# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:57:49 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: 5'-O-(D-valylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(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
 54H  54H  5'-O-(D-valylsulfamoyl)adenosine  ligand  53  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_54H
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
 54H  C4    C  CR56  0   0.492   3.3140   0.0629   0.3284
 54H  C5    C  CR56  0  -0.009   3.2382  -1.3137   0.4749
 54H  C6    C  CR6   0   0.455   4.4633  -1.9991   0.5662
 54H  C8    C  CR15  0   0.117   1.2422  -0.6350   0.4031
 54H  N1    N  N     0  -0.473   5.5890  -1.2806   0.5004
 54H  N3    N  N     0  -0.453   4.4251   0.7917   0.2634
 54H  CB    C  CH1   0  -0.265  -1.4690  -2.8292  -1.3303
 54H  CG1   C  CH3   0  -0.674  -1.3046  -1.5795  -2.1891
 54H  CA    C  CH1   0  -0.188  -2.7664  -2.7696  -0.4965
 54H  N     N  NH2   0  -0.786  -3.0663  -3.9345   0.3150
 54H  C     C  C     0   0.598  -2.6994  -1.5907   0.4627
 54H  O     O  O     0  -0.424  -1.9545  -1.5614   1.4141
 54H  NAP   N  NC1   0  -0.832  -3.5309  -0.5343   0.1632
 54H  SBD   S  S     0   1.627  -3.7051   0.8157   1.1297
 54H  OAF   O  OS    0  -0.625  -4.6613   1.6404   0.4371
 54H  OAG   O  OS    0  -0.604  -3.8947   0.4354   2.4999
 54H  O5'   O  OC2   0  -0.564  -2.2658   1.4805   1.0997
 54H  C4'   C  CH1   0  -0.036  -0.5318   2.8467   0.2029
 54H  O4'   O  O2    0  -0.490   0.4246   2.0437   0.8920
 54H  C3'   C  CH1   0  -0.040   0.1506   3.3233  -1.0756
 54H  O3'   O  OH1   0  -0.662   0.8326   4.5147  -0.7978
 54H  C2'   C  CH1   0  -0.032   1.1301   2.1711  -1.3259
 54H  O2'   O  OH1   0  -0.647   2.2393   2.4936  -2.1030
 54H  C1'   C  CH1   0   0.219   1.5636   1.8428   0.1016
 54H  N9    N  NR5   0  -0.541   2.0165   0.4864   0.2815
 54H  N7    N  N     0  -0.448   1.9326  -1.7289   0.5223
 54H  C2    C  CR16  0   0.044   5.5081   0.0400   0.3579
 54H  N6    N  NH2   0  -0.815   4.5391  -3.3253   0.7008
 54H  H8    H  HCR5  0   0.278   0.1661  -0.5804   0.4311
 54H  HG2   H  HCH3  0   0.241  -0.5519  -4.0896  -2.8246
 54H  HG2A  H  HCH3  0   0.232  -1.4701  -4.9937  -1.6344
 54H  HG2B  H  HCH3  0   0.224  -2.3135  -4.0806  -2.8912
 54H  HG1   H  HCH3  0   0.251  -0.3702  -1.6129  -2.7495
 54H  HG1A  H  HCH3  0   0.237  -2.1212  -1.4846  -2.9085
 54H  HG1B  H  HCH3  0   0.207  -1.2872  -0.6592  -1.6029
 54H  HA    H  HCH1  0   0.264  -3.6045  -2.6305  -1.1877
 54H  HN    H  HNH2  0   0.366  -3.2760  -4.7190  -0.2881
 54H  HNA   H  HNH2  0   0.351  -2.2548  -4.2011   0.8601
 54H  HNAP  H  HNC1  0   0.457  -4.1653  -0.5869  -0.6256
 54H  H4'   H  HCH1  0   0.287  -0.8076   3.6903   0.8416
 54H  H3'   H  HCH1  0   0.264  -0.5633   3.4413  -1.9018
 54H  HO3'  H  HOH1  0   0.453   1.4921   4.6506  -1.4882
 54H  H2'   H  HCH1  0   0.237   0.5795   1.3155  -1.7399
 54H  HO2'  H  HOH1  0   0.471   2.0046   2.4108  -3.0330
 54H  H1'   H  HCH1  0   0.267   2.3922   2.4916   0.4069
 54H  H2    H  HCR6  0   0.252   6.4579   0.5628   0.3155
 54H  HN6   H  HNH2  0   0.410   3.7114  -3.8697   0.8700
 54H  HN6A  H  HNH2  0   0.403   5.4294  -3.7601   0.8727
 54H  C5'   C  CH2   0  -0.210  -1.7780   2.0508  -0.1265
 54H  HB    H  HCH1  0   0.240  -0.6236  -2.8951  -0.6348
 54H  CG2   C  CH3   0  -0.665  -1.4558  -4.0714  -2.2147
 54H  H5'   H  HCH2  0   0.249  -1.5726   1.2518  -0.8438
 54H  H5'A  H  HCH2  0   0.287  -2.5194   2.7212  -0.5646

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
 54H  C4   C5    aromatic  1.387  0.020  1.387
 54H  C4   N3    aromatic  1.330  0.020  1.330
 54H  C4   N9    aromatic  1.366  0.020  1.366
 54H  C5   C6    aromatic  1.407  0.020  1.407
 54H  C5   N7    aromatic  1.371  0.020  1.371
 54H  C6   N1    aromatic  1.337  0.020  1.337
 54H  C6   N6    single    1.335  0.020  1.335
 54H  C8   N9    aromatic  1.368  0.020  1.368
 54H  C8   N7    aromatic  1.299  0.020  1.299
 54H  N1   C2    aromatic  1.331  0.020  1.331
 54H  N3   C2    aromatic  1.322  0.020  1.322
 54H  CG2  CB    single    1.525  0.020  1.525
 54H  CB   CG1   single    1.525  0.020  1.525
 54H  CB   CA    single    1.543  0.020  1.543
 54H  CA   N     single    1.451  0.020  1.451
 54H  CA   C     single    1.521  0.020  1.521
 54H  C    O     double    1.209  0.020  1.209
 54H  C    NAP   single    1.377  0.020  1.377
 54H  NAP  SBD   single    1.669  0.020  1.669
 54H  SBD  OAF   deloc     1.440  0.020  1.440
 54H  SBD  OAG   deloc     1.435  0.020  1.435
 54H  SBD  O5'   single    1.586  0.020  1.586
 54H  O5'  C5'   single    1.438  0.020  1.438
 54H  C5'  C4'   single    1.515  0.020  1.515
 54H  C4'  O4'   single    1.426  0.020  1.426
 54H  C4'  C3'   single    1.526  0.020  1.526
 54H  O4'  C1'   single    1.401  0.020  1.401
 54H  C3'  O3'   single    1.401  0.020  1.401
 54H  C3'  C2'   single    1.533  0.020  1.533
 54H  C2'  O2'   single    1.392  0.020  1.392
 54H  C2'  C1'   single    1.528  0.020  1.528
 54H  C1'  N9    single    1.441  0.020  1.441
 54H  C8   H8    single    0.930  0.020  1.080
 54H  CG2  HG2   single    0.970  0.020  1.090
 54H  CG2  HG2A  single    0.970  0.020  1.090
 54H  CG2  HG2B  single    0.970  0.020  1.090
 54H  CB   HB    single    0.970  0.020  1.090
 54H  CG1  HG1   single    0.970  0.020  1.090
 54H  CG1  HG1A  single    0.970  0.020  1.090
 54H  CG1  HG1B  single    0.970  0.020  1.090
 54H  CA   HA    single    0.970  0.020  1.090
 54H  N    HN    single    0.890  0.020  1.040
 54H  N    HNA   single    0.890  0.020  1.040
 54H  NAP  HNAP  single    0.860  0.020  1.020
 54H  C5'  H5'   single    0.970  0.020  1.090
 54H  C5'  H5'A  single    0.970  0.020  1.090
 54H  C4'  H4'   single    0.970  0.020  1.090
 54H  C3'  H3'   single    0.970  0.020  1.090
 54H  O3'  HO3'  single    0.850  0.020  0.980
 54H  C2'  H2'   single    0.970  0.020  1.090
 54H  O2'  HO2'  single    0.850  0.020  0.980
 54H  C1'  H1'   single    0.970  0.020  1.090
 54H  C2   H2    single    0.930  0.020  1.080
 54H  N6   HN6   single    0.860  0.020  1.020
 54H  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
 54H  N9    C4   N3    128.46  3.000
 54H  N9    C4   C5    105.05  3.000
 54H  N3    C4   C5    126.49  3.000
 54H  N7    C5   C6    132.81  3.000
 54H  N7    C5   C4    110.88  3.000
 54H  C6    C5   C4    116.30  3.000
 54H  N6    C6   N1    119.40  3.000
 54H  N6    C6   C5    122.68  3.000
 54H  N1    C6   C5    117.92  3.000
 54H  H8    C8   N7    124.81  3.000
 54H  H8    C8   N9    121.72  3.000
 54H  N7    C8   N9    113.43  3.000
 54H  C2    N1   C6    119.17  3.000
 54H  C2    N3   C4    111.68  3.000
 54H  HB    CB   CA    107.93  3.000
 54H  HB    CB   CG1   108.86  3.000
 54H  CA    CB   CG1   111.29  3.000
 54H  HB    CB   CG2   108.19  3.000
 54H  CA    CB   CG2   110.61  3.000
 54H  CG1   CB   CG2   109.87  3.000
 54H  HG1B  CG1  HG1A  107.00  3.000
 54H  HG1B  CG1  HG1   106.76  3.000
 54H  HG1A  CG1  HG1   107.75  3.000
 54H  HG1B  CG1  CB    112.97  3.000
 54H  HG1A  CG1  CB    111.19  3.000
 54H  HG1   CG1  CB    110.90  3.000
 54H  HA    CA   C     109.46  3.000
 54H  HA    CA   N     107.26  3.000
 54H  C     CA   N     106.18  3.000
 54H  HA    CA   CB    107.89  3.000
 54H  C     CA   CB    109.48  3.000
 54H  N     CA   CB    116.42  3.000
 54H  HNA   N    HN    106.43  3.000
 54H  HNA   N    CA    110.28  3.000
 54H  HN    N    CA    109.39  3.000
 54H  NAP   C    O     121.64  3.000
 54H  NAP   C    CA    115.51  3.000
 54H  O     C    CA    122.84  3.000
 54H  HNAP  NAP  SBD   115.29  3.000
 54H  HNAP  NAP  C     120.48  3.000
 54H  SBD   NAP  C     123.88  3.000
 54H  O5'   SBD  OAG   104.43  3.000
 54H  O5'   SBD  OAF   110.70  3.000
 54H  OAG   SBD  OAF   121.56  3.000
 54H  O5'   SBD  NAP   103.49  3.000
 54H  OAG   SBD  NAP   110.63  3.000
 54H  OAF   SBD  NAP   104.72  3.000
 54H  C5'   O5'  SBD   119.37  3.000
 54H  H4'   C4'  C3'   111.18  3.000
 54H  H4'   C4'  O4'   108.74  3.000
 54H  C3'   C4'  O4'   106.31  3.000
 54H  H4'   C4'  C5'   108.95  3.000
 54H  C3'   C4'  C5'   110.48  3.000
 54H  O4'   C4'  C5'   111.16  3.000
 54H  C1'   O4'  C4'   110.69  3.000
 54H  H3'   C3'  C2'   111.92  3.000
 54H  H3'   C3'  O3'   111.98  3.000
 54H  C2'   C3'  O3'   111.14  3.000
 54H  H3'   C3'  C4'   111.91  3.000
 54H  C2'   C3'  C4'   100.82  3.000
 54H  O3'   C3'  C4'   108.50  3.000
 54H  HO3'  O3'  C3'   108.11  3.000
 54H  H2'   C2'  C1'   109.09  3.000
 54H  H2'   C2'  O2'   111.68  3.000
 54H  C1'   C2'  O2'   110.20  3.000
 54H  H2'   C2'  C3'   109.07  3.000
 54H  C1'   C2'  C3'   100.97  3.000
 54H  O2'   C2'  C3'   115.22  3.000
 54H  HO2'  O2'  C2'   108.97  3.000
 54H  H1'   C1'  N9    106.55  3.000
 54H  H1'   C1'  C2'   110.35  3.000
 54H  N9    C1'  C2'   114.08  3.000
 54H  H1'   C1'  O4'   111.88  3.000
 54H  N9    C1'  O4'   108.67  3.000
 54H  C2'   C1'  O4'   105.41  3.000
 54H  C1'   N9   C8    127.20  3.000
 54H  C1'   N9   C4    126.49  3.000
 54H  C8    N9   C4    106.29  3.000
 54H  C8    N7   C5    104.36  3.000
 54H  H2    C2   N3    116.13  3.000
 54H  H2    C2   N1    115.41  3.000
 54H  N3    C2   N1    128.45  3.000
 54H  HN6A  N6   HN6   117.78  3.000
 54H  HN6A  N6   C6    119.80  3.000
 54H  HN6   N6   C6    120.55  3.000
 54H  H5'A  C5'  H5'   108.26  3.000
 54H  H5'A  C5'  C4'   108.87  3.000
 54H  H5'   C5'  C4'   111.84  3.000
 54H  H5'A  C5'  O5'   110.83  3.000
 54H  H5'   C5'  O5'   109.48  3.000
 54H  C4'   C5'  O5'   107.58  3.000
 54H  HG2B  CG2  HG2A  108.20  3.000
 54H  HG2B  CG2  HG2   107.71  3.000
 54H  HG2A  CG2  HG2   107.13  3.000
 54H  HG2B  CG2  CB    111.05  3.000
 54H  HG2A  CG2  CB    112.37  3.000
 54H  HG2   CG2  CB    110.19  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
 54H  CONST_01  N1    C6   C5   C4      0.00   0.0  0
 54H  CONST_02  C8    N7   C5   C4      0.00   0.0  0
 54H  CONST_03  N1    C2   N3   C4      0.00   0.0  0
 54H  CONST_04  N7    C8   N9   C4      0.00   0.0  0
 54H  CONST_05  C2    N3   C4   C5      0.00   0.0  0
 54H  CONST_06  C8    N9   C4   C5      0.00   0.0  0
 54H  CONST_07  C2    N1   C6   C5      0.00   0.0  0
 54H  CONST_08  N9    C8   N7   C5      0.00   0.0  0
 54H  CONST_09  N3    C4   C5   C6      0.00   0.0  0
 54H  CONST_10  N9    C4   C5   C6    180.00   0.0  0
 54H  CONST_11  C8    N7   C5   C6    180.00   0.0  0
 54H  CONST_12  N3    C2   N1   C6      0.00   0.0  0
 54H  CONST_13  N3    C4   N9   C8    180.00   0.0  0
 54H  CONST_14  N7    C5   C6   N1    180.00   0.0  0
 54H  CONST_15  N7    C5   C4   N3    180.00   0.0  0
 54H  CONST_16  N7    C5   C4   N9      0.00   0.0  0
 54H  CONST_17  C2    N3   C4   N9    180.00   0.0  0
 54H  CONST_18  C1'   N9   C4   C5    180.00   0.0  0
 54H  CONST_19  C1'   N9   C4   N3      0.00   0.0  0
 54H  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 54H  CONST_21  N6    C6   C5   C4    180.00   0.0  0
 54H  CONST_22  N6    C6   C5   N7      0.00   0.0  0
 54H  CONST_23  N6    C6   N1   C2    180.00   0.0  0
 54H  CONST_24  H2    C2   N3   C4    180.00   0.0  0
 54H  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 54H  CONST_26  HN6   N6   C6   C5      0.00   0.0  0
 54H  CONST_27  HN6A  N6   C6   C5    180.00   0.0  0
 54H  CONST_28  SBD   NAP  C    CA    180.00   0.0  0
 54H  CONST_29  SBD   NAP  C    O       0.00   0.0  0
 54H  CONST_30  HNAP  NAP  C    CA      0.00   0.0  0
 54H  Var_01    C4'   C5'  O5'  SBD   168.70  30.0  3
 54H  Var_02    OAF   SBD  NAP  C    -179.85  30.0  3
 54H  Var_03    HG1   CG1  CB   CG2   -59.06  30.0  3
 54H  Var_04    HG2   CG2  CB   CG1    54.87  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
 54H  chir_01  CA   CB   N    C    negativ
 54H  chir_02  C4'  O4'  C5'  C3'  positiv
 54H  chir_03  C3'  O3'  C4'  C2'  positiv
 54H  chir_04  C2'  O2'  C3'  C1'  positiv
 54H  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
 54H  plan-1  C4    0.020
 54H  plan-1  C5    0.020
 54H  plan-1  C6    0.020
 54H  plan-1  C8    0.020
 54H  plan-1  N1    0.020
 54H  plan-1  N3    0.020
 54H  plan-1  C1'   0.020
 54H  plan-1  N9    0.020
 54H  plan-1  N7    0.020
 54H  plan-1  C2    0.020
 54H  plan-1  N6    0.020
 54H  plan-1  H8    0.020
 54H  plan-1  H2    0.020
 54H  plan-2  C6    0.020
 54H  plan-2  N6    0.020
 54H  plan-2  HN6   0.020
 54H  plan-2  HN6A  0.020
 54H  plan-3  CA    0.020
 54H  plan-3  C     0.020
 54H  plan-3  O     0.020
 54H  plan-3  NAP   0.020
 54H  plan-3  SBD   0.020
 54H  plan-3  HNAP  0.020

