# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun  3 06:25:05 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 5'-O-(L-cysteinylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CS)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
 5CA  5CA  5'-O-(L-cysteinylsulfamoyl)adenosine  ligand  48  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5CA
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
 5CA  N     N  NH2   0  -0.778  -1.6451   2.2210   1.1450
 5CA  CA    C  CH1   0  -0.208  -2.9049   1.8712   0.5269
 5CA  CB    C  CH2   0  -0.586  -3.5993   2.9815  -0.2680
 5CA  SG    S  S2    0  -0.226  -4.0220   4.4130   0.7655
 5CA  C     C  C     0   0.612  -2.6326   0.7042  -0.4107
 5CA  O     O  O     0  -0.414  -1.9094   0.7856  -1.3728
 5CA  N3S   N  NC1   0  -0.837  -3.2687  -0.4662  -0.0630
 5CA  S     S  S     0   1.630  -3.2208  -1.8601  -0.9744
 5CA  O1S   O  OS    0  -0.629  -4.0062  -2.8116  -0.2305
 5CA  O2S   O  OS    0  -0.607  -3.5009  -1.5705  -2.3516
 5CA  O5'   O  OC2   0  -0.565  -1.6900  -2.2594  -0.9552
 5CA  C5'   C  CH2   0  -0.194  -1.0803  -2.6577   0.2878
 5CA  C4'   C  CH1   0  -0.039   0.3424  -3.0564  -0.0410
 5CA  O4'   O  O2    0  -0.484   1.0370  -1.9736  -0.6525
 5CA  C3'   C  CH1   0  -0.039   1.1274  -3.4154   1.2174
 5CA  O3'   O  OH1   0  -0.663   2.1073  -4.3546   0.8675
 5CA  C2'   C  CH1   0  -0.048   1.7594  -2.0638   1.5649
 5CA  O2'   O  OH1   0  -0.651   2.9225  -2.1364   2.3295
 5CA  C1'   C  CH1   0   0.210   2.0853  -1.5311   0.1711
 5CA  N9    N  NR5   0  -0.543   2.1826  -0.1006   0.0919
 5CA  C8    C  CR15  0   0.124   1.2235   0.8164   0.4309
 5CA  N7    N  N     0  -0.457   1.5789   2.0430   0.1969
 5CA  C5    C  CR56  0  -0.006   2.8421   1.9401  -0.3298
 5CA  C6    C  CR6   0   0.461   3.7716   2.8942  -0.7826
 5CA  N6    N  NH2   0  -0.816   3.5254   4.2049  -0.7692
 5CA  N1    N  N     0  -0.474   4.9434   2.4516  -1.2532
 5CA  C2    C  CR16  0   0.047   5.1808   1.1432  -1.2748
 5CA  N3    N  N     0  -0.457   4.3938   0.1585  -0.8760
 5CA  C4    C  CR56  0   0.490   3.2348   0.6143  -0.4098
 5CA  H     H  HNH2  0   0.360  -1.0263   2.6836   0.4891
 5CA  HN2   H  HNH2  0   0.365  -1.8049   2.8628   1.9108
 5CA  HA    H  HCH1  0   0.283  -3.5827   1.5530   1.3219
 5CA  HB1   H  HCH2  0   0.289  -2.9861   3.3085  -1.1080
 5CA  HB2   H  HCH2  0   0.294  -4.5475   2.6244  -0.6735
 5CA  HG    H  HSH1  0   0.224  -2.7973   4.9434   0.8514
 5CA  H3S   H  HNC1  0   0.459  -3.8449  -0.5076   0.7697
 5CA  H5'1  H  HCH2  0   0.251  -1.1210  -1.8282   1.0002
 5CA  H5'2  H  HCH2  0   0.281  -1.6100  -3.5124   0.7115
 5CA  H4'   H  HCH1  0   0.283   0.3198  -3.9032  -0.7337
 5CA  H3'   H  HCH1  0   0.263   0.4773  -3.7850   2.0214
 5CA  H3T   H  HOH1  0   0.453   2.7813  -4.3550   1.5573
 5CA  H2'   H  HCH1  0   0.252   1.0016  -1.4269   2.0402
 5CA  HO'2  H  HOH1  0   0.471   2.6825  -2.1787   3.2606
 5CA  H1'   H  HCH1  0   0.266   3.0512  -1.9224  -0.1659
 5CA  H8    H  HCR5  0   0.285   0.2709   0.5307   0.8516
 5CA  H61   H  HNH2  0   0.411   2.6817   4.5687  -0.3626
 5CA  H62   H  HNH2  0   0.404   4.2404   4.8568  -1.0429
 5CA  H2    H  HCR6  0   0.253   6.1475   0.8512  -1.6707

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
 5CA  N    CA    single    1.446  0.020  1.446
 5CA  N    H     single    0.860  0.020  1.020
 5CA  N    HN2   single    0.890  0.020  1.040
 5CA  CA   CB    single    1.532  0.020  1.532
 5CA  CA   C     single    1.522  0.020  1.522
 5CA  CA   HA    single    0.970  0.020  1.090
 5CA  CB   SG    single    1.815  0.020  1.815
 5CA  CB   HB1   single    0.970  0.020  1.090
 5CA  CB   HB2   single    0.970  0.020  1.090
 5CA  SG   HG    single    1.200  0.020  1.300
 5CA  C    O     double    1.206  0.020  1.206
 5CA  C    N3S   single    1.377  0.020  1.377
 5CA  N3S  S     single    1.666  0.020  1.666
 5CA  N3S  H3S   single    0.860  0.020  1.020
 5CA  S    O1S   deloc     1.441  0.020  1.441
 5CA  S    O2S   deloc     1.435  0.020  1.435
 5CA  S    O5'   single    1.582  0.020  1.582
 5CA  O5'  C5'   single    1.441  0.020  1.441
 5CA  C5'  C4'   single    1.514  0.020  1.514
 5CA  C5'  H5'1  single    0.970  0.020  1.090
 5CA  C5'  H5'2  single    0.970  0.020  1.090
 5CA  C4'  O4'   single    1.424  0.020  1.424
 5CA  C4'  C3'   single    1.526  0.020  1.526
 5CA  C4'  H4'   single    0.970  0.020  1.090
 5CA  O4'  C1'   single    1.405  0.020  1.405
 5CA  C3'  O3'   single    1.402  0.020  1.402
 5CA  C3'  C2'   single    1.532  0.020  1.532
 5CA  C3'  H3'   single    0.970  0.020  1.090
 5CA  O3'  H3T   single    0.850  0.020  0.980
 5CA  C2'  O2'   single    1.394  0.020  1.394
 5CA  C2'  C1'   single    1.527  0.020  1.527
 5CA  C2'  H2'   single    0.970  0.020  1.090
 5CA  O2'  HO'2  single    0.850  0.020  0.980
 5CA  C1'  N9    single    1.436  0.020  1.436
 5CA  C1'  H1'   single    0.970  0.020  1.090
 5CA  N9   C8    aromatic  1.370  0.020  1.370
 5CA  N9   C4    aromatic  1.367  0.020  1.367
 5CA  C8   N7    aromatic  1.298  0.020  1.298
 5CA  C8   H8    single    0.930  0.020  1.080
 5CA  N7   C5    aromatic  1.372  0.020  1.372
 5CA  C5   C6    aromatic  1.407  0.020  1.407
 5CA  C5   C4    aromatic  1.385  0.020  1.385
 5CA  C6   N6    single    1.334  0.020  1.334
 5CA  C6   N1    aromatic  1.338  0.020  1.338
 5CA  N6   H61   single    0.860  0.020  1.020
 5CA  N6   H62   single    0.860  0.020  1.020
 5CA  N1   C2    aromatic  1.330  0.020  1.330
 5CA  C2   N3    aromatic  1.322  0.020  1.322
 5CA  C2   H2    single    0.930  0.020  1.080
 5CA  N3   C4    aromatic  1.330  0.020  1.330

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
 5CA  HN2   N    H     107.26  3.000
 5CA  HN2   N    CA    109.84  3.000
 5CA  H     N    CA    111.45  3.000
 5CA  HA    CA   C     109.64  3.000
 5CA  HA    CA   CB    107.91  3.000
 5CA  C     CA   CB    108.50  3.000
 5CA  HA    CA   N     107.46  3.000
 5CA  C     CA   N     107.04  3.000
 5CA  CB    CA   N     116.19  3.000
 5CA  HB2   CB   HB1   107.49  3.000
 5CA  HB2   CB   SG    105.50  3.000
 5CA  HB1   CB   SG    109.46  3.000
 5CA  HB2   CB   CA    110.45  3.000
 5CA  HB1   CB   CA    111.24  3.000
 5CA  SG    CB   CA    112.44  3.000
 5CA  HG    SG   CB     97.82  3.000
 5CA  N3S   C    O     122.40  3.000
 5CA  N3S   C    CA    114.44  3.000
 5CA  O     C    CA    123.16  3.000
 5CA  H3S   N3S  S     115.57  3.000
 5CA  H3S   N3S  C     120.33  3.000
 5CA  S     N3S  C     124.04  3.000
 5CA  O5'   S    O2S   104.56  3.000
 5CA  O5'   S    O1S   110.77  3.000
 5CA  O2S   S    O1S   121.50  3.000
 5CA  O5'   S    N3S   103.43  3.000
 5CA  O2S   S    N3S   110.52  3.000
 5CA  O1S   S    N3S   104.74  3.000
 5CA  C5'   O5'  S     119.32  3.000
 5CA  H5'2  C5'  H5'1  108.84  3.000
 5CA  H5'2  C5'  C4'   109.53  3.000
 5CA  H5'1  C5'  C4'   112.09  3.000
 5CA  H5'2  C5'  O5'   110.25  3.000
 5CA  H5'1  C5'  O5'   109.66  3.000
 5CA  C4'   C5'  O5'   106.45  3.000
 5CA  H4'   C4'  C3'   110.53  3.000
 5CA  H4'   C4'  O4'   109.07  3.000
 5CA  C3'   C4'  O4'   106.38  3.000
 5CA  H4'   C4'  C5'   108.78  3.000
 5CA  C3'   C4'  C5'   111.49  3.000
 5CA  O4'   C4'  C5'   110.57  3.000
 5CA  C1'   O4'  C4'   110.59  3.000
 5CA  H3'   C3'  C2'   112.03  3.000
 5CA  H3'   C3'  O3'   111.79  3.000
 5CA  C2'   C3'  O3'   111.06  3.000
 5CA  H3'   C3'  C4'   112.24  3.000
 5CA  C2'   C3'  C4'   101.05  3.000
 5CA  O3'   C3'  C4'   108.14  3.000
 5CA  H3T   O3'  C3'   108.08  3.000
 5CA  H2'   C2'  C1'   109.87  3.000
 5CA  H2'   C2'  O2'   111.63  3.000
 5CA  C1'   C2'  O2'   109.92  3.000
 5CA  H2'   C2'  C3'   108.98  3.000
 5CA  C1'   C2'  C3'   100.88  3.000
 5CA  O2'   C2'  C3'   115.01  3.000
 5CA  HO'2  O2'  C2'   108.96  3.000
 5CA  H1'   C1'  N9    106.21  3.000
 5CA  H1'   C1'  C2'   110.14  3.000
 5CA  N9    C1'  C2'   114.35  3.000
 5CA  H1'   C1'  O4'   111.42  3.000
 5CA  N9    C1'  O4'   109.39  3.000
 5CA  C2'   C1'  O4'   105.42  3.000
 5CA  C4    N9   C8    106.24  3.000
 5CA  C4    N9   C1'   126.38  3.000
 5CA  C8    N9   C1'   127.29  3.000
 5CA  H8    C8   N7    124.17  3.000
 5CA  H8    C8   N9    122.49  3.000
 5CA  N7    C8   N9    113.35  3.000
 5CA  C5    N7   C8    104.50  3.000
 5CA  C4    C5   C6    116.31  3.000
 5CA  C4    C5   N7    110.79  3.000
 5CA  C6    C5   N7    132.91  3.000
 5CA  N1    C6   N6    119.36  3.000
 5CA  N1    C6   C5    117.87  3.000
 5CA  N6    C6   C5    122.77  3.000
 5CA  H62   N6   H61   118.20  3.000
 5CA  H62   N6   C6    120.21  3.000
 5CA  H61   N6   C6    120.99  3.000
 5CA  C2    N1   C6    119.18  3.000
 5CA  H2    C2   N3    116.11  3.000
 5CA  H2    C2   N1    115.46  3.000
 5CA  N3    C2   N1    128.43  3.000
 5CA  C4    N3   C2    111.67  3.000
 5CA  N3    C4   C5    126.55  3.000
 5CA  N3    C4   N9    128.32  3.000
 5CA  C5    C4   N9    105.13  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
 5CA  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 5CA  CONST_02  N7   C5   C4   N9     0.00   0.0  0
 5CA  CONST_03  C6   C5   C4   N9   180.00   0.0  0
 5CA  CONST_04  C2   N3   C4   N9   180.00   0.0  0
 5CA  CONST_05  C5   C4   N9   C8     0.00   0.0  0
 5CA  CONST_06  N3   C4   N9   C8   180.00   0.0  0
 5CA  CONST_07  C6   C5   N7   C8   180.00   0.0  0
 5CA  CONST_08  C4   C5   N7   C8     0.00   0.0  0
 5CA  CONST_09  C4   N9   C8   N7     0.00   0.0  0
 5CA  CONST_10  N1   C6   C5   N7   180.00   0.0  0
 5CA  CONST_11  N3   C4   C5   N7   180.00   0.0  0
 5CA  CONST_12  C2   N1   C6   C5     0.00   0.0  0
 5CA  CONST_13  C2   N3   C4   C5     0.00   0.0  0
 5CA  CONST_14  N3   C4   C5   C6     0.00   0.0  0
 5CA  CONST_15  N3   C2   N1   C6     0.00   0.0  0
 5CA  CONST_16  C4   C5   C6   N1     0.00   0.0  0
 5CA  CONST_17  C4   N3   C2   N1     0.00   0.0  0
 5CA  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 5CA  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 5CA  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 5CA  CONST_21  N6   C6   C5   N7     0.00   0.0  0
 5CA  CONST_22  C4   C5   C6   N6   180.00   0.0  0
 5CA  CONST_23  C2   N1   C6   N6   180.00   0.0  0
 5CA  CONST_24  H8   C8   N9   C1'    0.00   0.0  0
 5CA  CONST_25  H2   C2   N1   C6   180.00   0.0  0
 5CA  CONST_26  H61  N6   C6   C5     0.00   0.0  0
 5CA  CONST_27  H62  N6   C6   C5   180.00   0.0  0
 5CA  CONST_28  S    N3S  C    CA   180.00   0.0  0
 5CA  CONST_29  S    N3S  C    O      0.00   0.0  0
 5CA  CONST_30  H3S  N3S  C    CA     0.00   0.0  0
 5CA  Var_01    C4'  C5'  O5'  S    176.44  30.0  3
 5CA  Var_02    O1S  S    N3S  C    179.60  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
 5CA  chir_01  CA   N    CB   C    negativ
 5CA  chir_02  C4'  O4'  C5'  C3'  positiv
 5CA  chir_03  C3'  O3'  C4'  C2'  positiv
 5CA  chir_04  C2'  O2'  C3'  C1'  positiv
 5CA  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
 5CA  plan-1  C1'  0.020
 5CA  plan-1  N9   0.020
 5CA  plan-1  C8   0.020
 5CA  plan-1  N7   0.020
 5CA  plan-1  C5   0.020
 5CA  plan-1  C6   0.020
 5CA  plan-1  N6   0.020
 5CA  plan-1  N1   0.020
 5CA  plan-1  C2   0.020
 5CA  plan-1  N3   0.020
 5CA  plan-1  C4   0.020
 5CA  plan-1  H8   0.020
 5CA  plan-1  H2   0.020
 5CA  plan-2  C6   0.020
 5CA  plan-2  N6   0.020
 5CA  plan-2  H61  0.020
 5CA  plan-2  H62  0.020
 5CA  plan-3  CA   0.020
 5CA  plan-3  C    0.020
 5CA  plan-3  O    0.020
 5CA  plan-3  N3S  0.020
 5CA  plan-3  S    0.020
 5CA  plan-3  H3S  0.020

