# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 12:42:40 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: 9-(5-O-{(S)-hydroxy[(2-hydroxy-5-methylbenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(O)c(c1)C(=O)O[P](O)(=O)OC[C@@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
#
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
 B5Y  B5Y  9-(5-O-{(S)-hydroxy[(2-hydroxy-5-methylbenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine  ligand  53  33  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B5Y
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
 B5Y  C13  C  CH1   0  -0.084  -13.7509  58.6305   0.7518
 B5Y  C20  C  CR16  0  -0.314   -9.6079  58.1678   3.3020
 B5Y  C21  C  CR6   0   0.095   -8.3670  58.5903   2.8753
 B5Y  C22  C  CR16  0  -0.253   -7.8308  57.9645   1.7450
 B5Y  C24  C  CR6   0   0.327   -9.7831  56.5676   1.4962
 B5Y  C26  C  CH3   0  -0.726   -7.6160  59.6793   3.5818
 B5Y  C02  C  CR6   0   0.451   -7.8525  61.8661   0.3052
 B5Y  C03  C  CR56  0   0.011   -8.9758  61.0245   0.2150
 B5Y  C05  C  CR15  0   0.115  -10.4567  59.5741  -0.1791
 B5Y  C07  C  CR56  0   0.495  -10.0000  61.2746   1.1141
 B5Y  C09  C  CR16  0   0.035   -8.9303  62.9624   2.0199
 B5Y  C11  C  CH1   0   0.162  -12.2264  60.2210   1.5310
 B5Y  C14  C  CH2   0  -0.164  -14.9599  58.2977   1.6153
 B5Y  C18  C  C     0   0.628  -11.6679  56.8724   3.1843
 B5Y  C19  C  CR6   0  -0.182  -10.3370  57.1701   2.6374
 B5Y  C23  C  CR16  0  -0.313   -8.5130  56.9724   1.0782
 B5Y  C30  C  CH1   0  -0.002  -13.9318  59.9108  -0.0874
 B5Y  C32  C  CH1   0  -0.039  -13.3535  60.9923   0.8250
 B5Y  N04  N  N     0  -0.447   -9.2844  59.9586  -0.5878
 B5Y  N06  N  NR5   0  -0.531  -10.9497  60.3334   0.8475
 B5Y  N08  N  N     0  -0.455  -10.0336  62.2344   2.0358
 B5Y  N10  N  N     0  -0.473   -7.8676  62.8351   1.2288
 B5Y  O12  O  O2    0  -0.491  -12.6153  58.8823   1.5635
 B5Y  O15  O  O2    0  -0.581  -14.6312  57.3708   2.6644
 B5Y  O17  O  O2    0  -0.654  -12.4223  56.0970   2.3479
 B5Y  O27  O  O     0  -0.402  -12.0891  57.2419   4.2423
 B5Y  O28  O  O     0  -0.677  -14.4659  55.1983   1.2080
 B5Y  O29  O  OH1   0  -0.712  -14.3802  55.2931   3.8374
 B5Y  O31  O  OH1   0  -0.650  -15.2430  60.1985  -0.4575
 B5Y  O33  O  OH1   0  -0.652  -14.3380  61.3949   1.7331
 B5Y  P16  P  P     0   1.508  -14.0600  55.9207   2.4229
 B5Y  H1   H  HCH1  0   0.272  -13.5201  57.7739   0.1092
 B5Y  H2   H  HCR6  0   0.260  -10.0504  58.6323   4.1744
 B5Y  H3   H  HCR6  0   0.256   -6.8568  58.2660   1.3777
 B5Y  H4   H  HCH3  0   0.243   -7.4893  60.5520   2.9400
 B5Y  H5   H  HCH3  0   0.244   -8.1383  60.0051   4.4798
 B5Y  H6   H  HCH3  0   0.247   -6.6180  59.3506   3.8748
 B5Y  H7   H  HCR5  0   0.294  -11.0018  58.7349  -0.5827
 B5Y  H8   H  HCR6  0   0.252   -8.8784  63.7680   2.7442
 B5Y  H9   H  HCH1  0   0.284  -12.0646  60.5950   2.5456
 B5Y  H10  H  HCH2  0   0.269  -15.3376  59.1733   2.1354
 B5Y  H11  H  HCH2  0   0.257  -15.7586  57.8855   0.9976
 B5Y  H12  H  HCR6  0   0.267   -8.0804  56.5051   0.2025
 B5Y  H13  H  HCH1  0   0.262  -13.2785  59.8365  -0.9661
 B5Y  H14  H  HCH1  0   0.270  -12.9557  61.8390   0.2539
 B5Y  H17  H  HOH1  0   0.482  -11.2522  55.4163   1.0904
 B5Y  H18  H  HOH1  0   0.512  -14.2130  54.3425   3.9071
 B5Y  H19  H  HOH1  0   0.466  -15.4728  59.6534  -1.2165
 B5Y  H20  H  HOH1  0   0.465  -14.0022  62.1414   2.2398
 B5Y  N01  N  NH2   0  -0.817   -6.7879  61.7384  -0.4888
 B5Y  O25  O  OH1   0  -0.622  -10.3640  55.6096   0.7618
 B5Y  H15  H  HNH2  0   0.403   -5.9828  62.3252  -0.3541
 B5Y  H16  H  HNH2  0   0.410   -6.7245  60.9897  -1.1557

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
 B5Y  O31  C30  single    1.392  0.020  1.392
 B5Y  C30  C32  single    1.529  0.020  1.529
 B5Y  C30  C13  single    1.542  0.020  1.542
 B5Y  C32  O33  single    1.399  0.020  1.399
 B5Y  C32  C11  single    1.537  0.020  1.537
 B5Y  C13  C14  single    1.523  0.020  1.523
 B5Y  C13  O12  single    1.418  0.020  1.418
 B5Y  N01  C02  single    1.334  0.020  1.334
 B5Y  C02  N10  aromatic  1.339  0.020  1.339
 B5Y  C02  C03  aromatic  1.406  0.020  1.406
 B5Y  N10  C09  aromatic  1.331  0.020  1.331
 B5Y  C03  N04  aromatic  1.370  0.020  1.370
 B5Y  C03  C07  aromatic  1.386  0.020  1.386
 B5Y  C09  N08  aromatic  1.322  0.020  1.322
 B5Y  N04  C05  aromatic  1.300  0.020  1.300
 B5Y  C14  O15  single    1.438  0.020  1.438
 B5Y  C23  C22  aromatic  1.376  0.020  1.376
 B5Y  C23  C24  aromatic  1.397  0.020  1.397
 B5Y  C22  C21  aromatic  1.399  0.020  1.399
 B5Y  C07  N08  aromatic  1.331  0.020  1.331
 B5Y  C07  N06  aromatic  1.363  0.020  1.363
 B5Y  C05  N06  aromatic  1.369  0.020  1.369
 B5Y  N06  C11  single    1.452  0.020  1.452
 B5Y  C11  O12  single    1.394  0.020  1.394
 B5Y  O25  C24  single    1.340  0.020  1.340
 B5Y  C24  C19  aromatic  1.404  0.020  1.404
 B5Y  O28  P16  double    1.471  0.020  1.471
 B5Y  C21  C26  single    1.500  0.020  1.500
 B5Y  C21  C20  aromatic  1.379  0.020  1.379
 B5Y  C19  C20  aromatic  1.403  0.020  1.403
 B5Y  C19  C18  single    1.469  0.020  1.469
 B5Y  O15  P16  single    1.577  0.020  1.577
 B5Y  O17  P16  single    1.649  0.020  1.649
 B5Y  O17  C18  single    1.367  0.020  1.367
 B5Y  P16  O29  single    1.580  0.020  1.580
 B5Y  C18  O27  double    1.197  0.020  1.197
 B5Y  C13  H1   single    0.970  0.020  1.090
 B5Y  C20  H2   single    0.930  0.020  1.080
 B5Y  C22  H3   single    0.930  0.020  1.080
 B5Y  C26  H4   single    0.970  0.020  1.090
 B5Y  C26  H5   single    0.970  0.020  1.090
 B5Y  C26  H6   single    0.970  0.020  1.090
 B5Y  C05  H7   single    0.930  0.020  1.080
 B5Y  C09  H8   single    0.930  0.020  1.080
 B5Y  C11  H9   single    0.970  0.020  1.090
 B5Y  C14  H10  single    0.970  0.020  1.090
 B5Y  C14  H11  single    0.970  0.020  1.090
 B5Y  C23  H12  single    0.930  0.020  1.080
 B5Y  C30  H13  single    0.970  0.020  1.090
 B5Y  C32  H14  single    0.970  0.020  1.090
 B5Y  N01  H15  single    0.860  0.020  1.020
 B5Y  N01  H16  single    0.860  0.020  1.020
 B5Y  O25  H17  single    0.850  0.020  0.980
 B5Y  O29  H18  single    0.850  0.020  0.980
 B5Y  O31  H19  single    0.850  0.020  0.980
 B5Y  O33  H20  single    0.850  0.020  0.980

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
 B5Y  H1   C13  O12  107.81  3.000
 B5Y  H1   C13  C30  110.78  3.000
 B5Y  O12  C13  C30  104.95  3.000
 B5Y  H1   C13  C14  109.21  3.000
 B5Y  O12  C13  C14  110.49  3.000
 B5Y  C30  C13  C14  113.40  3.000
 B5Y  H2   C20  C19  118.31  3.000
 B5Y  H2   C20  C21  119.06  3.000
 B5Y  C19  C20  C21  122.62  3.000
 B5Y  C26  C21  C22  120.90  3.000
 B5Y  C26  C21  C20  121.83  3.000
 B5Y  C22  C21  C20  117.26  3.000
 B5Y  H3   C22  C23  118.81  3.000
 B5Y  H3   C22  C21  119.59  3.000
 B5Y  C23  C22  C21  121.59  3.000
 B5Y  O25  C24  C23  115.94  3.000
 B5Y  O25  C24  C19  125.54  3.000
 B5Y  C23  C24  C19  118.51  3.000
 B5Y  H6   C26  H5   107.91  3.000
 B5Y  H6   C26  H4   107.04  3.000
 B5Y  H5   C26  H4   107.55  3.000
 B5Y  H6   C26  C21  111.46  3.000
 B5Y  H5   C26  C21  111.44  3.000
 B5Y  H4   C26  C21  111.23  3.000
 B5Y  N10  C02  N01  119.26  3.000
 B5Y  N10  C02  C03  117.93  3.000
 B5Y  N01  C02  C03  122.81  3.000
 B5Y  N04  C03  C07  110.75  3.000
 B5Y  C07  C03  C02  116.15  3.000
 B5Y  N04  C03  C02  133.10  3.000
 B5Y  H7   C05  N06  122.01  3.000
 B5Y  H7   C05  N04  124.62  3.000
 B5Y  N06  C05  N04  113.36  3.000
 B5Y  N08  C07  N06  128.00  3.000
 B5Y  N06  C07  C03  105.27  3.000
 B5Y  N08  C07  C03  126.73  3.000
 B5Y  H8   C09  N10  115.45  3.000
 B5Y  H8   C09  N08  116.16  3.000
 B5Y  N10  C09  N08  128.38  3.000
 B5Y  H9   C11  O12  110.37  3.000
 B5Y  H9   C11  N06  106.27  3.000
 B5Y  O12  C11  N06  109.29  3.000
 B5Y  H9   C11  C32  111.29  3.000
 B5Y  O12  C11  C32  106.73  3.000
 B5Y  N06  C11  C32  112.92  3.000
 B5Y  H11  C14  H10  108.73  3.000
 B5Y  H11  C14  O15  109.70  3.000
 B5Y  H10  C14  O15  104.46  3.000
 B5Y  H11  C14  C13  110.06  3.000
 B5Y  H10  C14  C13  111.81  3.000
 B5Y  O15  C14  C13  111.91  3.000
 B5Y  O27  C18  O17  121.43  3.000
 B5Y  O27  C18  C19  125.80  3.000
 B5Y  O17  C18  C19  112.77  3.000
 B5Y  C18  C19  C24  124.94  3.000
 B5Y  C18  C19  C20  116.01  3.000
 B5Y  C24  C19  C20  119.02  3.000
 B5Y  H12  C23  C24  118.70  3.000
 B5Y  H12  C23  C22  120.32  3.000
 B5Y  C24  C23  C22  120.97  3.000
 B5Y  H13  C30  O31  111.21  3.000
 B5Y  H13  C30  C32  107.50  3.000
 B5Y  O31  C30  C32  111.63  3.000
 B5Y  H13  C30  C13  108.05  3.000
 B5Y  C32  C30  C13  102.61  3.000
 B5Y  O31  C30  C13  115.26  3.000
 B5Y  H14  C32  O33  111.81  3.000
 B5Y  H14  C32  C30  111.89  3.000
 B5Y  O33  C32  C30  108.96  3.000
 B5Y  H14  C32  C11  111.14  3.000
 B5Y  O33  C32  C11  111.24  3.000
 B5Y  C30  C32  C11  101.33  3.000
 B5Y  C05  N04  C03  104.43  3.000
 B5Y  C11  N06  C07  125.00  3.000
 B5Y  C11  N06  C05  128.80  3.000
 B5Y  C07  N06  C05  106.19  3.000
 B5Y  C09  N08  C07  111.57  3.000
 B5Y  C09  N10  C02  119.23  3.000
 B5Y  C11  O12  C13  112.36  3.000
 B5Y  P16  O15  C14  124.31  3.000
 B5Y  P16  O17  C18  125.51  3.000
 B5Y  H18  O29  P16  114.81  3.000
 B5Y  H19  O31  C30  108.51  3.000
 B5Y  H20  O33  C32  108.63  3.000
 B5Y  O29  P16  O28  119.24  3.000
 B5Y  O29  P16  O17  106.53  3.000
 B5Y  O28  P16  O17  106.80  3.000
 B5Y  O29  P16  O15   98.90  3.000
 B5Y  O17  P16  O15  105.57  3.000
 B5Y  O28  P16  O15  118.57  3.000
 B5Y  H16  N01  H15  118.26  3.000
 B5Y  H16  N01  C02  121.11  3.000
 B5Y  H15  N01  C02  120.23  3.000
 B5Y  H17  O25  C24  110.80  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
 B5Y  CONST_01  C23  C22  C21  C20     0.00   0.0  0
 B5Y  CONST_02  C23  C24  C19  C20     0.00   0.0  0
 B5Y  CONST_03  C24  C23  C22  C21     0.00   0.0  0
 B5Y  CONST_04  C24  C19  C20  C21     0.00   0.0  0
 B5Y  CONST_05  C19  C24  C23  C22     0.00   0.0  0
 B5Y  CONST_06  C19  C20  C21  C22     0.00   0.0  0
 B5Y  CONST_07  N08  C09  N10  C02     0.00   0.0  0
 B5Y  CONST_08  C05  N04  C03  C02   180.00   0.0  0
 B5Y  CONST_09  N08  C07  C03  C02     0.00   0.0  0
 B5Y  CONST_10  N06  C07  C03  C02   180.00   0.0  0
 B5Y  CONST_11  C09  N10  C02  C03     0.00   0.0  0
 B5Y  CONST_12  N06  C05  N04  C03     0.00   0.0  0
 B5Y  CONST_13  C09  N08  C07  C03     0.00   0.0  0
 B5Y  CONST_14  C05  N06  C07  C03     0.00   0.0  0
 B5Y  CONST_15  C07  C03  N04  C05     0.00   0.0  0
 B5Y  CONST_16  N08  C07  N06  C05   180.00   0.0  0
 B5Y  CONST_17  N10  C02  C03  C07     0.00   0.0  0
 B5Y  CONST_18  N10  C09  N08  C07     0.00   0.0  0
 B5Y  CONST_19  N04  C05  N06  C07     0.00   0.0  0
 B5Y  CONST_20  N06  C07  N08  C09   180.00   0.0  0
 B5Y  CONST_21  N10  C02  C03  N04   180.00   0.0  0
 B5Y  CONST_22  N08  C07  C03  N04   180.00   0.0  0
 B5Y  CONST_23  N06  C07  C03  N04     0.00   0.0  0
 B5Y  CONST_24  C11  N06  C07  C03   180.00   0.0  0
 B5Y  CONST_25  N08  C07  N06  C11     0.00   0.0  0
 B5Y  CONST_26  N04  C05  N06  C11   180.00   0.0  0
 B5Y  CONST_27  O25  C24  C19  C20   180.00   0.0  0
 B5Y  CONST_28  C18  C19  C20  C21   180.00   0.0  0
 B5Y  CONST_29  O25  C24  C23  C22   180.00   0.0  0
 B5Y  CONST_30  C23  C22  C21  C26   180.00   0.0  0
 B5Y  CONST_31  C19  C20  C21  C26   180.00   0.0  0
 B5Y  CONST_32  N01  C02  C03  C07   180.00   0.0  0
 B5Y  CONST_33  N01  C02  N10  C09   180.00   0.0  0
 B5Y  CONST_34  C23  C24  C19  C18   180.00   0.0  0
 B5Y  CONST_35  N04  C03  C02  N01     0.00   0.0  0
 B5Y  CONST_36  H3   C22  C21  C20   180.00   0.0  0
 B5Y  CONST_37  H12  C23  C22  C21   180.00   0.0  0
 B5Y  CONST_38  H2   C20  C21  C22   180.00   0.0  0
 B5Y  CONST_39  H8   C09  N10  C02   180.00   0.0  0
 B5Y  CONST_40  H7   C05  N04  C03   180.00   0.0  0
 B5Y  CONST_41  H15  N01  C02  C03   180.00   0.0  0
 B5Y  CONST_42  H16  N01  C02  C03     0.00   0.0  0
 B5Y  Var_01    O17  C18  C19  C20   167.77  30.0  2
 B5Y  Var_02    H4   C26  C21  C20  -115.50  30.0  2
 B5Y  Var_03    O28  P16  O15  C14   -31.46  30.0  3
 B5Y  Var_04    H10  C14  O15  P16   178.91  30.0  2

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
 B5Y  chir_01  C13  C30  C14  O12  positiv
 B5Y  chir_02  C11  O12  N06  C32  negativ
 B5Y  chir_03  C30  O31  C32  C13  negativ
 B5Y  chir_04  C32  O33  C11  C30  negativ
 B5Y  chir_05  P16  O15  O17  O29  both

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
 B5Y  plan-1  C20  0.020
 B5Y  plan-1  C21  0.020
 B5Y  plan-1  C22  0.020
 B5Y  plan-1  C24  0.020
 B5Y  plan-1  C26  0.020
 B5Y  plan-1  C18  0.020
 B5Y  plan-1  C19  0.020
 B5Y  plan-1  C23  0.020
 B5Y  plan-1  H2   0.020
 B5Y  plan-1  H3   0.020
 B5Y  plan-1  H12  0.020
 B5Y  plan-1  O25  0.020
 B5Y  plan-2  C02  0.020
 B5Y  plan-2  C03  0.020
 B5Y  plan-2  C05  0.020
 B5Y  plan-2  C07  0.020
 B5Y  plan-2  C09  0.020
 B5Y  plan-2  C11  0.020
 B5Y  plan-2  N04  0.020
 B5Y  plan-2  N06  0.020
 B5Y  plan-2  N08  0.020
 B5Y  plan-2  N10  0.020
 B5Y  plan-2  H7   0.020
 B5Y  plan-2  H8   0.020
 B5Y  plan-2  N01  0.020
 B5Y  plan-3  C02  0.020
 B5Y  plan-3  N01  0.020
 B5Y  plan-3  H15  0.020
 B5Y  plan-3  H16  0.020
 B5Y  plan-4  C18  0.020
 B5Y  plan-4  C19  0.020
 B5Y  plan-4  O17  0.020
 B5Y  plan-4  O27  0.020

