# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 08:36:40 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 3'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)C[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
 3AD  3AD  '3'-deoxyadenosine        '  ligand  31  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_3AD
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
 3AD  O5'   O  OH1   0  -0.669   1.7056  -0.5825  -4.3732
 3AD  C5'   C  CH2   0  -0.155   1.0792   0.4890  -3.7125
 3AD  C4'   C  CH1   0   0.022  -0.2622   0.0344  -3.1919
 3AD  O4'   O  O2    0  -0.498  -0.1090  -1.0539  -2.2625
 3AD  C3'   C  CH2   0  -0.546  -1.0043   1.1155  -2.4186
 3AD  C2'   C  CH1   0  -0.019  -1.8183   0.3033  -1.4229
 3AD  O2'   O  OH1   0  -0.666  -2.9337  -0.3151  -2.0160
 3AD  C1'   C  CH1   0   0.185  -0.8355  -0.8256  -1.1028
 3AD  N9    N  NR5   0  -0.539   0.0772  -0.4422  -0.0241
 3AD  C8    C  CR15  0   0.102   1.4374  -0.3110  -0.0779
 3AD  N7    N  N     0  -0.452   1.9751  -0.0134   1.0700
 3AD  C5    C  CR56  0  -0.003   0.9163   0.0434   1.9357
 3AD  C6    C  CR6   0   0.454   0.8201   0.3004   3.3158
 3AD  N6    N  NH2   0  -0.816   1.8806   0.5938   4.0713
 3AD  N1    N  N     0  -0.474  -0.3923   0.2556   3.8788
 3AD  C2    C  CR16  0   0.038  -1.4493  -0.0258   3.1207
 3AD  N3    N  N     0  -0.459  -1.4870  -0.2795   1.8246
 3AD  C4    C  CR56  0   0.486  -0.2728  -0.2298   1.2772
 3AD  HO5'  H  HOH1  0   0.458   2.5504  -0.2744  -4.7131
 3AD  H5'1  H  HCH2  0   0.214   0.8980   1.3379  -4.3851
 3AD  H5'2  H  HCH2  0   0.193   1.6861   0.8709  -2.8804
 3AD  H4'   H  HCH1  0   0.243  -0.8673  -0.3272  -4.0302
 3AD  H3'1  H  HCH2  0   0.255  -0.3065   1.7716  -1.8896
 3AD  H3'2  H  HCH2  0   0.282  -1.6222   1.7437  -3.0602
 3AD  H2'   H  HCH1  0   0.261  -2.0983   0.8770  -0.5339
 3AD  HO2'  H  HOH1  0   0.459  -3.4960   0.3694  -2.3916
 3AD  H1'   H  HCH1  0   0.283  -1.3481  -1.7396  -0.7902
 3AD  H8    H  HCR5  0   0.295   1.9903  -0.4648  -0.9902
 3AD  HN61  H  HNH2  0   0.402   1.7784   0.6828   5.0675
 3AD  HN62  H  HNH2  0   0.410   2.8109   0.5539   3.6935
 3AD  H2    H  HCR6  0   0.251  -2.4015  -0.0499   3.6402

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
 3AD  O5'  C5'   single    1.406  0.020  1.406
 3AD  O5'  HO5'  single    0.850  0.020  0.980
 3AD  C5'  C4'   single    1.509  0.020  1.509
 3AD  C5'  H5'1  single    0.970  0.020  1.090
 3AD  C5'  H5'2  single    0.970  0.020  1.090
 3AD  C4'  O4'   single    1.439  0.020  1.439
 3AD  C4'  C3'   single    1.522  0.020  1.522
 3AD  C4'  H4'   single    0.970  0.020  1.090
 3AD  O4'  C1'   single    1.387  0.020  1.387
 3AD  C3'  C2'   single    1.521  0.020  1.521
 3AD  C3'  H3'1  single    0.970  0.020  1.090
 3AD  C3'  H3'2  single    0.970  0.020  1.090
 3AD  C2'  O2'   single    1.406  0.020  1.406
 3AD  C2'  C1'   single    1.531  0.020  1.531
 3AD  C2'  H2'   single    0.970  0.020  1.090
 3AD  O2'  HO2'  single    0.850  0.020  0.980
 3AD  C1'  N9    single    1.464  0.020  1.464
 3AD  C1'  H1'   single    0.970  0.020  1.090
 3AD  N9   C8    aromatic  1.368  0.020  1.368
 3AD  N9   C4    aromatic  1.364  0.020  1.364
 3AD  C8   N7    aromatic  1.302  0.020  1.302
 3AD  C8   H8    single    0.930  0.020  1.080
 3AD  N7   C5    aromatic  1.369  0.020  1.369
 3AD  C5   C6    aromatic  1.407  0.020  1.407
 3AD  C5   C4    aromatic  1.386  0.020  1.386
 3AD  C6   N6    single    1.335  0.020  1.335
 3AD  C6   N1    aromatic  1.337  0.020  1.337
 3AD  N6   HN61  single    0.860  0.020  1.020
 3AD  N6   HN62  single    0.860  0.020  1.020
 3AD  N1   C2    aromatic  1.331  0.020  1.331
 3AD  C2   N3    aromatic  1.321  0.020  1.321
 3AD  C2   H2    single    0.930  0.020  1.080
 3AD  N3   C4    aromatic  1.333  0.020  1.333

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
 3AD  HO5'  O5'  C5'   108.27  3.000
 3AD  H5'2  C5'  H5'1  106.64  3.000
 3AD  H5'2  C5'  C4'   109.54  3.000
 3AD  H5'1  C5'  C4'   107.31  3.000
 3AD  H5'2  C5'  O5'   112.01  3.000
 3AD  H5'1  C5'  O5'   112.01  3.000
 3AD  C4'   C5'  O5'   109.18  3.000
 3AD  H4'   C4'  C3'   110.73  3.000
 3AD  H4'   C4'  O4'   107.66  3.000
 3AD  C3'   C4'  O4'   105.12  3.000
 3AD  H4'   C4'  C5'   109.06  3.000
 3AD  C3'   C4'  C5'   113.24  3.000
 3AD  O4'   C4'  C5'   110.85  3.000
 3AD  C1'   O4'  C4'   111.08  3.000
 3AD  H3'2  C3'  H3'1  107.49  3.000
 3AD  H3'2  C3'  C2'   112.94  3.000
 3AD  H3'1  C3'  C2'   110.18  3.000
 3AD  H3'2  C3'  C4'   112.74  3.000
 3AD  H3'1  C3'  C4'   111.13  3.000
 3AD  C2'   C3'  C4'   102.37  3.000
 3AD  H2'   C2'  C1'   112.40  3.000
 3AD  H2'   C2'  O2'   111.73  3.000
 3AD  C1'   C2'  O2'   105.85  3.000
 3AD  H2'   C2'  C3'   112.87  3.000
 3AD  C1'   C2'  C3'   100.78  3.000
 3AD  O2'   C2'  C3'   112.53  3.000
 3AD  HO2'  O2'  C2'   108.38  3.000
 3AD  H1'   C1'  N9    107.49  3.000
 3AD  H1'   C1'  C2'   112.03  3.000
 3AD  N9    C1'  C2'   111.18  3.000
 3AD  H1'   C1'  O4'   110.29  3.000
 3AD  N9    C1'  O4'   109.42  3.000
 3AD  C2'   C1'  O4'   106.43  3.000
 3AD  C4    N9   C8    106.13  3.000
 3AD  C4    N9   C1'   125.71  3.000
 3AD  C8    N9   C1'   128.03  3.000
 3AD  H8    C8   N7    124.54  3.000
 3AD  H8    C8   N9    122.00  3.000
 3AD  N7    C8   N9    113.45  3.000
 3AD  C5    N7   C8    104.34  3.000
 3AD  C4    C5   C6    116.31  3.000
 3AD  C4    C5   N7    110.78  3.000
 3AD  C6    C5   N7    132.90  3.000
 3AD  N1    C6   N6    119.29  3.000
 3AD  N1    C6   C5    117.95  3.000
 3AD  N6    C6   C5    122.75  3.000
 3AD  HN62  N6   HN61  118.04  3.000
 3AD  HN62  N6   C6    120.94  3.000
 3AD  HN61  N6   C6    119.98  3.000
 3AD  C2    N1   C6    119.16  3.000
 3AD  H2    C2   N3    116.13  3.000
 3AD  H2    C2   N1    115.41  3.000
 3AD  N3    C2   N1    128.46  3.000
 3AD  C4    N3   C2    111.70  3.000
 3AD  N3    C4   C5    126.41  3.000
 3AD  N3    C4   N9    128.30  3.000
 3AD  C5    C4   N9    105.29  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
 3AD  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 3AD  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 3AD  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 3AD  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 3AD  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 3AD  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 3AD  CONST_07  C6    C5  N7  C8   180.00  0.0  0
 3AD  CONST_08  C4    C5  N7  C8     0.00  0.0  0
 3AD  CONST_09  C4    N9  C8  N7     0.00  0.0  0
 3AD  CONST_10  N1    C6  C5  N7   180.00  0.0  0
 3AD  CONST_11  N3    C4  C5  N7   180.00  0.0  0
 3AD  CONST_12  C2    N1  C6  C5     0.00  0.0  0
 3AD  CONST_13  C2    N3  C4  C5     0.00  0.0  0
 3AD  CONST_14  N3    C4  C5  C6     0.00  0.0  0
 3AD  CONST_15  N3    C2  N1  C6     0.00  0.0  0
 3AD  CONST_16  C4    C5  C6  N1     0.00  0.0  0
 3AD  CONST_17  C4    N3  C2  N1     0.00  0.0  0
 3AD  CONST_18  N7    C8  N9  C1'  180.00  0.0  0
 3AD  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 3AD  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 3AD  CONST_21  N6    C6  C5  N7     0.00  0.0  0
 3AD  CONST_22  C4    C5  C6  N6   180.00  0.0  0
 3AD  CONST_23  C2    N1  C6  N6   180.00  0.0  0
 3AD  CONST_24  H8    C8  N9  C1'    0.00  0.0  0
 3AD  CONST_25  H2    C2  N1  C6   180.00  0.0  0
 3AD  CONST_26  HN61  N6  C6  C5   180.00  0.0  0
 3AD  CONST_27  HN62  N6  C6  C5     0.00  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
 3AD  chir_01  C4'  C5'  O4'  C3'  negativ
 3AD  chir_02  C2'  O2'  C1'  C3'  negativ
 3AD  chir_03  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
 3AD  plan-1  C1'   0.020
 3AD  plan-1  N9    0.020
 3AD  plan-1  C8    0.020
 3AD  plan-1  N7    0.020
 3AD  plan-1  C5    0.020
 3AD  plan-1  C6    0.020
 3AD  plan-1  N6    0.020
 3AD  plan-1  N1    0.020
 3AD  plan-1  C2    0.020
 3AD  plan-1  N3    0.020
 3AD  plan-1  C4    0.020
 3AD  plan-1  H8    0.020
 3AD  plan-1  H2    0.020
 3AD  plan-2  C6    0.020
 3AD  plan-2  N6    0.020
 3AD  plan-2  HN61  0.020
 3AD  plan-2  HN62  0.020

