# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 03:20:07 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 5'-O-(L-lysylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](N)C(=O)N[S](=O)(=O)OC[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
 KAA  KAA  5'-O-(L-lysylsulfamoyl)adenosine  ligand  58  32  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KAA
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
 KAA  NZ    N  NH2   0  -0.795  -1.0483   5.6278   7.7061
 KAA  CE    C  CH2   0  -0.285  -0.6679   5.4110   6.3197
 KAA  CD    C  CH2   0  -0.414  -1.2786   6.4603   5.4073
 KAA  CG    C  CH2   0  -0.453  -0.8716   6.2788   3.9508
 KAA  CB    C  CH2   0  -0.415  -1.5115   7.3251   3.0474
 KAA  CA    C  CH1   0  -0.217  -1.1085   7.2241   1.5822
 KAA  N     N  NH2   0  -0.771  -1.7341   8.2841   0.8140
 KAA  C     C  C     0   0.579  -1.4931   5.8528   1.0286
 KAA  O     O  O     0  -0.415  -2.5875   5.3650   1.1643
 KAA  N8    N  NC1   0  -0.850  -0.4710   5.2324   0.3276
 KAA  S1    S  S     0   1.625  -0.5742   3.8191  -0.5501
 KAA  O1S   O  OS    0  -0.615   0.4910   3.8598  -1.5133
 KAA  O2S   O  OS    0  -0.604  -1.9391   3.5955  -0.9368
 KAA  O5'   O  OC2   0  -0.566  -0.1126   2.7100   0.4883
 KAA  C5'   C  CH2   0  -0.199  -0.9025   2.4282   1.6570
 KAA  C4'   C  CH1   0  -0.072  -0.3055   1.1768   2.2700
 KAA  O4'   O  O2    0  -0.483   1.0833   1.3504   2.5297
 KAA  C3'   C  CH1   0  -0.012  -0.9288   0.8200   3.6239
 KAA  O3'   O  OH1   0  -0.659  -0.7226  -0.5255   3.9446
 KAA  C2'   C  CH1   0  -0.035  -0.0816   1.6708   4.5667
 KAA  O2'   O  OH1   0  -0.668  -0.0789   1.1965   5.8703
 KAA  C1'   C  CH1   0   0.209   1.2985   1.6398   3.8719
 KAA  N9    N  NR5   0  -0.548   1.9725   2.9280   3.9856
 KAA  C8    C  CR15  0   0.103   2.4249   3.7698   3.0071
 KAA  N7    N  N     0  -0.450   3.0082   4.8351   3.4790
 KAA  C5    C  CR56  0   0.018   2.9443   4.6882   4.8391
 KAA  C4    C  CR56  0   0.516   2.3019   3.5078   5.1706
 KAA  N3    N  N     0  -0.510   2.0437   3.0558   6.4001
 KAA  C2    C  CR16  0   0.054   2.5014   3.8789   7.3308
 KAA  N1    N  N     0  -0.469   3.1410   5.0299   7.1612
 KAA  C6    C  CR6   0   0.460   3.3810   5.4779   5.9211
 KAA  N6    N  NH2   0  -0.811   4.0177   6.6349   5.7607
 KAA  HNZ1  H  HNH2  0   0.344  -0.5930   4.9397   8.2923
 KAA  HNZ2  H  HNH2  0   0.339  -2.0407   5.4531   7.8102
 KAA  HE1   H  HCH2  0   0.191  -0.9363   4.4111   5.9448
 KAA  HE2   H  HCH2  0   0.208   0.4197   5.4812   6.2486
 KAA  HD1   H  HCH2  0   0.220  -0.9777   7.4531   5.7550
 KAA  HD2   H  HCH2  0   0.217  -2.3708   6.4206   5.4844
 KAA  HG1   H  HCH2  0   0.223   0.2193   6.3301   3.8614
 KAA  HG2   H  HCH2  0   0.215  -1.1615   5.2717   3.6289
 KAA  HB1   H  HCH2  0   0.230  -2.6012   7.2629   3.1262
 KAA  HB2   H  HCH2  0   0.247  -1.2297   8.3239   3.3890
 KAA  HA    H  HCH1  0   0.260  -0.0245   7.3557   1.5094
 KAA  HN1   H  HNH2  0   0.353  -2.7417   8.1807   0.8272
 KAA  HN2   H  HNH2  0   0.362  -1.4466   8.2517  -0.1561
 KAA  HN8   H  HNC1  0   0.452   0.4218   5.7064   0.2511
 KAA  H5'1  H  HCH2  0   0.239  -0.8556   3.2813   2.3399
 KAA  H5'2  H  HCH2  0   0.286  -1.9450   2.2480   1.3895
 KAA  H4'   H  HCH1  0   0.292  -0.4111   0.3562   1.5557
 KAA  H3'   H  HCH1  0   0.266  -1.9887   1.0981   3.6695
 KAA  HO3'  H  HOH1  0   0.462  -1.3056  -1.0642   3.3999
 KAA  H2'   H  HCH1  0   0.229  -0.4609   2.7033   4.5175
 KAA  HO2'  H  HOH1  0   0.458   0.5715   1.7320   6.3620
 KAA  H1'   H  HCH1  0   0.280   1.9484   0.8836   4.3250
 KAA  H8    H  HCR5  0   0.293   2.3018   3.5424   1.9600
 KAA  H2    H  HCR6  0   0.264   2.3301   3.5807   8.3589
 KAA  HN61  H  HNH2  0   0.415   4.1715   7.0217   4.8459
 KAA  HN62  H  HNH2  0   0.407   4.2749   7.1876   6.5607

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
 KAA  NZ   CE    single    1.454  0.020  1.454
 KAA  NZ   HNZ1  single    0.890  0.020  1.040
 KAA  NZ   HNZ2  single    0.890  0.020  1.040
 KAA  CE   CD    single    1.519  0.020  1.519
 KAA  CE   HE1   single    0.970  0.020  1.090
 KAA  CE   HE2   single    0.970  0.020  1.090
 KAA  CD   CG    single    1.523  0.020  1.523
 KAA  CD   HD1   single    0.970  0.020  1.090
 KAA  CD   HD2   single    0.970  0.020  1.090
 KAA  CG   CB    single    1.523  0.020  1.523
 KAA  CG   HG1   single    0.970  0.020  1.090
 KAA  CG   HG2   single    0.970  0.020  1.090
 KAA  CB   CA    single    1.523  0.020  1.523
 KAA  CB   HB1   single    0.970  0.020  1.090
 KAA  CB   HB2   single    0.970  0.020  1.090
 KAA  CA   C     single    1.528  0.020  1.528
 KAA  CA   N     single    1.451  0.020  1.451
 KAA  CA   HA    single    0.970  0.020  1.090
 KAA  N    HN1   single    0.890  0.020  1.040
 KAA  N    HN2   single    0.890  0.020  1.040
 KAA  C    O     double    1.206  0.020  1.206
 KAA  C    N8    single    1.386  0.020  1.386
 KAA  N8   S1    single    1.667  0.020  1.667
 KAA  N8   HN8   single    0.860  0.020  1.020
 KAA  S1   O1S   deloc     1.437  0.020  1.437
 KAA  S1   O5'   single    1.588  0.020  1.588
 KAA  S1   O2S   deloc     1.436  0.020  1.436
 KAA  O5'  C5'   single    1.438  0.020  1.438
 KAA  C5'  C4'   single    1.516  0.020  1.516
 KAA  C5'  H5'1  single    0.970  0.020  1.090
 KAA  C5'  H5'2  single    0.970  0.020  1.090
 KAA  C4'  O4'   single    1.423  0.020  1.423
 KAA  C4'  C3'   single    1.533  0.020  1.533
 KAA  C4'  H4'   single    0.970  0.020  1.090
 KAA  O4'  C1'   single    1.390  0.020  1.390
 KAA  C3'  C2'   single    1.527  0.020  1.527
 KAA  C3'  O3'   single    1.398  0.020  1.398
 KAA  C3'  H3'   single    0.970  0.020  1.090
 KAA  O3'  HO3'  single    0.850  0.020  0.980
 KAA  C2'  C1'   single    1.545  0.020  1.545
 KAA  C2'  O2'   single    1.387  0.020  1.387
 KAA  C2'  H2'   single    0.970  0.020  1.090
 KAA  O2'  HO2'  single    0.850  0.020  0.980
 KAA  C1'  N9    single    1.458  0.020  1.458
 KAA  C1'  H1'   single    0.970  0.020  1.090
 KAA  N9   C4    aromatic  1.360  0.020  1.360
 KAA  N9   C8    aromatic  1.368  0.020  1.368
 KAA  C8   N7    aromatic  1.303  0.020  1.303
 KAA  C8   H8    single    0.930  0.020  1.080
 KAA  N7   C5    aromatic  1.369  0.020  1.369
 KAA  C5   C6    aromatic  1.409  0.020  1.409
 KAA  C5   C4    aromatic  1.384  0.020  1.384
 KAA  C4   N3    aromatic  1.335  0.020  1.335
 KAA  N3   C2    aromatic  1.324  0.020  1.324
 KAA  C2   N1    aromatic  1.328  0.020  1.328
 KAA  C2   H2    single    0.930  0.020  1.080
 KAA  N1   C6    aromatic  1.340  0.020  1.340
 KAA  C6   N6    single    1.330  0.020  1.330
 KAA  N6   HN61  single    0.860  0.020  1.020
 KAA  N6   HN62  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
 KAA  HNZ2  NZ   HNZ1  105.30  3.000
 KAA  HNZ2  NZ   CE    109.19  3.000
 KAA  HNZ1  NZ   CE    109.47  3.000
 KAA  HE2   CE   HE1   106.20  3.000
 KAA  HE2   CE   CD    108.48  3.000
 KAA  HE1   CE   CD    108.96  3.000
 KAA  HE2   CE   NZ    108.24  3.000
 KAA  HE1   CE   NZ    113.34  3.000
 KAA  CD    CE   NZ    111.38  3.000
 KAA  HD2   CD   HD1   106.54  3.000
 KAA  HD2   CD   CG    109.23  3.000
 KAA  HD1   CD   CG    109.78  3.000
 KAA  HD2   CD   CE    109.48  3.000
 KAA  HD1   CD   CE    108.99  3.000
 KAA  CG    CD   CE    112.63  3.000
 KAA  HG2   CG   HG1   106.40  3.000
 KAA  HG2   CG   CB    110.23  3.000
 KAA  HG1   CG   CB    109.74  3.000
 KAA  HG2   CG   CD    108.63  3.000
 KAA  HG1   CG   CD    109.78  3.000
 KAA  CB    CG   CD    111.90  3.000
 KAA  HB2   CB   HB1   106.64  3.000
 KAA  HB2   CB   CA    107.04  3.000
 KAA  HB1   CB   CA    109.21  3.000
 KAA  HB2   CB   CG    109.52  3.000
 KAA  HB1   CB   CG    109.67  3.000
 KAA  CA    CB   CG    114.45  3.000
 KAA  HA    CA   C     109.46  3.000
 KAA  HA    CA   N     107.70  3.000
 KAA  C     CA   N     110.81  3.000
 KAA  HA    CA   CB    108.55  3.000
 KAA  N     CA   CB    110.30  3.000
 KAA  C     CA   CB    109.96  3.000
 KAA  HN2   N    HN1   106.96  3.000
 KAA  HN2   N    CA    111.19  3.000
 KAA  HN1   N    CA    110.33  3.000
 KAA  N8    C    O     123.03  3.000
 KAA  N8    C    CA    113.54  3.000
 KAA  O     C    CA    123.41  3.000
 KAA  HN8   N8   S1    114.28  3.000
 KAA  HN8   N8   C     118.58  3.000
 KAA  S1    N8   C     126.89  3.000
 KAA  O5'   S1   O2S   110.09  3.000
 KAA  O2S   S1   O1S   121.91  3.000
 KAA  O5'   S1   O1S   104.05  3.000
 KAA  O2S   S1   N8    109.43  3.000
 KAA  O5'   S1   N8    103.29  3.000
 KAA  O1S   S1   N8    106.45  3.000
 KAA  C5'   O5'  S1    120.56  3.000
 KAA  H5'2  C5'  H5'1  108.83  3.000
 KAA  H5'2  C5'  C4'   109.82  3.000
 KAA  H5'1  C5'  C4'   111.99  3.000
 KAA  H5'2  C5'  O5'   110.96  3.000
 KAA  H5'1  C5'  O5'   109.33  3.000
 KAA  C4'   C5'  O5'   105.90  3.000
 KAA  H4'   C4'  C3'   111.30  3.000
 KAA  H4'   C4'  O4'   107.76  3.000
 KAA  C3'   C4'  O4'   105.31  3.000
 KAA  H4'   C4'  C5'   108.50  3.000
 KAA  C3'   C4'  C5'   112.91  3.000
 KAA  O4'   C4'  C5'   110.93  3.000
 KAA  C1'   O4'  C4'   110.65  3.000
 KAA  H3'   C3'  C2'   111.67  3.000
 KAA  H3'   C3'  O3'   112.14  3.000
 KAA  C2'   C3'  O3'   108.23  3.000
 KAA  H3'   C3'  C4'   111.76  3.000
 KAA  O3'   C3'  C4'   111.51  3.000
 KAA  C2'   C3'  C4'   100.96  3.000
 KAA  HO3'  O3'  C3'   108.62  3.000
 KAA  H2'   C2'  C1'   107.84  3.000
 KAA  H2'   C2'  O2'   111.30  3.000
 KAA  C1'   C2'  O2'   114.45  3.000
 KAA  H2'   C2'  C3'   107.69  3.000
 KAA  O2'   C2'  C3'   113.01  3.000
 KAA  C1'   C2'  C3'   101.93  3.000
 KAA  HO2'  O2'  C2'   106.69  3.000
 KAA  H1'   C1'  N9    107.67  3.000
 KAA  H1'   C1'  C2'   110.96  3.000
 KAA  N9    C1'  C2'   111.10  3.000
 KAA  H1'   C1'  O4'   110.34  3.000
 KAA  N9    C1'  O4'   109.32  3.000
 KAA  C2'   C1'  O4'   107.46  3.000
 KAA  C4    N9   C8    106.31  3.000
 KAA  C8    N9   C1'   129.85  3.000
 KAA  C4    N9   C1'   123.82  3.000
 KAA  H8    C8   N7    125.10  3.000
 KAA  H8    C8   N9    121.81  3.000
 KAA  N7    C8   N9    113.09  3.000
 KAA  C5    N7   C8    104.54  3.000
 KAA  C6    C5   C4    115.97  3.000
 KAA  C4    C5   N7    110.55  3.000
 KAA  C6    C5   N7    133.48  3.000
 KAA  N3    C4   C5    126.80  3.000
 KAA  N3    C4   N9    127.69  3.000
 KAA  C5    C4   N9    105.50  3.000
 KAA  C2    N3   C4    111.71  3.000
 KAA  H2    C2   N1    115.83  3.000
 KAA  H2    C2   N3    116.16  3.000
 KAA  N1    C2   N3    128.00  3.000
 KAA  C6    N1   C2    119.62  3.000
 KAA  N6    C6   N1    119.21  3.000
 KAA  N6    C6   C5    122.90  3.000
 KAA  N1    C6   C5    117.89  3.000
 KAA  HN62  N6   HN61  118.26  3.000
 KAA  HN62  N6   C6    120.29  3.000
 KAA  HN61  N6   C6    121.18  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
 KAA  CONST_01  N7    C5   C4   N9      0.00   0.0  0
 KAA  CONST_02  C6    C5   C4   N9    180.00   0.0  0
 KAA  CONST_03  C2    N3   C4   N9    180.00   0.0  0
 KAA  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 KAA  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 KAA  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 KAA  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 KAA  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 KAA  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 KAA  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 KAA  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 KAA  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 KAA  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 KAA  CONST_14  N1    C6   C5   C4      0.00   0.0  0
 KAA  CONST_15  N1    C2   N3   C4      0.00   0.0  0
 KAA  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 KAA  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 KAA  CONST_18  C5    C4   N9   C1'   180.00   0.0  0
 KAA  CONST_19  N3    C4   N9   C1'     0.00   0.0  0
 KAA  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 KAA  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 KAA  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 KAA  CONST_23  N6    C6   N1   C2    180.00   0.0  0
 KAA  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 KAA  CONST_25  H2    C2   N3   C4    180.00   0.0  0
 KAA  CONST_26  HN61  N6   C6   C5      0.00   0.0  0
 KAA  CONST_27  HN62  N6   C6   C5    180.00   0.0  0
 KAA  CONST_28  S1    N8   C    CA    180.00   0.0  0
 KAA  CONST_29  S1    N8   C    O       0.00   0.0  0
 KAA  CONST_30  HN8   N8   C    CA      0.00   0.0  0
 KAA  Var_01    C4'   C5'  O5'  S1    170.25  30.0  3
 KAA  Var_02    CG    CD   CE   NZ    178.66  30.0  3
 KAA  Var_03    CB    CG   CD   CE    179.04  30.0  3
 KAA  Var_04    CA    CB   CG   CD    178.17  30.0  3
 KAA  Var_05    O1S   S1   N8   C     156.45  30.0  3
 KAA  Var_06    HNZ1  NZ   CE   CD   -177.44  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
 KAA  chir_01  CA   CB   C    N    negativ
 KAA  chir_02  C4'  O4'  C5'  C3'  positiv
 KAA  chir_03  C3'  O3'  C4'  C2'  positiv
 KAA  chir_04  C2'  O2'  C3'  C1'  positiv
 KAA  chir_05  C1'  O4'  N9   C2'  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
 KAA  plan-1  C1'   0.020
 KAA  plan-1  N9    0.020
 KAA  plan-1  C8    0.020
 KAA  plan-1  N7    0.020
 KAA  plan-1  C5    0.020
 KAA  plan-1  C4    0.020
 KAA  plan-1  N3    0.020
 KAA  plan-1  C2    0.020
 KAA  plan-1  N1    0.020
 KAA  plan-1  C6    0.020
 KAA  plan-1  N6    0.020
 KAA  plan-1  H8    0.020
 KAA  plan-1  H2    0.020
 KAA  plan-2  C6    0.020
 KAA  plan-2  N6    0.020
 KAA  plan-2  HN61  0.020
 KAA  plan-2  HN62  0.020
 KAA  plan-3  CA    0.020
 KAA  plan-3  C     0.020
 KAA  plan-3  O     0.020
 KAA  plan-3  N8    0.020
 KAA  plan-3  S1    0.020
 KAA  plan-3  HN8   0.020

