# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 14:07:58 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: adenosine 3',5'-bis(trihydrogen diphosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O[P](O)(=O)O[P](O)(O)=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
 N7Y  N7Y  'adenosine 3',5'-bis(trihydrogen diphosphate)'  ligand  52  35  .  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_N7Y
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
 N7Y  O3   O  O2    0  -0.703  58.0174  31.5251  -28.5893
 N7Y  C4   C  CR15  0   0.113  55.4794  25.3938  -31.9100
 N7Y  C5   C  CH1   0   0.206  57.1780  27.2221  -31.5980
 N7Y  O4   O  O     0  -0.702  55.5997  30.6849  -28.8658
 N7Y  C6   C  CH1   0   0.016  56.4717  28.1280  -30.5945
 N7Y  N1   N  N     0  -0.474  55.3203  26.1842  -36.2340
 N7Y  C7   C  CH1   0  -0.124  57.6037  28.3937  -29.6024
 N7Y  C8   C  CH1   0   0.030  58.3734  27.0709  -29.6140
 N7Y  N2   N  N     0  -0.456  56.6649  27.2856  -34.5964
 N7Y  C9   C  CH2   0  -0.224  58.0168  26.1642  -28.4430
 N7Y  O5   O  OH1   0  -0.706  56.1873  32.9498  -27.6926
 N7Y  O6   O  OH1   0  -0.756  56.6846  30.9123  -26.5043
 N7Y  N3   N  N     0  -0.447  54.7816  24.8301  -32.8486
 N7Y  O7   O  OH1   0  -0.782  59.5740  29.6193  -27.9310
 N7Y  O8   O  O2    0  -0.559  58.6583  26.6784  -27.2632
 N7Y  N4   N  NR5   0  -0.544  56.2973  26.3935  -32.3693
 N7Y  C    C  CR6   0   0.463  54.7561  25.3655  -35.3386
 N7Y  O    O  OH1   0  -0.670  55.9200  29.2340  -31.2138
 N7Y  C1   C  CR16  0   0.048  56.2203  27.0732  -35.8233
 N7Y  C2   C  CR56  0   0.493  56.0944  26.4649  -33.7189
 N7Y  C3   C  CR56  0  -0.011  55.1497  25.4902  -33.9934
 N7Y  O1   O  O2    0  -0.590  58.4007  29.4645  -30.0985
 N7Y  O10  O  O     0  -0.707  59.6782  30.1210  -25.4648
 N7Y  O11  O  OH1   0  -0.696  60.8534  28.6922  -23.6380
 N7Y  O12  O  OH1   0  -0.711  58.4317  29.2112  -23.3602
 N7Y  O13  O  O     0  -0.705  56.9261  28.3431  -26.2054
 N7Y  O14  O  OH1   0  -0.696  57.2722  25.9262  -25.3555
 N7Y  O15  O  O2    0  -0.493  58.0052  26.3998  -30.8149
 N7Y  O2   O  O     0  -0.669  60.1688  31.2685  -29.8803
 N7Y  O9   O  O2    0  -0.668  59.1376  27.6069  -25.0762
 N7Y  P    P  P     0   1.483  59.1474  30.5066  -29.1496
 N7Y  P1   P  P     0   1.474  56.5186  31.4310  -27.9748
 N7Y  P2   P  P     0   1.525  57.8807  27.2239  -26.0084
 N7Y  P3   P  P     0   1.524  59.5526  29.0419  -24.4524
 N7Y  H7   H  HCR5  0   0.298  55.4487  25.1172  -30.8669
 N7Y  H    H  HCH1  0   0.271  57.7499  27.8214  -32.3158
 N7Y  H1   H  HCH1  0   0.238  55.7151  27.5310  -30.0603
 N7Y  H2   H  HCH1  0   0.272  57.2102  28.6183  -28.6135
 N7Y  H3   H  HCH1  0   0.285  59.4529  27.2474  -29.6086
 N7Y  H9   H  HCH2  0   0.257  56.9347  26.0812  -28.3104
 N7Y  H10  H  HCH2  0   0.296  58.4103  25.1622  -28.6084
 N7Y  H11  H  HOH1  0   0.513  55.8771  33.4448  -28.4638
 N7Y  H12  H  HOH1  0   0.503  56.7573  29.9273  -26.3747
 N7Y  H13  H  HOH1  0   0.510  59.6620  29.9656  -26.9894
 N7Y  H5   H  HNH2  0   0.404  53.5984  24.4173  -36.7174
 N7Y  H4   H  HNH2  0   0.411  53.4198  23.8381  -35.1011
 N7Y  H8   H  HOH1  0   0.465  55.6586  29.8592  -30.5151
 N7Y  H6   H  HCR6  0   0.253  56.6387  27.7054  -36.5992
 N7Y  H14  H  HOH1  0   0.519  61.6861  28.7791  -24.1252
 N7Y  H15  H  HOH1  0   0.520  58.3711  30.0868  -22.9503
 N7Y  H16  H  HOH1  0   0.519  56.5128  26.0641  -24.7701
 N7Y  N    N  NH2   0  -0.816  53.8501  24.4771  -35.7460

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
 N7Y  N1   C1   aromatic  1.330  0.020  1.330
 N7Y  N1   C    aromatic  1.338  0.020  1.338
 N7Y  C1   N2   aromatic  1.322  0.020  1.322
 N7Y  N    C    single    1.333  0.020  1.333
 N7Y  C    C3   aromatic  1.407  0.020  1.407
 N7Y  N2   C2   aromatic  1.330  0.020  1.330
 N7Y  C2   C3   aromatic  1.385  0.020  1.385
 N7Y  C2   N4   aromatic  1.367  0.020  1.367
 N7Y  C3   N3   aromatic  1.372  0.020  1.372
 N7Y  N4   C5   single    1.434  0.020  1.434
 N7Y  N4   C4   aromatic  1.371  0.020  1.371
 N7Y  N3   C4   aromatic  1.298  0.020  1.298
 N7Y  C5   O15  single    1.405  0.020  1.405
 N7Y  C5   C6   single    1.525  0.020  1.525
 N7Y  O15  C8   single    1.424  0.020  1.424
 N7Y  O    C6   single    1.382  0.020  1.382
 N7Y  C6   C7   single    1.528  0.020  1.528
 N7Y  O1   C7   single    1.424  0.020  1.424
 N7Y  O1   P    single    1.595  0.020  1.595
 N7Y  O2   P    double    1.469  0.020  1.469
 N7Y  C8   C7   single    1.531  0.020  1.531
 N7Y  C8   C9   single    1.523  0.020  1.523
 N7Y  C9   O8   single    1.438  0.020  1.438
 N7Y  P    O3   single    1.621  0.020  1.621
 N7Y  P    O7   single    1.567  0.020  1.567
 N7Y  O4   P1   double    1.482  0.020  1.482
 N7Y  O3   P1   single    1.623  0.020  1.623
 N7Y  P1   O5   single    1.580  0.020  1.580
 N7Y  P1   O6   single    1.568  0.020  1.568
 N7Y  O8   P2   single    1.574  0.020  1.574
 N7Y  O13  P2   double    1.484  0.020  1.484
 N7Y  P2   O14  single    1.575  0.020  1.575
 N7Y  P2   O9   single    1.611  0.020  1.611
 N7Y  O10  P3   double    1.485  0.020  1.485
 N7Y  O9   P3   single    1.619  0.020  1.619
 N7Y  O12  P3   single    1.574  0.020  1.574
 N7Y  P3   O11  single    1.574  0.020  1.574
 N7Y  C4   H7   single    0.930  0.020  1.080
 N7Y  C5   H    single    0.970  0.020  1.090
 N7Y  C6   H1   single    0.970  0.020  1.090
 N7Y  C7   H2   single    0.970  0.020  1.090
 N7Y  C8   H3   single    0.970  0.020  1.090
 N7Y  C9   H9   single    0.970  0.020  1.090
 N7Y  C9   H10  single    0.970  0.020  1.090
 N7Y  O5   H11  single    0.850  0.020  0.980
 N7Y  O6   H12  single    0.850  0.020  0.980
 N7Y  O7   H13  single    0.850  0.020  0.980
 N7Y  N    H5   single    0.860  0.020  1.020
 N7Y  N    H4   single    0.860  0.020  1.020
 N7Y  O    H8   single    0.850  0.020  0.980
 N7Y  C1   H6   single    0.930  0.020  1.080
 N7Y  O11  H14  single    0.850  0.020  0.980
 N7Y  O12  H15  single    0.850  0.020  0.980
 N7Y  O14  H16  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
 N7Y  P1   O3   P    137.59  3.000
 N7Y  H7   C4   N4   121.84  3.000
 N7Y  H7   C4   N3   124.89  3.000
 N7Y  N4   C4   N3   113.27  3.000
 N7Y  H    C5   O15  112.20  3.000
 N7Y  H    C5   N4   106.50  3.000
 N7Y  O15  C5   N4   108.86  3.000
 N7Y  H    C5   C6   110.34  3.000
 N7Y  O15  C5   C6   104.69  3.000
 N7Y  N4   C5   C6   114.37  3.000
 N7Y  H1   C6   O    112.12  3.000
 N7Y  H1   C6   C7   106.74  3.000
 N7Y  O    C6   C7   116.57  3.000
 N7Y  H1   C6   C5   108.36  3.000
 N7Y  C7   C6   C5   100.80  3.000
 N7Y  O    C6   C5   111.42  3.000
 N7Y  C1   N1   C    119.19  3.000
 N7Y  H2   C7   O1   111.34  3.000
 N7Y  H2   C7   C8   111.55  3.000
 N7Y  O1   C7   C8   111.46  3.000
 N7Y  H2   C7   C6   110.98  3.000
 N7Y  C8   C7   C6   102.55  3.000
 N7Y  O1   C7   C6   108.61  3.000
 N7Y  H3   C8   O15  109.60  3.000
 N7Y  H3   C8   C9   108.86  3.000
 N7Y  O15  C8   C9   107.89  3.000
 N7Y  H3   C8   C7   110.91  3.000
 N7Y  C9   C8   C7   113.01  3.000
 N7Y  O15  C8   C7   106.48  3.000
 N7Y  C2   N2   C1   111.64  3.000
 N7Y  H10  C9   H9   107.83  3.000
 N7Y  H10  C9   O8   107.00  3.000
 N7Y  H9   C9   O8   111.67  3.000
 N7Y  H10  C9   C8   110.26  3.000
 N7Y  H9   C9   C8   111.72  3.000
 N7Y  O8   C9   C8   108.26  3.000
 N7Y  H11  O5   P1   114.63  3.000
 N7Y  H12  O6   P1   117.18  3.000
 N7Y  C3   N3   C4   104.49  3.000
 N7Y  H13  O7   P    123.79  3.000
 N7Y  P2   O8   C9   123.90  3.000
 N7Y  C2   N4   C5   126.30  3.000
 N7Y  C5   N4   C4   127.41  3.000
 N7Y  C2   N4   C4   106.28  3.000
 N7Y  C3   C    N    122.78  3.000
 N7Y  C3   C    N1   117.88  3.000
 N7Y  N    C    N1   119.34  3.000
 N7Y  H8   O    C6   107.43  3.000
 N7Y  H6   C1   N2   116.13  3.000
 N7Y  H6   C1   N1   115.45  3.000
 N7Y  N2   C1   N1   128.42  3.000
 N7Y  C3   C2   N4   105.08  3.000
 N7Y  N4   C2   N2   128.32  3.000
 N7Y  C3   C2   N2   126.60  3.000
 N7Y  C2   C3   C    116.27  3.000
 N7Y  C2   C3   N3   110.88  3.000
 N7Y  C    C3   N3   132.86  3.000
 N7Y  P    O1   C7   123.09  3.000
 N7Y  H14  O11  P3   115.48  3.000
 N7Y  H15  O12  P3   115.81  3.000
 N7Y  H16  O14  P2   115.85  3.000
 N7Y  C8   O15  C5   110.28  3.000
 N7Y  P3   O9   P2   129.33  3.000
 N7Y  O2   P    O1   111.62  3.000
 N7Y  O2   P    O7   119.43  3.000
 N7Y  O1   P    O7   102.72  3.000
 N7Y  O7   P    O3   106.07  3.000
 N7Y  O2   P    O3   109.32  3.000
 N7Y  O1   P    O3   106.84  3.000
 N7Y  O6   P1   O5    99.95  3.000
 N7Y  O6   P1   O4   117.58  3.000
 N7Y  O5   P1   O4   117.48  3.000
 N7Y  O6   P1   O3   106.05  3.000
 N7Y  O5   P1   O3   101.87  3.000
 N7Y  O4   P1   O3   111.98  3.000
 N7Y  O9   P2   O14  104.92  3.000
 N7Y  O9   P2   O13  113.54  3.000
 N7Y  O14  P2   O13  115.33  3.000
 N7Y  O9   P2   O8    99.11  3.000
 N7Y  O14  P2   O8   103.64  3.000
 N7Y  O13  P2   O8   118.25  3.000
 N7Y  O9   P3   O12  100.38  3.000
 N7Y  O12  P3   O11  104.67  3.000
 N7Y  O9   P3   O11  102.38  3.000
 N7Y  O11  P3   O10  116.38  3.000
 N7Y  O12  P3   O10  117.07  3.000
 N7Y  O9   P3   O10  113.78  3.000
 N7Y  H4   N    H5   118.37  3.000
 N7Y  H4   N    C    121.26  3.000
 N7Y  H5   N    C    120.35  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
 N7Y  CONST_01  N2   C2  N4  C4  180.00   0.0  0
 N7Y  CONST_02  C3   C2  N4  C4    0.00   0.0  0
 N7Y  CONST_03  C    C3  N3  C4  180.00   0.0  0
 N7Y  CONST_04  C2   C3  N3  C4    0.00   0.0  0
 N7Y  CONST_05  C2   N2  C1  N1    0.00   0.0  0
 N7Y  CONST_06  C2   C3  C   N1    0.00   0.0  0
 N7Y  CONST_07  N3   C3  C   N1  180.00   0.0  0
 N7Y  CONST_08  C    N1  C1  N2    0.00   0.0  0
 N7Y  CONST_09  C    C3  C2  N2    0.00   0.0  0
 N7Y  CONST_10  N3   C3  C2  N2  180.00   0.0  0
 N7Y  CONST_11  N4   C2  C3  N3    0.00   0.0  0
 N7Y  CONST_12  C2   N4  C4  N3    0.00   0.0  0
 N7Y  CONST_13  C1   N2  C2  N4  180.00   0.0  0
 N7Y  CONST_14  C    C3  C2  N4  180.00   0.0  0
 N7Y  CONST_15  C3   N3  C4  N4    0.00   0.0  0
 N7Y  CONST_16  C3   C   N1  C1    0.00   0.0  0
 N7Y  CONST_17  C3   C2  N2  C1    0.00   0.0  0
 N7Y  CONST_18  N2   C2  N4  C5    0.00   0.0  0
 N7Y  CONST_19  C3   C2  N4  C5  180.00   0.0  0
 N7Y  CONST_20  N3   C4  N4  C5  180.00   0.0  0
 N7Y  CONST_21  N    C   C3  N3    0.00   0.0  0
 N7Y  CONST_22  C1   N1  C   N   180.00   0.0  0
 N7Y  CONST_23  C2   C3  C   N   180.00   0.0  0
 N7Y  CONST_24  H7   C4  N4  C5    0.00   0.0  0
 N7Y  CONST_25  H6   C1  N1  C   180.00   0.0  0
 N7Y  CONST_26  H5   N   C   N1    0.00   0.0  0
 N7Y  CONST_27  H4   N   C   N1  180.00   0.0  0
 N7Y  Var_01    O2   P   O1  C7  164.72  30.0  3
 N7Y  Var_02    O13  P2  O8  C9  -57.75  30.0  3
 N7Y  Var_03    H9   C9  O8  P2   -7.24  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
 N7Y  chir_01  C5  N4   O15  C6  positiv
 N7Y  chir_02  C6  O    C5   C7  negativ
 N7Y  chir_03  C7  O1   C8   C6  positiv
 N7Y  chir_04  C8  O15  C7   C9  negativ
 N7Y  chir_05  P   O2   O3   O7  both
 N7Y  chir_06  P2  O13  O14  O9  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
 N7Y  plan-1  C4  0.020
 N7Y  plan-1  C5  0.020
 N7Y  plan-1  N1  0.020
 N7Y  plan-1  N2  0.020
 N7Y  plan-1  N3  0.020
 N7Y  plan-1  N4  0.020
 N7Y  plan-1  C   0.020
 N7Y  plan-1  C1  0.020
 N7Y  plan-1  C2  0.020
 N7Y  plan-1  C3  0.020
 N7Y  plan-1  H7  0.020
 N7Y  plan-1  H6  0.020
 N7Y  plan-1  N   0.020
 N7Y  plan-2  C   0.020
 N7Y  plan-2  H5  0.020
 N7Y  plan-2  H4  0.020
 N7Y  plan-2  N   0.020

