# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 12:14:10 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 2'-amino-2'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n2cnc3c(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
 2AD  2AD  2'-amino-2'-deoxyadenosine  L-peptide  33  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2AD
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
 2AD  O5'   O  OH1   0  -0.668  -2.5164   0.3644  -3.3378
 2AD  C5'   C  CH2   0  -0.166  -1.3584  -0.4203  -3.4725
 2AD  C4'   C  CH1   0  -0.051  -0.1435   0.4433  -3.1866
 2AD  O4'   O  O2    0  -0.493  -0.2477   1.0879  -1.9135
 2AD  C3'   C  CH1   0  -0.005   1.1357  -0.3853  -3.1122
 2AD  O3'   O  OH1   0  -0.673   2.2899   0.3891  -3.3187
 2AD  C2'   C  CH1   0  -0.175   1.1187  -0.8096  -1.6392
 2AD  C1'   C  CH1   0   0.235   0.5732   0.4605  -0.9737
 2AD  N9    N  NR5   0  -0.531  -0.1948   0.1935   0.2242
 2AD  C8    C  CR15  0   0.103  -1.4772  -0.2772   0.2933
 2AD  N7    N  N     0  -0.452  -1.8967  -0.4576   1.5113
 2AD  C5    C  CR56  0  -0.013  -0.8340  -0.0885   2.2937
 2AD  C6    C  CR6   0   0.456  -0.6443  -0.0427   3.6868
 2AD  N6    N  NH2   0  -0.818  -1.5874  -0.4108   4.5557
 2AD  N1    N  N     0  -0.476   0.5334   0.3955   4.1448
 2AD  C2    C  CR16  0   0.040   1.4679   0.7690   3.2734
 2AD  N3    N  N     0  -0.454   1.4115   0.7650   1.9537
 2AD  C4    C  CR56  0   0.491   0.2349   0.3242   1.5120
 2AD  N     N  NH2   0  -0.785   2.3324  -1.2621  -1.0182
 2AD  H5'   H  HOH1  0   0.459  -3.2786  -0.2023  -3.4861
 2AD  H5'1  H  HCH2  0   0.222  -1.2496  -0.8248  -4.4873
 2AD  H5'2  H  HCH2  0   0.200  -1.3787  -1.2812  -2.7898
 2AD  H4'   H  HCH1  0   0.259  -0.0768   1.2275  -3.9477
 2AD  H3'   H  HCH1  0   0.247   1.1011  -1.2504  -3.7868
 2AD  HA    H  HOH1  0   0.459   2.2926   0.7083  -4.2266
 2AD  H2'   H  HCH1  0   0.269   0.3752  -1.6053  -1.5328
 2AD  H1'   H  HCH1  0   0.257   1.3957   1.1151  -0.6639
 2AD  H8    H  HCR5  0   0.295  -2.0695  -0.4447  -0.5936
 2AD  H6N1  H  HNH2  0   0.403  -1.4046  -0.3852   5.5438
 2AD  H6N2  H  HNH2  0   0.410  -2.4699  -0.7745   4.2424
 2AD  H2    H  HCR6  0   0.250   2.3968   1.1201   3.7102
 2AD  HN1   H  HNH2  0   0.359   2.5939  -2.1655  -1.3901
 2AD  HN2   H  HNH2  0   0.348   3.0959  -0.6304  -1.2249

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
 2AD  O5'  C5'   single    1.405  0.020  1.405
 2AD  O5'  H5'   single    0.850  0.020  0.980
 2AD  C5'  C4'   single    1.518  0.020  1.518
 2AD  C5'  H5'1  single    0.970  0.020  1.090
 2AD  C5'  H5'2  single    0.970  0.020  1.090
 2AD  C4'  O4'   single    1.431  0.020  1.431
 2AD  C4'  C3'   single    1.526  0.020  1.526
 2AD  C4'  H4'   single    0.970  0.020  1.090
 2AD  O4'  C1'   single    1.397  0.020  1.397
 2AD  C3'  O3'   single    1.405  0.020  1.405
 2AD  C3'  C2'   single    1.533  0.020  1.533
 2AD  C3'  H3'   single    0.970  0.020  1.090
 2AD  O3'  HA    single    0.850  0.020  0.980
 2AD  C2'  C1'   single    1.534  0.020  1.534
 2AD  C2'  N     single    1.436  0.020  1.436
 2AD  C2'  H2'   single    0.970  0.020  1.090
 2AD  C1'  N9    single    1.448  0.020  1.448
 2AD  C1'  H1'   single    0.970  0.020  1.090
 2AD  N9   C8    aromatic  1.368  0.020  1.368
 2AD  N9   C4    aromatic  1.364  0.020  1.364
 2AD  C8   N7    aromatic  1.301  0.020  1.301
 2AD  C8   H8    single    0.930  0.020  1.080
 2AD  N7   C5    aromatic  1.370  0.020  1.370
 2AD  C5   C6    aromatic  1.407  0.020  1.407
 2AD  C5   C4    aromatic  1.387  0.020  1.387
 2AD  C6   N6    single    1.334  0.020  1.334
 2AD  C6   N1    aromatic  1.338  0.020  1.338
 2AD  N6   H6N1  single    0.860  0.020  1.020
 2AD  N6   H6N2  single    0.860  0.020  1.020
 2AD  N1   C2    aromatic  1.331  0.020  1.331
 2AD  C2   N3    aromatic  1.321  0.020  1.321
 2AD  C2   H2    single    0.930  0.020  1.080
 2AD  N3   C4    aromatic  1.332  0.020  1.332
 2AD  N    HN1   single    0.890  0.020  1.040
 2AD  N    HN2   single    0.890  0.020  1.040

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
 2AD  H5'   O5'  C5'   108.02  3.000
 2AD  H5'2  C5'  H5'1  106.71  3.000
 2AD  H5'2  C5'  C4'   110.10  3.000
 2AD  H5'1  C5'  C4'   107.73  3.000
 2AD  H5'2  C5'  O5'   111.27  3.000
 2AD  H5'1  C5'  O5'   112.08  3.000
 2AD  C4'   C5'  O5'   108.89  3.000
 2AD  H4'   C4'  C3'   111.82  3.000
 2AD  H4'   C4'  O4'   107.48  3.000
 2AD  C3'   C4'  O4'   105.21  3.000
 2AD  H4'   C4'  C5'   108.99  3.000
 2AD  C3'   C4'  C5'   111.79  3.000
 2AD  O4'   C4'  C5'   111.45  3.000
 2AD  C1'   O4'  C4'   110.70  3.000
 2AD  H3'   C3'  C2'   111.84  3.000
 2AD  H3'   C3'  O3'   111.71  3.000
 2AD  C2'   C3'  O3'   107.63  3.000
 2AD  H3'   C3'  C4'   111.82  3.000
 2AD  C2'   C3'  C4'   100.83  3.000
 2AD  O3'   C3'  C4'   112.47  3.000
 2AD  HA    O3'  C3'   108.89  3.000
 2AD  H2'   C2'  N     107.64  3.000
 2AD  H2'   C2'  C1'   108.56  3.000
 2AD  N     C2'  C1'   111.94  3.000
 2AD  H2'   C2'  C3'   107.59  3.000
 2AD  N     C2'  C3'   119.55  3.000
 2AD  C1'   C2'  C3'   101.05  3.000
 2AD  H1'   C1'  N9    105.93  3.000
 2AD  H1'   C1'  C2'   110.51  3.000
 2AD  N9    C1'  C2'   113.26  3.000
 2AD  H1'   C1'  O4'   111.28  3.000
 2AD  N9    C1'  O4'   109.13  3.000
 2AD  C2'   C1'  O4'   106.80  3.000
 2AD  C4    N9   C8    106.30  3.000
 2AD  C4    N9   C1'   126.62  3.000
 2AD  C8    N9   C1'   127.06  3.000
 2AD  H8    C8   N7    124.80  3.000
 2AD  H8    C8   N9    121.75  3.000
 2AD  N7    C8   N9    113.42  3.000
 2AD  C5    N7   C8    104.31  3.000
 2AD  C4    C5   C6    116.39  3.000
 2AD  C4    C5   N7    110.86  3.000
 2AD  C6    C5   N7    132.74  3.000
 2AD  N1    C6   N6    119.33  3.000
 2AD  N1    C6   C5    117.94  3.000
 2AD  N6    C6   C5    122.73  3.000
 2AD  H6N2  N6   H6N1  118.40  3.000
 2AD  H6N2  N6   C6    121.18  3.000
 2AD  H6N1  N6   C6    120.31  3.000
 2AD  C2    N1   C6    119.07  3.000
 2AD  H2    C2   N3    116.10  3.000
 2AD  H2    C2   N1    115.35  3.000
 2AD  N3    C2   N1    128.55  3.000
 2AD  C4    N3   C2    111.72  3.000
 2AD  N3    C4   C5    126.32  3.000
 2AD  N3    C4   N9    128.55  3.000
 2AD  C5    C4   N9    105.12  3.000
 2AD  HN2   N    HN1   106.69  3.000
 2AD  HN2   N    C2'   110.64  3.000
 2AD  HN1   N    C2'   109.93  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
 2AD  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 2AD  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 2AD  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 2AD  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 2AD  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 2AD  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 2AD  CONST_07  C6    C5  N7  C8   180.00  0.0  0
 2AD  CONST_08  C4    C5  N7  C8     0.00  0.0  0
 2AD  CONST_09  C4    N9  C8  N7     0.00  0.0  0
 2AD  CONST_10  N1    C6  C5  N7   180.00  0.0  0
 2AD  CONST_11  N3    C4  C5  N7   180.00  0.0  0
 2AD  CONST_12  C2    N1  C6  C5     0.00  0.0  0
 2AD  CONST_13  C2    N3  C4  C5     0.00  0.0  0
 2AD  CONST_14  N3    C4  C5  C6     0.00  0.0  0
 2AD  CONST_15  N3    C2  N1  C6     0.00  0.0  0
 2AD  CONST_16  C4    C5  C6  N1     0.00  0.0  0
 2AD  CONST_17  C4    N3  C2  N1     0.00  0.0  0
 2AD  CONST_18  N7    C8  N9  C1'  180.00  0.0  0
 2AD  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 2AD  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 2AD  CONST_21  N6    C6  C5  N7     0.00  0.0  0
 2AD  CONST_22  C4    C5  C6  N6   180.00  0.0  0
 2AD  CONST_23  C2    N1  C6  N6   180.00  0.0  0
 2AD  CONST_24  H8    C8  N9  C1'    0.00  0.0  0
 2AD  CONST_25  H2    C2  N1  C6   180.00  0.0  0
 2AD  CONST_26  H6N1  N6  C6  C5   180.00  0.0  0
 2AD  CONST_27  H6N2  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
 2AD  chir_01  C4'  C5'  O4'  C3'  negativ
 2AD  chir_02  C3'  O3'  C4'  C2'  positiv
 2AD  chir_03  C2'  N    C3'  C1'  positiv
 2AD  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
 2AD  plan-1  C1'   0.020
 2AD  plan-1  N9    0.020
 2AD  plan-1  C8    0.020
 2AD  plan-1  N7    0.020
 2AD  plan-1  C5    0.020
 2AD  plan-1  C6    0.020
 2AD  plan-1  N6    0.020
 2AD  plan-1  N1    0.020
 2AD  plan-1  C2    0.020
 2AD  plan-1  N3    0.020
 2AD  plan-1  C4    0.020
 2AD  plan-1  H8    0.020
 2AD  plan-1  H2    0.020
 2AD  plan-2  C6    0.020
 2AD  plan-2  N6    0.020
 2AD  plan-2  H6N1  0.020
 2AD  plan-2  H6N2  0.020

