# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 13:08:39 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[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
 ADN  ADN  'adenosine                '  ligand  32  19  .  2020-10-20  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ADN
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
 ADN  O5'   O  OH1   0  -0.668  -1.7855   1.7234  -3.8184
 ADN  C5'   C  CH2   0  -0.152  -1.3734   0.3993  -3.5875
 ADN  C4'   C  CH1   0   0.019   0.0067   0.4083  -2.9782
 ADN  O4'   O  O2    0  -0.490  -0.0315   0.9850  -1.6795
 ADN  C3'   C  CH1   0  -0.042   0.5726  -0.9925  -2.7670
 ADN  O3'   O  OH1   0  -0.656   1.1846  -1.4572  -3.9358
 ADN  C2'   C  CH1   0  -0.045   1.5502  -0.7700  -1.6054
 ADN  O2'   O  OH1   0  -0.664   2.7628  -0.2456  -2.0726
 ADN  C1'   C  CH1   0   0.163   0.8539   0.3354  -0.8037
 ADN  N9    N  NR5   0  -0.536   0.1250  -0.1466   0.3482
 ADN  C8    C  CR15  0   0.112  -0.8461  -1.1113   0.3985
 ADN  N7    N  N     0  -0.445  -1.3521  -1.2768   1.5832
 ADN  C5    C  CR56  0  -0.011  -0.6881  -0.3687   2.3670
 ADN  C6    C  CR6   0   0.461  -0.7701  -0.0423   3.7337
 ADN  N6    N  NH2   0  -0.816  -1.6144  -0.6464   4.5702
 ADN  N1    N  N     0  -0.475   0.0330   0.9231   4.1953
 ADN  C2    C  CR16  0   0.047   0.8671   1.5294   3.3551
 ADN  N3    N  N     0  -0.459   1.0351   1.3101   2.0627
 ADN  C4    C  CR56  0   0.498   0.2305   0.3482   1.6183
 ADN  HO5'  H  HOH1  0   0.459  -2.6443   1.6991  -4.2500
 ADN  H5'1  H  HCH2  0   0.210  -1.3197  -0.1818  -4.5173
 ADN  H5'2  H  HCH2  0   0.195  -2.0591  -0.1331  -2.9140
 ADN  H4'   H  HCH1  0   0.238   0.6861   0.9816  -3.6234
 ADN  H3'   H  HCH1  0   0.240  -0.2302  -1.6695  -2.4465
 ADN  HO3'  H  HOH1  0   0.470   1.2322  -2.4180  -3.9029
 ADN  H2'   H  HCH1  0   0.259   1.7054  -1.6743  -1.0039
 ADN  HO2'  H  HOH1  0   0.452   2.9741  -0.6886  -2.9040
 ADN  H1'   H  HCH1  0   0.276   1.5935   1.0359  -0.4075
 ADN  H8    H  HCR5  0   0.291  -1.1455  -1.6711  -0.4754
 ADN  HN61  H  HNH2  0   0.404  -1.6124  -0.4137   5.5483
 ADN  HN62  H  HNH2  0   0.412  -2.1906  -1.4102   4.2636
 ADN  H2    H  HCR6  0   0.253   1.4882   2.3033   3.7934

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
 ADN  O5'  C5'   single    1.406  0.020  1.406
 ADN  O5'  HO5'  single    0.850  0.020  0.980
 ADN  C5'  C4'   single    1.509  0.020  1.509
 ADN  C5'  H5'1  single    0.970  0.020  1.090
 ADN  C5'  H5'2  single    0.970  0.020  1.090
 ADN  C4'  O4'   single    1.422  0.020  1.422
 ADN  C4'  C3'   single    1.525  0.020  1.525
 ADN  C4'  H4'   single    0.970  0.020  1.090
 ADN  O4'  C1'   single    1.405  0.020  1.405
 ADN  C3'  O3'   single    1.399  0.020  1.399
 ADN  C3'  C2'   single    1.534  0.020  1.534
 ADN  C3'  H3'   single    0.970  0.020  1.090
 ADN  O3'  HO3'  single    0.850  0.020  0.980
 ADN  C2'  O2'   single    1.401  0.020  1.401
 ADN  C2'  C1'   single    1.533  0.020  1.533
 ADN  C2'  H2'   single    0.970  0.020  1.090
 ADN  O2'  HO2'  single    0.850  0.020  0.980
 ADN  C1'  N9    single    1.446  0.020  1.446
 ADN  C1'  H1'   single    0.970  0.020  1.090
 ADN  N9   C8    aromatic  1.370  0.020  1.370
 ADN  N9   C4    aromatic  1.367  0.020  1.367
 ADN  C8   N7    aromatic  1.299  0.020  1.299
 ADN  C8   H8    single    0.930  0.020  1.080
 ADN  N7   C5    aromatic  1.371  0.020  1.371
 ADN  C5   C6    aromatic  1.408  0.020  1.408
 ADN  C5   C4    aromatic  1.385  0.020  1.385
 ADN  C6   N6    single    1.333  0.020  1.333
 ADN  C6   N1    aromatic  1.338  0.020  1.338
 ADN  N6   HN61  single    0.860  0.020  1.020
 ADN  N6   HN62  single    0.860  0.020  1.020
 ADN  N1   C2    aromatic  1.330  0.020  1.330
 ADN  C2   N3    aromatic  1.322  0.020  1.322
 ADN  C2   H2    single    0.930  0.020  1.080
 ADN  N3   C4    aromatic  1.330  0.020  1.330

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
 ADN  HO5'  O5'  C5'   108.16  3.000
 ADN  H5'2  C5'  H5'1  107.05  3.000
 ADN  H5'2  C5'  C4'   109.04  3.000
 ADN  H5'1  C5'  C4'   107.48  3.000
 ADN  H5'2  C5'  O5'   111.98  3.000
 ADN  H5'1  C5'  O5'   111.95  3.000
 ADN  C4'   C5'  O5'   109.20  3.000
 ADN  H4'   C4'  C3'   109.33  3.000
 ADN  H4'   C4'  O4'   109.97  3.000
 ADN  C3'   C4'  O4'   104.83  3.000
 ADN  H4'   C4'  C5'   109.38  3.000
 ADN  C3'   C4'  C5'   112.94  3.000
 ADN  O4'   C4'  C5'   110.29  3.000
 ADN  C1'   O4'  C4'   111.41  3.000
 ADN  H3'   C3'  C2'   109.53  3.000
 ADN  H3'   C3'  O3'   111.04  3.000
 ADN  C2'   C3'  O3'   113.70  3.000
 ADN  H3'   C3'  C4'   109.60  3.000
 ADN  C2'   C3'  C4'   102.01  3.000
 ADN  O3'   C3'  C4'   110.59  3.000
 ADN  HO3'  O3'  C3'   108.95  3.000
 ADN  H2'   C2'  C1'   111.84  3.000
 ADN  H2'   C2'  O2'   111.64  3.000
 ADN  C1'   C2'  O2'   107.31  3.000
 ADN  H2'   C2'  C3'   112.69  3.000
 ADN  C1'   C2'  C3'   102.19  3.000
 ADN  O2'   C2'  C3'   110.68  3.000
 ADN  HO2'  O2'  C2'   107.74  3.000
 ADN  H1'   C1'  N9    105.42  3.000
 ADN  H1'   C1'  C2'   110.15  3.000
 ADN  N9    C1'  C2'   113.91  3.000
 ADN  H1'   C1'  O4'   110.87  3.000
 ADN  N9    C1'  O4'   109.46  3.000
 ADN  C2'   C1'  O4'   107.08  3.000
 ADN  C4    N9   C8    105.99  3.000
 ADN  C4    N9   C1'   125.49  3.000
 ADN  C8    N9   C1'   128.42  3.000
 ADN  H8    C8   N7    124.33  3.000
 ADN  H8    C8   N9    122.12  3.000
 ADN  N7    C8   N9    113.55  3.000
 ADN  C5    N7   C8    104.38  3.000
 ADN  C4    C5   C6    116.33  3.000
 ADN  C4    C5   N7    110.79  3.000
 ADN  C6    C5   N7    132.88  3.000
 ADN  N1    C6   N6    119.38  3.000
 ADN  N1    C6   C5    117.86  3.000
 ADN  N6    C6   C5    122.76  3.000
 ADN  HN62  N6   HN61  118.29  3.000
 ADN  HN62  N6   C6    121.08  3.000
 ADN  HN61  N6   C6    120.29  3.000
 ADN  C2    N1   C6    119.17  3.000
 ADN  H2    C2   N3    116.15  3.000
 ADN  H2    C2   N1    115.41  3.000
 ADN  N3    C2   N1    128.44  3.000
 ADN  C4    N3   C2    111.70  3.000
 ADN  N3    C4   C5    126.49  3.000
 ADN  N3    C4   N9    128.22  3.000
 ADN  C5    C4   N9    105.29  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
 ADN  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 ADN  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 ADN  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 ADN  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 ADN  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 ADN  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 ADN  CONST_07  C6    C5  N7  C8   180.00  0.0  0
 ADN  CONST_08  C4    C5  N7  C8     0.00  0.0  0
 ADN  CONST_09  C4    N9  C8  N7     0.00  0.0  0
 ADN  CONST_10  N1    C6  C5  N7   180.00  0.0  0
 ADN  CONST_11  N3    C4  C5  N7   180.00  0.0  0
 ADN  CONST_12  C2    N1  C6  C5     0.00  0.0  0
 ADN  CONST_13  C2    N3  C4  C5     0.00  0.0  0
 ADN  CONST_14  N3    C4  C5  C6     0.00  0.0  0
 ADN  CONST_15  N3    C2  N1  C6     0.00  0.0  0
 ADN  CONST_16  C4    C5  C6  N1     0.00  0.0  0
 ADN  CONST_17  C4    N3  C2  N1     0.00  0.0  0
 ADN  CONST_18  N7    C8  N9  C1'  180.00  0.0  0
 ADN  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 ADN  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 ADN  CONST_21  N6    C6  C5  N7     0.00  0.0  0
 ADN  CONST_22  C4    C5  C6  N6   180.00  0.0  0
 ADN  CONST_23  C2    N1  C6  N6   180.00  0.0  0
 ADN  CONST_24  H8    C8  N9  C1'    0.00  0.0  0
 ADN  CONST_25  H2    C2  N1  C6   180.00  0.0  0
 ADN  CONST_26  HN61  N6  C6  C5   180.00  0.0  0
 ADN  CONST_27  HN62  N6  C6  C5     0.00  0.0  0

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
 ADN  chir_01  C4'  C5'  O4'  C3'  negativ
 ADN  chir_02  C3'  O3'  C4'  C2'  positiv
 ADN  chir_03  C2'  O2'  C3'  C1'  positiv
 ADN  chir_04  C1'  O4'  N9   C2'  negativ

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
 ADN  plan-1  C1'   0.020
 ADN  plan-1  N9    0.020
 ADN  plan-1  C8    0.020
 ADN  plan-1  N7    0.020
 ADN  plan-1  C5    0.020
 ADN  plan-1  C6    0.020
 ADN  plan-1  N6    0.020
 ADN  plan-1  N1    0.020
 ADN  plan-1  C2    0.020
 ADN  plan-1  N3    0.020
 ADN  plan-1  C4    0.020
 ADN  plan-1  H8    0.020
 ADN  plan-1  H2    0.020
 ADN  plan-2  C6    0.020
 ADN  plan-2  N6    0.020
 ADN  plan-2  HN61  0.020
 ADN  plan-2  HN62  0.020

