# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 23:24:46 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 5'-O-(L-alanylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)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
 A5A  A5A  5'-O-(L-alanylsulfamoyl)adenosine  ligand  47  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A5A
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
 A5A  N     N  NH2   0  -0.778   2.6889  -1.6716   1.3385
 A5A  CA    C  CH1   0  -0.231   2.6074  -1.1078   2.6732
 A5A  CB    C  CH3   0  -0.667   3.9232  -0.5736   3.2392
 A5A  C     C  C     0   0.607   1.5967   0.0243   2.6249
 A5A  O     O  O     0  -0.417   1.6536   0.9315   1.8317
 A5A  N3S   N  NC1   0  -0.836   0.5928  -0.0612   3.5668
 A5A  S     S  S     0   1.627  -0.5877   1.0949   3.7660
 A5A  O1S   O  OS    0  -0.629  -1.4635   0.5644   4.7794
 A5A  O2S   O  OS    0  -0.609  -0.0055   2.4009   3.8921
 A5A  O5'   O  OC2   0  -0.565  -1.3126   1.1200   2.3583
 A5A  C5'   C  CH2   0  -0.192  -1.9692  -0.0674   1.8794
 A5A  C4'   C  CH1   0  -0.037  -2.6227   0.3004   0.5635
 A5A  O4'   O  O2    0  -0.483  -1.6536   0.7970  -0.3551
 A5A  C3'   C  CH1   0  -0.037  -3.2643  -0.9157  -0.1009
 A5A  O3'   O  OH1   0  -0.664  -4.3612  -0.4774  -0.8557
 A5A  C2'   C  CH1   0  -0.051  -2.1262  -1.3922  -1.0088
 A5A  O2'   O  OH1   0  -0.651  -2.5282  -2.1386  -2.1153
 A5A  C1'   C  CH1   0   0.212  -1.5430  -0.0574  -1.4652
 A5A  N9    N  NR5   0  -0.546  -0.1742  -0.1194  -1.8916
 A5A  C8    C  CR15  0   0.124   0.8988  -0.6134  -1.1961
 A5A  N7    N  N     0  -0.456   2.0274  -0.4659  -1.8208
 A5A  C5    C  CR56  0  -0.009   1.6926   0.1638  -2.9930
 A5A  C6    C  CR6   0   0.459   2.4507   0.6017  -4.0939
 A5A  N6    N  NH2   0  -0.816   3.7720   0.4379  -4.1699
 A5A  N1    N  N     0  -0.474   1.8037   1.1994  -5.1013
 A5A  C2    C  CR16  0   0.046   0.4851   1.3551  -5.0224
 A5A  N3    N  N     0  -0.458  -0.3288   0.9881  -4.0472
 A5A  C4    C  CR56  0   0.491   0.3289   0.3946  -3.0554
 A5A  H     H  HNH2  0   0.355   3.1474  -1.0226   0.7094
 A5A  HN2   H  HNH2  0   0.365   3.2692  -2.5011   1.3641
 A5A  HA    H  HCH1  0   0.272   2.2365  -1.8927   3.3366
 A5A  HB1   H  HCH3  0   0.250   4.6535  -1.3813   3.2851
 A5A  HB2   H  HCH3  0   0.235   4.3262   0.2160   2.6039
 A5A  HB3   H  HCH3  0   0.238   3.8018  -0.1750   4.2475
 A5A  H3S   H  HNC1  0   0.458   0.5500  -0.8507   4.2008
 A5A  H5'1  H  HCH2  0   0.249  -1.2352  -0.8697   1.7605
 A5A  H5'2  H  HCH2  0   0.279  -2.7348  -0.3923   2.5863
 A5A  H4'   H  HCH1  0   0.282  -3.3720   1.0764   0.7464
 A5A  H3'   H  HCH1  0   0.262  -3.5516  -1.6819   0.6312
 A5A  H3T   H  HOH1  0   0.452  -4.5506  -1.1480  -1.5226
 A5A  H2'   H  HCH1  0   0.252  -1.3933  -1.9355  -0.3990
 A5A  HO'2  H  HOH1  0   0.472  -2.6100  -3.0624  -1.8575
 A5A  H1'   H  HCH1  0   0.264  -2.1104   0.3256  -2.3203
 A5A  H8    H  HCR5  0   0.286   0.8031  -1.0792  -0.2262
 A5A  H61   H  HNH2  0   0.404   4.2855   0.8093  -4.9504
 A5A  H62   H  HNH2  0   0.411   4.2899   0.0456  -3.4033
 A5A  H2    H  HCR6  0   0.253   0.0225   1.8482  -5.8706

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
 A5A  N    CA    single    1.451  0.020  1.451
 A5A  N    H     single    0.860  0.020  1.020
 A5A  N    HN2   single    0.890  0.020  1.040
 A5A  CA   CB    single    1.529  0.020  1.529
 A5A  CA   C     single    1.518  0.020  1.518
 A5A  CA   HA    single    0.970  0.020  1.090
 A5A  CB   HB1   single    0.970  0.020  1.090
 A5A  CB   HB2   single    0.970  0.020  1.090
 A5A  CB   HB3   single    0.970  0.020  1.090
 A5A  C    O     double    1.206  0.020  1.206
 A5A  C    N3S   single    1.379  0.020  1.379
 A5A  N3S  S     single    1.664  0.020  1.664
 A5A  N3S  H3S   single    0.860  0.020  1.020
 A5A  S    O1S   deloc     1.441  0.020  1.441
 A5A  S    O2S   deloc     1.435  0.020  1.435
 A5A  S    O5'   single    1.584  0.020  1.584
 A5A  O5'  C5'   single    1.439  0.020  1.439
 A5A  C5'  C4'   single    1.515  0.020  1.515
 A5A  C5'  H5'1  single    0.970  0.020  1.090
 A5A  C5'  H5'2  single    0.970  0.020  1.090
 A5A  C4'  O4'   single    1.425  0.020  1.425
 A5A  C4'  C3'   single    1.527  0.020  1.527
 A5A  C4'  H4'   single    0.970  0.020  1.090
 A5A  O4'  C1'   single    1.405  0.020  1.405
 A5A  C3'  O3'   single    1.402  0.020  1.402
 A5A  C3'  C2'   single    1.532  0.020  1.532
 A5A  C3'  H3'   single    0.970  0.020  1.090
 A5A  O3'  H3T   single    0.850  0.020  0.980
 A5A  C2'  O2'   single    1.394  0.020  1.394
 A5A  C2'  C1'   single    1.527  0.020  1.527
 A5A  C2'  H2'   single    0.970  0.020  1.090
 A5A  O2'  HO'2  single    0.850  0.020  0.980
 A5A  C1'  N9    single    1.435  0.020  1.435
 A5A  C1'  H1'   single    0.970  0.020  1.090
 A5A  N9   C8    aromatic  1.371  0.020  1.371
 A5A  N9   C4    aromatic  1.368  0.020  1.368
 A5A  C8   N7    aromatic  1.298  0.020  1.298
 A5A  C8   H8    single    0.930  0.020  1.080
 A5A  N7   C5    aromatic  1.372  0.020  1.372
 A5A  C5   C6    aromatic  1.407  0.020  1.407
 A5A  C5   C4    aromatic  1.384  0.020  1.384
 A5A  C6   N6    single    1.334  0.020  1.334
 A5A  C6   N1    aromatic  1.338  0.020  1.338
 A5A  N6   H61   single    0.860  0.020  1.020
 A5A  N6   H62   single    0.860  0.020  1.020
 A5A  N1   C2    aromatic  1.330  0.020  1.330
 A5A  C2   N3    aromatic  1.322  0.020  1.322
 A5A  C2   H2    single    0.930  0.020  1.080
 A5A  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
 A5A  HN2   N    H     106.32  3.000
 A5A  HN2   N    CA    109.10  3.000
 A5A  H     N    CA    110.34  3.000
 A5A  HA    CA   C     109.20  3.000
 A5A  HA    CA   CB    108.57  3.000
 A5A  C     CA   CB    108.91  3.000
 A5A  HA    CA   N     107.36  3.000
 A5A  C     CA   N     107.32  3.000
 A5A  CB    CA   N     115.34  3.000
 A5A  HB3   CB   HB2   108.36  3.000
 A5A  HB3   CB   HB1   107.84  3.000
 A5A  HB2   CB   HB1   108.27  3.000
 A5A  HB3   CB   CA    111.97  3.000
 A5A  HB2   CB   CA    110.82  3.000
 A5A  HB1   CB   CA    109.47  3.000
 A5A  N3S   C    O     122.01  3.000
 A5A  N3S   C    CA    114.62  3.000
 A5A  O     C    CA    123.38  3.000
 A5A  H3S   N3S  S     115.87  3.000
 A5A  H3S   N3S  C     120.41  3.000
 A5A  S     N3S  C     123.71  3.000
 A5A  O5'   S    O2S   104.44  3.000
 A5A  O5'   S    O1S   110.66  3.000
 A5A  O2S   S    O1S   121.32  3.000
 A5A  O5'   S    N3S   103.26  3.000
 A5A  O2S   S    N3S   110.78  3.000
 A5A  O1S   S    N3S   105.05  3.000
 A5A  C5'   O5'  S     119.45  3.000
 A5A  H5'2  C5'  H5'1  108.83  3.000
 A5A  H5'2  C5'  C4'   109.41  3.000
 A5A  H5'1  C5'  C4'   111.91  3.000
 A5A  H5'2  C5'  O5'   110.50  3.000
 A5A  H5'1  C5'  O5'   109.59  3.000
 A5A  C4'   C5'  O5'   106.60  3.000
 A5A  H4'   C4'  C3'   110.47  3.000
 A5A  H4'   C4'  O4'   109.05  3.000
 A5A  C3'   C4'  O4'   106.43  3.000
 A5A  H4'   C4'  C5'   108.81  3.000
 A5A  C3'   C4'  C5'   111.46  3.000
 A5A  O4'   C4'  C5'   110.57  3.000
 A5A  C1'   O4'  C4'   110.55  3.000
 A5A  H3'   C3'  C2'   111.87  3.000
 A5A  H3'   C3'  O3'   111.87  3.000
 A5A  C2'   C3'  O3'   111.07  3.000
 A5A  H3'   C3'  C4'   112.06  3.000
 A5A  C2'   C3'  C4'   101.15  3.000
 A5A  O3'   C3'  C4'   108.30  3.000
 A5A  H3T   O3'  C3'   107.97  3.000
 A5A  H2'   C2'  C1'   110.11  3.000
 A5A  H2'   C2'  O2'   111.63  3.000
 A5A  C1'   C2'  O2'   109.94  3.000
 A5A  H2'   C2'  C3'   108.71  3.000
 A5A  C1'   C2'  C3'   100.90  3.000
 A5A  O2'   C2'  C3'   115.01  3.000
 A5A  HO'2  O2'  C2'   109.02  3.000
 A5A  H1'   C1'  N9    106.10  3.000
 A5A  H1'   C1'  C2'   109.95  3.000
 A5A  N9    C1'  C2'   114.55  3.000
 A5A  H1'   C1'  O4'   111.31  3.000
 A5A  N9    C1'  O4'   109.64  3.000
 A5A  C2'   C1'  O4'   105.39  3.000
 A5A  C4    N9   C8    106.21  3.000
 A5A  C4    N9   C1'   125.97  3.000
 A5A  C8    N9   C1'   127.70  3.000
 A5A  H8    C8   N7    123.92  3.000
 A5A  H8    C8   N9    122.79  3.000
 A5A  N7    C8   N9    113.29  3.000
 A5A  C5    N7   C8    104.54  3.000
 A5A  C4    C5   C6    116.34  3.000
 A5A  C4    C5   N7    110.81  3.000
 A5A  C6    C5   N7    132.84  3.000
 A5A  N1    C6   N6    119.41  3.000
 A5A  N1    C6   C5    117.89  3.000
 A5A  N6    C6   C5    122.71  3.000
 A5A  H62   N6   H61   118.25  3.000
 A5A  H62   N6   C6    121.01  3.000
 A5A  H61   N6   C6    120.32  3.000
 A5A  C2    N1   C6    119.14  3.000
 A5A  H2    C2   N3    116.12  3.000
 A5A  H2    C2   N1    115.44  3.000
 A5A  N3    C2   N1    128.43  3.000
 A5A  C4    N3   C2    111.69  3.000
 A5A  N3    C4   C5    126.52  3.000
 A5A  N3    C4   N9    128.33  3.000
 A5A  C5    C4   N9    105.15  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
 A5A  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 A5A  CONST_02  N7   C5   C4   N9     0.00   0.0  0
 A5A  CONST_03  C6   C5   C4   N9   180.00   0.0  0
 A5A  CONST_04  C2   N3   C4   N9   180.00   0.0  0
 A5A  CONST_05  C5   C4   N9   C8     0.00   0.0  0
 A5A  CONST_06  N3   C4   N9   C8   180.00   0.0  0
 A5A  CONST_07  C6   C5   N7   C8   180.00   0.0  0
 A5A  CONST_08  C4   C5   N7   C8     0.00   0.0  0
 A5A  CONST_09  C4   N9   C8   N7     0.00   0.0  0
 A5A  CONST_10  N1   C6   C5   N7   180.00   0.0  0
 A5A  CONST_11  N3   C4   C5   N7   180.00   0.0  0
 A5A  CONST_12  C2   N1   C6   C5     0.00   0.0  0
 A5A  CONST_13  C2   N3   C4   C5     0.00   0.0  0
 A5A  CONST_14  N3   C4   C5   C6     0.00   0.0  0
 A5A  CONST_15  N3   C2   N1   C6     0.00   0.0  0
 A5A  CONST_16  C4   C5   C6   N1     0.00   0.0  0
 A5A  CONST_17  C4   N3   C2   N1     0.00   0.0  0
 A5A  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 A5A  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 A5A  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 A5A  CONST_21  N6   C6   C5   N7     0.00   0.0  0
 A5A  CONST_22  C4   C5   C6   N6   180.00   0.0  0
 A5A  CONST_23  C2   N1   C6   N6   180.00   0.0  0
 A5A  CONST_24  H8   C8   N9   C1'    0.00   0.0  0
 A5A  CONST_25  H2   C2   N1   C6   180.00   0.0  0
 A5A  CONST_26  H61  N6   C6   C5   180.00   0.0  0
 A5A  CONST_27  H62  N6   C6   C5     0.00   0.0  0
 A5A  CONST_28  S    N3S  C    CA   180.00   0.0  0
 A5A  CONST_29  S    N3S  C    O      0.00   0.0  0
 A5A  CONST_30  H3S  N3S  C    CA     0.00   0.0  0
 A5A  Var_01    C4'  C5'  O5'  S    176.86  30.0  3
 A5A  Var_02    O1S  S    N3S  C    176.24  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
 A5A  chir_01  CA   N    CB   C    negativ
 A5A  chir_02  C4'  O4'  C5'  C3'  positiv
 A5A  chir_03  C3'  O3'  C4'  C2'  positiv
 A5A  chir_04  C2'  O2'  C3'  C1'  positiv
 A5A  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
 A5A  plan-1  C1'  0.020
 A5A  plan-1  N9   0.020
 A5A  plan-1  C8   0.020
 A5A  plan-1  N7   0.020
 A5A  plan-1  C5   0.020
 A5A  plan-1  C6   0.020
 A5A  plan-1  N6   0.020
 A5A  plan-1  N1   0.020
 A5A  plan-1  C2   0.020
 A5A  plan-1  N3   0.020
 A5A  plan-1  C4   0.020
 A5A  plan-1  H8   0.020
 A5A  plan-1  H2   0.020
 A5A  plan-2  C6   0.020
 A5A  plan-2  N6   0.020
 A5A  plan-2  H61  0.020
 A5A  plan-2  H62  0.020
 A5A  plan-3  CA   0.020
 A5A  plan-3  C    0.020
 A5A  plan-3  O    0.020
 A5A  plan-3  N3S  0.020
 A5A  plan-3  S    0.020
 A5A  plan-3  H3S  0.020

