# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:47:55 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 5'-amino-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[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
 5N5  5N5  5'-amino-5'-deoxyadenosine  ligand  33  19  .  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_5N5
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
 5N5  O2'  O  OH1   0  -0.653   1.1044  -2.5314  -0.9278
 5N5  C2'  C  CR15  0  -0.060   1.6310  -1.2558  -0.7093
 5N5  C3'  C  CR15  0  -0.006   3.1353  -1.2323  -0.4113
 5N5  O3'  O  OH1   0  -0.670   3.4928  -2.2997   0.4272
 5N5  C4'  C  CR15  0  -0.030   3.2478   0.0683   0.3650
 5N5  C5'  C  CH2   0  -0.305   3.3926   1.2750  -0.5546
 5N5  N5'  N  NH2   0  -0.791   3.2208   2.5197   0.1690
 5N5  O4'  O  O     0  -0.488   2.0542   0.1194   1.1524
 5N5  C1'  C  CR15  0   0.226   1.0511  -0.6582   0.5830
 5N5  N9   N  NR5   0  -0.542  -0.1164   0.1756   0.3558
 5N5  C8   C  CR15  0   0.090  -0.1389   1.5257   0.1280
 5N5  N7   N  N     0  -0.456  -1.3378   1.9889  -0.0833
 5N5  C5   C  CR56  0  -0.008  -2.1505   0.8904   0.0088
 5N5  C4   C  CR56  0   0.484  -1.4100  -0.2493   0.2865
 5N5  N3   N  N     0  -0.451  -1.8891  -1.4803   0.4592
 5N5  C2   C  CR16  0   0.038  -3.2036  -1.5149   0.3340
 5N5  N1   N  N     0  -0.474  -4.0377  -0.5126   0.0646
 5N5  C6   C  CR6   0   0.451  -3.5419   0.7174  -0.1055
 5N5  N6   N  NH2   0  -0.817  -4.3725   1.7246  -0.3872
 5N5  H1   H  HOH1  0   0.468   1.1957  -2.7492  -1.8606
 5N5  H2   H  HCR5  0   0.254   1.4162  -0.5850  -1.5488
 5N5  H3   H  HCR5  0   0.245   3.7375  -1.2156  -1.3295
 5N5  H4   H  HOH1  0   0.448   3.0530  -3.0934   0.1004
 5N5  H5   H  HCR5  0   0.261   4.0898   0.0486   1.0633
 5N5  H6   H  HCH2  0   0.228   4.3674   1.1766  -1.0529
 5N5  H7   H  HCH2  0   0.225   2.6433   1.2413  -1.3513
 5N5  H8   H  HNH2  0   0.348   3.9843   2.6480   0.8227
 5N5  H9   H  HNH2  0   0.356   3.2793   3.2928  -0.4803
 5N5  H11  H  HCR5  0   0.263   0.7375  -1.4586   1.2619
 5N5  H12  H  HCR5  0   0.307   0.7636   2.1222   0.1625
 5N5  H13  H  HCR6  0   0.249  -3.6701  -2.4855   0.4662
 5N5  H14  H  HNH2  0   0.409  -4.0386   2.6716  -0.4239
 5N5  H15  H  HNH2  0   0.402  -5.3666   1.5756  -0.3702

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
 5N5  N6   C6   single    1.336  0.020  1.336
 5N5  N7   C5   aromatic  1.370  0.020  1.370
 5N5  N7   C8   aromatic  1.303  0.020  1.303
 5N5  C6   C5   aromatic  1.407  0.020  1.407
 5N5  C6   N1   aromatic  1.337  0.020  1.337
 5N5  C5   C4   aromatic  1.387  0.020  1.387
 5N5  C8   N9   aromatic  1.369  0.020  1.369
 5N5  C2'  O2'  single    1.397  0.020  1.397
 5N5  C2'  C3'  single    1.534  0.020  1.534
 5N5  C2'  C1'  single    1.537  0.020  1.537
 5N5  N1   C2   aromatic  1.331  0.020  1.331
 5N5  O3'  C3'  single    1.404  0.020  1.404
 5N5  C3'  C4'  single    1.519  0.020  1.519
 5N5  C4   N9   aromatic  1.363  0.020  1.363
 5N5  C4   N3   aromatic  1.332  0.020  1.332
 5N5  N9   C1'  single    1.453  0.020  1.453
 5N5  C2   N3   aromatic  1.321  0.020  1.321
 5N5  C1'  O4'  single    1.391  0.020  1.391
 5N5  C4'  O4'  single    1.431  0.020  1.431
 5N5  C4'  C5'  single    1.524  0.020  1.524
 5N5  C5'  N5'  single    1.450  0.020  1.450
 5N5  O2'  H1   single    0.850  0.020  0.980
 5N5  C2'  H2   single    0.970  0.020  1.090
 5N5  C3'  H3   single    0.970  0.020  1.090
 5N5  O3'  H4   single    0.850  0.020  0.980
 5N5  C4'  H5   single    0.970  0.020  1.090
 5N5  C5'  H6   single    0.970  0.020  1.090
 5N5  C5'  H7   single    0.970  0.020  1.090
 5N5  N5'  H8   single    0.890  0.020  1.040
 5N5  N5'  H9   single    0.890  0.020  1.040
 5N5  C1'  H11  single    0.970  0.020  1.090
 5N5  C8   H12  single    0.930  0.020  1.080
 5N5  C2   H13  single    0.930  0.020  1.080
 5N5  N6   H14  single    0.860  0.020  1.020
 5N5  N6   H15  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
 5N5  H1   O2'  C2'  108.81  3.000
 5N5  H2   C2'  C1'  109.40  3.000
 5N5  H2   C2'  C3'  109.38  3.000
 5N5  C1'  C2'  C3'  101.58  3.000
 5N5  H2   C2'  O2'  111.42  3.000
 5N5  C1'  C2'  O2'  110.13  3.000
 5N5  C3'  C2'  O2'  114.46  3.000
 5N5  H3   C3'  C4'  111.94  3.000
 5N5  H3   C3'  O3'  111.80  3.000
 5N5  C4'  C3'  O3'  109.09  3.000
 5N5  H3   C3'  C2'  112.06  3.000
 5N5  C4'  C3'  C2'  100.66  3.000
 5N5  O3'  C3'  C2'  110.75  3.000
 5N5  H4   O3'  C3'  107.89  3.000
 5N5  H5   C4'  O4'  106.94  3.000
 5N5  H5   C4'  C5'  109.04  3.000
 5N5  O4'  C4'  C5'  112.52  3.000
 5N5  H5   C4'  C3'  111.58  3.000
 5N5  C5'  C4'  C3'  112.13  3.000
 5N5  O4'  C4'  C3'  104.48  3.000
 5N5  H7   C5'  H6   105.93  3.000
 5N5  H7   C5'  N5'  107.98  3.000
 5N5  H6   C5'  N5'  114.09  3.000
 5N5  H7   C5'  C4'  110.49  3.000
 5N5  H6   C5'  C4'  106.68  3.000
 5N5  N5'  C5'  C4'  111.55  3.000
 5N5  H9   N5'  H8   105.89  3.000
 5N5  H9   N5'  C5'  109.21  3.000
 5N5  H8   N5'  C5'  109.96  3.000
 5N5  C1'  O4'  C4'  110.87  3.000
 5N5  H11  C1'  N9   106.63  3.000
 5N5  H11  C1'  O4'  111.17  3.000
 5N5  N9   C1'  O4'  108.83  3.000
 5N5  H11  C1'  C2'  110.18  3.000
 5N5  O4'  C1'  C2'  106.82  3.000
 5N5  N9   C1'  C2'  113.26  3.000
 5N5  C4   N9   C8   106.46  3.000
 5N5  C4   N9   C1'  126.27  3.000
 5N5  C8   N9   C1'  127.24  3.000
 5N5  H12  C8   N7   125.22  3.000
 5N5  H12  C8   N9   121.62  3.000
 5N5  N7   C8   N9   113.12  3.000
 5N5  C5   N7   C8   104.48  3.000
 5N5  C6   C5   C4   116.31  3.000
 5N5  C4   C5   N7   110.83  3.000
 5N5  C6   C5   N7   132.85  3.000
 5N5  N3   C4   C5   126.38  3.000
 5N5  N3   C4   N9   128.51  3.000
 5N5  C5   C4   N9   105.10  3.000
 5N5  C2   N3   C4   111.70  3.000
 5N5  H13  C2   N1   115.38  3.000
 5N5  H13  C2   N3   116.09  3.000
 5N5  N1   C2   N3   128.53  3.000
 5N5  C6   N1   C2   119.07  3.000
 5N5  N6   C6   N1   119.34  3.000
 5N5  N1   C6   C5   118.01  3.000
 5N5  N6   C6   C5   122.65  3.000
 5N5  H15  N6   H14  117.97  3.000
 5N5  H15  N6   C6   119.98  3.000
 5N5  H14  N6   C6   120.78  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
 5N5  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 5N5  CONST_02  N7   C5   C4   N9     0.00   0.0  0
 5N5  CONST_03  C6   C5   C4   N9   180.00   0.0  0
 5N5  CONST_04  C2   N3   C4   N9   180.00   0.0  0
 5N5  CONST_05  C6   C5   N7   C8   180.00   0.0  0
 5N5  CONST_06  C4   C5   N7   C8     0.00   0.0  0
 5N5  CONST_07  C5   C4   N9   C8     0.00   0.0  0
 5N5  CONST_08  N3   C4   N9   C8   180.00   0.0  0
 5N5  CONST_09  N1   C6   C5   N7   180.00   0.0  0
 5N5  CONST_10  N3   C4   C5   N7   180.00   0.0  0
 5N5  CONST_11  C4   N9   C8   N7     0.00   0.0  0
 5N5  CONST_12  C2   N1   C6   C5     0.00   0.0  0
 5N5  CONST_13  C2   N3   C4   C5     0.00   0.0  0
 5N5  CONST_14  N1   C6   C5   C4     0.00   0.0  0
 5N5  CONST_15  N1   C2   N3   C4     0.00   0.0  0
 5N5  CONST_16  C6   C5   C4   N3     0.00   0.0  0
 5N5  CONST_17  C6   N1   C2   N3     0.00   0.0  0
 5N5  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 5N5  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 5N5  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 5N5  CONST_21  N6   C6   C5   N7     0.00   0.0  0
 5N5  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 5N5  CONST_23  N6   C6   N1   C2   180.00   0.0  0
 5N5  CONST_24  H12  C8   N9   C1'    0.00   0.0  0
 5N5  CONST_25  H13  C2   N3   C4   180.00   0.0  0
 5N5  CONST_26  H14  N6   C6   C5     0.00   0.0  0
 5N5  CONST_27  H15  N6   C6   C5   180.00   0.0  0
 5N5  Var_01    H8   N5'  C5'  C4'   66.92  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
 5N5  chir_01  C2'  O2'  C3'  C1'  positiv
 5N5  chir_02  C3'  O3'  C4'  C2'  positiv
 5N5  chir_03  C4'  O4'  C3'  C5'  negativ
 5N5  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
 5N5  plan-1  C1'  0.020
 5N5  plan-1  N9   0.020
 5N5  plan-1  C8   0.020
 5N5  plan-1  N7   0.020
 5N5  plan-1  C5   0.020
 5N5  plan-1  C4   0.020
 5N5  plan-1  N3   0.020
 5N5  plan-1  C2   0.020
 5N5  plan-1  N1   0.020
 5N5  plan-1  C6   0.020
 5N5  plan-1  N6   0.020
 5N5  plan-1  H12  0.020
 5N5  plan-1  H13  0.020
 5N5  plan-2  C6   0.020
 5N5  plan-2  N6   0.020
 5N5  plan-2  H14  0.020
 5N5  plan-2  H15  0.020

