# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 00:29:23 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2'-deoxyinosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[C@@H]1O)n2cnc3C(=O)NC=Nc23
#
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
 2ND  2ND  '2'-deoxyinosine          '  ligand  30  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2ND
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
 2ND  O6    O  O     0  -0.466  -4.2917   1.4900  -0.8945
 2ND  C6    C  CR6   0   0.510  -3.5233   0.6742  -0.4179
 2ND  N1    N  NR16  0  -0.664  -3.9658  -0.5802   0.0158
 2ND  C2    C  CR16  0   0.159  -3.1964  -1.5511   0.5586
 2ND  N3    N  N     0  -0.449  -1.9219  -1.4568   0.7541
 2ND  C4    C  CR56  0   0.482  -1.4248  -0.2671   0.3560
 2ND  C5    C  CR56  0  -0.054  -2.1126   0.7917  -0.2059
 2ND  N7    N  N     0  -0.445  -1.2635   1.8254  -0.4703
 2ND  C8    C  CR15  0   0.096  -0.0945   1.4000  -0.0800
 2ND  N9    N  NR5   0  -0.518  -0.1301   0.1341   0.4300
 2ND  C1'   C  CR15  0   0.186   0.9749  -0.6831   0.9467
 2ND  O4'   O  O     0  -0.497   2.0843   0.1395   1.1393
 2ND  C2'   C  CH2   0  -0.542   1.3965  -1.7626  -0.0383
 2ND  C3'   C  CR15  0   0.011   2.4748  -1.0502  -0.8488
 2ND  O3'   O  OH1   0  -0.661   3.4291  -1.8833  -1.4436
 2ND  C4'   C  CR15  0   0.007   3.1346  -0.1925   0.2275
 2ND  C5'   C  CH2   0  -0.155   3.7850   1.0591  -0.3047
 2ND  O5'   O  OH1   0  -0.669   4.3909   1.7491   0.7605
 2ND  HN1   H  HNR6  0   0.436  -4.9538  -0.7745  -0.0879
 2ND  H2    H  HCR6  0   0.305  -3.7191  -2.4567   0.8359
 2ND  H8    H  HCR5  0   0.298   0.8157   1.9755  -0.1293
 2ND  H1'   H  HCR5  0   0.281   0.6364  -1.0942   1.8997
 2ND  H2'1  H  HCH2  0   0.268   1.8454  -2.5929   0.5118
 2ND  H2'2  H  HCH2  0   0.282   0.5695  -2.1530  -0.6296
 2ND  H3'   H  HCR5  0   0.224   2.0024  -0.3982  -1.5982
 2ND  H1    H  HOH1  0   0.462   3.0402  -2.2788  -2.2293
 2ND  H4'   H  HCR5  0   0.242   3.8836  -0.7991   0.7544
 2ND  H5'1  H  HCH2  0   0.199   3.0310   1.6713  -0.8172
 2ND  H5'2  H  HCH2  0   0.213   4.5157   0.7549  -1.0653
 2ND  H5'   H  HOH1  0   0.459   4.7965   2.5472   0.4100

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
 2ND  O6   C6    double    1.218  0.020  1.218
 2ND  C6   N1    single    1.399  0.020  1.399
 2ND  C6   C5    single    1.431  0.020  1.431
 2ND  N1   C2    single    1.352  0.020  1.352
 2ND  N1   HN1   single    0.860  0.020  1.020
 2ND  C2   N3    double    1.293  0.020  1.293
 2ND  C2   H2    single    0.930  0.020  1.080
 2ND  N3   C4    single    1.349  0.020  1.349
 2ND  C4   C5    aromatic  1.382  0.020  1.382
 2ND  C4   N9    aromatic  1.357  0.020  1.357
 2ND  C5   N7    aromatic  1.364  0.020  1.364
 2ND  N7   C8    aromatic  1.304  0.020  1.304
 2ND  C8   N9    aromatic  1.365  0.020  1.365
 2ND  C8   H8    single    0.930  0.020  1.080
 2ND  N9   C1'   single    1.468  0.020  1.468
 2ND  C1'  O4'   single    1.394  0.020  1.394
 2ND  C1'  C2'   single    1.521  0.020  1.521
 2ND  C1'  H1'   single    0.970  0.020  1.090
 2ND  O4'  C4'   single    1.430  0.020  1.430
 2ND  C2'  C3'   single    1.526  0.020  1.526
 2ND  C2'  H2'1  single    0.970  0.020  1.090
 2ND  C2'  H2'2  single    0.970  0.020  1.090
 2ND  C3'  O3'   single    1.399  0.020  1.399
 2ND  C3'  C4'   single    1.526  0.020  1.526
 2ND  C3'  H3'   single    0.970  0.020  1.090
 2ND  O3'  H1    single    0.850  0.020  0.980
 2ND  C4'  C5'   single    1.508  0.020  1.508
 2ND  C4'  H4'   single    0.970  0.020  1.090
 2ND  C5'  O5'   single    1.406  0.020  1.406
 2ND  C5'  H5'1  single    0.970  0.020  1.090
 2ND  C5'  H5'2  single    0.970  0.020  1.090
 2ND  O5'  H5'   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
 2ND  C5    C6   N1    109.84  3.000
 2ND  C5    C6   O6    128.67  3.000
 2ND  N1    C6   O6    121.49  3.000
 2ND  HN1   N1   C2    117.30  3.000
 2ND  HN1   N1   C6    116.68  3.000
 2ND  C2    N1   C6    126.02  3.000
 2ND  H2    C2   N3    119.91  3.000
 2ND  H2    C2   N1    115.40  3.000
 2ND  N3    C2   N1    124.69  3.000
 2ND  C4    N3   C2    112.51  3.000
 2ND  N9    C4   C5    105.69  3.000
 2ND  N9    C4   N3    126.57  3.000
 2ND  C5    C4   N3    127.74  3.000
 2ND  N7    C5   C4    110.47  3.000
 2ND  N7    C5   C6    130.33  3.000
 2ND  C4    C5   C6    119.20  3.000
 2ND  C8    N7   C5    104.65  3.000
 2ND  H8    C8   N9    122.29  3.000
 2ND  H8    C8   N7    124.69  3.000
 2ND  N9    C8   N7    113.01  3.000
 2ND  C1'   N9   C8    128.89  3.000
 2ND  C1'   N9   C4    124.93  3.000
 2ND  C8    N9   C4    106.18  3.000
 2ND  H1'   C1'  C2'   112.58  3.000
 2ND  H1'   C1'  O4'   110.38  3.000
 2ND  C2'   C1'  O4'   106.72  3.000
 2ND  H1'   C1'  N9    106.46  3.000
 2ND  C2'   C1'  N9    112.07  3.000
 2ND  O4'   C1'  N9    108.61  3.000
 2ND  C4'   O4'  C1'   111.06  3.000
 2ND  H2'2  C2'  H2'1  108.24  3.000
 2ND  H2'2  C2'  C3'   114.56  3.000
 2ND  H2'1  C2'  C3'   109.39  3.000
 2ND  H2'2  C2'  C1'   113.31  3.000
 2ND  H2'1  C2'  C1'   109.10  3.000
 2ND  C3'   C2'  C1'   102.04  3.000
 2ND  H3'   C3'  C4'   109.45  3.000
 2ND  H3'   C3'  O3'   110.87  3.000
 2ND  C4'   C3'  O3'   109.85  3.000
 2ND  H3'   C3'  C2'   109.58  3.000
 2ND  C4'   C3'  C2'   101.14  3.000
 2ND  O3'   C3'  C2'   115.45  3.000
 2ND  H1    O3'  C3'   108.44  3.000
 2ND  H4'   C4'  C5'   109.48  3.000
 2ND  H4'   C4'  C3'   108.83  3.000
 2ND  C5'   C4'  C3'   113.83  3.000
 2ND  H4'   C4'  O4'   108.86  3.000
 2ND  C5'   C4'  O4'   110.44  3.000
 2ND  C3'   C4'  O4'   105.23  3.000
 2ND  H5'2  C5'  H5'1  106.75  3.000
 2ND  H5'2  C5'  O5'   111.96  3.000
 2ND  H5'1  C5'  O5'   112.07  3.000
 2ND  H5'2  C5'  C4'   107.56  3.000
 2ND  H5'1  C5'  C4'   109.35  3.000
 2ND  O5'   C5'  C4'   109.01  3.000
 2ND  H5'   O5'  C5'   108.24  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
 2ND  CONST_01  C8   N7  C5  C4    0.00  0.0  0
 2ND  CONST_02  N7   C8  N9  C4    0.00  0.0  0
 2ND  CONST_03  C8   N9  C4  C5    0.00  0.0  0
 2ND  CONST_04  N9   C8  N7  C5    0.00  0.0  0
 2ND  CONST_05  N9   C4  C5  N7    0.00  0.0  0
 2ND  CONST_06  C1'  N9  C4  N3    0.00  0.0  0
 2ND  CONST_07  C1'  N9  C4  C5  180.00  0.0  0
 2ND  CONST_08  C1'  N9  C8  N7  180.00  0.0  0
 2ND  CONST_09  N3   C2  N1  C6    0.00  0.0  0
 2ND  CONST_10  C4   N3  C2  N1    0.00  0.0  0
 2ND  CONST_11  C5   C6  N1  C2    0.00  0.0  0
 2ND  CONST_12  C2   N1  C6  O6  180.00  0.0  0
 2ND  CONST_13  H8   C8  N9  C4  180.00  0.0  0
 2ND  CONST_14  H2   C2  N1  C6  180.00  0.0  0
 2ND  CONST_15  HN1  N1  C2  N3  180.00  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
 2ND  chir_01  C1'  N9   O4'  C2'  positiv
 2ND  chir_02  C3'  O3'  C4'  C2'  positiv
 2ND  chir_03  C4'  O4'  C3'  C5'  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
 2ND  plan-1  O6   0.020
 2ND  plan-1  C6   0.020
 2ND  plan-1  N1   0.020
 2ND  plan-1  C2   0.020
 2ND  plan-1  N3   0.020
 2ND  plan-1  C4   0.020
 2ND  plan-1  C5   0.020
 2ND  plan-1  N7   0.020
 2ND  plan-1  C8   0.020
 2ND  plan-1  N9   0.020
 2ND  plan-1  C1'  0.020
 2ND  plan-1  HN1  0.020
 2ND  plan-1  H2   0.020
 2ND  plan-1  H8   0.020

