# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 09:11:24 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 9-(5-O-{(S)-hydroxy[(2-hydroxybenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@@H](CO[P](O)(=O)OC(=O)c4ccccc4O)[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
 B5V  B5V  9-(5-O-{(S)-hydroxy[(2-hydroxybenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine  ligand  50  32  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B5V
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
 B5V  C13  C  CH1   0  -0.009   0.3124   2.7952  -1.2741
 B5V  C20  C  CR16  0  -0.251  -1.6745  -1.0272  -0.9383
 B5V  C21  C  CR16  0  -0.258  -1.4919  -2.1021  -1.7771
 B5V  C22  C  CR16  0  -0.218  -1.6880  -3.3928  -1.2847
 B5V  C24  C  CR6   0   0.373  -2.2628  -2.5201   0.8838
 B5V  C02  C  CR6   0   0.485   1.1158  -3.1865   1.2846
 B5V  C03  C  CR56  0   0.015   1.4614  -2.3232   0.2280
 B5V  C05  C  CR15  0   0.121   2.0590  -1.3581  -1.5528
 B5V  C07  C  CR56  0   0.599   1.3630  -0.9682   0.4805
 B5V  C09  C  CR16  0   0.082   0.6802  -1.3207   2.5571
 B5V  C11  C  CH1   0   0.234   1.7755   1.0703  -0.8294
 B5V  C14  C  CH2   0  -0.183   0.0218   3.8066  -0.1861
 B5V  C18  C  C     0   0.636  -2.1745  -0.0897   1.3254
 B5V  C19  C  CR6   0  -0.241  -2.0579  -1.2115   0.3984
 B5V  C23  C  CR16  0  -0.325  -2.0716  -3.6031   0.0223
 B5V  C29  C  CH1   0  -0.046   1.5954   3.0386  -2.0801
 B5V  C31  C  CH1   0  -0.048   2.1578   1.6065  -2.2000
 B5V  N04  N  N     0  -0.447   1.9020  -2.5451  -1.0500
 B5V  N06  N  NR5   0  -0.560   1.7538  -0.3555  -0.6702
 B5V  N08  N  N     0  -0.595   0.9624  -0.4115   1.6295
 B5V  N10  N  N     0  -0.463   0.7400  -2.6352   2.4491
 B5V  O12  O  O2    0  -0.499   0.4621   1.5164  -0.6643
 B5V  O15  O  O2    0  -0.580  -1.1955   3.4641   0.4897
 B5V  O17  O  O2    0  -0.587  -1.9338   1.1088   0.7763
 B5V  O26  O  O     0  -0.462  -2.4398  -0.2059   2.5059
 B5V  O27  O  O     0  -0.679  -2.3846   2.8944   2.6374
 B5V  O28  O  OH1   0  -0.787  -0.0170   1.9667   2.2449
 B5V  O30  O  OH1   0  -0.662   2.4690   3.8606  -1.3546
 B5V  O32  O  OH1   0  -0.653   3.5331   1.5363  -2.4100
 B5V  P16  P  P     0   1.474  -1.4014   2.4056   1.6576
 B5V  H1   H  HCH1  0   0.273  -0.5436   2.7394  -1.9528
 B5V  H2   H  HCR6  0   0.278  -1.5036  -0.0287  -1.3113
 B5V  H3   H  HCR6  0   0.258  -1.1898  -1.9471  -2.8032
 B5V  H4   H  HCR6  0   0.264  -1.5378  -4.2456  -1.9338
 B5V  H5   H  HCR5  0   0.295   2.4094  -1.1500  -2.5520
 B5V  H6   H  HCR6  0   0.270   0.3558  -0.9338   3.5162
 B5V  H7   H  HCH1  0   0.257   2.4433   1.4822  -0.0616
 B5V  H8   H  HCH2  0   0.254   0.8403   3.8787   0.5304
 B5V  H9   H  HCH2  0   0.267  -0.1464   4.7940  -0.6149
 B5V  H10  H  HCR6  0   0.268  -2.2187  -4.6061   0.4009
 B5V  H11  H  HCH1  0   0.260   1.3649   3.4627  -3.0637
 B5V  H12  H  HCH1  0   0.261   1.5881   1.0707  -2.9702
 B5V  H15  H  HOH1  0   0.477  -2.6846  -1.9525   2.6365
 B5V  H16  H  HOH1  0   0.516   0.4325   1.1060   1.9228
 B5V  H17  H  HOH1  0   0.456   3.3433   3.8004  -1.7568
 B5V  H18  H  HOH1  0   0.473   3.7091   1.5753  -3.3556
 B5V  N01  N  NH2   0  -0.820   1.1648  -4.5091   1.1828
 B5V  O25  O  OH1   0  -0.620  -2.6261  -2.7892   2.1357
 B5V  H13  H  HNH2  0   0.428   1.3757  -4.9538   0.3063
 B5V  H14  H  HNH2  0   0.423   0.8521  -5.0869   1.9446

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
 B5V  O30  C29  single    1.402  0.020  1.402
 B5V  C29  C31  single    1.543  0.020  1.543
 B5V  C29  C13  single    1.535  0.020  1.535
 B5V  C31  O32  single    1.393  0.020  1.393
 B5V  C31  C11  single    1.521  0.020  1.521
 B5V  C13  C14  single    1.514  0.020  1.514
 B5V  C13  O12  single    1.425  0.020  1.425
 B5V  N10  C09  aromatic  1.320  0.020  1.320
 B5V  N10  C02  aromatic  1.342  0.020  1.342
 B5V  C09  N08  aromatic  1.329  0.020  1.329
 B5V  N01  C02  single    1.327  0.020  1.327
 B5V  C02  C03  aromatic  1.408  0.020  1.408
 B5V  N08  C07  aromatic  1.338  0.020  1.338
 B5V  C23  C22  aromatic  1.378  0.020  1.378
 B5V  C23  C24  aromatic  1.397  0.020  1.397
 B5V  C03  C07  aromatic  1.382  0.020  1.382
 B5V  C03  N04  aromatic  1.370  0.020  1.370
 B5V  C22  C21  aromatic  1.395  0.020  1.395
 B5V  C07  N06  aromatic  1.361  0.020  1.361
 B5V  N04  C05  aromatic  1.299  0.020  1.299
 B5V  N06  C11  single    1.435  0.020  1.435
 B5V  N06  C05  aromatic  1.370  0.020  1.370
 B5V  C11  O12  single    1.397  0.020  1.397
 B5V  C14  O15  single    1.434  0.020  1.434
 B5V  O25  C24  single    1.331  0.020  1.331
 B5V  C24  C19  aromatic  1.411  0.020  1.411
 B5V  C21  C20  aromatic  1.376  0.020  1.376
 B5V  O27  P16  double    1.472  0.020  1.472
 B5V  C19  C20  aromatic  1.403  0.020  1.403
 B5V  C19  C18  single    1.460  0.020  1.460
 B5V  O15  P16  single    1.590  0.020  1.590
 B5V  O17  C18  single    1.340  0.020  1.340
 B5V  O17  P16  single    1.656  0.020  1.656
 B5V  C18  O26  double    1.215  0.020  1.215
 B5V  P16  O28  single    1.567  0.020  1.567
 B5V  C13  H1   single    0.970  0.020  1.090
 B5V  C20  H2   single    0.930  0.020  1.080
 B5V  C21  H3   single    0.930  0.020  1.080
 B5V  C22  H4   single    0.930  0.020  1.080
 B5V  C05  H5   single    0.930  0.020  1.080
 B5V  C09  H6   single    0.930  0.020  1.080
 B5V  C11  H7   single    0.970  0.020  1.090
 B5V  C14  H8   single    0.970  0.020  1.090
 B5V  C14  H9   single    0.970  0.020  1.090
 B5V  C23  H10  single    0.930  0.020  1.080
 B5V  C29  H11  single    0.970  0.020  1.090
 B5V  C31  H12  single    0.970  0.020  1.090
 B5V  N01  H13  single    0.860  0.020  1.020
 B5V  N01  H14  single    0.860  0.020  1.020
 B5V  O25  H15  single    0.850  0.020  0.980
 B5V  O28  H16  single    0.850  0.020  0.980
 B5V  O30  H17  single    0.850  0.020  0.980
 B5V  O32  H18  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
 B5V  H1   C13  O12  107.58  3.000
 B5V  H1   C13  C29  109.66  3.000
 B5V  O12  C13  C29  106.22  3.000
 B5V  H1   C13  C14  109.26  3.000
 B5V  O12  C13  C14  108.19  3.000
 B5V  C29  C13  C14  115.60  3.000
 B5V  H2   C20  C19  119.61  3.000
 B5V  H2   C20  C21  119.41  3.000
 B5V  C19  C20  C21  120.97  3.000
 B5V  H3   C21  C22  120.46  3.000
 B5V  H3   C21  C20  120.26  3.000
 B5V  C22  C21  C20  119.28  3.000
 B5V  H4   C22  C23  119.15  3.000
 B5V  H4   C22  C21  119.86  3.000
 B5V  C23  C22  C21  120.99  3.000
 B5V  O25  C24  C23  117.43  3.000
 B5V  O25  C24  C19  123.42  3.000
 B5V  C23  C24  C19  119.15  3.000
 B5V  N10  C02  N01  119.09  3.000
 B5V  N01  C02  C03  122.99  3.000
 B5V  N10  C02  C03  117.92  3.000
 B5V  N04  C03  C07  110.62  3.000
 B5V  N04  C03  C02  132.84  3.000
 B5V  C07  C03  C02  116.54  3.000
 B5V  H5   C05  N06  121.84  3.000
 B5V  H5   C05  N04  125.04  3.000
 B5V  N06  C05  N04  113.11  3.000
 B5V  N08  C07  N06  128.66  3.000
 B5V  N06  C07  C03  105.46  3.000
 B5V  N08  C07  C03  125.88  3.000
 B5V  H6   C09  N10  116.19  3.000
 B5V  H6   C09  N08  115.91  3.000
 B5V  N10  C09  N08  127.90  3.000
 B5V  H7   C11  O12  111.69  3.000
 B5V  H7   C11  N06  107.72  3.000
 B5V  O12  C11  N06  106.86  3.000
 B5V  H7   C11  C31  110.19  3.000
 B5V  O12  C11  C31  103.32  3.000
 B5V  N06  C11  C31  117.01  3.000
 B5V  H9   C14  H8   108.34  3.000
 B5V  H9   C14  O15  105.72  3.000
 B5V  H8   C14  O15  110.09  3.000
 B5V  H9   C14  C13  110.62  3.000
 B5V  H8   C14  C13  111.87  3.000
 B5V  O15  C14  C13  110.01  3.000
 B5V  O26  C18  O17  121.51  3.000
 B5V  O26  C18  C19  124.10  3.000
 B5V  O17  C18  C19  114.37  3.000
 B5V  C18  C19  C24  118.86  3.000
 B5V  C18  C19  C20  121.73  3.000
 B5V  C24  C19  C20  119.31  3.000
 B5V  H10  C23  C24  118.96  3.000
 B5V  H10  C23  C22  120.73  3.000
 B5V  C24  C23  C22  120.30  3.000
 B5V  H11  C29  O30  111.64  3.000
 B5V  H11  C29  C31  111.48  3.000
 B5V  O30  C29  C31  110.93  3.000
 B5V  H11  C29  C13  110.92  3.000
 B5V  C31  C29  C13  101.44  3.000
 B5V  O30  C29  C13  110.01  3.000
 B5V  H12  C31  O32  112.47  3.000
 B5V  H12  C31  C29  108.56  3.000
 B5V  O32  C31  C29  114.72  3.000
 B5V  H12  C31  C11  109.26  3.000
 B5V  O32  C31  C11  111.49  3.000
 B5V  C29  C31  C11   99.53  3.000
 B5V  C05  N04  C03  104.60  3.000
 B5V  C11  N06  C07  123.06  3.000
 B5V  C11  N06  C05  130.72  3.000
 B5V  C07  N06  C05  106.21  3.000
 B5V  C09  N08  C07  112.23  3.000
 B5V  C09  N10  C02  119.51  3.000
 B5V  C11  O12  C13  109.56  3.000
 B5V  P16  O15  C14  127.98  3.000
 B5V  P16  O17  C18  122.69  3.000
 B5V  H16  O28  P16  120.39  3.000
 B5V  H17  O30  C29  108.22  3.000
 B5V  H18  O32  C31  109.06  3.000
 B5V  O28  P16  O27  115.71  3.000
 B5V  O28  P16  O17  105.32  3.000
 B5V  O27  P16  O17  113.55  3.000
 B5V  O28  P16  O15  110.34  3.000
 B5V  O17  P16  O15   99.91  3.000
 B5V  O27  P16  O15  110.77  3.000
 B5V  H14  N01  H13  118.12  3.000
 B5V  H14  N01  C02  120.18  3.000
 B5V  H13  N01  C02  121.03  3.000
 B5V  H15  O25  C24  108.99  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
 B5V  CONST_01  C23  C22  C21  C20    0.00   0.0  0
 B5V  CONST_02  C23  C24  C19  C20    0.00   0.0  0
 B5V  CONST_03  C24  C23  C22  C21    0.00   0.0  0
 B5V  CONST_04  C24  C19  C20  C21    0.00   0.0  0
 B5V  CONST_05  C19  C24  C23  C22    0.00   0.0  0
 B5V  CONST_06  C19  C20  C21  C22    0.00   0.0  0
 B5V  CONST_07  N08  C09  N10  C02    0.00   0.0  0
 B5V  CONST_08  N08  C07  C03  C02    0.00   0.0  0
 B5V  CONST_09  N06  C07  C03  C02  180.00   0.0  0
 B5V  CONST_10  C05  N04  C03  C02  180.00   0.0  0
 B5V  CONST_11  C09  N10  C02  C03    0.00   0.0  0
 B5V  CONST_12  C09  N08  C07  C03    0.00   0.0  0
 B5V  CONST_13  C05  N06  C07  C03    0.00   0.0  0
 B5V  CONST_14  N06  C05  N04  C03    0.00   0.0  0
 B5V  CONST_15  C07  C03  N04  C05    0.00   0.0  0
 B5V  CONST_16  N08  C07  N06  C05  180.00   0.0  0
 B5V  CONST_17  N10  C09  N08  C07    0.00   0.0  0
 B5V  CONST_18  N10  C02  C03  C07    0.00   0.0  0
 B5V  CONST_19  N04  C05  N06  C07    0.00   0.0  0
 B5V  CONST_20  N06  C07  N08  C09  180.00   0.0  0
 B5V  CONST_21  N10  C02  C03  N04  180.00   0.0  0
 B5V  CONST_22  N08  C07  C03  N04  180.00   0.0  0
 B5V  CONST_23  N06  C07  C03  N04    0.00   0.0  0
 B5V  CONST_24  C11  N06  C07  C03  180.00   0.0  0
 B5V  CONST_25  N08  C07  N06  C11    0.00   0.0  0
 B5V  CONST_26  N04  C05  N06  C11  180.00   0.0  0
 B5V  CONST_27  O25  C24  C19  C20  180.00   0.0  0
 B5V  CONST_28  C18  C19  C20  C21  180.00   0.0  0
 B5V  CONST_29  O25  C24  C23  C22  180.00   0.0  0
 B5V  CONST_30  N01  C02  C03  C07  180.00   0.0  0
 B5V  CONST_31  N01  C02  N10  C09  180.00   0.0  0
 B5V  CONST_32  C23  C24  C19  C18  180.00   0.0  0
 B5V  CONST_33  N04  C03  C02  N01    0.00   0.0  0
 B5V  CONST_34  H4   C22  C21  C20  180.00   0.0  0
 B5V  CONST_35  H10  C23  C22  C21  180.00   0.0  0
 B5V  CONST_36  H2   C20  C21  C22  180.00   0.0  0
 B5V  CONST_37  H6   C09  N10  C02  180.00   0.0  0
 B5V  CONST_38  H5   C05  N04  C03  180.00   0.0  0
 B5V  CONST_39  H3   C21  C20  C19  180.00   0.0  0
 B5V  CONST_40  H13  N01  C02  C03    0.00   0.0  0
 B5V  CONST_41  H14  N01  C02  C03  180.00   0.0  0
 B5V  Var_01    O17  C18  C19  C20    2.29  30.0  2
 B5V  Var_02    O27  P16  O15  C14  142.35  30.0  3
 B5V  Var_03    H8   C14  O15  P16  -41.68  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
 B5V  chir_01  C13  C29  C14  O12  positiv
 B5V  chir_02  C11  O12  N06  C31  negativ
 B5V  chir_03  C29  O30  C31  C13  negativ
 B5V  chir_04  C31  O32  C11  C29  negativ
 B5V  chir_05  P16  O15  O17  O28  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
 B5V  plan-1  C20  0.020
 B5V  plan-1  C21  0.020
 B5V  plan-1  C22  0.020
 B5V  plan-1  C24  0.020
 B5V  plan-1  C18  0.020
 B5V  plan-1  C19  0.020
 B5V  plan-1  C23  0.020
 B5V  plan-1  H2   0.020
 B5V  plan-1  H3   0.020
 B5V  plan-1  H4   0.020
 B5V  plan-1  H10  0.020
 B5V  plan-1  O25  0.020
 B5V  plan-2  C02  0.020
 B5V  plan-2  C03  0.020
 B5V  plan-2  C05  0.020
 B5V  plan-2  C07  0.020
 B5V  plan-2  C09  0.020
 B5V  plan-2  C11  0.020
 B5V  plan-2  N04  0.020
 B5V  plan-2  N06  0.020
 B5V  plan-2  N08  0.020
 B5V  plan-2  N10  0.020
 B5V  plan-2  H5   0.020
 B5V  plan-2  H6   0.020
 B5V  plan-2  N01  0.020
 B5V  plan-3  C02  0.020
 B5V  plan-3  N01  0.020
 B5V  plan-3  H13  0.020
 B5V  plan-3  H14  0.020
 B5V  plan-4  C18  0.020
 B5V  plan-4  C19  0.020
 B5V  plan-4  O17  0.020
 B5V  plan-4  O26  0.020

