# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 08:00:24 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: 5'-deoxy-5'-{[(3-hydroxybenzene-1-carbonyl)sulfamoyl]amino}adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CN[S](=O)(=O)NC(=O)c4cccc(O)c4)[C@@H](O)[C@H]3O
#
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
 R2V  R2V  5'-deoxy-5'-{[(3-hydroxybenzene-1-carbonyl)sulfamoyl]amino}adenosine  ligand  51  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R2V
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
 R2V  N10  N  NR5   0  -0.543  19.9476   -9.1403  11.9881
 R2V  C02  C  CR6   0   0.366  23.4222   -9.2609  12.4127
 R2V  C04  C  CR16  0   0.084  22.4319   -9.8955  14.3828
 R2V  C06  C  CR56  0   0.528  21.0708   -9.3804  12.7320
 R2V  C07  C  CR56  0   0.010  22.1305   -9.0952  11.8833
 R2V  C09  C  CR15  0   0.117  20.3899   -8.7211  10.7618
 R2V  C11  C  CH1   0   0.193  18.5523   -9.3104  12.3351
 R2V  C13  C  CH1   0  -0.008  17.7390   -9.5531  14.5042
 R2V  C14  C  CH2   0  -0.337  18.3178   -9.2438  15.8663
 R2V  C20  C  C     0   0.564  20.7240   -6.4582  15.3484
 R2V  C22  C  CR6   0   0.083  22.1234   -6.4345  14.8485
 R2V  C23  C  CR16  0  -0.335  23.2234   -6.5916  15.6895
 R2V  C24  C  CR16  0  -0.189  24.4989   -6.4958  15.1574
 R2V  C25  C  CR16  0  -0.336  24.6894   -6.2453  13.8084
 R2V  C26  C  CR6   0   0.363  23.5886   -6.0893  12.9693
 R2V  C28  C  CR16  0  -0.372  22.3054   -6.1828  13.4939
 R2V  C30  C  CH1   0  -0.023  18.1100  -10.9539  14.0205
 R2V  C32  C  CH1   0  -0.072  18.1100  -10.7700  12.4966
 R2V  N01  N  NH2   0  -0.772  24.5274   -9.0544  11.6890
 R2V  N03  N  N     0  -0.496  23.5358   -9.6686  13.6788
 R2V  N05  N  N     0  -0.512  21.1733   -9.7872  13.9950
 R2V  N08  N  N     0  -0.413  21.6830   -8.6847  10.6556
 R2V  N15  N  NC1   0  -0.708  17.9937   -7.8714  16.2666
 R2V  N19  N  NC1   0  -0.876  20.5223   -7.0856  16.5527
 R2V  O12  O  O2    0  -0.509  18.2761   -8.6598  13.5410
 R2V  O17  O  OS    0  -0.583  19.2292   -8.0055  18.4276
 R2V  O18  O  OS    0  -0.599  18.5446   -5.7786  17.4789
 R2V  O21  O  O     0  -0.405  19.8033   -5.9423  14.7528
 R2V  O27  O  OH1   0  -0.650  23.7064   -5.8514  11.6512
 R2V  O31  O  OH1   0  -0.671  17.1635  -11.8845  14.4675
 R2V  O33  O  OH1   0  -0.673  16.8078  -10.8696  11.9883
 R2V  S16  S  S     0   1.461  19.0092   -7.1322  17.2964
 R2V  H1   H  HCR6  0   0.258  22.5885  -10.2150  15.4075
 R2V  H2   H  HCR5  0   0.290  19.6913   -8.4585   9.9805
 R2V  H3   H  HCH1  0   0.273  17.9934   -8.8518  11.5136
 R2V  H4   H  HCH1  0   0.274  16.6457   -9.4493  14.5315
 R2V  H5   H  HCH2  0   0.288  17.8932   -9.9412  16.5895
 R2V  H6   H  HCR6  0   0.225  23.1103   -6.7493  16.7542
 R2V  H7   H  HCR6  0   0.267  25.3590   -6.6076  15.8036
 R2V  H8   H  HCR6  0   0.290  25.6950   -6.1698  13.4104
 R2V  H9   H  HCR6  0   0.265  21.4516   -6.0668  12.8386
 R2V  H10  H  HCH1  0   0.293  19.1210  -11.2035  14.3558
 R2V  H11  H  HCH1  0   0.302  18.7969  -11.4572  11.9872
 R2V  H12  H  HNH2  0   0.390  25.4230   -9.0602  12.1462
 R2V  H13  H  HNH2  0   0.387  24.4677   -8.6100  10.7892
 R2V  H14  H  HNC1  0   0.425  21.2408   -7.6547  16.9787
 R2V  H15  H  HOH1  0   0.469  24.6346   -5.7998  11.3974
 R2V  H16  H  HOH1  0   0.454  17.5658  -12.7594  14.4714
 R2V  H17  H  HOH1  0   0.460  16.3348  -11.5195  12.5247
 R2V  H18  H  HCH2  0   0.293  19.3974   -9.4068  15.8225
 R2V  H19  H  HNC1  0   0.408  17.7009   -7.2511  15.5169

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
 R2V  N03  C04  aromatic  1.329  0.020  1.329
 R2V  N03  C02  aromatic  1.335  0.020  1.335
 R2V  C04  N05  aromatic  1.321  0.020  1.321
 R2V  N01  C02  single    1.337  0.020  1.337
 R2V  C02  C07  aromatic  1.406  0.020  1.406
 R2V  N05  C06  aromatic  1.331  0.020  1.331
 R2V  C07  C06  aromatic  1.387  0.020  1.387
 R2V  C07  N08  aromatic  1.370  0.020  1.370
 R2V  C06  N10  aromatic  1.368  0.020  1.368
 R2V  N08  C09  aromatic  1.298  0.020  1.298
 R2V  N10  C09  aromatic  1.369  0.020  1.369
 R2V  N10  C11  single    1.448  0.020  1.448
 R2V  C11  O12  single    1.398  0.020  1.398
 R2V  C11  C32  single    1.534  0.020  1.534
 R2V  O33  C32  single    1.401  0.020  1.401
 R2V  O12  C13  single    1.419  0.020  1.419
 R2V  C32  C30  single    1.535  0.020  1.535
 R2V  O27  C26  single    1.345  0.020  1.345
 R2V  O21  C20  double    1.212  0.020  1.212
 R2V  C28  C26  aromatic  1.389  0.020  1.389
 R2V  C28  C22  aromatic  1.390  0.020  1.390
 R2V  C13  C30  single    1.528  0.020  1.528
 R2V  C13  C14  single    1.512  0.020  1.512
 R2V  C30  O31  single    1.401  0.020  1.401
 R2V  C26  C25  aromatic  1.393  0.020  1.393
 R2V  N15  C14  single    1.466  0.020  1.466
 R2V  N15  S16  single    1.624  0.020  1.624
 R2V  C20  C22  single    1.486  0.020  1.486
 R2V  C20  N19  single    1.373  0.020  1.373
 R2V  O18  S16  double    1.443  0.020  1.443
 R2V  C22  C23  aromatic  1.394  0.020  1.394
 R2V  S16  N19  single    1.687  0.020  1.687
 R2V  S16  O17  double    1.446  0.020  1.446
 R2V  C25  C24  aromatic  1.385  0.020  1.385
 R2V  C23  C24  aromatic  1.385  0.020  1.385
 R2V  C04  H1   single    0.930  0.020  1.080
 R2V  C09  H2   single    0.930  0.020  1.080
 R2V  C11  H3   single    0.970  0.020  1.090
 R2V  C13  H4   single    0.970  0.020  1.090
 R2V  C14  H5   single    0.970  0.020  1.090
 R2V  C23  H6   single    0.930  0.020  1.080
 R2V  C24  H7   single    0.930  0.020  1.080
 R2V  C25  H8   single    0.930  0.020  1.080
 R2V  C28  H9   single    0.930  0.020  1.080
 R2V  C30  H10  single    0.970  0.020  1.090
 R2V  C32  H11  single    0.970  0.020  1.090
 R2V  N01  H12  single    0.860  0.020  1.020
 R2V  N01  H13  single    0.860  0.020  1.020
 R2V  N19  H14  single    0.860  0.020  1.020
 R2V  O27  H15  single    0.850  0.020  0.980
 R2V  O31  H16  single    0.850  0.020  0.980
 R2V  O33  H17  single    0.850  0.020  0.980
 R2V  C14  H18  single    0.970  0.020  1.090
 R2V  N15  H19  single    0.890  0.020  1.040

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
 R2V  C11  N10  C09  124.19  3.000
 R2V  C11  N10  C06  129.80  3.000
 R2V  C09  N10  C06  105.99  3.000
 R2V  N03  C02  N01  119.35  3.000
 R2V  N01  C02  C07  122.51  3.000
 R2V  N03  C02  C07  118.12  3.000
 R2V  H1   C04  N05  116.03  3.000
 R2V  H1   C04  N03  115.52  3.000
 R2V  N05  C04  N03  128.45  3.000
 R2V  N05  C06  C07  125.78  3.000
 R2V  C07  C06  N10  104.97  3.000
 R2V  N05  C06  N10  129.25  3.000
 R2V  N08  C07  C06  111.13  3.000
 R2V  N08  C07  C02  132.31  3.000
 R2V  C06  C07  C02  116.57  3.000
 R2V  H2   C09  N08  125.32  3.000
 R2V  H2   C09  N10  120.88  3.000
 R2V  N08  C09  N10  113.80  3.000
 R2V  H3   C11  O12  110.59  3.000
 R2V  H3   C11  C32  109.30  3.000
 R2V  O12  C11  C32  107.17  3.000
 R2V  H3   C11  N10  105.25  3.000
 R2V  C32  C11  N10  114.51  3.000
 R2V  O12  C11  N10  110.03  3.000
 R2V  H4   C13  O12  109.51  3.000
 R2V  H4   C13  C30  109.65  3.000
 R2V  O12  C13  C30  105.69  3.000
 R2V  H4   C13  C14  109.83  3.000
 R2V  C30  C13  C14  112.32  3.000
 R2V  O12  C13  C14  109.74  3.000
 R2V  H18  C14  H5   108.41  3.000
 R2V  H18  C14  N15  111.66  3.000
 R2V  H5   C14  N15  109.36  3.000
 R2V  H18  C14  C13  108.16  3.000
 R2V  H5   C14  C13  108.51  3.000
 R2V  N15  C14  C13  110.66  3.000
 R2V  O21  C20  N19  120.94  3.000
 R2V  N19  C20  C22  116.14  3.000
 R2V  O21  C20  C22  122.90  3.000
 R2V  C28  C22  C23  120.35  3.000
 R2V  C23  C22  C20  122.58  3.000
 R2V  C28  C22  C20  117.01  3.000
 R2V  H6   C23  C24  118.96  3.000
 R2V  H6   C23  C22  121.84  3.000
 R2V  C24  C23  C22  119.16  3.000
 R2V  H7   C24  C25  119.42  3.000
 R2V  H7   C24  C23  119.70  3.000
 R2V  C25  C24  C23  120.88  3.000
 R2V  H8   C25  C26  120.27  3.000
 R2V  H8   C25  C24  119.85  3.000
 R2V  C26  C25  C24  119.88  3.000
 R2V  O27  C26  C28  117.57  3.000
 R2V  C28  C26  C25  119.66  3.000
 R2V  O27  C26  C25  122.76  3.000
 R2V  H9   C28  C26  119.51  3.000
 R2V  H9   C28  C22  120.41  3.000
 R2V  C26  C28  C22  120.08  3.000
 R2V  H10  C30  O31  112.03  3.000
 R2V  H10  C30  C32  109.36  3.000
 R2V  O31  C30  C32  113.36  3.000
 R2V  H10  C30  C13  109.67  3.000
 R2V  O31  C30  C13  110.13  3.000
 R2V  C32  C30  C13  101.80  3.000
 R2V  H11  C32  O33  111.64  3.000
 R2V  H11  C32  C30  112.70  3.000
 R2V  O33  C32  C30  110.58  3.000
 R2V  H11  C32  C11  111.52  3.000
 R2V  C30  C32  C11  102.62  3.000
 R2V  O33  C32  C11  107.30  3.000
 R2V  H13  N01  H12  117.54  3.000
 R2V  H13  N01  C02  120.24  3.000
 R2V  H12  N01  C02  119.29  3.000
 R2V  C04  N03  C02  118.94  3.000
 R2V  C06  N05  C04  112.14  3.000
 R2V  C09  N08  C07  104.11  3.000
 R2V  H19  N15  S16  111.72  3.000
 R2V  H19  N15  C14  115.71  3.000
 R2V  S16  N15  C14  117.45  3.000
 R2V  H14  N19  S16  115.87  3.000
 R2V  H14  N19  C20  121.51  3.000
 R2V  S16  N19  C20  122.08  3.000
 R2V  C13  O12  C11  111.55  3.000
 R2V  H15  O27  C26  110.61  3.000
 R2V  H16  O31  C30  108.83  3.000
 R2V  H17  O33  C32  107.54  3.000
 R2V  O18  S16  O17  121.11  3.000
 R2V  O17  S16  N19  103.01  3.000
 R2V  O18  S16  N19  108.59  3.000
 R2V  O17  S16  N15  108.44  3.000
 R2V  N19  S16  N15  107.09  3.000
 R2V  O18  S16  N15  107.81  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
 R2V  CONST_01  C04  N05  C06  N10   180.00   0.0  0
 R2V  CONST_02  C02  C07  C06  N10   180.00   0.0  0
 R2V  CONST_03  N08  C07  C06  N10     0.00   0.0  0
 R2V  CONST_04  C07  N08  C09  N10     0.00   0.0  0
 R2V  CONST_05  N05  C04  N03  C02     0.00   0.0  0
 R2V  CONST_06  N05  C06  C07  C02     0.00   0.0  0
 R2V  CONST_07  C09  N08  C07  C02   180.00   0.0  0
 R2V  CONST_08  C07  C02  N03  C04     0.00   0.0  0
 R2V  CONST_09  C07  C06  N05  C04     0.00   0.0  0
 R2V  CONST_10  N03  C04  N05  C06     0.00   0.0  0
 R2V  CONST_11  N03  C02  C07  C06     0.00   0.0  0
 R2V  CONST_12  C09  N08  C07  C06     0.00   0.0  0
 R2V  CONST_13  N08  C09  N10  C06     0.00   0.0  0
 R2V  CONST_14  C09  N10  C06  C07     0.00   0.0  0
 R2V  CONST_15  N05  C06  N10  C09   180.00   0.0  0
 R2V  CONST_16  C25  C26  C28  C22     0.00   0.0  0
 R2V  CONST_17  C25  C24  C23  C22     0.00   0.0  0
 R2V  CONST_18  C26  C28  C22  C23     0.00   0.0  0
 R2V  CONST_19  C26  C25  C24  C23     0.00   0.0  0
 R2V  CONST_20  C28  C26  C25  C24     0.00   0.0  0
 R2V  CONST_21  C28  C22  C23  C24     0.00   0.0  0
 R2V  CONST_22  N08  C07  C02  N03   180.00   0.0  0
 R2V  CONST_23  N08  C07  C06  N05   180.00   0.0  0
 R2V  CONST_24  C11  N10  C06  C07   180.00   0.0  0
 R2V  CONST_25  N05  C06  N10  C11     0.00   0.0  0
 R2V  CONST_26  N08  C09  N10  C11   180.00   0.0  0
 R2V  CONST_27  N01  C02  N03  C04   180.00   0.0  0
 R2V  CONST_28  N01  C02  C07  C06   180.00   0.0  0
 R2V  CONST_29  C26  C28  C22  C20   180.00   0.0  0
 R2V  CONST_30  C24  C23  C22  C20   180.00   0.0  0
 R2V  CONST_31  O27  C26  C28  C22   180.00   0.0  0
 R2V  CONST_32  O27  C26  C25  C24   180.00   0.0  0
 R2V  CONST_33  N08  C07  C02  N01     0.00   0.0  0
 R2V  CONST_34  H1   C04  N03  C02   180.00   0.0  0
 R2V  CONST_35  H2   C09  N10  C06   180.00   0.0  0
 R2V  CONST_36  H7   C24  C23  C22   180.00   0.0  0
 R2V  CONST_37  H9   C28  C22  C23   180.00   0.0  0
 R2V  CONST_38  H8   C25  C24  C23   180.00   0.0  0
 R2V  CONST_39  H6   C23  C24  C25   180.00   0.0  0
 R2V  CONST_40  H12  N01  C02  C07   180.00   0.0  0
 R2V  CONST_41  H13  N01  C02  C07     0.00   0.0  0
 R2V  CONST_42  S16  N19  C20  C22   180.00   0.0  0
 R2V  CONST_43  H14  N19  C20  C22     0.00   0.0  0
 R2V  CONST_44  S16  N19  C20  O21     0.00   0.0  0
 R2V  Var_01    O21  C20  C22  C23   157.12  30.0  2
 R2V  Var_02    S16  N15  C14  C13  -153.17  30.0  1
 R2V  Var_03    O18  S16  N15  C14   176.35  30.0  3
 R2V  Var_04    N15  S16  N19  C20    59.39  30.0  1

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
 R2V  chir_01  C11  N10  O12  C32  positiv
 R2V  chir_02  C13  O12  C14  C30  positiv
 R2V  chir_03  C30  O31  C13  C32  positiv
 R2V  chir_04  C32  O33  C30  C11  positiv

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
 R2V  plan-1  C20  0.020
 R2V  plan-1  C22  0.020
 R2V  plan-1  C23  0.020
 R2V  plan-1  C24  0.020
 R2V  plan-1  C25  0.020
 R2V  plan-1  C26  0.020
 R2V  plan-1  C28  0.020
 R2V  plan-1  O27  0.020
 R2V  plan-1  H6   0.020
 R2V  plan-1  H7   0.020
 R2V  plan-1  H8   0.020
 R2V  plan-1  H9   0.020
 R2V  plan-2  N10  0.020
 R2V  plan-2  C02  0.020
 R2V  plan-2  C04  0.020
 R2V  plan-2  C06  0.020
 R2V  plan-2  C07  0.020
 R2V  plan-2  C09  0.020
 R2V  plan-2  C11  0.020
 R2V  plan-2  N01  0.020
 R2V  plan-2  N03  0.020
 R2V  plan-2  N05  0.020
 R2V  plan-2  N08  0.020
 R2V  plan-2  H1   0.020
 R2V  plan-2  H2   0.020
 R2V  plan-3  C02  0.020
 R2V  plan-3  N01  0.020
 R2V  plan-3  H12  0.020
 R2V  plan-3  H13  0.020
 R2V  plan-4  C20  0.020
 R2V  plan-4  C22  0.020
 R2V  plan-4  N19  0.020
 R2V  plan-4  O21  0.020
 R2V  plan-4  S16  0.020
 R2V  plan-4  H14  0.020

