# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 11:25:08 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: 9-(5-O-{(S)-hydroxy[(2-hydroxy-6-methylbenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(O)c1C(=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
 B5M  B5M  9-(5-O-{(S)-hydroxy[(2-hydroxy-6-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 PERFECT
;

data_comp_B5M
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
 B5M  C13  C  CR15  0  -0.040  -12.4478  60.1817   0.4670
 B5M  C20  C  CR6   0   0.120   -8.2703  54.6525   2.3697
 B5M  C21  C  CR16  0  -0.333   -7.7035  53.3923   2.2791
 B5M  C22  C  CR16  0  -0.210   -8.4901  52.2466   2.2761
 B5M  C24  C  CR6   0   0.372  -10.4705  53.5906   2.4832
 B5M  C26  C  CH3   0  -0.717   -7.3238  55.8206   2.3730
 B5M  C02  C  CR6   0   0.459  -10.1482  66.3112   1.2235
 B5M  C03  C  CR56  0  -0.003  -10.3201  64.9189   1.1089
 B5M  C05  C  CR15  0   0.101  -10.2383  62.8363   0.7716
 B5M  C07  C  CR56  0   0.485  -11.4957  64.4030   1.6309
 B5M  C09  C  CR16  0   0.039  -12.1958  66.3807   2.2738
 B5M  C11  C  CR15  0   0.149  -12.4503  62.0904   1.7964
 B5M  C14  C  CH2   0  -0.175  -13.2620  58.9594   0.8280
 B5M  C18  C  C     0   0.621  -10.2777  56.1149   2.5217
 B5M  C19  C  CR6   0  -0.261   -9.6834  54.7696   2.4687
 B5M  C23  C  CR16  0  -0.352   -9.8578  52.3404   2.3789
 B5M  C30  C  CR15  0  -0.008  -13.2606  61.2784  -0.2546
 B5M  C32  C  CR15  0  -0.037  -13.6848  62.1883   0.8934
 B5M  N04  N  N     0  -0.451   -9.5473  63.9218   0.5756
 B5M  N06  N  NR5   0  -0.535  -11.4311  63.0605   1.4033
 B5M  N08  N  N     0  -0.458  -12.4708  65.0887   2.2258
 B5M  N10  N  N     0  -0.474  -11.1187  67.0149   1.8175
 B5M  O12  O  O     0  -0.482  -11.9441  60.8044   1.6465
 B5M  O15  O  O2    0  -0.584  -12.3774  57.9839   1.4142
 B5M  O17  O  O2    0  -0.650  -11.6160  56.0969   2.8230
 B5M  O27  O  O     0  -0.392   -9.7206  57.1565   2.3326
 B5M  O28  O  O     0  -0.676  -13.9582  56.9603   3.2314
 B5M  O29  O  OH1   0  -0.714  -11.9206  58.4580   3.8311
 B5M  O31  O  OH1   0  -0.651  -14.3608  60.8303  -0.9835
 B5M  O33  O  OH1   0  -0.653  -14.8091  61.6354   1.5151
 B5M  P16  P  P     0   1.504  -12.6067  57.4094   2.8640
 B5M  H1   H  HCR5  0   0.269  -11.5950  59.8640  -0.1421
 B5M  H2   H  HCR6  0   0.258   -6.6276  53.3010   2.2113
 B5M  H3   H  HCR6  0   0.269   -8.0247  51.2726   2.1977
 B5M  H4   H  HCH3  0   0.252   -7.4405  56.4502   1.4922
 B5M  H5   H  HCH3  0   0.248   -7.4550  56.4618   3.2435
 B5M  H6   H  HCH3  0   0.245   -6.3003  55.4508   2.3832
 B5M  H7   H  HCR5  0   0.300   -9.9224  61.8465   0.4810
 B5M  H8   H  HCR6  0   0.252  -12.9427  67.0112   2.7443
 B5M  H9   H  HCR5  0   0.292  -12.6896  62.2778   2.8467
 B5M  H10  H  HCH2  0   0.252  -14.0833  59.2080   1.5007
 B5M  H11  H  HCH2  0   0.262  -13.6792  58.5042  -0.0685
 B5M  H12  H  HCR6  0   0.273  -10.4799  51.4550   2.3858
 B5M  H13  H  HCR5  0   0.263  -12.5701  61.8449  -0.8915
 B5M  H14  H  HCR5  0   0.268  -13.8640  63.2171   0.5623
 B5M  H17  H  HOH1  0   0.488  -12.1662  54.4368   2.7052
 B5M  H18  H  HOH1  0   0.506  -12.2141  58.3957   4.7513
 B5M  H19  H  HOH1  0   0.465  -14.0479  60.4721  -1.8202
 B5M  H20  H  HOH1  0   0.464  -15.1132  62.2406   2.1993
 B5M  N01  N  NH2   0  -0.817   -9.0643  66.9437   0.7731
 B5M  O25  O  OH1   0  -0.619  -11.8018  53.5497   2.5767
 B5M  H15  H  HNH2  0   0.404   -8.9929  67.9440   0.8442
 B5M  H16  H  HNH2  0   0.411   -8.3375  66.4476   0.2884

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
 B5M  O31  C30  single    1.394  0.020  1.394
 B5M  C30  C32  single    1.525  0.020  1.525
 B5M  C30  C13  single    1.544  0.020  1.544
 B5M  C32  O33  single    1.399  0.020  1.399
 B5M  C32  C11  single    1.533  0.020  1.533
 B5M  C22  C23  aromatic  1.375  0.020  1.375
 B5M  C22  C21  aromatic  1.390  0.020  1.390
 B5M  C23  C24  aromatic  1.396  0.020  1.396
 B5M  N10  C09  aromatic  1.331  0.020  1.331
 B5M  N10  C02  aromatic  1.338  0.020  1.338
 B5M  N01  C02  single    1.333  0.020  1.333
 B5M  C13  C14  single    1.512  0.020  1.512
 B5M  C13  O12  single    1.426  0.020  1.426
 B5M  C09  N08  aromatic  1.322  0.020  1.322
 B5M  C02  C03  aromatic  1.407  0.020  1.407
 B5M  N08  C07  aromatic  1.332  0.020  1.332
 B5M  C03  C07  aromatic  1.386  0.020  1.386
 B5M  C03  N04  aromatic  1.370  0.020  1.370
 B5M  C07  N06  aromatic  1.363  0.020  1.363
 B5M  N04  C05  aromatic  1.302  0.020  1.302
 B5M  N06  C05  aromatic  1.368  0.020  1.368
 B5M  N06  C11  single    1.461  0.020  1.461
 B5M  C21  C20  aromatic  1.385  0.020  1.385
 B5M  C11  O12  single    1.390  0.020  1.390
 B5M  C24  O25  single    1.335  0.020  1.335
 B5M  C24  C19  aromatic  1.418  0.020  1.418
 B5M  O15  C14  single    1.441  0.020  1.441
 B5M  O15  P16  single    1.576  0.020  1.576
 B5M  C20  C19  aromatic  1.421  0.020  1.421
 B5M  C20  C26  single    1.503  0.020  1.503
 B5M  C19  C18  single    1.472  0.020  1.472
 B5M  O28  P16  double    1.471  0.020  1.471
 B5M  O17  P16  single    1.645  0.020  1.645
 B5M  O17  C18  single    1.372  0.020  1.372
 B5M  P16  O29  single    1.583  0.020  1.583
 B5M  C18  O27  double    1.196  0.020  1.196
 B5M  C13  H1   single    0.970  0.020  1.090
 B5M  C21  H2   single    0.930  0.020  1.080
 B5M  C22  H3   single    0.930  0.020  1.080
 B5M  C26  H4   single    0.970  0.020  1.090
 B5M  C26  H5   single    0.970  0.020  1.090
 B5M  C26  H6   single    0.970  0.020  1.090
 B5M  C05  H7   single    0.930  0.020  1.080
 B5M  C09  H8   single    0.930  0.020  1.080
 B5M  C11  H9   single    0.970  0.020  1.090
 B5M  C14  H10  single    0.970  0.020  1.090
 B5M  C14  H11  single    0.970  0.020  1.090
 B5M  C23  H12  single    0.930  0.020  1.080
 B5M  C30  H13  single    0.970  0.020  1.090
 B5M  C32  H14  single    0.970  0.020  1.090
 B5M  N01  H15  single    0.860  0.020  1.020
 B5M  N01  H16  single    0.860  0.020  1.020
 B5M  O25  H17  single    0.850  0.020  0.980
 B5M  O29  H18  single    0.850  0.020  0.980
 B5M  O31  H19  single    0.850  0.020  0.980
 B5M  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
 B5M  H1   C13  O12  108.16  3.000
 B5M  H1   C13  C30  110.86  3.000
 B5M  O12  C13  C30  105.21  3.000
 B5M  H1   C13  C14  108.52  3.000
 B5M  O12  C13  C14  110.23  3.000
 B5M  C30  C13  C14  113.72  3.000
 B5M  C19  C20  C26  124.18  3.000
 B5M  C26  C20  C21  116.71  3.000
 B5M  C19  C20  C21  119.11  3.000
 B5M  H2   C21  C22  119.55  3.000
 B5M  H2   C21  C20  119.20  3.000
 B5M  C22  C21  C20  121.24  3.000
 B5M  H3   C22  C23  119.65  3.000
 B5M  H3   C22  C21  119.91  3.000
 B5M  C23  C22  C21  120.44  3.000
 B5M  O25  C24  C23  114.54  3.000
 B5M  O25  C24  C19  125.43  3.000
 B5M  C23  C24  C19  120.02  3.000
 B5M  H6   C26  H5   107.81  3.000
 B5M  H6   C26  H4   107.74  3.000
 B5M  H5   C26  H4   107.05  3.000
 B5M  H6   C26  C20  109.16  3.000
 B5M  H5   C26  C20  112.54  3.000
 B5M  H4   C26  C20  112.33  3.000
 B5M  N10  C02  N01  119.35  3.000
 B5M  N01  C02  C03  122.75  3.000
 B5M  N10  C02  C03  117.89  3.000
 B5M  N04  C03  C07  110.75  3.000
 B5M  N04  C03  C02  133.07  3.000
 B5M  C07  C03  C02  116.18  3.000
 B5M  H7   C05  N06  122.01  3.000
 B5M  H7   C05  N04  124.68  3.000
 B5M  N06  C05  N04  113.31  3.000
 B5M  N08  C07  N06  128.03  3.000
 B5M  N06  C07  C03  105.28  3.000
 B5M  N08  C07  C03  126.69  3.000
 B5M  H8   C09  N10  115.41  3.000
 B5M  H8   C09  N08  116.14  3.000
 B5M  N10  C09  N08  128.45  3.000
 B5M  H9   C11  O12  109.99  3.000
 B5M  H9   C11  N06  107.29  3.000
 B5M  O12  C11  N06  109.34  3.000
 B5M  H9   C11  C32  112.26  3.000
 B5M  O12  C11  C32  106.79  3.000
 B5M  N06  C11  C32  111.16  3.000
 B5M  H11  C14  H10  108.34  3.000
 B5M  H11  C14  O15  106.69  3.000
 B5M  H10  C14  O15  111.45  3.000
 B5M  H11  C14  C13  110.35  3.000
 B5M  H10  C14  C13  111.63  3.000
 B5M  O15  C14  C13  108.28  3.000
 B5M  O27  C18  O17  120.03  3.000
 B5M  O27  C18  C19  127.03  3.000
 B5M  O17  C18  C19  112.94  3.000
 B5M  C18  C19  C24  122.39  3.000
 B5M  C18  C19  C20  118.64  3.000
 B5M  C24  C19  C20  118.96  3.000
 B5M  H12  C23  C24  118.68  3.000
 B5M  H12  C23  C22  121.10  3.000
 B5M  C24  C23  C22  120.22  3.000
 B5M  H13  C30  O31  111.05  3.000
 B5M  H13  C30  C32  107.70  3.000
 B5M  O31  C30  C32  111.46  3.000
 B5M  H13  C30  C13  107.87  3.000
 B5M  C32  C30  C13  102.62  3.000
 B5M  O31  C30  C13  115.57  3.000
 B5M  H14  C32  O33  111.97  3.000
 B5M  H14  C32  C30  112.23  3.000
 B5M  O33  C32  C30  108.80  3.000
 B5M  H14  C32  C11  111.71  3.000
 B5M  O33  C32  C11  111.12  3.000
 B5M  C30  C32  C11  100.45  3.000
 B5M  C05  N04  C03  104.41  3.000
 B5M  C11  N06  C07  125.17  3.000
 B5M  C11  N06  C05  128.58  3.000
 B5M  C07  N06  C05  106.24  3.000
 B5M  C09  N08  C07  111.53  3.000
 B5M  C09  N10  C02  119.26  3.000
 B5M  C11  O12  C13  111.38  3.000
 B5M  P16  O15  C14  122.10  3.000
 B5M  P16  O17  C18  125.63  3.000
 B5M  H18  O29  P16  114.01  3.000
 B5M  H19  O31  C30  108.52  3.000
 B5M  H20  O33  C32  108.74  3.000
 B5M  O29  P16  O28  116.61  3.000
 B5M  O29  P16  O17  106.43  3.000
 B5M  O28  P16  O17  108.42  3.000
 B5M  O29  P16  O15  104.92  3.000
 B5M  O17  P16  O15  100.39  3.000
 B5M  O28  P16  O15  118.34  3.000
 B5M  H16  N01  H15  118.30  3.000
 B5M  H16  N01  C02  121.12  3.000
 B5M  H15  N01  C02  120.39  3.000
 B5M  H17  O25  C24  110.90  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
 B5M  CONST_01  C23  C22  C21  C20     0.00   0.0  0
 B5M  CONST_02  C23  C24  C19  C20     0.00   0.0  0
 B5M  CONST_03  C24  C23  C22  C21     0.00   0.0  0
 B5M  CONST_04  C24  C19  C20  C21     0.00   0.0  0
 B5M  CONST_05  C19  C24  C23  C22     0.00   0.0  0
 B5M  CONST_06  C19  C20  C21  C22     0.00   0.0  0
 B5M  CONST_07  N08  C09  N10  C02     0.00   0.0  0
 B5M  CONST_08  N08  C07  C03  C02     0.00   0.0  0
 B5M  CONST_09  N06  C07  C03  C02   180.00   0.0  0
 B5M  CONST_10  C05  N04  C03  C02   180.00   0.0  0
 B5M  CONST_11  C09  N10  C02  C03     0.00   0.0  0
 B5M  CONST_12  C09  N08  C07  C03     0.00   0.0  0
 B5M  CONST_13  C05  N06  C07  C03     0.00   0.0  0
 B5M  CONST_14  N06  C05  N04  C03     0.00   0.0  0
 B5M  CONST_15  C07  C03  N04  C05     0.00   0.0  0
 B5M  CONST_16  N08  C07  N06  C05   180.00   0.0  0
 B5M  CONST_17  N10  C09  N08  C07     0.00   0.0  0
 B5M  CONST_18  N10  C02  C03  C07     0.00   0.0  0
 B5M  CONST_19  N04  C05  N06  C07     0.00   0.0  0
 B5M  CONST_20  N06  C07  N08  C09   180.00   0.0  0
 B5M  CONST_21  N10  C02  C03  N04   180.00   0.0  0
 B5M  CONST_22  N08  C07  C03  N04   180.00   0.0  0
 B5M  CONST_23  N06  C07  C03  N04     0.00   0.0  0
 B5M  CONST_24  C11  N06  C07  C03   180.00   0.0  0
 B5M  CONST_25  N08  C07  N06  C11     0.00   0.0  0
 B5M  CONST_26  N04  C05  N06  C11   180.00   0.0  0
 B5M  CONST_27  O25  C24  C19  C20   180.00   0.0  0
 B5M  CONST_28  C18  C19  C20  C21   180.00   0.0  0
 B5M  CONST_29  O25  C24  C23  C22   180.00   0.0  0
 B5M  CONST_30  C26  C20  C21  C22   180.00   0.0  0
 B5M  CONST_31  C26  C20  C19  C24   180.00   0.0  0
 B5M  CONST_32  N01  C02  C03  C07   180.00   0.0  0
 B5M  CONST_33  N01  C02  N10  C09   180.00   0.0  0
 B5M  CONST_34  C23  C24  C19  C18   180.00   0.0  0
 B5M  CONST_35  N04  C03  C02  N01     0.00   0.0  0
 B5M  CONST_36  H3   C22  C21  C20   180.00   0.0  0
 B5M  CONST_37  H12  C23  C22  C21   180.00   0.0  0
 B5M  CONST_38  H8   C09  N10  C02   180.00   0.0  0
 B5M  CONST_39  H7   C05  N04  C03   180.00   0.0  0
 B5M  CONST_40  H2   C21  C20  C19   180.00   0.0  0
 B5M  CONST_41  H15  N01  C02  C03   180.00   0.0  0
 B5M  CONST_42  H16  N01  C02  C03     0.00   0.0  0
 B5M  Var_01    O17  C18  C19  C20  -170.52  30.0  2
 B5M  Var_02    H4   C26  C20  C21   114.78  30.0  2
 B5M  Var_03    O28  P16  O15  C14    47.06  30.0  3
 B5M  Var_04    O15  P16  O17  C18    55.43  30.0  3
 B5M  Var_05    H10  C14  O15  P16    -1.19  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
 B5M  chir_01  C13  C30  C14  O12  positiv
 B5M  chir_02  C11  O12  N06  C32  negativ
 B5M  chir_03  C30  O31  C32  C13  negativ
 B5M  chir_04  C32  O33  C11  C30  negativ
 B5M  chir_05  P16  O28  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
 B5M  plan-1  C20  0.020
 B5M  plan-1  C21  0.020
 B5M  plan-1  C22  0.020
 B5M  plan-1  C24  0.020
 B5M  plan-1  C26  0.020
 B5M  plan-1  C18  0.020
 B5M  plan-1  C19  0.020
 B5M  plan-1  C23  0.020
 B5M  plan-1  H2   0.020
 B5M  plan-1  H3   0.020
 B5M  plan-1  H12  0.020
 B5M  plan-1  O25  0.020
 B5M  plan-2  C02  0.020
 B5M  plan-2  C03  0.020
 B5M  plan-2  C05  0.020
 B5M  plan-2  C07  0.020
 B5M  plan-2  C09  0.020
 B5M  plan-2  C11  0.020
 B5M  plan-2  N04  0.020
 B5M  plan-2  N06  0.020
 B5M  plan-2  N08  0.020
 B5M  plan-2  N10  0.020
 B5M  plan-2  H7   0.020
 B5M  plan-2  H8   0.020
 B5M  plan-2  N01  0.020
 B5M  plan-3  C02  0.020
 B5M  plan-3  N01  0.020
 B5M  plan-3  H15  0.020
 B5M  plan-3  H16  0.020
 B5M  plan-4  C18  0.020
 B5M  plan-4  C19  0.020
 B5M  plan-4  O17  0.020
 B5M  plan-4  O27  0.020

