# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 19:59:02 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 5'-deoxy-5'-(prop-2-yn-1-ylamino)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CNCC#C)[C@@H](O)[C@H]3O
#
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
 A3N  A3N  5'-deoxy-5'-(prop-2-yn-1-ylamino)adenosine  ligand  38  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A3N
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
 A3N  C13  C  CSP1  0  -0.536  -5.2069  -3.5184   0.9811
 A3N  C12  C  CSP   0   0.261  -4.8650  -2.5752   0.3196
 A3N  C11  C  CH2   0  -0.404  -4.4345  -1.4332  -0.4813
 A3N  N5   N  NH1   0  -0.603  -3.5971  -0.5345   0.2939
 A3N  C10  C  CH2   0  -0.282  -3.1649   0.6040  -0.4888
 A3N  C9   C  CH1   0  -0.029  -2.3004   1.5306   0.3472
 A3N  O1   O  O2    0  -0.495  -1.1485   0.8277   0.8368
 A3N  C8   C  CH1   0  -0.020  -1.7521   2.7125  -0.4402
 A3N  O2   O  OH1   0  -0.668  -1.5047   3.7694   0.4503
 A3N  C7   C  CH1   0  -0.056  -0.4417   2.1305  -0.9756
 A3N  O3   O  OH1   0  -0.653   0.5397   3.0690  -1.2983
 A3N  C6   C  CH1   0   0.214   0.0185   1.2915   0.2164
 A3N  N3   N  NR5   0  -0.541   0.8559   0.1760  -0.1431
 A3N  C5   C  CR15  0   0.114   0.5481  -0.8611  -0.9835
 A3N  N4   N  N     0  -0.447   1.4934  -1.7454  -1.0815
 A3N  C2   C  CR56  0  -0.012   2.4865  -1.2755  -0.2602
 A3N  C3   C  CR56  0   0.493   2.1081  -0.0845   0.3381
 A3N  N2   N  N     0  -0.458   2.8281   0.6342   1.1952
 A3N  C4   C  CR16  0   0.046   4.0023   0.0762   1.4349
 A3N  N1   N  N     0  -0.474   4.4996  -1.0516   0.9353
 A3N  C1   C  CR6   0   0.462   3.7635  -1.7636   0.0738
 A3N  N6   N  NH2   0  -0.816   4.2596  -2.8927  -0.4317
 A3N  H1   H  H     0   0.279  -5.5097  -4.3547   1.5684
 A3N  H2   H  HCH2  0   0.243  -3.9441  -1.8045  -1.3935
 A3N  H3   H  HCH2  0   0.269  -5.3199  -0.8857  -0.8164
 A3N  H4   H  HNH1  0   0.352  -2.7865  -1.0447   0.6238
 A3N  H6   H  HCH2  0   0.203  -2.6367   0.3134  -1.4129
 A3N  H7   H  HCH2  0   0.251  -4.0490   1.1639  -0.8077
 A3N  H8   H  HCH1  0   0.262  -2.8806   1.8700   1.2098
 A3N  H9   H  HCH1  0   0.253  -2.4280   3.0124  -1.2521
 A3N  H10  H  HOH1  0   0.450  -0.8776   4.3709   0.0323
 A3N  H11  H  HCH1  0   0.250  -0.6689   1.4795  -1.8288
 A3N  H12  H  HOH1  0   0.470   0.3843   3.3856  -2.1939
 A3N  H13  H  HCH1  0   0.264   0.6130   1.9066   0.9001
 A3N  H14  H  HCR5  0   0.290  -0.3984  -0.9150  -1.5010
 A3N  H15  H  HCR6  0   0.253   4.6480   0.6026   2.1295
 A3N  H16  H  HNH2  0   0.412   3.7266  -3.4561  -1.0704
 A3N  H17  H  HNH2  0   0.404   5.1730  -3.2127  -0.1595

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
 A3N  N6   C1   single    1.333  0.020  1.333
 A3N  N4   C2   aromatic  1.372  0.020  1.372
 A3N  N4   C5   aromatic  1.298  0.020  1.298
 A3N  C1   C2   aromatic  1.407  0.020  1.407
 A3N  C1   N1   aromatic  1.338  0.020  1.338
 A3N  C2   C3   aromatic  1.385  0.020  1.385
 A3N  C5   N3   aromatic  1.370  0.020  1.370
 A3N  C7   O3   single    1.396  0.020  1.396
 A3N  C7   C8   single    1.530  0.020  1.530
 A3N  C7   C6   single    1.529  0.020  1.529
 A3N  N1   C4   aromatic  1.330  0.020  1.330
 A3N  O2   C8   single    1.404  0.020  1.404
 A3N  C8   C9   single    1.522  0.020  1.522
 A3N  C3   N3   aromatic  1.367  0.020  1.367
 A3N  C3   N2   aromatic  1.330  0.020  1.330
 A3N  N3   C6   single    1.440  0.020  1.440
 A3N  C4   N2   aromatic  1.322  0.020  1.322
 A3N  C6   O1   single    1.401  0.020  1.401
 A3N  C9   O1   single    1.435  0.020  1.435
 A3N  C9   C10  single    1.518  0.020  1.518
 A3N  C10  N5   single    1.448  0.020  1.448
 A3N  N5   C11  single    1.452  0.020  1.452
 A3N  C11  C12  single    1.460  0.020  1.460
 A3N  C12  C13  triple    1.202  0.020  1.202
 A3N  C13  H1   single    0.913  0.020  1.066
 A3N  C11  H2   single    0.939  0.020  1.096
 A3N  C11  H3   single    0.939  0.020  1.096
 A3N  N5   H4   single    0.868  0.020  1.013
 A3N  C10  H6   single    0.939  0.020  1.096
 A3N  C10  H7   single    0.939  0.020  1.096
 A3N  C9   H8   single    0.939  0.020  1.096
 A3N  C8   H9   single    0.939  0.020  1.096
 A3N  O2   H10  single    0.832  0.020  0.971
 A3N  C7   H11  single    0.939  0.020  1.096
 A3N  O3   H12  single    0.832  0.020  0.971
 A3N  C6   H13  single    0.939  0.020  1.096
 A3N  C5   H14  single    0.929  0.020  1.085
 A3N  C4   H15  single    0.929  0.020  1.085
 A3N  N6   H16  single    0.868  0.020  1.013
 A3N  N6   H17  single    0.868  0.020  1.013

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
 A3N  H1   C13  C12  180.00  3.000
 A3N  C11  C12  C13  180.00  3.000
 A3N  H3   C11  H2   106.00  3.000
 A3N  H3   C11  N5   108.69  3.000
 A3N  H2   C11  N5   113.22  3.000
 A3N  H3   C11  C12  108.73  3.000
 A3N  H2   C11  C12  108.81  3.000
 A3N  N5   C11  C12  111.18  3.000
 A3N  H4   N5   C10  109.46  3.000
 A3N  H4   N5   C11  108.88  3.000
 A3N  C10  N5   C11  111.73  3.000
 A3N  H7   C10  H6   106.11  3.000
 A3N  H7   C10  C9   107.96  3.000
 A3N  H6   C10  C9   110.45  3.000
 A3N  H7   C10  N5   108.59  3.000
 A3N  H6   C10  N5   112.87  3.000
 A3N  C9   C10  N5   110.63  3.000
 A3N  H8   C9   C8   110.98  3.000
 A3N  H8   C9   O1   107.98  3.000
 A3N  C8   C9   O1   105.52  3.000
 A3N  H8   C9   C10  108.76  3.000
 A3N  O1   C9   C10  110.24  3.000
 A3N  C8   C9   C10  113.21  3.000
 A3N  C6   O1   C9   110.82  3.000
 A3N  H9   C8   C7   111.85  3.000
 A3N  H9   C8   O2   111.82  3.000
 A3N  C7   C8   O2   110.94  3.000
 A3N  H9   C8   C9   111.88  3.000
 A3N  O2   C8   C9   108.65  3.000
 A3N  C7   C8   C9   101.19  3.000
 A3N  H10  O2   C8   108.01  3.000
 A3N  H11  C7   C6   110.06  3.000
 A3N  H11  C7   O3   111.40  3.000
 A3N  C6   C7   O3   109.73  3.000
 A3N  H11  C7   C8   108.69  3.000
 A3N  C6   C7   C8   101.17  3.000
 A3N  O3   C7   C8   115.29  3.000
 A3N  H12  O3   C7   108.83  3.000
 A3N  H13  C6   N3   105.98  3.000
 A3N  H13  C6   C7   109.99  3.000
 A3N  N3   C6   C7   113.92  3.000
 A3N  H13  C6   O1   111.21  3.000
 A3N  N3   C6   O1   109.78  3.000
 A3N  C7   C6   O1   106.04  3.000
 A3N  C3   N3   C5   106.12  3.000
 A3N  C3   N3   C6   126.33  3.000
 A3N  C5   N3   C6   127.50  3.000
 A3N  H14  C5   N4   124.61  3.000
 A3N  H14  C5   N3   121.92  3.000
 A3N  N4   C5   N3   113.48  3.000
 A3N  C2   N4   C5   104.40  3.000
 A3N  C1   C2   C3   116.33  3.000
 A3N  C3   C2   N4   110.81  3.000
 A3N  C1   C2   N4   132.86  3.000
 A3N  N2   C3   C2   126.50  3.000
 A3N  N2   C3   N3   128.30  3.000
 A3N  C2   C3   N3   105.19  3.000
 A3N  C4   N2   C3   111.69  3.000
 A3N  H15  C4   N1   115.43  3.000
 A3N  H15  C4   N2   116.11  3.000
 A3N  N1   C4   N2   128.46  3.000
 A3N  C1   N1   C4   119.16  3.000
 A3N  N6   C1   N1   119.34  3.000
 A3N  N1   C1   C2   117.87  3.000
 A3N  N6   C1   C2   122.79  3.000
 A3N  H17  N6   H16  118.39  3.000
 A3N  H17  N6   C1   120.34  3.000
 A3N  H16  N6   C1   121.24  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
 A3N  CONST_01  C2   N4   C5   N3      0.00   0.0  0
 A3N  CONST_02  N4   C2   C3   N3      0.00   0.0  0
 A3N  CONST_03  C1   C2   C3   N3    180.00   0.0  0
 A3N  CONST_04  C4   N2   C3   N3    180.00   0.0  0
 A3N  CONST_05  C1   C2   N4   C5    180.00   0.0  0
 A3N  CONST_06  C3   C2   N4   C5      0.00   0.0  0
 A3N  CONST_07  C2   C3   N3   C5      0.00   0.0  0
 A3N  CONST_08  N2   C3   N3   C5    180.00   0.0  0
 A3N  CONST_09  N1   C1   C2   N4    180.00   0.0  0
 A3N  CONST_10  N2   C3   C2   N4    180.00   0.0  0
 A3N  CONST_11  C3   N3   C5   N4      0.00   0.0  0
 A3N  CONST_12  C4   N1   C1   C2      0.00   0.0  0
 A3N  CONST_13  C4   N2   C3   C2      0.00   0.0  0
 A3N  CONST_14  N1   C1   C2   C3      0.00   0.0  0
 A3N  CONST_15  N1   C4   N2   C3      0.00   0.0  0
 A3N  CONST_16  C1   C2   C3   N2      0.00   0.0  0
 A3N  CONST_17  C1   N1   C4   N2      0.00   0.0  0
 A3N  CONST_18  N4   C5   N3   C6    180.00   0.0  0
 A3N  CONST_19  C2   C3   N3   C6    180.00   0.0  0
 A3N  CONST_20  N2   C3   N3   C6      0.00   0.0  0
 A3N  CONST_21  N6   C1   C2   N4      0.00   0.0  0
 A3N  CONST_22  N6   C1   C2   C3    180.00   0.0  0
 A3N  CONST_23  N6   C1   N1   C4    180.00   0.0  0
 A3N  CONST_24  H14  C5   N3   C6      0.00   0.0  0
 A3N  CONST_25  H15  C4   N2   C3    180.00   0.0  0
 A3N  CONST_26  H16  N6   C1   C2      0.00   0.0  0
 A3N  CONST_27  H17  N6   C1   C2    180.00   0.0  0
 A3N  Var_01    C9   C10  N5   C11   179.61  30.0  1
 A3N  Var_02    N5   C11  C12  C13   -57.99  30.0  2
 A3N  Var_03    C10  N5   C11  C12  -179.91  30.0  2

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
 A3N  chir_01  C9  C8  O1  C10  positiv
 A3N  chir_02  C8  O2  C7  C9   negativ
 A3N  chir_03  C7  O3  C6  C8   negativ
 A3N  chir_04  C6  O1  N3  C7   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
 A3N  plan-1  C6   0.020
 A3N  plan-1  N3   0.020
 A3N  plan-1  C5   0.020
 A3N  plan-1  N4   0.020
 A3N  plan-1  C2   0.020
 A3N  plan-1  C3   0.020
 A3N  plan-1  N2   0.020
 A3N  plan-1  C4   0.020
 A3N  plan-1  N1   0.020
 A3N  plan-1  C1   0.020
 A3N  plan-1  N6   0.020
 A3N  plan-1  H14  0.020
 A3N  plan-1  H15  0.020
 A3N  plan-2  C1   0.020
 A3N  plan-2  N6   0.020
 A3N  plan-2  H16  0.020
 A3N  plan-2  H17  0.020

