# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 17:43:55 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (2S,3S,4R,5R)-N-(2-aminoethyl)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-carboxamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCNC(=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 N5A  N5A  '(2S,3S,4R,5R)-N-(2-aminoethyl)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-carboxamide (non-preferred name)'  ligand  40  23  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N5A
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
 N5A  N53   N  NH2   0  -0.800   7.2604   1.4755  -0.5491
 N5A  C52   C  CH2   0  -0.301   6.1738   0.5198  -0.4280
 N5A  C51   C  CH2   0  -0.272   5.0336   1.1428   0.3657
 N5A  N5'   N  NH1   0  -0.631   3.9737   0.1816   0.5774
 N5A  C5'   C  C     0   0.537   2.6694   0.4516   0.4848
 N5A  O5'   O  O     0  -0.482   2.2046   1.5547   0.2376
 N5A  C4'   C  CR15  0  -0.067   1.7746  -0.7684   0.6495
 N5A  O4'   O  O     0  -0.487   0.6168  -0.4121   1.3738
 N5A  C3'   C  CR15  0  -0.035   1.2626  -1.2840  -0.6987
 N5A  O3'   O  OH1   0  -0.652   2.1947  -2.1548  -1.2658
 N5A  C2'   C  CR15  0  -0.048  -0.0475  -1.9587  -0.2744
 N5A  O2'   O  OH1   0  -0.661   0.1993  -3.2105   0.3013
 N5A  C1'   C  CR15  0   0.171  -0.5232  -1.0237   0.8378
 N5A  N9    N  NR5   0  -0.537  -1.4330   0.0007   0.3545
 N5A  C8    C  CR15  0   0.089  -1.1523   1.2752  -0.0600
 N5A  N7    N  N     0  -0.453  -2.2099   1.9352  -0.4355
 N5A  C5    C  CR56  0  -0.003  -3.2447   1.0539  -0.2631
 N5A  C4    C  CR56  0   0.486  -2.7819  -0.1563   0.2280
 N5A  N3    N  N     0  -0.459  -3.5131  -1.2320   0.5134
 N5A  C2    C  CR16  0   0.041  -4.7969  -1.0230   0.2782
 N5A  N1    N  N     0  -0.474  -5.3835   0.0773  -0.1858
 N5A  C6    C  CR6   0   0.454  -4.6333   1.1478  -0.4710
 N5A  N6    N  NH2   0  -0.816  -5.2203   2.2481  -0.9451
 N5A  H531  H  HNH2  0   0.344   7.7140   1.5862   0.3495
 N5A  H532  H  HNH2  0   0.354   7.9690   1.1037  -1.1676
 N5A  H521  H  HCH2  0   0.231   5.8115   0.2686  -1.4268
 N5A  H522  H  HCH2  0   0.203   6.4665  -0.4278   0.0475
 N5A  H511  H  HCH2  0   0.239   5.4065   1.5041   1.3299
 N5A  H512  H  HCH2  0   0.250   4.6335   2.0015  -0.1705
 N5A  HN5'  H  HNH1  0   0.405   4.2487  -0.7454   0.8623
 N5A  H4'   H  HCR5  0   0.268   2.3105  -1.5728   1.1685
 N5A  H3'   H  HCR5  0   0.260   1.0409  -0.4398  -1.3632
 N5A  HO3'  H  HOH1  0   0.472   2.0350  -2.2103  -2.2134
 N5A  H2'   H  HCR5  0   0.265  -0.7745  -2.0178  -1.0934
 N5A  HO2'  H  HOH1  0   0.454   0.8810  -3.6491  -0.2230
 N5A  H1'   H  HCR5  0   0.283  -1.0593  -1.5809   1.6110
 N5A  H8    H  HCR5  0   0.306  -0.1447   1.6632  -0.0525
 N5A  H2    H  HCR6  0   0.252  -5.4636  -1.8524   0.4896
 N5A  HN61  H  HNH2  0   0.411  -4.6930   3.0888  -1.1028
 N5A  HN62  H  HNH2  0   0.403  -6.2224   2.2974  -1.0090

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
 N5A  N53  C52   single    1.452  0.020  1.452
 N5A  N53  H531  single    0.890  0.020  1.040
 N5A  N53  H532  single    0.890  0.020  1.040
 N5A  C52  C51   single    1.523  0.020  1.523
 N5A  C52  H521  single    0.970  0.020  1.090
 N5A  C52  H522  single    0.970  0.020  1.090
 N5A  C51  N5'   single    1.446  0.020  1.446
 N5A  C51  H511  single    0.970  0.020  1.090
 N5A  C51  H512  single    0.970  0.020  1.090
 N5A  N5'  C5'   single    1.335  0.020  1.335
 N5A  N5'  HN5'  single    0.860  0.020  1.020
 N5A  C5'  O5'   double    1.222  0.020  1.222
 N5A  C5'  C4'   single    1.522  0.020  1.522
 N5A  C4'  O4'   single    1.411  0.020  1.411
 N5A  C4'  C3'   single    1.532  0.020  1.532
 N5A  C4'  H4'   single    0.970  0.020  1.090
 N5A  O4'  C1'   single    1.400  0.020  1.400
 N5A  C3'  O3'   single    1.396  0.020  1.396
 N5A  C3'  C2'   single    1.533  0.020  1.533
 N5A  C3'  H3'   single    0.970  0.020  1.090
 N5A  O3'  HO3'  single    0.850  0.020  0.980
 N5A  C2'  O2'   single    1.400  0.020  1.400
 N5A  C2'  C1'   single    1.529  0.020  1.529
 N5A  C2'  H2'   single    0.970  0.020  1.090
 N5A  O2'  HO2'  single    0.850  0.020  0.980
 N5A  C1'  N9    single    1.453  0.020  1.453
 N5A  C1'  H1'   single    0.970  0.020  1.090
 N5A  N9   C8    aromatic  1.369  0.020  1.369
 N5A  N9   C4    aromatic  1.364  0.020  1.364
 N5A  C8   N7    aromatic  1.302  0.020  1.302
 N5A  C8   H8    single    0.930  0.020  1.080
 N5A  N7   C5    aromatic  1.370  0.020  1.370
 N5A  C5   C4    aromatic  1.386  0.020  1.386
 N5A  C5   C6    aromatic  1.407  0.020  1.407
 N5A  C4   N3    aromatic  1.332  0.020  1.332
 N5A  N3   C2    aromatic  1.322  0.020  1.322
 N5A  C2   N1    aromatic  1.330  0.020  1.330
 N5A  C2   H2    single    0.930  0.020  1.080
 N5A  N1   C6    aromatic  1.338  0.020  1.338
 N5A  C6   N6    single    1.334  0.020  1.334
 N5A  N6   HN61  single    0.860  0.020  1.020
 N5A  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
 N5A  H532  N53  H531  105.61  3.000
 N5A  H532  N53  C52   109.46  3.000
 N5A  H531  N53  C52   109.46  3.000
 N5A  H522  C52  H521  106.60  3.000
 N5A  H522  C52  C51   109.05  3.000
 N5A  H521  C52  C51   108.81  3.000
 N5A  H522  C52  N53   113.83  3.000
 N5A  H521  C52  N53   108.87  3.000
 N5A  C51   C52  N53   109.54  3.000
 N5A  H512  C51  H511  107.37  3.000
 N5A  H512  C51  N5'   109.08  3.000
 N5A  H511  C51  N5'   109.87  3.000
 N5A  H512  C51  C52   109.95  3.000
 N5A  H511  C51  C52   109.81  3.000
 N5A  N5'   C51  C52   110.68  3.000
 N5A  HN5'  N5'  C5'   118.16  3.000
 N5A  HN5'  N5'  C51   116.91  3.000
 N5A  C5'   N5'  C51   124.85  3.000
 N5A  C4'   C5'  O5'   121.45  3.000
 N5A  C4'   C5'  N5'   113.88  3.000
 N5A  O5'   C5'  N5'   124.61  3.000
 N5A  H4'   C4'  C3'   109.44  3.000
 N5A  H4'   C4'  O4'   110.06  3.000
 N5A  C3'   C4'  O4'   105.22  3.000
 N5A  H4'   C4'  C5'   110.60  3.000
 N5A  C3'   C4'  C5'   111.79  3.000
 N5A  O4'   C4'  C5'   109.60  3.000
 N5A  C1'   O4'  C4'   111.17  3.000
 N5A  H3'   C3'  C2'   109.48  3.000
 N5A  H3'   C3'  O3'   111.65  3.000
 N5A  C2'   C3'  O3'   114.10  3.000
 N5A  H3'   C3'  C4'   109.98  3.000
 N5A  C2'   C3'  C4'   100.96  3.000
 N5A  O3'   C3'  C4'   110.15  3.000
 N5A  HO3'  O3'  C3'   108.97  3.000
 N5A  H2'   C2'  C1'   111.71  3.000
 N5A  H2'   C2'  O2'   112.08  3.000
 N5A  C1'   C2'  O2'   107.62  3.000
 N5A  H2'   C2'  C3'   112.54  3.000
 N5A  C1'   C2'  C3'   101.42  3.000
 N5A  O2'   C2'  C3'   110.89  3.000
 N5A  HO2'  O2'  C2'   107.91  3.000
 N5A  H1'   C1'  N9    106.71  3.000
 N5A  H1'   C1'  C2'   110.81  3.000
 N5A  N9    C1'  C2'   112.59  3.000
 N5A  H1'   C1'  O4'   110.55  3.000
 N5A  N9    C1'  O4'   109.22  3.000
 N5A  C2'   C1'  O4'   106.99  3.000
 N5A  C4    N9   C8    106.37  3.000
 N5A  C4    N9   C1'   124.68  3.000
 N5A  C8    N9   C1'   128.95  3.000
 N5A  H8    C8   N7    125.30  3.000
 N5A  H8    C8   N9    121.58  3.000
 N5A  N7    C8   N9    113.12  3.000
 N5A  C5    N7   C8    104.55  3.000
 N5A  C6    C5   C4    116.12  3.000
 N5A  C6    C5   N7    133.14  3.000
 N5A  C4    C5   N7    110.74  3.000
 N5A  N3    C4   C5    126.74  3.000
 N5A  N3    C4   N9    128.03  3.000
 N5A  C5    C4   N9    105.23  3.000
 N5A  C2    N3   C4    111.55  3.000
 N5A  H2    C2   N1    115.42  3.000
 N5A  H2    C2   N3    116.18  3.000
 N5A  N1    C2   N3    128.40  3.000
 N5A  C6    N1   C2    119.26  3.000
 N5A  N6    C6   N1    119.27  3.000
 N5A  N6    C6   C5    122.80  3.000
 N5A  N1    C6   C5    117.93  3.000
 N5A  HN62  N6   HN61  118.17  3.000
 N5A  HN62  N6   C6    120.10  3.000
 N5A  HN61  N6   C6    120.99  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
 N5A  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 N5A  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 N5A  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 N5A  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 N5A  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 N5A  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 N5A  CONST_07  C4    C5   N7   C8      0.00   0.0  0
 N5A  CONST_08  C6    C5   N7   C8    180.00   0.0  0
 N5A  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 N5A  CONST_10  N3    C4   C5   N7    180.00   0.0  0
 N5A  CONST_11  N1    C6   C5   N7    180.00   0.0  0
 N5A  CONST_12  C2    N3   C4   C5      0.00   0.0  0
 N5A  CONST_13  C2    N1   C6   C5      0.00   0.0  0
 N5A  CONST_14  N1    C6   C5   C4      0.00   0.0  0
 N5A  CONST_15  N1    C2   N3   C4      0.00   0.0  0
 N5A  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 N5A  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 N5A  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 N5A  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 N5A  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 N5A  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 N5A  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 N5A  CONST_23  N6    C6   N1   C2    180.00   0.0  0
 N5A  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 N5A  CONST_25  H2    C2   N3   C4    180.00   0.0  0
 N5A  CONST_26  HN61  N6   C6   C5      0.00   0.0  0
 N5A  CONST_27  HN62  N6   C6   C5    180.00   0.0  0
 N5A  CONST_28  C4'   C5'  N5'  C51   180.00   0.0  0
 N5A  CONST_29  HN5'  N5'  C5'  C4'     0.00   0.0  0
 N5A  CONST_30  O5'   C5'  N5'  C51     0.00   0.0  0
 N5A  Var_01    N5'   C51  C52  N53  -176.22  30.0  3
 N5A  Var_02    C5'   N5'  C51  C52  -138.65  30.0  3
 N5A  Var_03    H531  N53  C52  C51    71.41  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
 N5A  chir_01  C4'  C5'  O4'  C3'  negativ
 N5A  chir_02  C3'  O3'  C4'  C2'  positiv
 N5A  chir_03  C2'  O2'  C3'  C1'  positiv
 N5A  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
 N5A  plan-1  C1'   0.020
 N5A  plan-1  N9    0.020
 N5A  plan-1  C8    0.020
 N5A  plan-1  N7    0.020
 N5A  plan-1  C5    0.020
 N5A  plan-1  C4    0.020
 N5A  plan-1  N3    0.020
 N5A  plan-1  C2    0.020
 N5A  plan-1  N1    0.020
 N5A  plan-1  C6    0.020
 N5A  plan-1  N6    0.020
 N5A  plan-1  H8    0.020
 N5A  plan-1  H2    0.020
 N5A  plan-2  C6    0.020
 N5A  plan-2  N6    0.020
 N5A  plan-2  HN61  0.020
 N5A  plan-2  HN62  0.020
 N5A  plan-3  C51   0.020
 N5A  plan-3  N5'   0.020
 N5A  plan-3  C5'   0.020
 N5A  plan-3  O5'   0.020
 N5A  plan-3  C4'   0.020
 N5A  plan-3  HN5'  0.020

