# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Sep 21 15:02:14 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: 5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)N[P](O)(O)=O)[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
 AU1  AU1  "5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]adenosine"  ligand  43  27  .  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_AU1
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
 AU1  O1A  O  OH1   0  -0.718  -3.1966  -0.0148  -2.2731
 AU1  PA   P  P     0   1.428  -2.5892  -0.1327  -0.8083
 AU1  O2A  O  O     0  -0.724  -3.6172   0.0545   0.2307
 AU1  N3A  N  NH1   0  -0.875  -1.2957   0.9231  -0.6578
 AU1  PB   P  P     0   1.391  -1.4378   2.5155  -0.1072
 AU1  O2B  O  O     0  -0.681  -2.7935   3.0644  -0.2982
 AU1  O1B  O  OH1   0  -0.695  -1.0072   2.5669   1.4217
 AU1  O3B  O  OH1   0  -0.709  -0.2666   3.1989  -0.9483
 AU1  O5'  O  O2    0  -0.612  -1.8833  -1.5705  -0.8624
 AU1  C5'  C  CH2   0  -0.150  -1.3214  -2.1104   0.3329
 AU1  C4'  C  CR15  0  -0.012  -0.0253  -2.8273   0.0169
 AU1  C3'  C  CR15  0   0.060   0.6799  -3.2672   1.3080
 AU1  O3'  O  OH1   0  -0.658   0.4211  -4.6176   1.5666
 AU1  C2'  C  CR15  0  -0.023   2.1643  -2.9825   1.0138
 AU1  O2'  O  OH1   0  -0.674   2.7509  -4.0720   0.3610
 AU1  C1'  C  CR15  0   0.155   2.0964  -1.8429   0.0010
 AU1  O4'  O  O     0  -0.494   0.8714  -1.9633  -0.6667
 AU1  N9   N  NR5   0  -0.456   2.1906  -0.5071   0.5686
 AU1  C4   C  CR56  0   0.436   2.7659   0.5530  -0.0850
 AU1  C5   C  CR56  0   0.026   2.2753   1.6870   0.5396
 AU1  N7   N  N     0  -0.517   1.4114   1.3365   1.5485
 AU1  C8   C  CR15  0   0.088   1.3895   0.0348   1.5277
 AU1  N3   N  N     0  -0.531   3.5898   0.5284  -1.1221
 AU1  C2   C  CR16  0   0.028   3.9138   1.7428  -1.5306
 AU1  N1   N  N     0  -0.397   3.4934   2.9096  -1.0423
 AU1  C6   C  CR6   0   0.436   2.6559   2.9148  -0.0127
 AU1  N6   N  NH2   0  -0.853   2.1069   4.0899   0.4005
 AU1  H1   H  HOH1  0   0.492  -2.5622   0.0345  -3.0004
 AU1  H2   H  HNH1  0   0.422  -0.4239   0.6542  -1.1004
 AU1  H3   H  HOH1  0   0.482  -0.1381   2.1453   1.6524
 AU1  H4   H  HOH1  0   0.499   0.3692   3.7650  -0.4609
 AU1  H5   H  HCH2  0   0.261  -1.1490  -1.3252   1.0756
 AU1  H6   H  HCH2  0   0.216  -2.0217  -2.8224   0.7750
 AU1  H7   H  HCR5  0   0.236  -0.2268  -3.6965  -0.6188
 AU1  H8   H  HCR5  0   0.199   0.3513  -2.6483   2.1522
 AU1  H9   H  HOH1  0   0.461   0.5437  -4.7846   2.5074
 AU1  H10  H  HCR5  0   0.318   2.7201  -2.6974   1.9154
 AU1  H11  H  HOH1  0   0.435   2.3129  -4.8722   0.6803
 AU1  H12  H  HCR5  0   0.305   2.9180  -1.9144  -0.7131
 AU1  H13  H  HCR5  0   0.318   0.8030  -0.5650   2.2059
 AU1  H14  H  HCR6  0   0.275   4.5993   1.8026  -2.3673
 AU1  H15  H  HNH2  0   0.396   2.5617   4.9264   0.0634
 AU1  H16  H  HNH2  0   0.418   1.8376   4.1524   1.3720

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
 AU1  O2A  PA   double    1.473  0.020  1.473
 AU1  O2B  PB   double    1.475  0.020  1.475
 AU1  O1B  PB   single    1.589  0.020  1.589
 AU1  O1A  PA   single    1.590  0.020  1.590
 AU1  PB   N3A  single    1.691  0.020  1.691
 AU1  PB   O3B  single    1.596  0.020  1.596
 AU1  PA   N3A  single    1.676  0.020  1.676
 AU1  PA   O5'  single    1.603  0.020  1.603
 AU1  N6   C6   single    1.361  0.020  1.361
 AU1  N1   C6   aromatic  1.327  0.020  1.327
 AU1  N1   C2   aromatic  1.333  0.020  1.333
 AU1  O5'  C5'  single    1.427  0.020  1.427
 AU1  C5'  C4'  single    1.515  0.020  1.515
 AU1  C6   C5   aromatic  1.399  0.020  1.399
 AU1  C2   N3   aromatic  1.322  0.020  1.322
 AU1  N3   C4   aromatic  1.325  0.020  1.325
 AU1  C5   C4   aromatic  1.384  0.020  1.384
 AU1  C5   N7   aromatic  1.374  0.020  1.374
 AU1  O4'  C4'  single    1.420  0.020  1.420
 AU1  O4'  C1'  single    1.400  0.020  1.400
 AU1  C4   N9   aromatic  1.372  0.020  1.372
 AU1  N7   C8   aromatic  1.302  0.020  1.302
 AU1  C4'  C3'  single    1.535  0.020  1.535
 AU1  N9   C8   aromatic  1.362  0.020  1.362
 AU1  N9   C1'  single    1.454  0.020  1.454
 AU1  C1'  C2'  single    1.526  0.020  1.526
 AU1  C3'  C2'  single    1.540  0.020  1.540
 AU1  C3'  O3'  single    1.399  0.020  1.399
 AU1  C2'  O2'  single    1.399  0.020  1.399
 AU1  O1A  H1   single    0.850  0.020  0.980
 AU1  N3A  H2   single    0.860  0.020  1.020
 AU1  O1B  H3   single    0.850  0.020  0.980
 AU1  O3B  H4   single    0.850  0.020  0.980
 AU1  C5'  H5   single    0.970  0.020  1.090
 AU1  C5'  H6   single    0.970  0.020  1.090
 AU1  C4'  H7   single    0.970  0.020  1.090
 AU1  C3'  H8   single    0.970  0.020  1.090
 AU1  O3'  H9   single    0.850  0.020  0.980
 AU1  C2'  H10  single    0.970  0.020  1.090
 AU1  O2'  H11  single    0.850  0.020  0.980
 AU1  C1'  H12  single    0.970  0.020  1.090
 AU1  C8   H13  single    0.930  0.020  1.080
 AU1  C2   H14  single    0.930  0.020  1.080
 AU1  N6   H15  single    0.890  0.020  1.040
 AU1  N6   H16  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
 AU1  H1   O1A  PA   116.51  3.000
 AU1  O5'  PA   N3A  103.19  3.000
 AU1  O5'  PA   O2A  116.43  3.000
 AU1  N3A  PA   O2A  113.26  3.000
 AU1  O5'  PA   O1A  101.75  3.000
 AU1  N3A  PA   O1A  109.31  3.000
 AU1  O2A  PA   O1A  111.94  3.000
 AU1  H2   N3A  PB   117.66  3.000
 AU1  H2   N3A  PA   117.20  3.000
 AU1  PB   N3A  PA   123.89  3.000
 AU1  O3B  PB   O1B  107.12  3.000
 AU1  O3B  PB   O2B  116.55  3.000
 AU1  O1B  PB   O2B  111.20  3.000
 AU1  O3B  PB   N3A   99.79  3.000
 AU1  O1B  PB   N3A  108.72  3.000
 AU1  O2B  PB   N3A  112.67  3.000
 AU1  H3   O1B  PB   116.54  3.000
 AU1  H4   O3B  PB   117.45  3.000
 AU1  C5'  O5'  PA   118.99  3.000
 AU1  H6   C5'  H5   107.10  3.000
 AU1  H6   C5'  C4'  108.94  3.000
 AU1  H5   C5'  C4'  110.27  3.000
 AU1  H6   C5'  O5'  109.46  3.000
 AU1  H5   C5'  O5'  111.04  3.000
 AU1  C4'  C5'  O5'  109.96  3.000
 AU1  H7   C4'  O4'  108.63  3.000
 AU1  H7   C4'  C3'  110.19  3.000
 AU1  O4'  C4'  C3'  106.80  3.000
 AU1  H7   C4'  C5'  109.83  3.000
 AU1  C3'  C4'  C5'  110.68  3.000
 AU1  O4'  C4'  C5'  110.65  3.000
 AU1  H8   C3'  C2'  109.35  3.000
 AU1  H8   C3'  O3'  110.29  3.000
 AU1  C2'  C3'  O3'  113.09  3.000
 AU1  H8   C3'  C4'  110.36  3.000
 AU1  O3'  C3'  C4'  110.30  3.000
 AU1  C2'  C3'  C4'  103.25  3.000
 AU1  H9   O3'  C3'  108.93  3.000
 AU1  H10  C2'  C1'  111.96  3.000
 AU1  H10  C2'  O2'  111.93  3.000
 AU1  C1'  C2'  O2'  106.89  3.000
 AU1  H10  C2'  C3'  112.30  3.000
 AU1  O2'  C2'  C3'  110.45  3.000
 AU1  C1'  C2'  C3'  102.82  3.000
 AU1  H11  O2'  C2'  107.49  3.000
 AU1  H12  C1'  N9   105.48  3.000
 AU1  H12  C1'  O4'  109.94  3.000
 AU1  N9   C1'  O4'  108.77  3.000
 AU1  H12  C1'  C2'  110.61  3.000
 AU1  N9   C1'  C2'  115.09  3.000
 AU1  O4'  C1'  C2'  106.93  3.000
 AU1  C1'  O4'  C4'  112.02  3.000
 AU1  C8   N9   C4   105.94  3.000
 AU1  C8   N9   C1'  127.02  3.000
 AU1  C4   N9   C1'  123.44  3.000
 AU1  N3   C4   C5   126.07  3.000
 AU1  C5   C4   N9   105.63  3.000
 AU1  N3   C4   N9   128.27  3.000
 AU1  C6   C5   N7   133.22  3.000
 AU1  N7   C5   C4   110.20  3.000
 AU1  C6   C5   C4   116.38  3.000
 AU1  C8   N7   C5   104.71  3.000
 AU1  H13  C8   N7   123.71  3.000
 AU1  H13  C8   N9   122.76  3.000
 AU1  N7   C8   N9   113.52  3.000
 AU1  C2   N3   C4   112.17  3.000
 AU1  H14  C2   N1   115.73  3.000
 AU1  H14  C2   N3   116.40  3.000
 AU1  N1   C2   N3   127.87  3.000
 AU1  C6   N1   C2   119.12  3.000
 AU1  N6   C6   N1   119.56  3.000
 AU1  N1   C6   C5   118.32  3.000
 AU1  N6   C6   C5   121.88  3.000
 AU1  H16  N6   H15  112.94  3.000
 AU1  H16  N6   C6   116.93  3.000
 AU1  H15  N6   C6   115.60  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
 AU1  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 AU1  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 AU1  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 AU1  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 AU1  CONST_05  N1   C2   N3   C4      0.00   0.0  0
 AU1  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 AU1  CONST_07  C8   N7   C5   C4      0.00   0.0  0
 AU1  CONST_08  N7   C8   N9   C4      0.00   0.0  0
 AU1  CONST_09  C2   N1   C6   C5      0.00   0.0  0
 AU1  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 AU1  CONST_11  C8   N9   C4   C5      0.00   0.0  0
 AU1  CONST_12  N1   C6   C5   N7    180.00   0.0  0
 AU1  CONST_13  N3   C4   C5   N7    180.00   0.0  0
 AU1  CONST_14  C6   C5   N7   C8    180.00   0.0  0
 AU1  CONST_15  N3   C4   N9   C8    180.00   0.0  0
 AU1  CONST_16  C6   N1   C2   N3      0.00   0.0  0
 AU1  CONST_17  C6   C5   C4   N3      0.00   0.0  0
 AU1  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 AU1  CONST_22  N6   C6   C5   N7      0.00   0.0  0
 AU1  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 AU1  CONST_25  H14  C2   N3   C4    180.00   0.0  0
 AU1  CONST_26  H13  C8   N9   C4    180.00   0.0  0
 AU1  CONST_27  H13  C8   N7   C5    180.00   0.0  0
 AU1  CONST_28  H14  C2   N1   C6    180.00   0.0  0
 AU1  CONST_29  H15  N6   C6   C5    180.00   0.0  0
 AU1  Var_01    C4'  C5'  O5'  PA   -141.48  30.0  3
 AU1  Var_02    PB   N3A  PA   O1A    91.00  30.0  3
 AU1  Var_03    C5'  O5'  PA   O1A  -173.86  30.0  3
 AU1  Var_04    O2B  PB   N3A  PA    -23.71  30.0  2
 AU1  Var_05    O1B  PB   N3A  PA    100.02  30.0  2
 AU1  Var_06    O3B  PB   N3A  PA   -148.02  30.0  2
 AU1  Var_07    PB   N3A  PA   O2A   -34.56  30.0  3
 AU1  Var_08    C5'  O5'  PA   O2A   -51.88  30.0  3
 AU1  Var_09    C5'  O5'  PA   N3A    72.83  30.0  3
 AU1  Var_10    O5'  PA   N3A  PB   -161.31  30.0  1
 AU1  Var_11    H2   N3A  PA   O1A   -75.85  30.0  3
 AU1  Var_12    H5   C5'  O5'  PA    -19.16  30.0  3
 AU1  Var_13    H6   C5'  O5'  PA     98.88  30.0  3
 AU1  Var_14    H2   N3A  PA   O2A   158.59  30.0  3
 AU1  Var_15    H2   N3A  PB   O2B   143.08  30.0  3
 AU1  Var_16    H2   N3A  PB   O1B   -93.18  30.0  3
 AU1  Var_17    H2   N3A  PB   O3B    18.77  30.0  3
 AU1  Var_18    H2   N3A  PA   O5'    31.84  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
 AU1  chir_02  C4'  C5'  O4'  C3'  negativ
 AU1  chir_03  C3'  O3'  C4'  C2'  positiv
 AU1  chir_04  C2'  O2'  C3'  C1'  positiv
 AU1  chir_05  C1'  O4'  N9   C2'  negativ
 AU1  chir_06  PA   O1A  N3A  O5'  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
 AU1  plan-1  C1'  0.020
 AU1  plan-1  N9   0.020
 AU1  plan-1  C4   0.020
 AU1  plan-1  C5   0.020
 AU1  plan-1  N7   0.020
 AU1  plan-1  C8   0.020
 AU1  plan-1  N3   0.020
 AU1  plan-1  C2   0.020
 AU1  plan-1  N1   0.020
 AU1  plan-1  C6   0.020
 AU1  plan-1  N6   0.020
 AU1  plan-1  H13  0.020
 AU1  plan-1  H14  0.020
 AU1  plan-2  C6   0.020
 AU1  plan-2  N6   0.020
 AU1  plan-2  H15  0.020
 AU1  plan-2  H16  0.020

