# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:15:28 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 5'-O-(glycylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=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
 G5A  G5A  5'-O-(glycylsulfamoyl)adenosine  ligand  44  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G5A
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
 G5A  C     C  C     0   0.576  -2.5053   1.9283   0.1557
 G5A  N     N  NH2   0  -0.782  -1.0878   3.0891   1.7371
 G5A  O     O  O     0  -0.412  -1.6804   1.9303  -0.7234
 G5A  S     S  S     0   1.625  -3.8973  -0.0063  -1.0892
 G5A  N1    N  N     0  -0.474   5.2751   1.3578  -1.2217
 G5A  C2    C  CR16  0   0.046   4.9923   0.0697  -1.3926
 G5A  N3    N  N     0  -0.459   3.9120  -0.5915  -1.0134
 G5A  C4    C  CR56  0   0.490   3.0454   0.2002  -0.3880
 G5A  C5    C  CR56  0  -0.011   3.1969   1.5529  -0.1373
 G5A  C6    C  CR6   0   0.460   4.3912   2.1411  -0.5922
 G5A  N6    N  NH2   0  -0.817   4.6694   3.4339  -0.4212
 G5A  N7    N  N     0  -0.453   2.1034   2.0510   0.5251
 G5A  C8    C  CR15  0   0.125   1.3160   1.0293   0.6728
 G5A  N9    N  NR5   0  -0.549   1.8297  -0.1294   0.1467
 G5A  CA    C  CH2   0  -0.400  -2.4606   2.8412   1.3584
 G5A  C1'   C  CH1   0   0.215   1.2188  -1.4251   0.0844
 G5A  O1S   O  OS    0  -0.631  -5.0169  -0.7843  -0.6228
 G5A  C2'   C  CH1   0  -0.044   0.7131  -1.9648   1.4174
 G5A  O2'   O  OH1   0  -0.651   1.7739  -2.4762   2.1632
 G5A  O2S   O  OS    0  -0.609  -3.9273   0.6492  -2.3657
 G5A  C3'   C  CH1   0  -0.046  -0.2975  -3.0125   0.9339
 G5A  O3'   O  OH1   0  -0.664   0.3502  -4.1828   0.5147
 G5A  N3S   N  NC1   0  -0.831  -3.5945   1.0791   0.1338
 G5A  C4'   C  CH1   0  -0.026  -0.8883  -2.3178  -0.2937
 G5A  O4'   O  O2    0  -0.482   0.0815  -1.3732  -0.7382
 G5A  C5'   C  CH2   0  -0.194  -2.1846  -1.6158   0.0474
 G5A  O5'   O  OC2   0  -0.564  -2.5800  -0.8837  -1.1259
 G5A  HN    H  HNH2  0   0.356  -0.6048   3.5927   1.0051
 G5A  HNA   H  HNH2  0   0.367  -1.0735   3.6866   2.5530
 G5A  HN6   H  HNH2  0   0.411   4.0192   4.0501   0.0335
 G5A  HN6A  H  HNH2  0   0.403   5.5276   3.8201  -0.7744
 G5A  H8    H  HCR5  0   0.287   0.3519   1.0787   1.1575
 G5A  HA    H  HCH2  0   0.263  -3.0412   3.7356   1.0853
 G5A  HAA   H  HCH2  0   0.265  -2.9864   2.3823   2.1969
 G5A  H1'   H  HCH1  0   0.261   1.9814  -2.0972  -0.3250
 G5A  H2'   H  HCH1  0   0.251   0.1762  -1.1762   1.9606
 G5A  HO2'  H  HOH1  0   0.472   1.5079  -2.5357   3.0863
 G5A  HN3S  H  HNC1  0   0.457  -4.2456   1.0586   0.9098
 G5A  H4'   H  HCH1  0   0.279  -1.0759  -3.0465  -1.0884
 G5A  H5'   H  HCH2  0   0.280  -2.9433  -2.3566   0.3062
 G5A  H5'A  H  HCH2  0   0.248  -2.0592  -0.9284   0.8887
 G5A  H16   H  HCH1  0   0.261  -1.0617  -3.2197   1.6947
 G5A  H17   H  HOH1  0   0.452   0.9932  -4.4248   1.1918
 G5A  H2    H  HCR6  0   0.252   5.7490  -0.5089  -1.9117

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
 G5A  C    N3S   single    1.381  0.020  1.381
 G5A  N    CA    single    1.445  0.020  1.445
 G5A  N    HN    single    0.890  0.020  1.040
 G5A  N    HNA   single    0.890  0.020  1.040
 G5A  O    C     double    1.206  0.020  1.206
 G5A  S    O5'   single    1.583  0.020  1.583
 G5A  S    O2S   deloc     1.435  0.020  1.435
 G5A  N1   C2    aromatic  1.330  0.020  1.330
 G5A  C2   H2    single    0.930  0.020  1.080
 G5A  N3   C2    aromatic  1.322  0.020  1.322
 G5A  C4   N3    aromatic  1.330  0.020  1.330
 G5A  C5   C4    aromatic  1.384  0.020  1.384
 G5A  C5   C6    aromatic  1.407  0.020  1.407
 G5A  C6   N1    aromatic  1.338  0.020  1.338
 G5A  N6   C6    single    1.333  0.020  1.333
 G5A  N6   HN6   single    0.860  0.020  1.020
 G5A  N6   HN6A  single    0.860  0.020  1.020
 G5A  N7   C5    aromatic  1.372  0.020  1.372
 G5A  N7   C8    aromatic  1.298  0.020  1.298
 G5A  C8   N9    aromatic  1.372  0.020  1.372
 G5A  C8   H8    single    0.930  0.020  1.080
 G5A  N9   C4    aromatic  1.368  0.020  1.368
 G5A  N9   C1'   single    1.434  0.020  1.434
 G5A  CA   C     single    1.511  0.020  1.511
 G5A  CA   HA    single    0.970  0.020  1.090
 G5A  CA   HAA   single    0.970  0.020  1.090
 G5A  C1'  C2'   single    1.524  0.020  1.524
 G5A  C1'  H1'   single    0.970  0.020  1.090
 G5A  O1S  S     deloc     1.441  0.020  1.441
 G5A  C2'  O2'   single    1.394  0.020  1.394
 G5A  C2'  H2'   single    0.970  0.020  1.090
 G5A  O2'  HO2'  single    0.850  0.020  0.980
 G5A  C3'  C2'   single    1.534  0.020  1.534
 G5A  C3'  O3'   single    1.402  0.020  1.402
 G5A  N3S  S     single    1.663  0.020  1.663
 G5A  N3S  HN3S  single    0.860  0.020  1.020
 G5A  C4'  C3'   single    1.529  0.020  1.529
 G5A  C4'  O4'   single    1.425  0.020  1.425
 G5A  C4'  H4'   single    0.970  0.020  1.090
 G5A  O4'  C1'   single    1.405  0.020  1.405
 G5A  C5'  C4'   single    1.513  0.020  1.513
 G5A  C5'  H5'   single    0.970  0.020  1.090
 G5A  C5'  H5'A  single    0.970  0.020  1.090
 G5A  O5'  C5'   single    1.438  0.020  1.438
 G5A  C3'  H16   single    0.970  0.020  1.090
 G5A  O3'  H17   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
 G5A  N3S   C    CA   114.05  3.000
 G5A  CA    C    O    124.01  3.000
 G5A  N3S   C    O    121.94  3.000
 G5A  HNA   N    HN   106.43  3.000
 G5A  HNA   N    CA   109.03  3.000
 G5A  HN    N    CA   110.45  3.000
 G5A  O5'   S    N3S  103.14  3.000
 G5A  N3S   S    O2S  111.08  3.000
 G5A  O5'   S    O2S  104.47  3.000
 G5A  N3S   S    O1S  104.83  3.000
 G5A  O2S   S    O1S  121.21  3.000
 G5A  O5'   S    O1S  110.78  3.000
 G5A  C6    N1   C2   119.14  3.000
 G5A  H2    C2   N3   116.14  3.000
 G5A  N3    C2   N1   128.41  3.000
 G5A  H2    C2   N1   115.45  3.000
 G5A  C4    N3   C2   111.69  3.000
 G5A  N9    C4   C5   105.18  3.000
 G5A  N9    C4   N3   128.26  3.000
 G5A  C5    C4   N3   126.55  3.000
 G5A  N7    C5   C6   132.91  3.000
 G5A  N7    C5   C4   110.79  3.000
 G5A  C6    C5   C4   116.30  3.000
 G5A  N6    C6   C5   122.75  3.000
 G5A  N6    C6   N1   119.34  3.000
 G5A  C5    C6   N1   117.91  3.000
 G5A  HN6A  N6   HN6  118.42  3.000
 G5A  HN6A  N6   C6   120.37  3.000
 G5A  HN6   N6   C6   121.18  3.000
 G5A  C8    N7   C5   104.63  3.000
 G5A  H8    C8   N9   123.00  3.000
 G5A  H8    C8   N7   123.80  3.000
 G5A  N9    C8   N7   113.19  3.000
 G5A  C1'   N9   C8   128.33  3.000
 G5A  C1'   N9   C4   125.39  3.000
 G5A  C8    N9   C4   106.20  3.000
 G5A  HAA   CA   HA   106.15  3.000
 G5A  HAA   CA   N    109.18  3.000
 G5A  HA    CA   N    115.26  3.000
 G5A  HAA   CA   C    110.09  3.000
 G5A  HA    CA   C    106.13  3.000
 G5A  N     CA   C    109.90  3.000
 G5A  H1'   C1'  O4'  111.55  3.000
 G5A  O4'   C1'  C2'  104.87  3.000
 G5A  H1'   C1'  C2'  109.90  3.000
 G5A  O4'   C1'  N9   109.69  3.000
 G5A  H1'   C1'  N9   105.91  3.000
 G5A  C2'   C1'  N9   115.04  3.000
 G5A  H2'   C2'  C3'  108.93  3.000
 G5A  C3'   C2'  O2'  114.80  3.000
 G5A  H2'   C2'  O2'  111.78  3.000
 G5A  C3'   C2'  C1'  100.64  3.000
 G5A  H2'   C2'  C1'  109.91  3.000
 G5A  O2'   C2'  C1'  110.20  3.000
 G5A  HO2'  O2'  C2'  109.00  3.000
 G5A  H16   C3'  C4'  111.90  3.000
 G5A  H16   C3'  O3'  111.79  3.000
 G5A  C4'   C3'  O3'  108.53  3.000
 G5A  H16   C3'  C2'  111.65  3.000
 G5A  C4'   C3'  C2'  101.38  3.000
 G5A  O3'   C3'  C2'  111.11  3.000
 G5A  H17   O3'  C3'  107.91  3.000
 G5A  HN3S  N3S  S    115.66  3.000
 G5A  HN3S  N3S  C    120.47  3.000
 G5A  S     N3S  C    123.81  3.000
 G5A  H4'   C4'  C5'  109.01  3.000
 G5A  C5'   C4'  O4'  110.24  3.000
 G5A  H4'   C4'  O4'  109.36  3.000
 G5A  C5'   C4'  C3'  111.15  3.000
 G5A  H4'   C4'  C3'  110.28  3.000
 G5A  O4'   C4'  C3'  106.77  3.000
 G5A  C4'   O4'  C1'  110.12  3.000
 G5A  H5'A  C5'  H5'  108.90  3.000
 G5A  H5'A  C5'  O5'  109.82  3.000
 G5A  H5'   C5'  O5'  110.35  3.000
 G5A  O5'   C5'  C4'  106.72  3.000
 G5A  H5'A  C5'  C4'  111.52  3.000
 G5A  H5'   C5'  C4'  109.52  3.000
 G5A  C5'   O5'  S    119.46  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
 G5A  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 G5A  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 G5A  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 G5A  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 G5A  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 G5A  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 G5A  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 G5A  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 G5A  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 G5A  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 G5A  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 G5A  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 G5A  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 G5A  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 G5A  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 G5A  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 G5A  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 G5A  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 G5A  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 G5A  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 G5A  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 G5A  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 G5A  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 G5A  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 G5A  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 G5A  CONST_26  HN6   N6   C6   N1   180.00   0.0  0
 G5A  CONST_27  HN6A  N6   C6   N1     0.00   0.0  0
 G5A  CONST_28  S     N3S  C    O      0.00   0.0  0
 G5A  CONST_29  CA    C    N3S  S    180.00   0.0  0
 G5A  CONST_30  HN3S  N3S  C    O    180.00   0.0  0
 G5A  Var_01    C4'   C5'  O5'  S   -178.73  30.0  3
 G5A  Var_02    O5'   S    N3S  C     56.93  30.0  3
 G5A  Var_03    N3S   C    CA   N    146.95  30.0  3
 G5A  Var_04    HN    N    CA   C     64.45  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
 G5A  chir_01  C1'  N9   C2'  O4'  negativ
 G5A  chir_02  C2'  O2'  C3'  C1'  positiv
 G5A  chir_03  C3'  O3'  C4'  C2'  positiv
 G5A  chir_04  C4'  O4'  C3'  C5'  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
 G5A  plan-1  N1    0.020
 G5A  plan-1  C2    0.020
 G5A  plan-1  N3    0.020
 G5A  plan-1  C4    0.020
 G5A  plan-1  C5    0.020
 G5A  plan-1  C6    0.020
 G5A  plan-1  N6    0.020
 G5A  plan-1  N7    0.020
 G5A  plan-1  C8    0.020
 G5A  plan-1  N9    0.020
 G5A  plan-1  C1'   0.020
 G5A  plan-1  H8    0.020
 G5A  plan-1  H2    0.020
 G5A  plan-2  C6    0.020
 G5A  plan-2  N6    0.020
 G5A  plan-2  HN6   0.020
 G5A  plan-2  HN6A  0.020
 G5A  plan-3  C     0.020
 G5A  plan-3  O     0.020
 G5A  plan-3  S     0.020
 G5A  plan-3  CA    0.020
 G5A  plan-3  N3S   0.020
 G5A  plan-3  HN3S  0.020

