# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:44:49 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: 5'-O-(L-phenylalanylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)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
 W5Y  W5Y  5'-O-(L-phenylalanylsulfamoyl)adenosine  ligand  57  34  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W5Y
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
 W5Y  CD1  C  CR16  0  -0.313  -16.0620   4.3969  -67.4042
 W5Y  CE1  C  CR16  0  -0.241  -16.8407   4.0694  -68.5067
 W5Y  CZ   C  CR16  0  -0.269  -16.6961   4.7715  -69.6958
 W5Y  CE2  C  CR16  0  -0.238  -15.7716   5.8057  -69.7726
 W5Y  CD2  C  CR16  0  -0.303  -14.9987   6.1313  -68.6666
 W5Y  CG   C  CR6   0   0.160  -15.1319   5.4301  -67.4702
 W5Y  CB   C  CH2   0  -0.534  -14.2708   5.7817  -66.2906
 W5Y  CA   C  CH1   0  -0.216  -12.8552   5.1857  -66.4180
 W5Y  N    N  NH2   0  -0.763  -12.9129   3.7509  -66.4515
 W5Y  C    C  C     0   0.560  -11.9822   5.7302  -65.2855
 W5Y  O    O  O     0  -0.404  -11.6608   5.0966  -64.3121
 W5Y  NAT  N  NC1   0  -0.828  -11.5970   7.0479  -65.4598
 W5Y  SBI  S  S     0   1.623  -10.5543   7.8541  -64.4498
 W5Y  OAD  O  OS    0  -0.607   -9.3721   7.0761  -64.2050
 W5Y  OAE  O  OS    0  -0.621  -10.4730   9.1891  -64.9871
 W5Y  O5'  O  OC2   0  -0.570  -11.3101   7.8489  -63.0579
 W5Y  C5'  C  CH2   0  -0.233  -12.5139   8.6159  -62.8563
 W5Y  C4'  C  CH1   0   0.026  -12.3107   9.6275  -61.7564
 W5Y  O4'  O  O2    0  -0.491  -11.9053   8.9760  -60.5622
 W5Y  C3'  C  CH1   0   0.006  -11.2476  10.6970  -61.9947
 W5Y  O3'  O  OH1   0  -0.652  -11.7410  11.6731  -62.8556
 W5Y  C2'  C  CH1   0  -0.061  -10.9497  11.1431  -60.5600
 W5Y  O2'  O  OH1   0  -0.653  -11.9453  12.0385  -60.1590
 W5Y  C1'  C  CH1   0   0.162  -11.0667   9.8029  -59.8061
 W5Y  N9   N  NR5   0  -0.534   -9.7838   9.1459  -59.6190
 W5Y  C8   C  CR15  0   0.103   -9.1210   8.2862  -60.4533
 W5Y  N7   N  N     0  -0.448   -7.9615   7.9142  -59.9954
 W5Y  C5   C  CR56  0  -0.003   -7.8435   8.5635  -58.7953
 W5Y  C4   C  CR56  0   0.486   -8.9664   9.3350  -58.5423
 W5Y  N3   N  N     0  -0.456   -9.1843  10.0921  -57.4690
 W5Y  C2   C  CR16  0   0.042   -8.1766  10.0288  -56.6161
 W5Y  N1   N  N     0  -0.470   -7.0453   9.3369  -56.7226
 W5Y  C6   C  CR6   0   0.454   -6.8391   8.5859  -57.8103
 W5Y  N6   N  NH2   0  -0.815   -5.6975   7.9043  -57.9266
 W5Y  H1   H  HCR6  0   0.245  -16.1817   3.8457  -66.4791
 W5Y  H2   H  HCR6  0   0.251  -17.5604   3.2635  -68.4366
 W5Y  H3   H  HCR6  0   0.251  -17.3022   4.5170  -70.5558
 W5Y  H4   H  HCR6  0   0.251  -15.6559   6.3626  -70.6936
 W5Y  H5   H  HCR6  0   0.246  -14.2845   6.9448  -68.7335
 W5Y  H6   H  HCH2  0   0.268  -14.2078   6.8683  -66.1965
 W5Y  H7   H  HCH2  0   0.267  -14.7240   5.4128  -65.3662
 W5Y  H8   H  HCH1  0   0.284  -12.4223   5.5344  -67.3624
 W5Y  H9   H  HNH2  0   0.358  -11.9931   3.3572  -66.6020
 W5Y  H10  H  HNH2  0   0.349  -13.2486   3.3862  -65.5685
 W5Y  H12  H  HNC1  0   0.456  -11.8630   7.5532  -66.2979
 W5Y  H13  H  HCH2  0   0.274  -12.8263   9.1353  -63.7643
 W5Y  H14  H  HCH2  0   0.289  -13.2925   7.9000  -62.5934
 W5Y  H15  H  HCH1  0   0.259  -13.2847  10.1160  -61.6145
 W5Y  H16  H  HCH1  0   0.238  -10.3350  10.2326  -62.3896
 W5Y  H17  H  HOH1  0   0.461  -11.0064  12.2017  -63.1821
 W5Y  H18  H  HCH1  0   0.264   -9.9446  11.5667  -60.4501
 W5Y  H19  H  HOH1  0   0.460  -11.7480  12.3382  -59.2654
 W5Y  H20  H  HCH1  0   0.278  -11.4779   9.9569  -58.8036
 W5Y  H21  H  HCR5  0   0.291   -9.5444   7.9546  -61.3863
 W5Y  H22  H  HCR6  0   0.250   -8.2794  10.6168  -55.7102
 W5Y  H23  H  HNH2  0   0.402   -5.0398   7.8907  -57.1661
 W5Y  H24  H  HNH2  0   0.410   -5.5487   7.2715  -58.6930

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
 W5Y  CE2  CZ   aromatic  1.389  0.020  1.389
 W5Y  CE2  CD2  aromatic  1.388  0.020  1.388
 W5Y  CZ   CE1  aromatic  1.388  0.020  1.388
 W5Y  CD2  CG   aromatic  1.393  0.020  1.393
 W5Y  CE1  CD1  aromatic  1.389  0.020  1.389
 W5Y  CG   CD1  aromatic  1.392  0.020  1.392
 W5Y  CG   CB   single    1.502  0.020  1.502
 W5Y  CA   CB   single    1.541  0.020  1.541
 W5Y  CA   N    single    1.436  0.020  1.436
 W5Y  CA   C    single    1.530  0.020  1.530
 W5Y  NAT  C    single    1.384  0.020  1.384
 W5Y  NAT  SBI  single    1.661  0.020  1.661
 W5Y  C    O    double    1.205  0.020  1.205
 W5Y  OAE  SBI  deloc     1.441  0.020  1.441
 W5Y  SBI  OAD  deloc     1.436  0.020  1.436
 W5Y  SBI  O5'  single    1.584  0.020  1.584
 W5Y  O5'  C5'  single    1.442  0.020  1.442
 W5Y  C5'  C4'  single    1.508  0.020  1.508
 W5Y  O3'  C3'  single    1.392  0.020  1.392
 W5Y  C3'  C4'  single    1.527  0.020  1.527
 W5Y  C3'  C2'  single    1.532  0.020  1.532
 W5Y  C4'  O4'  single    1.420  0.020  1.420
 W5Y  O4'  C1'  single    1.400  0.020  1.400
 W5Y  C2'  O2'  single    1.398  0.020  1.398
 W5Y  C2'  C1'  single    1.542  0.020  1.542
 W5Y  C8   N7   aromatic  1.301  0.020  1.301
 W5Y  C8   N9   aromatic  1.369  0.020  1.369
 W5Y  N7   C5   aromatic  1.370  0.020  1.370
 W5Y  C1'  N9   single    1.453  0.020  1.453
 W5Y  N9   C4   aromatic  1.365  0.020  1.365
 W5Y  C5   C4   aromatic  1.386  0.020  1.386
 W5Y  C5   C6   aromatic  1.407  0.020  1.407
 W5Y  C4   N3   aromatic  1.331  0.020  1.331
 W5Y  N6   C6   single    1.335  0.020  1.335
 W5Y  C6   N1   aromatic  1.338  0.020  1.338
 W5Y  N3   C2   aromatic  1.322  0.020  1.322
 W5Y  N1   C2   aromatic  1.330  0.020  1.330
 W5Y  CD1  H1   single    0.930  0.020  1.080
 W5Y  CE1  H2   single    0.930  0.020  1.080
 W5Y  CZ   H3   single    0.930  0.020  1.080
 W5Y  CE2  H4   single    0.930  0.020  1.080
 W5Y  CD2  H5   single    0.930  0.020  1.080
 W5Y  CB   H6   single    0.970  0.020  1.090
 W5Y  CB   H7   single    0.970  0.020  1.090
 W5Y  CA   H8   single    0.970  0.020  1.090
 W5Y  N    H9   single    0.890  0.020  1.040
 W5Y  N    H10  single    0.890  0.020  1.040
 W5Y  NAT  H12  single    0.860  0.020  1.020
 W5Y  C5'  H13  single    0.970  0.020  1.090
 W5Y  C5'  H14  single    0.970  0.020  1.090
 W5Y  C4'  H15  single    0.970  0.020  1.090
 W5Y  C3'  H16  single    0.970  0.020  1.090
 W5Y  O3'  H17  single    0.850  0.020  0.980
 W5Y  C2'  H18  single    0.970  0.020  1.090
 W5Y  O2'  H19  single    0.850  0.020  0.980
 W5Y  C1'  H20  single    0.970  0.020  1.090
 W5Y  C8   H21  single    0.930  0.020  1.080
 W5Y  C2   H22  single    0.930  0.020  1.080
 W5Y  N6   H23  single    0.860  0.020  1.020
 W5Y  N6   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
 W5Y  H1   CD1  CG   119.47  3.000
 W5Y  H1   CD1  CE1  119.72  3.000
 W5Y  CG   CD1  CE1  120.81  3.000
 W5Y  H2   CE1  CZ   120.08  3.000
 W5Y  H2   CE1  CD1  119.79  3.000
 W5Y  CZ   CE1  CD1  120.14  3.000
 W5Y  H3   CZ   CE2  120.25  3.000
 W5Y  H3   CZ   CE1  120.21  3.000
 W5Y  CE2  CZ   CE1  119.55  3.000
 W5Y  H4   CE2  CD2  119.85  3.000
 W5Y  H4   CE2  CZ   120.07  3.000
 W5Y  CD2  CE2  CZ   120.08  3.000
 W5Y  H5   CD2  CG   119.57  3.000
 W5Y  H5   CD2  CE2  119.57  3.000
 W5Y  CG   CD2  CE2  120.86  3.000
 W5Y  CB   CG   CD2  120.12  3.000
 W5Y  CB   CG   CD1  121.31  3.000
 W5Y  CD2  CG   CD1  118.57  3.000
 W5Y  H7   CB   H6   106.66  3.000
 W5Y  H7   CB   CA   108.66  3.000
 W5Y  H6   CB   CA   109.80  3.000
 W5Y  H7   CB   CG   110.32  3.000
 W5Y  H6   CB   CG   109.48  3.000
 W5Y  CA   CB   CG   111.78  3.000
 W5Y  H8   CA   C    107.41  3.000
 W5Y  H8   CA   N    108.28  3.000
 W5Y  C    CA   N    113.31  3.000
 W5Y  H8   CA   CB   108.12  3.000
 W5Y  C    CA   CB   108.98  3.000
 W5Y  N    CA   CB   110.57  3.000
 W5Y  H10  N    H9   106.92  3.000
 W5Y  H10  N    CA   110.66  3.000
 W5Y  H9   N    CA   110.83  3.000
 W5Y  NAT  C    O    121.88  3.000
 W5Y  O    C    CA   124.25  3.000
 W5Y  NAT  C    CA   113.86  3.000
 W5Y  H12  NAT  SBI  115.18  3.000
 W5Y  H12  NAT  C    120.37  3.000
 W5Y  SBI  NAT  C    124.09  3.000
 W5Y  O5'  SBI  OAE  110.95  3.000
 W5Y  O5'  SBI  OAD  103.96  3.000
 W5Y  OAE  SBI  OAD  121.25  3.000
 W5Y  O5'  SBI  NAT  103.49  3.000
 W5Y  OAD  SBI  NAT  110.95  3.000
 W5Y  OAE  SBI  NAT  104.97  3.000
 W5Y  C5'  O5'  SBI  121.31  3.000
 W5Y  H14  C5'  H13  107.99  3.000
 W5Y  H14  C5'  C4'  111.16  3.000
 W5Y  H13  C5'  C4'  109.02  3.000
 W5Y  H14  C5'  O5'  106.31  3.000
 W5Y  H13  C5'  O5'  112.07  3.000
 W5Y  C4'  C5'  O5'  110.27  3.000
 W5Y  H15  C4'  C3'  109.03  3.000
 W5Y  H15  C4'  O4'  110.40  3.000
 W5Y  C3'  C4'  O4'  104.71  3.000
 W5Y  H15  C4'  C5'  105.84  3.000
 W5Y  O4'  C4'  C5'  110.13  3.000
 W5Y  C3'  C4'  C5'  116.73  3.000
 W5Y  C1'  O4'  C4'  110.76  3.000
 W5Y  H16  C3'  C2'  107.37  3.000
 W5Y  H16  C3'  O3'  111.65  3.000
 W5Y  C2'  C3'  O3'  116.36  3.000
 W5Y  H16  C3'  C4'  109.81  3.000
 W5Y  C2'  C3'  C4'  101.14  3.000
 W5Y  O3'  C3'  C4'  109.94  3.000
 W5Y  H17  O3'  C3'  108.94  3.000
 W5Y  H18  C2'  C1'  110.88  3.000
 W5Y  H18  C2'  O2'  112.13  3.000
 W5Y  C1'  C2'  O2'  111.25  3.000
 W5Y  H18  C2'  C3'  112.63  3.000
 W5Y  C1'  C2'  C3'  100.96  3.000
 W5Y  O2'  C2'  C3'  108.47  3.000
 W5Y  H19  O2'  C2'  108.64  3.000
 W5Y  H20  C1'  N9   106.10  3.000
 W5Y  H20  C1'  C2'  110.73  3.000
 W5Y  N9   C1'  C2'  112.88  3.000
 W5Y  H20  C1'  O4'  110.66  3.000
 W5Y  N9   C1'  O4'  109.35  3.000
 W5Y  C2'  C1'  O4'  107.15  3.000
 W5Y  C4   N9   C8   106.13  3.000
 W5Y  C4   N9   C1'  124.57  3.000
 W5Y  C8   N9   C1'  129.25  3.000
 W5Y  H21  C8   N7   124.56  3.000
 W5Y  H21  C8   N9   122.07  3.000
 W5Y  N7   C8   N9   113.36  3.000
 W5Y  C5   N7   C8   104.46  3.000
 W5Y  C6   C5   C4   116.22  3.000
 W5Y  C6   C5   N7   133.04  3.000
 W5Y  C4   C5   N7   110.74  3.000
 W5Y  N3   C4   C5   126.61  3.000
 W5Y  N3   C4   N9   128.08  3.000
 W5Y  C5   C4   N9   105.32  3.000
 W5Y  C2   N3   C4   111.61  3.000
 W5Y  H22  C2   N1   115.43  3.000
 W5Y  H22  C2   N3   116.14  3.000
 W5Y  N1   C2   N3   128.43  3.000
 W5Y  C6   N1   C2   119.22  3.000
 W5Y  N6   C6   N1   119.30  3.000
 W5Y  N1   C6   C5   117.91  3.000
 W5Y  N6   C6   C5   122.78  3.000
 W5Y  H24  N6   H23  118.12  3.000
 W5Y  H24  N6   C6   120.98  3.000
 W5Y  H23  N6   C6   120.03  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
 W5Y  CONST_01  CE2  CZ   CE1  CD1     0.00   0.0  0
 W5Y  CONST_02  CE2  CD2  CG   CD1     0.00   0.0  0
 W5Y  CONST_03  CD2  CE2  CZ   CE1     0.00   0.0  0
 W5Y  CONST_04  CD2  CG   CD1  CE1     0.00   0.0  0
 W5Y  CONST_05  CG   CD2  CE2  CZ      0.00   0.0  0
 W5Y  CONST_06  CG   CD1  CE1  CZ      0.00   0.0  0
 W5Y  CONST_07  C5   N7   C8   N9      0.00   0.0  0
 W5Y  CONST_08  N7   C5   C4   N9      0.00   0.0  0
 W5Y  CONST_09  C6   C5   C4   N9    180.00   0.0  0
 W5Y  CONST_10  C2   N3   C4   N9    180.00   0.0  0
 W5Y  CONST_11  C4   C5   N7   C8      0.00   0.0  0
 W5Y  CONST_12  C6   C5   N7   C8    180.00   0.0  0
 W5Y  CONST_13  C5   C4   N9   C8      0.00   0.0  0
 W5Y  CONST_14  N3   C4   N9   C8    180.00   0.0  0
 W5Y  CONST_15  C4   N9   C8   N7      0.00   0.0  0
 W5Y  CONST_16  N3   C4   C5   N7    180.00   0.0  0
 W5Y  CONST_17  N1   C6   C5   N7    180.00   0.0  0
 W5Y  CONST_18  C2   N3   C4   C5      0.00   0.0  0
 W5Y  CONST_19  C2   N1   C6   C5      0.00   0.0  0
 W5Y  CONST_20  N1   C6   C5   C4      0.00   0.0  0
 W5Y  CONST_21  N1   C2   N3   C4      0.00   0.0  0
 W5Y  CONST_22  C6   C5   C4   N3      0.00   0.0  0
 W5Y  CONST_23  C6   N1   C2   N3      0.00   0.0  0
 W5Y  CONST_24  N7   C8   N9   C1'   180.00   0.0  0
 W5Y  CONST_25  C5   C4   N9   C1'   180.00   0.0  0
 W5Y  CONST_26  N3   C4   N9   C1'     0.00   0.0  0
 W5Y  CONST_27  CB   CG   CD1  CE1   180.00   0.0  0
 W5Y  CONST_28  CB   CG   CD2  CE2   180.00   0.0  0
 W5Y  CONST_29  N6   C6   C5   N7      0.00   0.0  0
 W5Y  CONST_30  N6   C6   C5   C4    180.00   0.0  0
 W5Y  CONST_31  N6   C6   N1   C2    180.00   0.0  0
 W5Y  CONST_32  H3   CZ   CE1  CD1   180.00   0.0  0
 W5Y  CONST_33  H5   CD2  CG   CD1   180.00   0.0  0
 W5Y  CONST_34  H4   CE2  CZ   CE1   180.00   0.0  0
 W5Y  CONST_35  H1   CD1  CE1  CZ    180.00   0.0  0
 W5Y  CONST_36  H2   CE1  CZ   CE2   180.00   0.0  0
 W5Y  CONST_37  H21  C8   N9   C1'     0.00   0.0  0
 W5Y  CONST_38  H22  C2   N3   C4    180.00   0.0  0
 W5Y  CONST_39  H23  N6   C6   C5    180.00   0.0  0
 W5Y  CONST_40  H24  N6   C6   C5      0.00   0.0  0
 W5Y  CONST_41  SBI  NAT  C    CA    180.00   0.0  0
 W5Y  CONST_42  SBI  NAT  C    O       0.00   0.0  0
 W5Y  CONST_43  H12  NAT  C    CA      0.00   0.0  0
 W5Y  Var_01    CA   CB   CG   CD1   100.01  30.0  2
 W5Y  Var_02    C4'  C5'  O5'  SBI  -119.48  30.0  3
 W5Y  Var_03    OAE  SBI  NAT  C    -178.46  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
 W5Y  chir_01  CA   CB   N    C    positiv
 W5Y  chir_02  C4'  O4'  C5'  C3'  positiv
 W5Y  chir_03  C3'  O3'  C4'  C2'  positiv
 W5Y  chir_04  C2'  O2'  C3'  C1'  positiv
 W5Y  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
 W5Y  plan-1  CD1  0.020
 W5Y  plan-1  CE1  0.020
 W5Y  plan-1  CZ   0.020
 W5Y  plan-1  CE2  0.020
 W5Y  plan-1  CD2  0.020
 W5Y  plan-1  CG   0.020
 W5Y  plan-1  CB   0.020
 W5Y  plan-1  H1   0.020
 W5Y  plan-1  H2   0.020
 W5Y  plan-1  H3   0.020
 W5Y  plan-1  H4   0.020
 W5Y  plan-1  H5   0.020
 W5Y  plan-2  C1'  0.020
 W5Y  plan-2  N9   0.020
 W5Y  plan-2  C8   0.020
 W5Y  plan-2  N7   0.020
 W5Y  plan-2  C5   0.020
 W5Y  plan-2  C4   0.020
 W5Y  plan-2  N3   0.020
 W5Y  plan-2  C2   0.020
 W5Y  plan-2  N1   0.020
 W5Y  plan-2  C6   0.020
 W5Y  plan-2  N6   0.020
 W5Y  plan-2  H21  0.020
 W5Y  plan-2  H22  0.020
 W5Y  plan-3  C6   0.020
 W5Y  plan-3  N6   0.020
 W5Y  plan-3  H23  0.020
 W5Y  plan-3  H24  0.020
 W5Y  plan-4  CA   0.020
 W5Y  plan-4  C    0.020
 W5Y  plan-4  O    0.020
 W5Y  plan-4  NAT  0.020
 W5Y  plan-4  SBI  0.020
 W5Y  plan-4  H12  0.020

