# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:56:54 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 5'-O-[(3-methyl-D-valyl)sulfamoyl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(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
 53H  53H  5'-O-[(3-methyl-D-valyl)sulfamoyl]adenosine  ligand  56  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_53H
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
 53H  C1    C  C     0   0.576  -2.7982  -1.0777   0.8434
 53H  C2    C  CR16  0   0.041   3.5475  -1.8320   1.4382
 53H  C3    C  CH1   0  -0.188  -2.6150  -2.5452   0.4556
 53H  C4    C  CR56  0   0.510   2.7074  -0.5156  -0.1028
 53H  C5    C  CR56  0  -0.001   2.9396  -1.4408  -1.1060
 53H  C6    C  CR6   0   0.458   3.5348  -2.6536  -0.7118
 53H  C7    C  CT    0  -0.077  -1.1877  -2.8214  -0.0916
 53H  N1    N  N     0  -0.473   3.8259  -2.8138   0.5845
 53H  N2    N  NC1   0  -0.836  -3.4449  -0.3075  -0.1057
 53H  O1    O  O     0  -0.415  -2.4404  -0.6093   1.8969
 53H  C8    C  CR15  0   0.108   2.0497   0.2210  -2.0535
 53H  O2    O  OH1   0  -0.661   2.2019   4.0558   0.0271
 53H  N3    N  N     0  -0.458   2.9935  -0.6581   1.1880
 53H  C9    C  CH3   0  -0.657  -0.1351  -2.7478   1.0147
 53H  C10   C  CH3   0  -0.637  -1.1830  -4.2290  -0.6920
 53H  C11   C  CH3   0  -0.681  -0.8335  -1.8177  -1.1896
 53H  N4    N  NH2   0  -0.777  -2.9464  -3.4242   1.5539
 53H  S1    S  S     0   1.628  -3.9283   1.2643   0.1449
 53H  O1A   O  OS    0  -0.632  -4.5815   1.6521  -1.0809
 53H  O2A   O  OS    0  -0.608  -4.5863   1.3943   1.4141
 53H  O5    O  OC2   0  -0.571  -2.5621   2.0432   0.3177
 53H  C25   C  CH2   0  -0.193  -1.7528   2.3070  -0.8485
 53H  C24   C  CR15  0   0.011  -0.4022   2.7512  -0.3560
 53H  C23   C  CR15  0  -0.037   0.4934   3.2568  -1.4834
 53H  O3    O  OH1   0  -0.653   0.2074   4.5916  -1.7745
 53H  C22   C  CR15  0  -0.062   1.8870   3.0346  -0.8775
 53H  C21   C  CR15  0   0.175   1.6814   1.7548  -0.0613
 53H  O4    O  O     0  -0.481   0.2994   1.6579   0.2055
 53H  N9    N  NR5   0  -0.542   2.1384   0.5598  -0.7278
 53H  N7    N  N     0  -0.448   2.5231  -0.9580  -2.3199
 53H  H2    H  HCR6  0   0.254   3.8113  -2.0255   2.4723
 53H  H3    H  HCH1  0   0.265  -3.3118  -2.7678  -0.3598
 53H  HN2   H  HNC1  0   0.452  -3.7615  -0.7237  -0.9734
 53H  H8    H  HCR5  0   0.299   1.6323   0.8893  -2.7917
 53H  HO2   H  HOH1  0   0.454   1.9280   4.8944  -0.3649
 53H  H9    H  HCH3  0   0.230  -0.3197  -3.4843   1.7982
 53H  H9A   H  HCH3  0   0.229   0.8491  -2.9678   0.5977
 53H  H9B   H  HCH3  0   0.233  -0.0782  -1.7619   1.4760
 53H  H10   H  HCH3  0   0.223  -1.8875  -4.3096  -1.5230
 53H  H10A  H  HCH3  0   0.224  -0.1889  -4.4702  -1.0741
 53H  H10B  H  HCH3  0   0.234  -1.4499  -4.9786   0.0523
 53H  H11   H  HCH3  0   0.231  -0.6739  -0.8106  -0.7980
 53H  H11A  H  HCH3  0   0.244   0.0979  -2.1156  -1.6724
 53H  H11B  H  HCH3  0   0.232  -1.5996  -1.7671  -1.9678
 53H  HN4   H  HNH2  0   0.353  -2.4593  -3.1430   2.3954
 53H  HN4A  H  HNH2  0   0.360  -3.9349  -3.3681   1.7626
 53H  H25   H  HCH2  0   0.254  -1.6625   1.4117  -1.4700
 53H  H25A  H  HCH2  0   0.281  -2.2137   3.1042  -1.4332
 53H  H24   H  HCR5  0   0.260  -0.5329   3.5495   0.3868
 53H  H23   H  HCR5  0   0.250   0.3721   2.6188  -2.3685
 53H  HO3   H  HOH1  0   0.473   0.5236   4.7947  -2.6609
 53H  H22   H  HCR5  0   0.265   2.6652   2.9174  -1.6410
 53H  H21   H  HCR5  0   0.281   2.2411   1.8057   0.8750
 53H  HN6   H  HNH2  0   0.412   3.6193  -3.5387  -2.5511
 53H  HN6A  H  HNH2  0   0.404   4.2660  -4.4740  -1.2526
 53H  N6    N  NH2   0  -0.815   3.8096  -3.6359  -1.5694

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
 53H  C1   C3    single    1.529  0.020  1.529
 53H  C1   N2    single    1.383  0.020  1.383
 53H  C1   O1    double    1.207  0.020  1.207
 53H  C2   N1    aromatic  1.330  0.020  1.330
 53H  C2   N3    aromatic  1.322  0.020  1.322
 53H  C3   C7    single    1.553  0.020  1.553
 53H  C3   N4    single    1.445  0.020  1.445
 53H  C4   C5    aromatic  1.384  0.020  1.384
 53H  C4   N3    aromatic  1.330  0.020  1.330
 53H  C4   N9    aromatic  1.368  0.020  1.368
 53H  C5   C6    aromatic  1.407  0.020  1.407
 53H  C5   N7    aromatic  1.371  0.020  1.371
 53H  C6   N1    aromatic  1.338  0.020  1.338
 53H  C6   N6    single    1.333  0.020  1.333
 53H  C7   C9    single    1.529  0.020  1.529
 53H  C7   C10   single    1.530  0.020  1.530
 53H  C7   C11   single    1.529  0.020  1.529
 53H  N2   S1    single    1.663  0.020  1.663
 53H  C8   N9    aromatic  1.371  0.020  1.371
 53H  C8   N7    aromatic  1.298  0.020  1.298
 53H  O2   C22   single    1.400  0.020  1.400
 53H  S1   O1A   deloc     1.442  0.020  1.442
 53H  S1   O2A   deloc     1.435  0.020  1.435
 53H  S1   O5    single    1.582  0.020  1.582
 53H  O5   C25   single    1.444  0.020  1.444
 53H  C25  C24   single    1.505  0.020  1.505
 53H  C24  C23   single    1.526  0.020  1.526
 53H  C24  O4    single    1.415  0.020  1.415
 53H  C23  O3    single    1.396  0.020  1.396
 53H  C23  C22   single    1.536  0.020  1.536
 53H  C22  C21   single    1.532  0.020  1.532
 53H  C21  O4    single    1.411  0.020  1.411
 53H  C21  N9    single    1.443  0.020  1.443
 53H  C2   H2    single    0.930  0.020  1.080
 53H  C3   H3    single    0.970  0.020  1.090
 53H  N2   HN2   single    0.860  0.020  1.020
 53H  C8   H8    single    0.930  0.020  1.080
 53H  O2   HO2   single    0.850  0.020  0.980
 53H  C9   H9    single    0.970  0.020  1.090
 53H  C9   H9A   single    0.970  0.020  1.090
 53H  C9   H9B   single    0.970  0.020  1.090
 53H  C10  H10   single    0.970  0.020  1.090
 53H  C10  H10A  single    0.970  0.020  1.090
 53H  C10  H10B  single    0.970  0.020  1.090
 53H  C11  H11   single    0.970  0.020  1.090
 53H  C11  H11A  single    0.970  0.020  1.090
 53H  C11  H11B  single    0.970  0.020  1.090
 53H  N4   HN4   single    0.890  0.020  1.040
 53H  N4   HN4A  single    0.890  0.020  1.040
 53H  C25  H25   single    0.970  0.020  1.090
 53H  C25  H25A  single    0.970  0.020  1.090
 53H  C24  H24   single    0.970  0.020  1.090
 53H  C23  H23   single    0.970  0.020  1.090
 53H  O3   HO3   single    0.850  0.020  0.980
 53H  C22  H22   single    0.970  0.020  1.090
 53H  C21  H21   single    0.970  0.020  1.090
 53H  N6   HN6   single    0.860  0.020  1.020
 53H  N6   HN6A  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
 53H  O1    C1   N2    121.44  3.000
 53H  O1    C1   C3    123.93  3.000
 53H  N2    C1   C3    114.62  3.000
 53H  H2    C2   N3    116.15  3.000
 53H  H2    C2   N1    115.42  3.000
 53H  N3    C2   N1    128.43  3.000
 53H  H3    C3   N4    107.23  3.000
 53H  H3    C3   C7    106.62  3.000
 53H  N4    C3   C7    111.73  3.000
 53H  H3    C3   C1    107.92  3.000
 53H  N4    C3   C1    111.32  3.000
 53H  C7    C3   C1    111.72  3.000
 53H  N9    C4   N3    128.12  3.000
 53H  N9    C4   C5    105.31  3.000
 53H  N3    C4   C5    126.57  3.000
 53H  N7    C5   C6    132.84  3.000
 53H  N7    C5   C4    110.81  3.000
 53H  C6    C5   C4    116.35  3.000
 53H  N6    C6   N1    119.36  3.000
 53H  N6    C6   C5    122.83  3.000
 53H  N1    C6   C5    117.81  3.000
 53H  C11   C7   C10   108.74  3.000
 53H  C11   C7   C9    109.18  3.000
 53H  C10   C7   C9    109.03  3.000
 53H  C11   C7   C3    110.43  3.000
 53H  C10   C7   C3    107.73  3.000
 53H  C9    C7   C3    111.66  3.000
 53H  C6    N1   C2    119.19  3.000
 53H  HN2   N2   S1    115.24  3.000
 53H  HN2   N2   C1    120.34  3.000
 53H  S1    N2   C1    123.97  3.000
 53H  H8    C8   N7    124.25  3.000
 53H  H8    C8   N9    122.22  3.000
 53H  N7    C8   N9    113.53  3.000
 53H  HO2   O2   C22   107.91  3.000
 53H  C4    N3   C2    111.65  3.000
 53H  H9B   C9   H9A   107.28  3.000
 53H  H9B   C9   H9    108.39  3.000
 53H  H9A   C9   H9    106.91  3.000
 53H  H9B   C9   C7    112.69  3.000
 53H  H9A   C9   C7    109.56  3.000
 53H  H9    C9   C7    111.76  3.000
 53H  H10B  C10  H10A  108.06  3.000
 53H  H10B  C10  H10   108.12  3.000
 53H  H10A  C10  H10   107.73  3.000
 53H  H10B  C10  C7    111.35  3.000
 53H  H10A  C10  C7    110.08  3.000
 53H  H10   C10  C7    111.37  3.000
 53H  H11B  C11  H11A  107.22  3.000
 53H  H11B  C11  H11   108.36  3.000
 53H  H11A  C11  H11   106.60  3.000
 53H  H11B  C11  C7    112.29  3.000
 53H  H11A  C11  C7    109.66  3.000
 53H  H11   C11  C7    112.43  3.000
 53H  HN4A  N4   HN4   106.45  3.000
 53H  HN4A  N4   C3    110.31  3.000
 53H  HN4   N4   C3    110.64  3.000
 53H  O5    S1   O2A   104.75  3.000
 53H  O5    S1   O1A   110.59  3.000
 53H  O2A   S1   O1A   121.30  3.000
 53H  O5    S1   N2    103.34  3.000
 53H  O2A   S1   N2    110.61  3.000
 53H  O1A   S1   N2    104.93  3.000
 53H  C25   O5   S1    119.06  3.000
 53H  H25A  C25  H25   109.19  3.000
 53H  H25A  C25  C24   109.81  3.000
 53H  H25   C25  C24   110.70  3.000
 53H  H25A  C25  O5    109.25  3.000
 53H  H25   C25  O5    110.85  3.000
 53H  C24   C25  O5    107.02  3.000
 53H  H24   C24  O4    110.62  3.000
 53H  H24   C24  C23   109.19  3.000
 53H  O4    C24  C23   104.96  3.000
 53H  H24   C24  C25   109.22  3.000
 53H  O4    C24  C25   110.29  3.000
 53H  C23   C24  C25   112.50  3.000
 53H  H23   C23  C22   109.53  3.000
 53H  H23   C23  O3    111.41  3.000
 53H  C22   C23  O3    113.99  3.000
 53H  H23   C23  C24   109.77  3.000
 53H  C22   C23  C24   101.14  3.000
 53H  O3    C23  C24   110.53  3.000
 53H  HO3   O3   C23   109.06  3.000
 53H  H22   C22  C21   112.14  3.000
 53H  H22   C22  C23   112.63  3.000
 53H  C21   C22  C23   102.08  3.000
 53H  H22   C22  O2    111.61  3.000
 53H  C21   C22  O2    107.18  3.000
 53H  C23   C22  O2    110.70  3.000
 53H  H21   C21  N9    105.81  3.000
 53H  H21   C21  O4    110.06  3.000
 53H  N9    C21  O4    109.93  3.000
 53H  H21   C21  C22   110.43  3.000
 53H  N9    C21  C22   113.79  3.000
 53H  O4    C21  C22   106.84  3.000
 53H  C21   O4   C24   110.95  3.000
 53H  C21   N9   C8    129.12  3.000
 53H  C21   N9   C4    124.89  3.000
 53H  C8    N9   C4    105.93  3.000
 53H  C8    N7   C5    104.41  3.000
 53H  HN6A  N6   HN6   118.32  3.000
 53H  HN6A  N6   C6    120.35  3.000
 53H  HN6   N6   C6    121.23  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
 53H  CONST_01  C5    C6   N1  C2      0.00   0.0  0
 53H  CONST_02  C5    C4   N3  C2      0.00   0.0  0
 53H  CONST_03  N9    C4   N3  C2    180.00   0.0  0
 53H  CONST_04  N1    C6   C5  C4      0.00   0.0  0
 53H  CONST_05  C8    N7   C5  C4      0.00   0.0  0
 53H  CONST_06  N1    C2   N3  C4      0.00   0.0  0
 53H  CONST_07  N7    C8   N9  C4      0.00   0.0  0
 53H  CONST_08  C8    N9   C4  C5      0.00   0.0  0
 53H  CONST_09  N9    C8   N7  C5      0.00   0.0  0
 53H  CONST_10  N3    C4   C5  C6      0.00   0.0  0
 53H  CONST_11  N9    C4   C5  C6    180.00   0.0  0
 53H  CONST_12  C8    N7   C5  C6    180.00   0.0  0
 53H  CONST_13  N3    C2   N1  C6      0.00   0.0  0
 53H  CONST_14  N7    C5   C6  N1    180.00   0.0  0
 53H  CONST_15  N3    C4   N9  C8    180.00   0.0  0
 53H  CONST_16  N7    C5   C4  N3    180.00   0.0  0
 53H  CONST_17  N7    C5   C4  N9      0.00   0.0  0
 53H  CONST_18  C21   N9   C4  C5    180.00   0.0  0
 53H  CONST_19  C21   N9   C4  N3      0.00   0.0  0
 53H  CONST_20  N7    C8   N9  C21   180.00   0.0  0
 53H  CONST_21  N6    C6   N1  C2    180.00   0.0  0
 53H  CONST_22  N6    C6   C5  C4    180.00   0.0  0
 53H  CONST_23  N6    C6   C5  N7      0.00   0.0  0
 53H  CONST_24  H2    C2   N3  C4    180.00   0.0  0
 53H  CONST_25  H8    C8   N9  C4    180.00   0.0  0
 53H  CONST_26  HN6   N6   C6  C5      0.00   0.0  0
 53H  CONST_27  HN6A  N6   C6  C5    180.00   0.0  0
 53H  CONST_28  S1    N2   C1  C3    180.00   0.0  0
 53H  CONST_29  S1    N2   C1  O1      0.00   0.0  0
 53H  CONST_30  HN2   N2   C1  C3      0.00   0.0  0
 53H  Var_01    C24   C25  O5  S1   -166.89  30.0  3
 53H  Var_02    O1A   S1   N2  C1   -178.49  30.0  3
 53H  Var_03    H9    C9   C7  C3     60.48  30.0  3
 53H  Var_04    H10   C10  C7  C3     61.56  30.0  3
 53H  Var_05    H11   C11  C7  C3     70.50  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
 53H  chir_01  C3   C1  C7   N4   negativ
 53H  chir_02  C24  O4  C25  C23  positiv
 53H  chir_03  C23  O3  C24  C22  positiv
 53H  chir_04  C22  O2  C23  C21  positiv
 53H  chir_05  C21  O4  N9   C22  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
 53H  plan-1  C2    0.020
 53H  plan-1  C4    0.020
 53H  plan-1  C5    0.020
 53H  plan-1  C6    0.020
 53H  plan-1  N1    0.020
 53H  plan-1  C8    0.020
 53H  plan-1  N3    0.020
 53H  plan-1  C21   0.020
 53H  plan-1  N9    0.020
 53H  plan-1  N7    0.020
 53H  plan-1  H2    0.020
 53H  plan-1  H8    0.020
 53H  plan-1  N6    0.020
 53H  plan-2  C6    0.020
 53H  plan-2  HN6   0.020
 53H  plan-2  HN6A  0.020
 53H  plan-2  N6    0.020
 53H  plan-3  C1    0.020
 53H  plan-3  C3    0.020
 53H  plan-3  N2    0.020
 53H  plan-3  O1    0.020
 53H  plan-3  S1    0.020
 53H  plan-3  HN2   0.020

