# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:14:55 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 9-beta-D-ribofuranosyl-1,9-dihydro-6H-purine-6-selone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=[Se])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
 SNI  SNI  9-beta-D-ribofuranosyl-1,9-dihydro-6H-purine-6-selone  ligand  31  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SNI
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
 SNI  O5'   O   OH1   0  -0.666   2.7273   0.3880   4.0383
 SNI  C5'   C   CH2   0  -0.167   1.6361  -0.4656   4.2733
 SNI  C4'   C   CH1   0  -0.058   0.3593   0.3535   4.2345
 SNI  O4'   O   O2    0  -0.489   0.2597   1.1201   3.0282
 SNI  C1'   C   CH1   0   0.211  -0.6400   0.5346   2.1437
 SNI  N9    N   NR5   0  -0.531   0.0064   0.4016   0.8470
 SNI  C4    C   CR56  0   0.505  -0.5983   0.4324  -0.3634
 SNI  N3    N   N     0  -0.420  -1.8955   0.6404  -0.6213
 SNI  C2    C   CR16  0   0.162  -2.1652   0.6231  -1.8886
 SNI  N1    N   NR16  0  -0.606  -1.2496   0.4131  -2.8597
 SNI  C6    C   CR6   0   0.148   0.0888   0.1983  -2.6620
 SNI  SE    SE  SE    0  -0.411   1.2241  -0.0666  -4.0550
 SNI  C5    C   CR56  0   0.069   0.4157   0.2168  -1.2963
 SNI  N7    N   N     0  -0.430   1.6131   0.0639  -0.6619
 SNI  C8    C   CR15  0   0.117   1.3352   0.1782   0.6036
 SNI  C2'   C   CH1   0  -0.013  -1.0379  -0.8151   2.7531
 SNI  O2'   O   OH1   0  -0.649  -2.3014  -1.1814   2.3057
 SNI  C3'   C   CH1   0  -0.031  -0.8913  -0.5237   4.2483
 SNI  O3'   O   OH1   0  -0.666  -2.0337   0.1734   4.6644
 SNI  H5'   H   HOH1  0   0.461   3.5304  -0.1402   4.0617
 SNI  H5'1  H   HCH2  0   0.229   1.6891  -0.9438   5.2602
 SNI  H5'2  H   HCH2  0   0.200   1.5979  -1.2787   3.5350
 SNI  H4'   H   HCH1  0   0.268   0.3658   1.0615   5.0684
 SNI  H1'   H   HCH1  0   0.273  -1.5224   1.1647   1.9886
 SNI  H2    H   HCR6  0   0.318  -3.1775   0.7826  -2.2326
 SNI  HN1   H   HNR6  0   0.447  -1.5850   0.4220  -3.8156
 SNI  H8    H   HCR5  0   0.306   2.0607   0.1377   1.4019
 SNI  H2'   H   HCH1  0   0.246  -0.2809  -1.5632   2.4810
 SNI  H1    H   HOH1  0   0.464  -2.4464  -2.1093   2.5150
 SNI  H3'   H   HCH1  0   0.256  -0.7356  -1.4400   4.8325
 SNI  H3    H   HOH1  0   0.458  -1.9372   0.3885   5.5977

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
 SNI  O5'  C5'   single    1.405  0.020  1.405
 SNI  O5'  H5'   single    0.850  0.020  0.980
 SNI  C5'  C4'   single    1.517  0.020  1.517
 SNI  C5'  H5'1  single    0.970  0.020  1.090
 SNI  C5'  H5'2  single    0.970  0.020  1.090
 SNI  C4'  O4'   single    1.433  0.020  1.433
 SNI  C4'  C3'   single    1.528  0.020  1.528
 SNI  C4'  H4'   single    0.970  0.020  1.090
 SNI  O4'  C1'   single    1.391  0.020  1.391
 SNI  C1'  N9    single    1.455  0.020  1.455
 SNI  C1'  C2'   single    1.533  0.020  1.533
 SNI  C1'  H1'   single    0.970  0.020  1.090
 SNI  N9   C4    aromatic  1.354  0.020  1.354
 SNI  N9   C8    aromatic  1.369  0.020  1.369
 SNI  C4   N3    aromatic  1.339  0.020  1.339
 SNI  C4   C5    aromatic  1.395  0.020  1.395
 SNI  N3   C2    aromatic  1.296  0.020  1.296
 SNI  C2   N1    aromatic  1.351  0.020  1.351
 SNI  C2   H2    single    0.930  0.020  1.080
 SNI  N1   C6    aromatic  1.370  0.020  1.370
 SNI  N1   HN1   single    0.860  0.020  1.020
 SNI  C6   SE    double    1.816  0.020  1.816
 SNI  C6   C5    aromatic  1.404  0.020  1.404
 SNI  C5   N7    aromatic  1.364  0.020  1.364
 SNI  N7   C8    aromatic  1.301  0.020  1.301
 SNI  C8   H8    single    0.930  0.020  1.080
 SNI  C2'  O2'   single    1.390  0.020  1.390
 SNI  C2'  C3'   single    1.530  0.020  1.530
 SNI  C2'  H2'   single    0.970  0.020  1.090
 SNI  O2'  H1    single    0.850  0.020  0.980
 SNI  C3'  O3'   single    1.402  0.020  1.402
 SNI  C3'  H3'   single    0.970  0.020  1.090
 SNI  O3'  H3    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
 SNI  H5'   O5'  C5'   108.10  3.000
 SNI  H5'2  C5'  H5'1  106.46  3.000
 SNI  H5'2  C5'  C4'   110.66  3.000
 SNI  H5'1  C5'  C4'   107.37  3.000
 SNI  H5'2  C5'  O5'   111.36  3.000
 SNI  H5'1  C5'  O5'   112.18  3.000
 SNI  C4'   C5'  O5'   108.73  3.000
 SNI  H4'   C4'  C3'   111.69  3.000
 SNI  H4'   C4'  O4'   107.22  3.000
 SNI  C3'   C4'  O4'   104.95  3.000
 SNI  H4'   C4'  C5'   108.95  3.000
 SNI  C3'   C4'  C5'   112.25  3.000
 SNI  O4'   C4'  C5'   111.64  3.000
 SNI  C1'   O4'  C4'   110.80  3.000
 SNI  H1'   C1'  C2'   110.70  3.000
 SNI  H1'   C1'  N9    106.52  3.000
 SNI  C2'   C1'  N9    112.89  3.000
 SNI  H1'   C1'  O4'   111.65  3.000
 SNI  C2'   C1'  O4'   106.59  3.000
 SNI  N9    C1'  O4'   108.53  3.000
 SNI  C8    N9   C4    106.16  3.000
 SNI  C8    N9   C1'   127.20  3.000
 SNI  C4    N9   C1'   126.61  3.000
 SNI  C5    C4   N3    126.85  3.000
 SNI  C5    C4   N9    105.65  3.000
 SNI  N3    C4   N9    127.49  3.000
 SNI  C2    N3   C4    112.83  3.000
 SNI  H2    C2   N1    115.39  3.000
 SNI  H2    C2   N3    120.28  3.000
 SNI  N1    C2   N3    124.33  3.000
 SNI  HN1   N1   C6    117.45  3.000
 SNI  HN1   N1   C2    116.91  3.000
 SNI  C6    N1   C2    125.64  3.000
 SNI  C5    C6   SE    127.02  3.000
 SNI  C5    C6   N1    111.45  3.000
 SNI  SE    C6   N1    121.53  3.000
 SNI  N7    C5   C6    130.94  3.000
 SNI  N7    C5   C4    110.16  3.000
 SNI  C6    C5   C4    118.90  3.000
 SNI  C8    N7   C5    104.78  3.000
 SNI  H8    C8   N7    124.93  3.000
 SNI  H8    C8   N9    121.79  3.000
 SNI  N7    C8   N9    113.25  3.000
 SNI  H2'   C2'  C3'   107.79  3.000
 SNI  H2'   C2'  O2'   111.55  3.000
 SNI  C3'   C2'  O2'   116.86  3.000
 SNI  H2'   C2'  C1'   108.79  3.000
 SNI  C3'   C2'  C1'   101.30  3.000
 SNI  O2'   C2'  C1'   109.88  3.000
 SNI  H1    O2'  C2'   108.74  3.000
 SNI  H3'   C3'  O3'   111.89  3.000
 SNI  H3'   C3'  C2'   112.00  3.000
 SNI  O3'   C3'  C2'   107.86  3.000
 SNI  H3'   C3'  C4'   111.59  3.000
 SNI  O3'   C3'  C4'   112.60  3.000
 SNI  C2'   C3'  C4'   100.30  3.000
 SNI  H3    O3'  C3'   108.50  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
 SNI  CONST_01  C2   N3  C4  N9   180.00  0.0  0
 SNI  CONST_02  C6   C5  C4  N9   180.00  0.0  0
 SNI  CONST_03  N7   C5  C4  N9     0.00  0.0  0
 SNI  CONST_04  C5   N7  C8  N9     0.00  0.0  0
 SNI  CONST_05  N7   C8  N9  C4     0.00  0.0  0
 SNI  CONST_06  N1   C2  N3  C4     0.00  0.0  0
 SNI  CONST_07  N1   C6  C5  C4     0.00  0.0  0
 SNI  CONST_08  C8   N7  C5  C4     0.00  0.0  0
 SNI  CONST_09  C8   N9  C4  N3   180.00  0.0  0
 SNI  CONST_10  C6   C5  C4  N3     0.00  0.0  0
 SNI  CONST_11  N7   C5  C4  N3   180.00  0.0  0
 SNI  CONST_12  C6   N1  C2  N3     0.00  0.0  0
 SNI  CONST_13  C5   C4  N3  C2     0.00  0.0  0
 SNI  CONST_14  C5   C6  N1  C2     0.00  0.0  0
 SNI  CONST_15  N7   C5  C6  N1   180.00  0.0  0
 SNI  CONST_16  C8   N7  C5  C6   180.00  0.0  0
 SNI  CONST_17  C8   N9  C4  C5     0.00  0.0  0
 SNI  CONST_18  N3   C4  N9  C1'    0.00  0.0  0
 SNI  CONST_19  C5   C4  N9  C1'  180.00  0.0  0
 SNI  CONST_20  N7   C8  N9  C1'  180.00  0.0  0
 SNI  CONST_21  SE   C6  C5  C4   180.00  0.0  0
 SNI  CONST_22  SE   C6  N1  C2   180.00  0.0  0
 SNI  CONST_23  N7   C5  C6  SE     0.00  0.0  0
 SNI  CONST_24  H8   C8  N9  C1'    0.00  0.0  0
 SNI  CONST_25  H2   C2  N3  C4   180.00  0.0  0
 SNI  CONST_26  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
 SNI  chir_01  C4'  C5'  O4'  C3'  negativ
 SNI  chir_02  C1'  O4'  N9   C2'  negativ
 SNI  chir_03  C2'  O2'  C1'  C3'  negativ
 SNI  chir_04  C3'  O3'  C4'  C2'  positiv

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
 SNI  plan-1  C1'  0.020
 SNI  plan-1  N9   0.020
 SNI  plan-1  C4   0.020
 SNI  plan-1  N3   0.020
 SNI  plan-1  C2   0.020
 SNI  plan-1  N1   0.020
 SNI  plan-1  C6   0.020
 SNI  plan-1  SE   0.020
 SNI  plan-1  C5   0.020
 SNI  plan-1  N7   0.020
 SNI  plan-1  C8   0.020
 SNI  plan-1  H2   0.020
 SNI  plan-1  HN1  0.020
 SNI  plan-1  H8   0.020

