.00   0.0  0
 ILA  Var_01    C4'  C5'  N5'  SA    174.48  30.0  3
 ILA  Var_02    O1A  SA   N3A  C     173.49  30.0  1
 ILA  Var_03    C5'  N5'  SA   O1A   -49.59  30.0  3
 ILA  Var_04    HD1  CD   CG1  CB   -172.72  30.0  3

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
 ILA  chir_01  CA   N    CB   C    negativ
 ILA  chir_02  CB   CA   CG2  CG1  negativ
 ILA  chir_03  C4'  C5'  O4'  C3'  negativ
 ILA  chir_04  C1'  O4'  N9   C2'  negativ
 ILA  chir_05  C2'  O2'  C1'  C3'  negativ
 ILA  chir_06  C3'  O3'  C4'  C2'  positiv

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
 ILA  plan-1  C1'  0.020
 ILA  plan-1  N9   0.020
 ILA  plan-1  C4   0.020
 ILA  plan-1  N3   0.020
 ILA  plan-1  C2   0.020
 ILA  plan-1  N1   0.020
 ILA  plan-1  C6   0.020
 ILA  plan-1  N6   0.020
 ILA  plan-1  C5   0.020
 ILA  plan-1  N7   0.020
 ILA  plan-1  C8   0.020
 ILA  plan-1  H2   0.020
 ILA  plan-1  H8   0.020
 ILA  plan-2  C6   0.020
 ILA  plan-2  N6   0.020
 ILA  plan-2  H61  0.020
 ILA  plan-2  H62  0.020
 ILA  plan-3  CA   0.020
 ILA  plan-3  C    0.020
 ILA  plan-3  O    0.020
 ILA  plan-3  SA   0.020
 ILA  plan-3  N3A  0.020
 ILA  plan-3  HNA  0.020

