# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 06:12:14 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2S)-2-amino-N-({[5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfamoyl)-4-(methylsulfanyl)butanamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N)C(=O)N[S](=O)(=O)NCC1OC(C(O)C1O)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
 MDS  MDS  '(2S)-2-amino-N-({[5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfamoyl)-4-(methylsulfanyl)butanamide (non-preferred name)'  ligand  55  31  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MDS
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
 MDS  O1    O  OH1   0  -0.651   2.5024  -0.0346   3.2050
 MDS  C1    C  CH1   0  -0.054   2.0022  -1.0411   2.3806
 MDS  C2    C  CH1   0   0.219   1.8216  -0.5088   0.9594
 MDS  O2    O  O2    0  -0.504   0.8859  -1.3646   0.3619
 MDS  C3    C  CH1   0   0.001   0.1859  -2.1129   1.3634
 MDS  C4    C  CH2   0  -0.292  -1.2972  -2.0813   1.0646
 MDS  N1    N  NC1   0  -0.746  -1.5323  -2.7466  -0.2171
 MDS  S1    S  S     0   1.542  -3.0687  -2.8844  -0.7455
 MDS  O3    O  OS    0  -0.630  -3.0212  -3.4618  -2.0664
 MDS  O4    O  OS    0  -0.648  -3.8656  -3.4807   0.3020
 MDS  N2    N  NC1   0  -0.815  -3.6721  -1.3145  -0.8592
 MDS  C5    C  C     0   0.560  -3.0799  -0.3432  -1.6230
 MDS  O5    O  O     0  -0.434  -2.1090  -0.5736  -2.3101
 MDS  C6    C  CH1   0  -0.215  -3.6939   1.0461  -1.4700
 MDS  N3    N  NH2   0  -0.770  -3.5489   1.8739  -2.6391
 MDS  C7    C  CH2   0  -0.434  -3.0258   1.7028  -0.2521
 MDS  C8    C  CH2   0  -0.540  -3.6749   3.0300   0.1050
 MDS  S2    S  S2    0  -0.044  -2.8155   3.7493   1.5328
 MDS  C9    C  CH3   0  -0.763  -3.7662   5.2713   1.7324
 MDS  C10   C  CH1   0  -0.034   0.5781  -1.4993   2.7012
 MDS  O6    O  OH1   0  -0.663  -0.2505  -0.4053   2.9852
 MDS  N4    N  NR5   0  -0.542   3.0297  -0.4970   0.1810
 MDS  C11   C  CR15  0   0.111   3.8141  -1.5703  -0.1501
 MDS  N5    N  N     0  -0.449   4.8379  -1.2531  -0.8835
 MDS  C12   C  CR56  0  -0.012   4.7305   0.1042  -1.0519
 MDS  C13   C  CR6   0   0.461   5.5156   1.0488  -1.7387
 MDS  N6    N  N     0  -0.474   5.1211   2.3272  -1.7138
 MDS  C14   C  CR16  0   0.046   4.0155   2.6517  -1.0495
 MDS  N7    N  N     0  -0.457   3.2037   1.8608  -0.3690
 MDS  C15   C  CR56  0   0.492   3.6093   0.5942  -0.4024
 MDS  N8    N  NH2   0  -0.816   6.6246   0.7201  -2.4011
 MDS  HO1   H  HOH1  0   0.471   2.8740  -0.4357   3.9974
 MDS  H1    H  HCH1  0   0.258   2.6577  -1.9219   2.3623
 MDS  H2    H  HCH1  0   0.263   1.4637   0.5261   0.9851
 MDS  H3    H  HCH1  0   0.265   0.5314  -3.1527   1.3343
 MDS  H41   H  HCH2  0   0.255  -1.6564  -1.0489   1.0612
 MDS  H42   H  HCH2  0   0.282  -1.8257  -2.6267   1.8461
 MDS  HN1   H  HNC1  0   0.421  -0.9110  -2.4456  -0.9632
 MDS  HN2   H  HNC1  0   0.448  -4.4903  -1.1054  -0.2992
 MDS  H6    H  HCH1  0   0.274  -4.7616   0.9301  -1.2589
 MDS  HN31  H  HNH2  0   0.349  -2.5757   1.9241  -2.9153
 MDS  HN32  H  HNH2  0   0.361  -4.0541   1.4770  -3.4210
 MDS  H71   H  HCH2  0   0.250  -1.9635   1.8531  -0.4688
 MDS  H72   H  HCH2  0   0.252  -3.0823   1.0294   0.6079
 MDS  H81   H  HCH2  0   0.260  -4.7273   2.8808   0.3570
 MDS  H82   H  HCH2  0   0.269  -3.6217   3.7207  -0.7363
 MDS  H91   H  HCH3  0   0.261  -3.7070   5.8928   0.8401
 MDS  H92   H  HCH3  0   0.261  -4.8106   5.0591   1.9566
 MDS  H93   H  HCH3  0   0.273  -3.3359   5.8209   2.5678
 MDS  H10   H  HCH1  0   0.260   0.5543  -2.2530   3.4976
 MDS  HO6   H  HOH1  0   0.454   0.2002   0.1573   3.6257
 MDS  H11   H  HCR5  0   0.301   3.5739  -2.5714   0.1762
 MDS  H14   H  HCR6  0   0.253   3.7498   3.7032  -1.0719
 MDS  HN81  H  HNH2  0   0.412   6.9348  -0.2338  -2.4561
 MDS  HN82  H  HNH2  0   0.404   7.1442   1.4204  -2.9014

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
 MDS  O1   C1    single    1.394  0.020  1.394
 MDS  O1   HO1   single    0.850  0.020  0.980
 MDS  C1   C2    single    1.528  0.020  1.528
 MDS  C1   C10   single    1.530  0.020  1.530
 MDS  C1   H1    single    0.970  0.020  1.090
 MDS  C2   O2    single    1.402  0.020  1.402
 MDS  C2   N4    single    1.437  0.020  1.437
 MDS  C2   H2    single    0.970  0.020  1.090
 MDS  O2   C3    single    1.433  0.020  1.433
 MDS  C3   C4    single    1.513  0.020  1.513
 MDS  C3   C10   single    1.523  0.020  1.523
 MDS  C3   H3    single    0.970  0.020  1.090
 MDS  C4   N1    single    1.463  0.020  1.463
 MDS  C4   H41   single    0.970  0.020  1.090
 MDS  C4   H42   single    0.970  0.020  1.090
 MDS  N1   S1    single    1.631  0.020  1.631
 MDS  N1   HN1   single    0.890  0.020  1.040
 MDS  S1   O3    double    1.442  0.020  1.442
 MDS  S1   O4    double    1.445  0.020  1.445
 MDS  S1   N2    single    1.686  0.020  1.686
 MDS  N2   C5    single    1.370  0.020  1.370
 MDS  N2   HN2   single    0.860  0.020  1.020
 MDS  C5   O5    double    1.212  0.020  1.212
 MDS  C5   C6    single    1.527  0.020  1.527
 MDS  C6   N3    single    1.440  0.020  1.440
 MDS  C6   C7    single    1.537  0.020  1.537
 MDS  C6   H6    single    0.970  0.020  1.090
 MDS  N3   HN31  single    0.890  0.020  1.040
 MDS  N3   HN32  single    0.890  0.020  1.040
 MDS  C7   C8    single    1.520  0.020  1.520
 MDS  C7   H71   single    0.970  0.020  1.090
 MDS  C7   H72   single    0.970  0.020  1.090
 MDS  C8   S2    single    1.815  0.020  1.815
 MDS  C8   H81   single    0.970  0.020  1.090
 MDS  C8   H82   single    0.970  0.020  1.090
 MDS  S2   C9    single    1.806  0.020  1.806
 MDS  C9   H91   single    0.970  0.020  1.090
 MDS  C9   H92   single    0.970  0.020  1.090
 MDS  C9   H93   single    0.970  0.020  1.090
 MDS  C10  O6    single    1.401  0.020  1.401
 MDS  C10  H10   single    0.970  0.020  1.090
 MDS  O6   HO6   single    0.850  0.020  0.980
 MDS  N4   C11   aromatic  1.370  0.020  1.370
 MDS  N4   C15   aromatic  1.366  0.020  1.366
 MDS  C11  N5    aromatic  1.299  0.020  1.299
 MDS  C11  H11   single    0.930  0.020  1.080
 MDS  N5   C12   aromatic  1.372  0.020  1.372
 MDS  C12  C13   aromatic  1.407  0.020  1.407
 MDS  C12  C15   aromatic  1.385  0.020  1.385
 MDS  C13  N6    aromatic  1.338  0.020  1.338
 MDS  C13  N8    single    1.333  0.020  1.333
 MDS  N6   C14   aromatic  1.330  0.020  1.330
 MDS  C14  N7    aromatic  1.322  0.020  1.322
 MDS  C14  H14   single    0.930  0.020  1.080
 MDS  N7   C15   aromatic  1.330  0.020  1.330
 MDS  N8   HN81  single    0.860  0.020  1.020
 MDS  N8   HN82  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
 MDS  HO1   O1   C1    108.93  3.000
 MDS  H1    C1   C10   108.59  3.000
 MDS  H1    C1   C2    109.54  3.000
 MDS  C10   C1   C2    100.91  3.000
 MDS  H1    C1   O1    112.01  3.000
 MDS  C10   C1   O1    115.24  3.000
 MDS  C2    C1   O1    109.93  3.000
 MDS  H2    C2   N4    106.24  3.000
 MDS  H2    C2   O2    111.63  3.000
 MDS  N4    C2   O2    109.59  3.000
 MDS  H2    C2   C1    110.23  3.000
 MDS  N4    C2   C1    114.03  3.000
 MDS  O2    C2   C1    105.23  3.000
 MDS  C3    O2   C2    110.30  3.000
 MDS  H3    C3   C10   108.92  3.000
 MDS  H3    C3   C4    108.88  3.000
 MDS  C10   C3   C4    114.67  3.000
 MDS  H3    C3   O2    108.84  3.000
 MDS  C10   C3   O2    106.12  3.000
 MDS  C4    C3   O2    109.26  3.000
 MDS  H42   C4   H41   108.39  3.000
 MDS  H42   C4   N1    108.83  3.000
 MDS  H41   C4   N1    111.96  3.000
 MDS  H42   C4   C3    108.86  3.000
 MDS  H41   C4   C3    110.02  3.000
 MDS  N1    C4   C3    108.72  3.000
 MDS  HN1   N1   S1    111.29  3.000
 MDS  HN1   N1   C4    114.21  3.000
 MDS  S1    N1   C4    118.27  3.000
 MDS  N2    S1   O4    103.64  3.000
 MDS  N2    S1   O3    108.83  3.000
 MDS  O4    S1   O3    121.11  3.000
 MDS  N2    S1   N1    106.29  3.000
 MDS  O4    S1   N1    108.65  3.000
 MDS  O3    S1   N1    107.43  3.000
 MDS  HN2   N2   C5    120.72  3.000
 MDS  HN2   N2   S1    116.35  3.000
 MDS  C5    N2   S1    122.89  3.000
 MDS  C6    C5   O5    123.52  3.000
 MDS  C6    C5   N2    114.55  3.000
 MDS  O5    C5   N2    121.85  3.000
 MDS  H6    C6   C7    108.45  3.000
 MDS  H6    C6   N3    108.41  3.000
 MDS  C7    C6   N3    110.74  3.000
 MDS  H6    C6   C5    108.37  3.000
 MDS  C7    C6   C5    107.07  3.000
 MDS  N3    C6   C5    113.66  3.000
 MDS  HN32  N3   HN31  106.76  3.000
 MDS  HN32  N3   C6    110.59  3.000
 MDS  HN31  N3   C6    110.29  3.000
 MDS  H72   C7   H71   106.88  3.000
 MDS  H72   C7   C8    109.32  3.000
 MDS  H71   C7   C8    109.94  3.000
 MDS  H72   C7   C6    109.74  3.000
 MDS  H71   C7   C6    108.89  3.000
 MDS  C8    C7   C6    111.95  3.000
 MDS  H82   C8   H81   108.16  3.000
 MDS  H82   C8   S2    109.45  3.000
 MDS  H81   C8   S2    109.20  3.000
 MDS  H82   C8   C7    110.56  3.000
 MDS  H81   C8   C7    110.27  3.000
 MDS  S2    C8   C7    109.19  3.000
 MDS  C9    S2   C8     99.89  3.000
 MDS  H93   C9   H92   108.63  3.000
 MDS  H93   C9   H91   108.62  3.000
 MDS  H92   C9   H91   109.39  3.000
 MDS  H93   C9   S2    107.59  3.000
 MDS  H92   C9   S2    111.31  3.000
 MDS  H91   C9   S2    111.21  3.000
 MDS  H10   C10  O6    112.12  3.000
 MDS  H10   C10  C3    110.81  3.000
 MDS  O6    C10  C3    109.89  3.000
 MDS  H10   C10  C1    112.22  3.000
 MDS  O6    C10  C1    111.04  3.000
 MDS  C3    C10  C1    100.15  3.000
 MDS  HO6   O6   C10   108.29  3.000
 MDS  C15   N4   C11   106.23  3.000
 MDS  C15   N4   C2    126.47  3.000
 MDS  C11   N4   C2    127.28  3.000
 MDS  H11   C11  N5    124.92  3.000
 MDS  H11   C11  N4    121.72  3.000
 MDS  N5    C11  N4    113.36  3.000
 MDS  C12   N5   C11   104.43  3.000
 MDS  C15   C12  C13   116.29  3.000
 MDS  C15   C12  N5    110.84  3.000
 MDS  C13   C12  N5    132.87  3.000
 MDS  N8    C13  N6    119.35  3.000
 MDS  N8    C13  C12   122.77  3.000
 MDS  N6    C13  C12   117.89  3.000
 MDS  C14   N6   C13   119.17  3.000
 MDS  H14   C14  N7    116.12  3.000
 MDS  H14   C14  N6    115.45  3.000
 MDS  N7    C14  N6    128.43  3.000
 MDS  C15   N7   C14   111.68  3.000
 MDS  N7    C15  C12   126.53  3.000
 MDS  N7    C15  N4    128.33  3.000
 MDS  C12   C15  N4    105.14  3.000
 MDS  HN82  N8   HN81  118.34  3.000
 MDS  HN82  N8   C13   120.37  3.000
 MDS  HN81  N8   C13   121.21  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
 MDS  CONST_01  C12   N5   C11  N4      0.00   0.0  0
 MDS  CONST_02  N5    C12  C15  N4      0.00   0.0  0
 MDS  CONST_03  C13   C12  C15  N4    180.00   0.0  0
 MDS  CONST_04  C14   N7   C15  N4    180.00   0.0  0
 MDS  CONST_05  C12   C15  N4   C11     0.00   0.0  0
 MDS  CONST_06  N7    C15  N4   C11   180.00   0.0  0
 MDS  CONST_07  C13   C12  N5   C11   180.00   0.0  0
 MDS  CONST_08  C15   C12  N5   C11     0.00   0.0  0
 MDS  CONST_09  C15   N4   C11  N5      0.00   0.0  0
 MDS  CONST_10  N6    C13  C12  N5    180.00   0.0  0
 MDS  CONST_11  N7    C15  C12  N5    180.00   0.0  0
 MDS  CONST_12  C14   N6   C13  C12     0.00   0.0  0
 MDS  CONST_13  C14   N7   C15  C12     0.00   0.0  0
 MDS  CONST_14  N7    C15  C12  C13     0.00   0.0  0
 MDS  CONST_15  N7    C14  N6   C13     0.00   0.0  0
 MDS  CONST_16  C15   C12  C13  N6      0.00   0.0  0
 MDS  CONST_17  C15   N7   C14  N6      0.00   0.0  0
 MDS  CONST_18  N5    C11  N4   C2    180.00   0.0  0
 MDS  CONST_19  C12   C15  N4   C2    180.00   0.0  0
 MDS  CONST_20  N7    C15  N4   C2      0.00   0.0  0
 MDS  CONST_21  N8    C13  C12  N5      0.00   0.0  0
 MDS  CONST_22  N8    C13  N6   C14   180.00   0.0  0
 MDS  CONST_23  N8    C13  C12  C15   180.00   0.0  0
 MDS  CONST_24  H11   C11  N4   C2      0.00   0.0  0
 MDS  CONST_25  H14   C14  N6   C13   180.00   0.0  0
 MDS  CONST_26  HN81  N8   C13  C12     0.00   0.0  0
 MDS  CONST_27  HN82  N8   C13  C12   180.00   0.0  0
 MDS  CONST_28  O5    C5   N2   S1      0.00   0.0  0
 MDS  CONST_29  C6    C5   N2   S1    180.00   0.0  0
 MDS  CONST_30  HN2   N2   C5   O5    180.00   0.0  0
 MDS  Var_01    S1    N1   C4   C3    178.20  30.0  3
 MDS  Var_02    O3    S1   N1   C4    175.03  30.0  3
 MDS  Var_03    C5    N2   S1   N1     57.02  30.0  3
 MDS  Var_04    S2    C8   C7   C6   -179.18  30.0  3
 MDS  Var_05    H91   C9   S2   C8    -60.32  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
 MDS  chir_01  C1   O1  C2   C10  positiv
 MDS  chir_02  C2   O2  N4   C1   positiv
 MDS  chir_03  C3   O2  C10  C4   negativ
 MDS  chir_04  C6   C5  N3   C7   positiv
 MDS  chir_05  C10  O6  C3   C1   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
 MDS  plan-1  C2    0.020
 MDS  plan-1  N4    0.020
 MDS  plan-1  C11   0.020
 MDS  plan-1  N5    0.020
 MDS  plan-1  C12   0.020
 MDS  plan-1  C13   0.020
 MDS  plan-1  N6    0.020
 MDS  plan-1  C14   0.020
 MDS  plan-1  N7    0.020
 MDS  plan-1  C15   0.020
 MDS  plan-1  N8    0.020
 MDS  plan-1  H11   0.020
 MDS  plan-1  H14   0.020
 MDS  plan-2  C13   0.020
 MDS  plan-2  N8    0.020
 MDS  plan-2  HN81  0.020
 MDS  plan-2  HN82  0.020
 MDS  plan-3  S1    0.020
 MDS  plan-3  N2    0.020
 MDS  plan-3  C5    0.020
 MDS  plan-3  O5    0.020
 MDS  plan-3  C6    0.020
 MDS  plan-3  HN2   0.020

