# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:12:41 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxy-N-(2-hydroxyethyl)tetrahydrofuran-2-carboxamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]([C@@H](O)[C@H]3O)C(=O)NCCO
#
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
 N5O  N5O  '(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxy-N-(2-hydroxyethyl)tetrahydrofuran-2-carboxamide (non-preferred name)'  ligand  39  23  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N5O
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
 N5O  O53   O  OH1   0  -0.673  -6.5876   0.2291  -0.7715
 N5O  C52   C  CH2   0  -0.153  -5.8505   1.4100  -0.5536
 N5O  C51   C  CH2   0  -0.328  -4.8976   1.1798   0.6019
 N5O  N5'   N  NH1   0  -0.614  -3.9366   0.1293   0.3451
 N5O  C5'   C  C     0   0.526  -2.7520   0.3399  -0.2388
 N5O  O5'   O  O     0  -0.480  -2.3549   1.4346  -0.6077
 N5O  C4'   C  CH1   0  -0.064  -1.8995  -0.9159  -0.3491
 N5O  O4'   O  O2    0  -0.485  -0.8580  -0.7216  -1.2800
 N5O  C3'   C  CH1   0  -0.042  -1.2079  -1.2569   0.9772
 N5O  O3'   O  OH1   0  -0.651  -2.0524  -2.0309   1.7753
 N5O  C2'   C  CH1   0  -0.041   0.0340  -2.0022   0.4760
 N5O  O2'   O  OH1   0  -0.661  -0.2873  -3.3090   0.0923
 N5O  C1'   C  CH1   0   0.168   0.3558  -1.2160  -0.7933
 N5O  N9    N  NR5   0  -0.537   1.2616  -0.1067  -0.5276
 N5O  C8    C  CR15  0   0.086   0.9825   1.2279  -0.4032
 N5O  N7    N  N     0  -0.454   2.0388   1.9513  -0.1649
 N5O  C5    C  CR56  0  -0.001   3.0714   1.0517  -0.1308
 N5O  C4    C  CR56  0   0.485   2.6084  -0.2347  -0.3560
 N5O  N3    N  N     0  -0.459   3.3375  -1.3487  -0.3942
 N5O  C2    C  CR16  0   0.039   4.6188  -1.0975  -0.1889
 N5O  N1    N  N     0  -0.473   5.2050   0.0752   0.0374
 N5O  C6    C  CR6   0   0.453   4.4572   1.1839   0.0746
 N5O  N6    N  NH2   0  -0.816   5.0437   2.3582   0.3159
 N5O  HO53  H  HOH1  0   0.457  -7.1053   0.3393  -1.5737
 N5O  H521  H  HCH2  0   0.204  -6.4993   2.2577  -0.2971
 N5O  H522  H  HCH2  0   0.204  -5.2771   1.7022  -1.4413
 N5O  H511  H  HCH2  0   0.259  -5.4550   0.9116   1.5004
 N5O  H512  H  HCH2  0   0.254  -4.3701   2.1082   0.8176
 N5O  HN5'  H  HNH1  0   0.405  -4.2053  -0.8151   0.5686
 N5O  H4'   H  HCH1  0   0.276  -2.5266  -1.7611  -0.6610
 N5O  H3'   H  HCH1  0   0.263  -0.8963  -0.3375   1.4885
 N5O  HO3'  H  HOH1  0   0.473  -1.7714  -1.9583   2.6933
 N5O  H2'   H  HCH1  0   0.267   0.8589  -1.9735   1.1974
 N5O  HO2'  H  HOH1  0   0.454  -0.8951  -3.6703   0.7492
 N5O  H1'   H  HCH1  0   0.288   0.8360  -1.8489  -1.5440
 N5O  H8    H  HCR5  0   0.307  -0.0225   1.6087  -0.5062
 N5O  H2    H  HCR6  0   0.252   5.2836  -1.9545  -0.2066
 N5O  HN61  H  HNH2  0   0.403   6.0460   2.4172   0.3710
 N5O  HN62  H  HNH2  0   0.410   4.5232   3.2163   0.2616

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
 N5O  O53  C52   single    1.409  0.020  1.409
 N5O  O53  HO53  single    0.850  0.020  0.980
 N5O  C52  C51   single    1.515  0.020  1.515
 N5O  C52  H521  single    0.970  0.020  1.090
 N5O  C52  H522  single    0.970  0.020  1.090
 N5O  C51  N5'   single    1.447  0.020  1.447
 N5O  C51  H511  single    0.970  0.020  1.090
 N5O  C51  H512  single    0.970  0.020  1.090
 N5O  N5'  C5'   single    1.337  0.020  1.337
 N5O  N5'  HN5'  single    0.860  0.020  1.020
 N5O  C5'  O5'   double    1.221  0.020  1.221
 N5O  C5'  C4'   single    1.522  0.020  1.522
 N5O  C4'  O4'   single    1.410  0.020  1.410
 N5O  C4'  C3'   single    1.534  0.020  1.534
 N5O  C4'  H4'   single    0.970  0.020  1.090
 N5O  O4'  C1'   single    1.398  0.020  1.398
 N5O  C3'  O3'   single    1.396  0.020  1.396
 N5O  C3'  C2'   single    1.533  0.020  1.533
 N5O  C3'  H3'   single    0.970  0.020  1.090
 N5O  O3'  HO3'  single    0.850  0.020  0.980
 N5O  C2'  O2'   single    1.399  0.020  1.399
 N5O  C2'  C1'   single    1.527  0.020  1.527
 N5O  C2'  H2'   single    0.970  0.020  1.090
 N5O  O2'  HO2'  single    0.850  0.020  0.980
 N5O  C1'  N9    single    1.457  0.020  1.457
 N5O  C1'  H1'   single    0.970  0.020  1.090
 N5O  N9   C8    aromatic  1.369  0.020  1.369
 N5O  N9   C4    aromatic  1.364  0.020  1.364
 N5O  C8   N7    aromatic  1.302  0.020  1.302
 N5O  C8   H8    single    0.930  0.020  1.080
 N5O  N7   C5    aromatic  1.370  0.020  1.370
 N5O  C5   C4    aromatic  1.386  0.020  1.386
 N5O  C5   C6    aromatic  1.407  0.020  1.407
 N5O  C4   N3    aromatic  1.332  0.020  1.332
 N5O  N3   C2    aromatic  1.322  0.020  1.322
 N5O  C2   N1    aromatic  1.331  0.020  1.331
 N5O  C2   H2    single    0.930  0.020  1.080
 N5O  N1   C6    aromatic  1.338  0.020  1.338
 N5O  C6   N6    single    1.335  0.020  1.335
 N5O  N6   HN61  single    0.860  0.020  1.020
 N5O  N6   HN62  single    0.860  0.020  1.020

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
 N5O  HO53  O53  C52   108.35  3.000
 N5O  H522  C52  H521  107.00  3.000
 N5O  H522  C52  C51   109.21  3.000
 N5O  H521  C52  C51   108.10  3.000
 N5O  H522  C52  O53   111.82  3.000
 N5O  H521  C52  O53   111.97  3.000
 N5O  C51   C52  O53   108.64  3.000
 N5O  H512  C51  H511  107.09  3.000
 N5O  H512  C51  N5'   109.41  3.000
 N5O  H511  C51  N5'   107.88  3.000
 N5O  H512  C51  C52   109.03  3.000
 N5O  H511  C51  C52   110.13  3.000
 N5O  N5'   C51  C52   113.12  3.000
 N5O  HN5'  N5'  C5'   118.75  3.000
 N5O  HN5'  N5'  C51   117.66  3.000
 N5O  C5'   N5'  C51   123.47  3.000
 N5O  C4'   C5'  O5'   122.38  3.000
 N5O  C4'   C5'  N5'   113.44  3.000
 N5O  O5'   C5'  N5'   124.13  3.000
 N5O  H4'   C4'  C3'   109.39  3.000
 N5O  H4'   C4'  O4'   109.90  3.000
 N5O  C3'   C4'  O4'   105.57  3.000
 N5O  H4'   C4'  C5'   109.63  3.000
 N5O  C3'   C4'  C5'   111.92  3.000
 N5O  O4'   C4'  C5'   110.36  3.000
 N5O  C1'   O4'  C4'   111.26  3.000
 N5O  H3'   C3'  C2'   109.25  3.000
 N5O  H3'   C3'  O3'   111.71  3.000
 N5O  C2'   C3'  O3'   114.04  3.000
 N5O  H3'   C3'  C4'   110.16  3.000
 N5O  C2'   C3'  C4'   100.99  3.000
 N5O  O3'   C3'  C4'   110.17  3.000
 N5O  HO3'  O3'  C3'   109.07  3.000
 N5O  H2'   C2'  C1'   112.02  3.000
 N5O  H2'   C2'  O2'   112.19  3.000
 N5O  C1'   C2'  O2'   107.53  3.000
 N5O  H2'   C2'  C3'   112.45  3.000
 N5O  C1'   C2'  C3'   101.08  3.000
 N5O  O2'   C2'  C3'   110.96  3.000
 N5O  HO2'  O2'  C2'   107.91  3.000
 N5O  H1'   C1'  N9    107.04  3.000
 N5O  H1'   C1'  C2'   111.43  3.000
 N5O  N9    C1'  C2'   111.80  3.000
 N5O  H1'   C1'  O4'   110.31  3.000
 N5O  N9    C1'  O4'   109.52  3.000
 N5O  C2'   C1'  O4'   106.77  3.000
 N5O  C4    N9   C8    106.34  3.000
 N5O  C4    N9   C1'   124.45  3.000
 N5O  C8    N9   C1'   129.21  3.000
 N5O  H8    C8   N7    125.21  3.000
 N5O  H8    C8   N9    121.66  3.000
 N5O  N7    C8   N9    113.13  3.000
 N5O  C5    N7   C8    104.55  3.000
 N5O  C6    C5   C4    116.11  3.000
 N5O  C6    C5   N7    133.18  3.000
 N5O  C4    C5   N7    110.71  3.000
 N5O  N3    C4   C5    126.74  3.000
 N5O  N3    C4   N9    127.99  3.000
 N5O  C5    C4   N9    105.27  3.000
 N5O  C2    N3   C4    111.55  3.000
 N5O  H2    C2   N1    115.41  3.000
 N5O  H2    C2   N3    116.20  3.000
 N5O  N1    C2   N3    128.39  3.000
 N5O  C6    N1   C2    119.27  3.000
 N5O  N6    C6   N1    119.25  3.000
 N5O  N6    C6   C5    122.81  3.000
 N5O  N1    C6   C5    117.94  3.000
 N5O  HN62  N6   HN61  117.98  3.000
 N5O  HN62  N6   C6    120.92  3.000
 N5O  HN61  N6   C6    119.97  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
 N5O  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 N5O  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 N5O  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 N5O  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 N5O  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 N5O  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 N5O  CONST_07  C4    C5   N7   C8     0.00   0.0  0
 N5O  CONST_08  C6    C5   N7   C8   180.00   0.0  0
 N5O  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 N5O  CONST_10  N3    C4   C5   N7   180.00   0.0  0
 N5O  CONST_11  N1    C6   C5   N7   180.00   0.0  0
 N5O  CONST_12  C2    N3   C4   C5     0.00   0.0  0
 N5O  CONST_13  C2    N1   C6   C5     0.00   0.0  0
 N5O  CONST_14  N1    C6   C5   C4     0.00   0.0  0
 N5O  CONST_15  N1    C2   N3   C4     0.00   0.0  0
 N5O  CONST_16  C6    C5   C4   N3     0.00   0.0  0
 N5O  CONST_17  C6    N1   C2   N3     0.00   0.0  0
 N5O  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 N5O  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 N5O  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 N5O  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 N5O  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 N5O  CONST_23  N6    C6   N1   C2   180.00   0.0  0
 N5O  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 N5O  CONST_25  H2    C2   N3   C4   180.00   0.0  0
 N5O  CONST_26  HN61  N6   C6   C5   180.00   0.0  0
 N5O  CONST_27  HN62  N6   C6   C5     0.00   0.0  0
 N5O  CONST_28  C4'   C5'  N5'  C51  180.00   0.0  0
 N5O  CONST_29  HN5'  N5'  C5'  C4'    0.00   0.0  0
 N5O  CONST_30  O5'   C5'  N5'  C51    0.00   0.0  0
 N5O  Var_01    N5'   C51  C52  O53   61.64  30.0  3
 N5O  Var_02    C5'   N5'  C51  C52   88.77  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
 N5O  chir_01  C4'  C5'  O4'  C3'  negativ
 N5O  chir_02  C3'  O3'  C4'  C2'  positiv
 N5O  chir_03  C2'  O2'  C3'  C1'  positiv
 N5O  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
 N5O  plan-1  C1'   0.020
 N5O  plan-1  N9    0.020
 N5O  plan-1  C8    0.020
 N5O  plan-1  N7    0.020
 N5O  plan-1  C5    0.020
 N5O  plan-1  C4    0.020
 N5O  plan-1  N3    0.020
 N5O  plan-1  C2    0.020
 N5O  plan-1  N1    0.020
 N5O  plan-1  C6    0.020
 N5O  plan-1  N6    0.020
 N5O  plan-1  H8    0.020
 N5O  plan-1  H2    0.020
 N5O  plan-2  C6    0.020
 N5O  plan-2  N6    0.020
 N5O  plan-2  HN61  0.020
 N5O  plan-2  HN62  0.020
 N5O  plan-3  C51   0.020
 N5O  plan-3  N5'   0.020
 N5O  plan-3  C5'   0.020
 N5O  plan-3  O5'   0.020
 N5O  plan-3  C4'   0.020
 N5O  plan-3  HN5'  0.020

