# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul 10 06:19:31 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 5'-O-(L-tyrosylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)cc1)C(=O)N[S](=O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
#
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
 YSA  YSA  5'-O-(L-tyrosylsulfamoyl)adenosine  ligand  58  35  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YSA
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
 YSA  CD1   C  CR16  0  -0.187  -4.4121   2.0099  -1.6425
 YSA  CE1   C  CR16  0  -0.313  -5.3654   3.0041  -1.4965
 YSA  CZ    C  CR6   0   0.307  -5.2338   3.9485  -0.4815
 YSA  OH    O  OH1   0  -0.607  -6.1837   4.9013  -0.3804
 YSA  CE2   C  CR16  0  -0.384  -4.1406   3.8762   0.3772
 YSA  CD2   C  CR16  0  -0.168  -3.1974   2.8719   0.2148
 YSA  CG    C  CR6   0  -0.088  -3.3095   1.9215  -0.7954
 YSA  CB    C  CH2   0  -0.518  -2.3083   0.8121  -0.9534
 YSA  CA    C  CH1   0  -0.274  -2.6199  -0.3677  -0.0246
 YSA  N     N  NH2   0  -0.750  -2.5213  -0.1000   1.3966
 YSA  C     C  C     0   0.623  -1.7962  -1.6020  -0.3903
 YSA  O     O  O     0  -0.422  -1.4407  -1.8814  -1.5068
 YSA  NAT   N  NC1   0  -0.791  -1.5623  -2.4088   0.7051
 YSA  SBI   S  S     0   1.590  -1.1418  -4.0020   0.6101
 YSA  OAD   O  OS    0  -0.598  -1.1759  -4.4947   1.9648
 YSA  OAE   O  OS    0  -0.640  -1.8780  -4.6478  -0.4416
 YSA  O5'   O  OC2   0  -0.572   0.3492  -3.9636   0.0757
 YSA  C5'   C  CH2   0  -0.231   1.4205  -3.6602   0.9857
 YSA  C4'   C  CH1   0   0.004   2.5396  -3.0606   0.1651
 YSA  O4'   O  O2    0  -0.484   2.1326  -1.8083  -0.3765
 YSA  C3'   C  CH1   0  -0.055   3.7839  -2.7883   1.0072
 YSA  O3'   O  OH1   0  -0.632   4.9112  -2.9210   0.1859
 YSA  C2'   C  CH1   0  -0.012   3.5633  -1.3277   1.4079
 YSA  O2'   O  OH1   0  -0.654   4.7270  -0.6177   1.7032
 YSA  C1'   C  CH1   0   0.168   2.9202  -0.7684   0.1399
 YSA  N9    N  NR5   0  -0.488   2.0998   0.3880   0.3691
 YSA  C8    C  CR15  0   0.093   1.0796   0.5149   1.2713
 YSA  N7    N  N     0  -0.457   0.4767   1.6644   1.2114
 YSA  C5    C  CR56  0   0.015   1.1259   2.3401   0.2064
 YSA  C4    C  CR56  0   0.421   2.1334   1.5584  -0.3365
 YSA  N3    N  N     0  -0.507   2.9470   1.8905  -1.3322
 YSA  C2    C  CR16  0   0.010   2.6923   3.1055  -1.7858
 YSA  N1    N  N     0  -0.353   1.7711   3.9661  -1.3642
 YSA  C6    C  CR6   0   0.460   0.9630   3.6189  -0.3581
 YSA  N6    N  NH2   0  -0.861   0.0382   4.4871   0.0572
 YSA  HD1   H  HCR6  0   0.259  -4.5300   1.2854  -2.4400
 YSA  HE1   H  HCR6  0   0.223  -6.2117   3.0527  -2.1702
 YSA  HOH   H  HOH1  0   0.476  -5.9831   5.5014   0.3456
 YSA  HE2   H  HCR6  0   0.255  -4.0217   4.6010   1.1748
 YSA  HD2   H  HCR6  0   0.265  -2.3586   2.8306   0.8984
 YSA  HB1   H  HCH2  0   0.261  -1.3010   1.1788  -0.7420
 YSA  HB2   H  HCH2  0   0.276  -2.3114   0.4634  -1.9863
 YSA  HA    H  HCH1  0   0.312  -3.6501  -0.6877  -0.2232
 YSA  HN1   H  HNH2  0   0.309  -1.7783   0.5625   1.5915
 YSA  HN2   H  HNH2  0   0.378  -3.3790   0.2953   1.7533
 YSA  HAT   H  HNC1  0   0.453  -1.8819  -2.0204   1.5961
 YSA  H5'1  H  HCH2  0   0.248   1.0888  -2.9759   1.7714
 YSA  H5'2  H  HCH2  0   0.302   1.7539  -4.5864   1.4548
 YSA  H4'   H  HCH1  0   0.280   2.7846  -3.7453  -0.6526
 YSA  H3'   H  HCH1  0   0.208   3.8370  -3.4493   1.8823
 YSA  H3    H  HOH1  0   0.451   5.6239  -2.3977   0.5706
 YSA  H2'   H  HCH1  0   0.296   2.8485  -1.2924   2.2408
 YSA  H1    H  HOH1  0   0.470   4.9359  -0.7299   2.6356
 YSA  H1'   H  HCH1  0   0.326   3.6932  -0.4616  -0.5725
 YSA  H8    H  HCR5  0   0.266   0.8229  -0.2800   1.9558
 YSA  H2    H  HCR6  0   0.265   3.3124   3.4500  -2.6061
 YSA  HN61  H  HNH2  0   0.397  -0.5043   4.3119   0.8836
 YSA  HN62  H  HNH2  0   0.379   0.0083   5.4110  -0.3374

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
 YSA  CD1  CE1   aromatic  1.385  0.020  1.385
 YSA  CD1  CG    aromatic  1.393  0.020  1.393
 YSA  CD1  HD1   single    0.930  0.020  1.080
 YSA  CE1  CZ    aromatic  1.393  0.020  1.393
 YSA  CE1  HE1   single    0.930  0.020  1.080
 YSA  CZ   OH    single    1.349  0.020  1.349
 YSA  CZ   CE2   aromatic  1.392  0.020  1.392
 YSA  OH   HOH   single    0.850  0.020  0.980
 YSA  CE2  CD2   aromatic  1.387  0.020  1.387
 YSA  CE2  HE2   single    0.930  0.020  1.080
 YSA  CD2  CG    aromatic  1.391  0.020  1.391
 YSA  CD2  HD2   single    0.930  0.020  1.080
 YSA  CG   CB    single    1.503  0.020  1.503
 YSA  CB   CA    single    1.534  0.020  1.534
 YSA  CB   HB1   single    0.970  0.020  1.090
 YSA  CB   HB2   single    0.970  0.020  1.090
 YSA  CA   N     single    1.450  0.020  1.450
 YSA  CA   C     single    1.528  0.020  1.528
 YSA  CA   HA    single    0.970  0.020  1.090
 YSA  N    HN1   single    0.890  0.020  1.040
 YSA  N    HN2   single    0.890  0.020  1.040
 YSA  C    O     double    1.205  0.020  1.205
 YSA  C    NAT   single    1.380  0.020  1.380
 YSA  NAT  SBI   single    1.650  0.020  1.650
 YSA  NAT  HAT   single    0.860  0.020  1.020
 YSA  SBI  OAD   deloc     1.442  0.020  1.442
 YSA  SBI  OAE   deloc     1.437  0.020  1.437
 YSA  SBI  O5'   single    1.584  0.020  1.584
 YSA  O5'  C5'   single    1.438  0.020  1.438
 YSA  C5'  C4'   single    1.512  0.020  1.512
 YSA  C5'  H5'1  single    0.970  0.020  1.090
 YSA  C5'  H5'2  single    0.970  0.020  1.090
 YSA  C4'  O4'   single    1.424  0.020  1.424
 YSA  C4'  C3'   single    1.527  0.020  1.527
 YSA  C4'  H4'   single    0.970  0.020  1.090
 YSA  O4'  C1'   single    1.403  0.020  1.403
 YSA  C3'  O3'   single    1.401  0.020  1.401
 YSA  C3'  C2'   single    1.530  0.020  1.530
 YSA  C3'  H3'   single    0.970  0.020  1.090
 YSA  O3'  H3    single    0.850  0.020  0.980
 YSA  C2'  O2'   single    1.395  0.020  1.395
 YSA  C2'  C1'   single    1.528  0.020  1.528
 YSA  C2'  H2'   single    0.970  0.020  1.090
 YSA  O2'  H1    single    0.850  0.020  0.980
 YSA  C1'  N9    single    1.436  0.020  1.436
 YSA  C1'  H1'   single    0.970  0.020  1.090
 YSA  N9   C8    aromatic  1.368  0.020  1.368
 YSA  N9   C4    aromatic  1.367  0.020  1.367
 YSA  C8   N7    aromatic  1.299  0.020  1.299
 YSA  C8   H8    single    0.930  0.020  1.080
 YSA  N7   C5    aromatic  1.374  0.020  1.374
 YSA  C5   C4    aromatic  1.386  0.020  1.386
 YSA  C5   C6    aromatic  1.407  0.020  1.407
 YSA  C4   N3    aromatic  1.328  0.020  1.328
 YSA  N3   C2    aromatic  1.322  0.020  1.322
 YSA  C2   N1    aromatic  1.329  0.020  1.329
 YSA  C2   H2    single    0.930  0.020  1.080
 YSA  N1   C6    aromatic  1.336  0.020  1.336
 YSA  C6   N6    single    1.335  0.020  1.335
 YSA  N6   HN61  single    0.860  0.020  1.020
 YSA  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
 YSA  HD1   CD1  CG    119.41  3.000
 YSA  HD1   CD1  CE1   118.85  3.000
 YSA  CG    CD1  CE1   121.75  3.000
 YSA  HE1   CE1  CZ    119.80  3.000
 YSA  HE1   CE1  CD1   120.30  3.000
 YSA  CZ    CE1  CD1   119.90  3.000
 YSA  CE2   CZ   OH    122.91  3.000
 YSA  CE2   CZ   CE1   119.25  3.000
 YSA  OH    CZ   CE1   117.84  3.000
 YSA  HOH   OH   CZ    110.48  3.000
 YSA  HE2   CE2  CD2   119.70  3.000
 YSA  HE2   CE2  CZ    120.35  3.000
 YSA  CD2   CE2  CZ    119.95  3.000
 YSA  HD2   CD2  CG    119.65  3.000
 YSA  HD2   CD2  CE2   118.70  3.000
 YSA  CG    CD2  CE2   121.65  3.000
 YSA  CB    CG   CD2   121.80  3.000
 YSA  CB    CG   CD1   120.68  3.000
 YSA  CD2   CG   CD1   117.50  3.000
 YSA  HB2   CB   HB1   107.06  3.000
 YSA  HB2   CB   CA    109.10  3.000
 YSA  HB1   CB   CA    109.17  3.000
 YSA  HB2   CB   CG    109.50  3.000
 YSA  HB1   CB   CG    110.25  3.000
 YSA  CA    CB   CG    111.65  3.000
 YSA  HA    CA   C     103.14  3.000
 YSA  HA    CA   N     107.18  3.000
 YSA  C     CA   N     110.30  3.000
 YSA  HA    CA   CB    107.80  3.000
 YSA  C     CA   CB    111.53  3.000
 YSA  N     CA   CB    115.97  3.000
 YSA  HN2   N    HN1   107.38  3.000
 YSA  HN2   N    CA    111.15  3.000
 YSA  HN1   N    CA    111.03  3.000
 YSA  NAT   C    O     123.36  3.000
 YSA  NAT   C    CA    111.93  3.000
 YSA  O     C    CA    124.62  3.000
 YSA  HAT   NAT  SBI   119.75  3.000
 YSA  HAT   NAT  C     114.60  3.000
 YSA  SBI   NAT  C     124.17  3.000
 YSA  O5'   SBI  OAE   104.25  3.000
 YSA  O5'   SBI  OAD   110.33  3.000
 YSA  OAE   SBI  OAD   121.46  3.000
 YSA  O5'   SBI  NAT   103.64  3.000
 YSA  OAE   SBI  NAT   110.21  3.000
 YSA  OAD   SBI  NAT   105.65  3.000
 YSA  C5'   O5'  SBI   119.52  3.000
 YSA  H5'2  C5'  H5'1  108.37  3.000
 YSA  H5'2  C5'  C4'   110.13  3.000
 YSA  H5'1  C5'  C4'   111.50  3.000
 YSA  H5'2  C5'  O5'   108.71  3.000
 YSA  H5'1  C5'  O5'   111.14  3.000
 YSA  C4'   C5'  O5'   106.96  3.000
 YSA  H4'   C4'  C3'   109.95  3.000
 YSA  H4'   C4'  O4'   109.28  3.000
 YSA  C3'   C4'  O4'   106.61  3.000
 YSA  H4'   C4'  C5'   108.86  3.000
 YSA  C3'   C4'  C5'   112.00  3.000
 YSA  O4'   C4'  C5'   110.10  3.000
 YSA  C1'   O4'  C4'   110.58  3.000
 YSA  H3'   C3'  C2'   111.90  3.000
 YSA  H3'   C3'  O3'   111.80  3.000
 YSA  C2'   C3'  O3'   111.09  3.000
 YSA  H3'   C3'  C4'   111.81  3.000
 YSA  C2'   C3'  C4'   101.36  3.000
 YSA  O3'   C3'  C4'   108.38  3.000
 YSA  H3    O3'  C3'   108.02  3.000
 YSA  H2'   C2'  C1'   110.11  3.000
 YSA  H2'   C2'  O2'   111.47  3.000
 YSA  C1'   C2'  O2'   109.91  3.000
 YSA  H2'   C2'  C3'   108.85  3.000
 YSA  C1'   C2'  C3'   101.12  3.000
 YSA  O2'   C2'  C3'   114.89  3.000
 YSA  H1    O2'  C2'   109.09  3.000
 YSA  H1'   C1'  N9    106.34  3.000
 YSA  H1'   C1'  C2'   110.20  3.000
 YSA  N9    C1'  C2'   113.75  3.000
 YSA  H1'   C1'  O4'   111.38  3.000
 YSA  N9    C1'  O4'   109.56  3.000
 YSA  C2'   C1'  O4'   105.69  3.000
 YSA  C4    N9   C8    106.22  3.000
 YSA  C4    N9   C1'   126.36  3.000
 YSA  C8    N9   C1'   127.30  3.000
 YSA  H8    C8   N7    124.75  3.000
 YSA  H8    C8   N9    121.80  3.000
 YSA  N7    C8   N9    113.44  3.000
 YSA  C5    N7   C8    104.44  3.000
 YSA  C6    C5   C4    116.08  3.000
 YSA  C6    C5   N7    133.27  3.000
 YSA  C4    C5   N7    110.65  3.000
 YSA  N3    C4   C5    126.73  3.000
 YSA  N3    C4   N9    128.03  3.000
 YSA  C5    C4   N9    105.24  3.000
 YSA  C2    N3   C4    111.66  3.000
 YSA  H2    C2   N1    115.49  3.000
 YSA  H2    C2   N3    116.19  3.000
 YSA  N1    C2   N3    128.31  3.000
 YSA  C6    N1   C2    119.31  3.000
 YSA  N6    C6   N1    118.96  3.000
 YSA  N6    C6   C5    123.13  3.000
 YSA  N1    C6   C5    117.91  3.000
 YSA  HN62  N6   HN61  117.88  3.000
 YSA  HN62  N6   C6    119.76  3.000
 YSA  HN61  N6   C6    121.13  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
 YSA  CONST_01  CE2   CZ   CE1  CD1     0.00   0.0  0
 YSA  CONST_02  CE2   CD2  CG   CD1     0.00   0.0  0
 YSA  CONST_03  CD2   CG   CD1  CE1     0.00   0.0  0
 YSA  CONST_04  CD2   CE2  CZ   CE1     0.00   0.0  0
 YSA  CONST_05  CG    CD1  CE1  CZ      0.00   0.0  0
 YSA  CONST_06  CG    CD2  CE2  CZ      0.00   0.0  0
 YSA  CONST_07  C5    N7   C8   N9      0.00   0.0  0
 YSA  CONST_08  N7    C5   C4   N9      0.00   0.0  0
 YSA  CONST_09  C6    C5   C4   N9    180.00   0.0  0
 YSA  CONST_10  C2    N3   C4   N9    180.00   0.0  0
 YSA  CONST_11  C5    C4   N9   C8      0.00   0.0  0
 YSA  CONST_12  N3    C4   N9   C8    180.00   0.0  0
 YSA  CONST_13  C4    C5   N7   C8      0.00   0.0  0
 YSA  CONST_14  C6    C5   N7   C8    180.00   0.0  0
 YSA  CONST_15  C4    N9   C8   N7      0.00   0.0  0
 YSA  CONST_16  N3    C4   C5   N7    180.00   0.0  0
 YSA  CONST_17  N1    C6   C5   N7    180.00   0.0  0
 YSA  CONST_18  C2    N3   C4   C5      0.00   0.0  0
 YSA  CONST_19  C2    N1   C6   C5      0.00   0.0  0
 YSA  CONST_20  N1    C6   C5   C4      0.00   0.0  0
 YSA  CONST_21  N1    C2   N3   C4      0.00   0.0  0
 YSA  CONST_22  C6    C5   C4   N3      0.00   0.0  0
 YSA  CONST_23  C6    N1   C2   N3      0.00   0.0  0
 YSA  CONST_24  N7    C8   N9   C1'   180.00   0.0  0
 YSA  CONST_25  C5    C4   N9   C1'   180.00   0.0  0
 YSA  CONST_26  N3    C4   N9   C1'     0.00   0.0  0
 YSA  CONST_27  OH    CZ   CE1  CD1   180.00   0.0  0
 YSA  CONST_28  CB    CG   CD1  CE1   180.00   0.0  0
 YSA  CONST_29  CD2   CE2  CZ   OH    180.00   0.0  0
 YSA  CONST_30  CB    CG   CD2  CE2   180.00   0.0  0
 YSA  CONST_31  N6    C6   C5   N7      0.00   0.0  0
 YSA  CONST_32  N6    C6   C5   C4    180.00   0.0  0
 YSA  CONST_33  N6    C6   N1   C2    180.00   0.0  0
 YSA  CONST_34  HD2   CD2  CG   CD1   180.00   0.0  0
 YSA  CONST_35  HE2   CE2  CZ   CE1   180.00   0.0  0
 YSA  CONST_36  HD1   CD1  CE1  CZ    180.00   0.0  0
 YSA  CONST_37  HE1   CE1  CZ   CE2   180.00   0.0  0
 YSA  CONST_38  H8    C8   N9   C1'     0.00   0.0  0
 YSA  CONST_39  H2    C2   N3   C4    180.00   0.0  0
 YSA  CONST_40  HN61  N6   C6   C5      0.00   0.0  0
 YSA  CONST_41  HN62  N6   C6   C5    180.00   0.0  0
 YSA  CONST_44  HAT   NAT  C    CA      0.00   0.0  0
 YSA  Var_01    CA    CB   CG   CD1   -94.88  30.0  2
 YSA  Var_02    C4'   C5'  O5'  SBI  -153.62  30.0  3
 YSA  Var_03    OAD   SBI  NAT  C    -172.42  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
 YSA  chir_01  CA   CB   N    C    positiv
 YSA  chir_02  C4'  O4'  C5'  C3'  positiv
 YSA  chir_03  C3'  O3'  C4'  C2'  positiv
 YSA  chir_04  C2'  O2'  C3'  C1'  positiv
 YSA  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
 YSA  plan-1  CD1   0.020
 YSA  plan-1  CE1   0.020
 YSA  plan-1  CZ    0.020
 YSA  plan-1  OH    0.020
 YSA  plan-1  CE2   0.020
 YSA  plan-1  CD2   0.020
 YSA  plan-1  CG    0.020
 YSA  plan-1  CB    0.020
 YSA  plan-1  HD1   0.020
 YSA  plan-1  HE1   0.020
 YSA  plan-1  HE2   0.020
 YSA  plan-1  HD2   0.020
 YSA  plan-2  C1'   0.020
 YSA  plan-2  N9    0.020
 YSA  plan-2  C8    0.020
 YSA  plan-2  N7    0.020
 YSA  plan-2  C5    0.020
 YSA  plan-2  C4    0.020
 YSA  plan-2  N3    0.020
 YSA  plan-2  C2    0.020
 YSA  plan-2  N1    0.020
 YSA  plan-2  C6    0.020
 YSA  plan-2  N6    0.020
 YSA  plan-2  H8    0.020
 YSA  plan-2  H2    0.020
 YSA  plan-3  C6    0.020
 YSA  plan-3  N6    0.020
 YSA  plan-3  HN61  0.020
 YSA  plan-3  HN62  0.020
 YSA  plan-4  CA    0.020
 YSA  plan-4  C     0.020
 YSA  plan-4  O     0.020
 YSA  plan-4  NAT   0.020
 YSA  plan-4  SBI   0.020
 YSA  plan-4  HAT   0.020

