# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 13 04:16:06 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 5'-O-{[(2S)-4-amino-2-ammonio-4-oxobutanoyl]sulfamoyl}adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)C[C@H]([NH3+])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
 NSS  NSS  5'-O-{[(2S)-4-amino-2-ammonio-4-oxobutanoyl]sulfamoyl}adenosine  ligand  52  31  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NSS
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
 NSS  OAX   O  OS    0  -0.614  -3.0723   3.4694   0.2639
 NSS  SBE   S  S     0   1.620  -2.8162   4.1014   1.5324
 NSS  OAY   O  OS    0  -0.617  -2.3660   5.4680   1.5782
 NSS  NAT   N  NC1   0  -0.811  -4.1701   4.0368   2.4907
 NSS  C     C  C     0   0.628  -4.9034   2.8976   2.6938
 NSS  O     O  O     0  -0.382  -4.6805   1.8456   2.1565
 NSS  CA    C  CH1   0  -0.241  -6.1327   3.0834   3.5861
 NSS  N     N  NT3   1  -0.784  -7.3244   3.0069   2.6976
 NSS  CB    C  CH2   0  -0.594  -6.2223   1.9895   4.6331
 NSS  CG    C  C     0   0.561  -5.0035   2.0385   5.5307
 NSS  OD1   O  O     0  -0.475  -4.0585   2.7633   5.2527
 NSS  ND2   N  NH2   0  -0.805  -5.0516   1.2448   6.6014
 NSS  O5'   O  OC2   0  -0.562  -1.8707   3.1818   2.4092
 NSS  C5'   C  CH2   0  -0.195  -0.6440   2.6965   1.8277
 NSS  C4'   C  CH1   0  -0.039  -0.1947   1.5240   2.6759
 NSS  C3'   C  CH1   0  -0.055   1.0326   0.8545   2.0646
 NSS  O3'   O  OH1   0  -0.669   1.7765   0.2422   3.0878
 NSS  C2'   C  CH1   0  -0.034   0.3722  -0.1973   1.1650
 NSS  O2'   O  OH1   0  -0.646   1.1790  -1.2529   0.7592
 NSS  C1'   C  CH1   0   0.191  -0.8290  -0.6151   2.0249
 NSS  O4'   O  O2    0  -0.477  -1.2138   0.5305   2.7314
 NSS  N9    N  NR5   0  -0.539  -1.9512  -1.1033   1.2641
 NSS  C4    C  CR56  0   0.489  -2.3488  -2.4059   1.1633
 NSS  N3    N  N     0  -0.457  -1.8273  -3.4770   1.7565
 NSS  C2    C  CR16  0   0.045  -2.4818  -4.5797   1.4363
 NSS  N1    N  N     0  -0.475  -3.5326  -4.7139   0.6315
 NSS  C6    C  CR6   0   0.458  -4.0441  -3.6277   0.0409
 NSS  N6    N  NH2   0  -0.817  -5.0975  -3.7582  -0.7663
 NSS  C5    C  CR56  0  -0.011  -3.4370  -2.3865   0.3055
 NSS  N7    N  N     0  -0.453  -3.7082  -1.1080  -0.1089
 NSS  C8    C  CR15  0   0.125  -2.8078  -0.3784   0.4789
 NSS  HAT   H  HNC1  0   0.462  -4.3379   4.8582   3.0613
 NSS  HA    H  HCH1  0   0.355  -6.1626   4.0697   4.0469
 NSS  HN1   H  HNT3  0   0.491  -8.1896   3.0782   3.2364
 NSS  HN2   H  HNT3  0   0.478  -7.3699   2.1267   2.1794
 NSS  HN3   H  HNT3  0   0.489  -7.3497   3.7660   2.0149
 NSS  HB1   H  HCH2  0   0.312  -6.2852   1.0060   4.1589
 NSS  HB2   H  HCH2  0   0.321  -7.1336   2.1139   5.2225
 NSS  HD21  H  HNH2  0   0.416  -5.8422   0.6528   6.7917
 NSS  HD22  H  HNH2  0   0.409  -4.2632   1.1819   7.2251
 NSS  H5'1  H  HCH2  0   0.259  -0.8055   2.3995   0.7886
 NSS  H5'2  H  HCH2  0   0.283   0.1082   3.4865   1.8534
 NSS  H4'   H  HCH1  0   0.284   0.0152   1.8714   3.6910
 NSS  H3'   H  HCH1  0   0.277   1.6401   1.5610   1.4892
 NSS  H2    H  HOH1  0   0.467   2.6802   0.1150   2.7836
 NSS  H2'   H  HCH1  0   0.268   0.0128   0.2880   0.2513
 NSS  H1    H  HOH1  0   0.449   1.5629  -1.6707   1.5390
 NSS  H1'   H  HCH1  0   0.263  -0.5502  -1.4285   2.7053
 NSS  H3    H  HCR6  0   0.251  -2.1188  -5.4982   1.8850
 NSS  HN61  H  HNH2  0   0.404  -5.5191  -4.6595  -0.9102
 NSS  HN62  H  HNH2  0   0.411  -5.5062  -2.9614  -1.2217
 NSS  H8    H  HCR5  0   0.283  -2.7377   0.6947   0.3953

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
 NSS  OAX  SBE   deloc     1.440  0.020  1.440
 NSS  SBE  OAY   deloc     1.440  0.020  1.440
 NSS  SBE  NAT   single    1.660  0.020  1.660
 NSS  SBE  O5'   single    1.584  0.020  1.584
 NSS  NAT  C     single    1.370  0.020  1.370
 NSS  NAT  HAT   single    0.860  0.020  1.020
 NSS  C    O     double    1.202  0.020  1.202
 NSS  C    CA    single    1.530  0.020  1.530
 NSS  CA   N     single    1.488  0.020  1.488
 NSS  CA   CB    single    1.517  0.020  1.517
 NSS  CA   HA    single    0.970  0.020  1.090
 NSS  N    HN1   single    0.890  0.020  1.040
 NSS  N    HN2   single    0.890  0.020  1.040
 NSS  N    HN3   single    0.890  0.020  1.040
 NSS  CB   CG    single    1.514  0.020  1.514
 NSS  CB   HB1   single    0.970  0.020  1.090
 NSS  CB   HB2   single    0.970  0.020  1.090
 NSS  CG   OD1   double    1.223  0.020  1.223
 NSS  CG   ND2   single    1.334  0.020  1.334
 NSS  ND2  HD21  single    0.860  0.020  1.020
 NSS  ND2  HD22  single    0.860  0.020  1.020
 NSS  O5'  C5'   single    1.442  0.020  1.442
 NSS  C5'  C4'   single    1.515  0.020  1.515
 NSS  C5'  H5'1  single    0.970  0.020  1.090
 NSS  C5'  H5'2  single    0.970  0.020  1.090
 NSS  C4'  C3'   single    1.526  0.020  1.526
 NSS  C4'  O4'   single    1.424  0.020  1.424
 NSS  C4'  H4'   single    0.970  0.020  1.090
 NSS  C3'  O3'   single    1.405  0.020  1.405
 NSS  C3'  C2'   single    1.534  0.020  1.534
 NSS  C3'  H3'   single    0.970  0.020  1.090
 NSS  O3'  H2    single    0.850  0.020  0.980
 NSS  C2'  O2'   single    1.389  0.020  1.389
 NSS  C2'  C1'   single    1.535  0.020  1.535
 NSS  C2'  H2'   single    0.970  0.020  1.090
 NSS  O2'  H1    single    0.850  0.020  0.980
 NSS  C1'  O4'   single    1.400  0.020  1.400
 NSS  C1'  N9    single    1.441  0.020  1.441
 NSS  C1'  H1'   single    0.970  0.020  1.090
 NSS  N9   C4    aromatic  1.366  0.020  1.366
 NSS  N9   C8    aromatic  1.370  0.020  1.370
 NSS  C4   N3    aromatic  1.331  0.020  1.331
 NSS  C4   C5    aromatic  1.386  0.020  1.386
 NSS  N3   C2    aromatic  1.322  0.020  1.322
 NSS  C2   N1    aromatic  1.330  0.020  1.330
 NSS  C2   H3    single    0.930  0.020  1.080
 NSS  N1   C6    aromatic  1.338  0.020  1.338
 NSS  C6   N6    single    1.334  0.020  1.334
 NSS  C6   C5    aromatic  1.407  0.020  1.407
 NSS  N6   HN61  single    0.860  0.020  1.020
 NSS  N6   HN62  single    0.860  0.020  1.020
 NSS  C5   N7    aromatic  1.371  0.020  1.371
 NSS  N7   C8    aromatic  1.299  0.020  1.299
 NSS  C8   H8    single    0.930  0.020  1.080

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
 NSS  O5'   SBE  NAT    98.32  3.000
 NSS  O5'   SBE  OAY   110.30  3.000
 NSS  NAT   SBE  OAY   105.88  3.000
 NSS  O5'   SBE  OAX   109.81  3.000
 NSS  NAT   SBE  OAX   110.26  3.000
 NSS  OAY   SBE  OAX   120.01  3.000
 NSS  HAT   NAT  C     120.11  3.000
 NSS  HAT   NAT  SBE   115.35  3.000
 NSS  C     NAT  SBE   123.68  3.000
 NSS  CA    C    O     121.05  3.000
 NSS  CA    C    NAT   114.55  3.000
 NSS  O     C    NAT   124.21  3.000
 NSS  HA    CA   CB    111.07  3.000
 NSS  HA    CA   N     106.09  3.000
 NSS  CB    CA   N     109.12  3.000
 NSS  HA    CA   C     112.25  3.000
 NSS  CB    CA   C     111.25  3.000
 NSS  N     CA   C     106.79  3.000
 NSS  HN3   N    HN2   107.46  3.000
 NSS  HN3   N    HN1   106.24  3.000
 NSS  HN2   N    HN1   106.84  3.000
 NSS  HN3   N    CA    112.37  3.000
 NSS  HN2   N    CA    112.48  3.000
 NSS  HN1   N    CA    111.08  3.000
 NSS  HB2   CB   HB1   106.76  3.000
 NSS  HB2   CB   CG    110.36  3.000
 NSS  HB1   CB   CG    109.41  3.000
 NSS  HB2   CB   CA    109.85  3.000
 NSS  HB1   CB   CA    110.65  3.000
 NSS  CG    CB   CA    109.76  3.000
 NSS  ND2   CG   OD1   124.27  3.000
 NSS  ND2   CG   CB    115.31  3.000
 NSS  OD1   CG   CB    120.42  3.000
 NSS  HD22  ND2  HD21  117.47  3.000
 NSS  HD22  ND2  CG    120.40  3.000
 NSS  HD21  ND2  CG    122.04  3.000
 NSS  C5'   O5'  SBE   118.69  3.000
 NSS  H5'2  C5'  H5'1  108.73  3.000
 NSS  H5'2  C5'  C4'   110.04  3.000
 NSS  H5'1  C5'  C4'   111.45  3.000
 NSS  H5'2  C5'  O5'   109.48  3.000
 NSS  H5'1  C5'  O5'   110.45  3.000
 NSS  C4'   C5'  O5'   106.68  3.000
 NSS  H4'   C4'  O4'   108.84  3.000
 NSS  H4'   C4'  C3'   110.92  3.000
 NSS  O4'   C4'  C3'   106.56  3.000
 NSS  H4'   C4'  C5'   109.32  3.000
 NSS  O4'   C4'  C5'   110.45  3.000
 NSS  C3'   C4'  C5'   110.72  3.000
 NSS  H3'   C3'  C2'   111.91  3.000
 NSS  H3'   C3'  O3'   111.71  3.000
 NSS  C2'   C3'  O3'   110.87  3.000
 NSS  H3'   C3'  C4'   111.94  3.000
 NSS  C2'   C3'  C4'   100.93  3.000
 NSS  O3'   C3'  C4'   108.98  3.000
 NSS  H2    O3'  C3'   108.95  3.000
 NSS  H2'   C2'  C1'   109.34  3.000
 NSS  H2'   C2'  O2'   106.47  3.000
 NSS  C1'   C2'  O2'   114.28  3.000
 NSS  H2'   C2'  C3'   109.08  3.000
 NSS  C1'   C2'  C3'   101.25  3.000
 NSS  O2'   C2'  C3'   116.26  3.000
 NSS  H1    O2'  C2'   108.92  3.000
 NSS  H1'   C1'  N9    105.92  3.000
 NSS  H1'   C1'  O4'   111.33  3.000
 NSS  N9    C1'  O4'   109.24  3.000
 NSS  H1'   C1'  C2'   110.52  3.000
 NSS  N9    C1'  C2'   113.95  3.000
 NSS  O4'   C1'  C2'   105.96  3.000
 NSS  C1'   O4'  C4'   110.76  3.000
 NSS  C8    N9   C4    106.28  3.000
 NSS  C8    N9   C1'   127.62  3.000
 NSS  C4    N9   C1'   126.07  3.000
 NSS  C5    C4   N3    126.50  3.000
 NSS  C5    C4   N9    105.13  3.000
 NSS  N3    C4   N9    128.36  3.000
 NSS  C2    N3   C4    111.68  3.000
 NSS  H3    C2   N1    115.41  3.000
 NSS  H3    C2   N3    116.14  3.000
 NSS  N1    C2   N3    128.45  3.000
 NSS  C6    N1   C2    119.15  3.000
 NSS  C5    C6   N6    122.76  3.000
 NSS  C5    C6   N1    117.92  3.000
 NSS  N6    C6   N1    119.32  3.000
 NSS  HN62  N6   HN61  118.40  3.000
 NSS  HN62  N6   C6    121.20  3.000
 NSS  HN61  N6   C6    120.37  3.000
 NSS  N7    C5   C6    132.88  3.000
 NSS  N7    C5   C4    110.82  3.000
 NSS  C6    C5   C4    116.30  3.000
 NSS  C8    N7   C5    104.47  3.000
 NSS  H8    C8   N7    124.65  3.000
 NSS  H8    C8   N9    122.03  3.000
 NSS  N7    C8   N9    113.30  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
 NSS  CONST_01  C2    N3   C4   N9    180.00   0.0  0
 NSS  CONST_02  C6    C5   C4   N9    180.00   0.0  0
 NSS  CONST_03  N7    C5   C4   N9      0.00   0.0  0
 NSS  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 NSS  CONST_05  N7    C8   N9   C4      0.00   0.0  0
 NSS  CONST_06  N1    C2   N3   C4      0.00   0.0  0
 NSS  CONST_07  N1    C6   C5   C4      0.00   0.0  0
 NSS  CONST_08  C8    N7   C5   C4      0.00   0.0  0
 NSS  CONST_09  C8    N9   C4   N3    180.00   0.0  0
 NSS  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 NSS  CONST_11  N7    C5   C4   N3    180.00   0.0  0
 NSS  CONST_12  C6    N1   C2   N3      0.00   0.0  0
 NSS  CONST_13  C5    C4   N3   C2      0.00   0.0  0
 NSS  CONST_14  C5    C6   N1   C2      0.00   0.0  0
 NSS  CONST_15  N7    C5   C6   N1    180.00   0.0  0
 NSS  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 NSS  CONST_17  C8    N9   C4   C5      0.00   0.0  0
 NSS  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 NSS  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 NSS  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 NSS  CONST_21  N6    C6   C5   C4    180.00   0.0  0
 NSS  CONST_22  N6    C6   N1   C2    180.00   0.0  0
 NSS  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 NSS  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 NSS  CONST_25  H3    C2   N3   C4    180.00   0.0  0
 NSS  CONST_26  HN61  N6   C6   N1      0.00   0.0  0
 NSS  CONST_27  HN62  N6   C6   N1    180.00   0.0  0
 NSS  CONST_28  O     C    NAT  SBE     0.00   0.0  0
 NSS  CONST_29  CA    C    NAT  SBE   180.00   0.0  0
 NSS  CONST_30  HAT   NAT  C    O     180.00   0.0  0
 NSS  CONST_31  HD21  ND2  CG   CB      0.00   0.0  0
 NSS  CONST_32  HD22  ND2  CG   CB    180.00   0.0  0
 NSS  Var_01    C4'   C5'  O5'  SBE  -161.83  30.0  3
 NSS  Var_02    C     NAT  SBE  OAX    48.07  30.0  3
 NSS  Var_03    OD1   CG   CB   CA     -9.15  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
 NSS  chir_01  CA   C    N    CB   negativ
 NSS  chir_02  C4'  O4'  C5'  C3'  positiv
 NSS  chir_03  C3'  O3'  C4'  C2'  positiv
 NSS  chir_04  C2'  O2'  C3'  C1'  positiv
 NSS  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
 NSS  plan-1  C1'   0.020
 NSS  plan-1  N9    0.020
 NSS  plan-1  C4    0.020
 NSS  plan-1  N3    0.020
 NSS  plan-1  C2    0.020
 NSS  plan-1  N1    0.020
 NSS  plan-1  C6    0.020
 NSS  plan-1  N6    0.020
 NSS  plan-1  C5    0.020
 NSS  plan-1  N7    0.020
 NSS  plan-1  C8    0.020
 NSS  plan-1  H3    0.020
 NSS  plan-1  H8    0.020
 NSS  plan-2  CB    0.020
 NSS  plan-2  CG    0.020
 NSS  plan-2  OD1   0.020
 NSS  plan-2  ND2   0.020
 NSS  plan-2  HD21  0.020
 NSS  plan-2  HD22  0.020
 NSS  plan-3  C6    0.020
 NSS  plan-3  N6    0.020
 NSS  plan-3  HN61  0.020
 NSS  plan-3  HN62  0.020
 NSS  plan-4  SBE   0.020
 NSS  plan-4  NAT   0.020
 NSS  plan-4  C     0.020
 NSS  plan-4  O     0.020
 NSS  plan-4  CA    0.020
 NSS  plan-4  HAT   0.020

