# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 05:55:58 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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
 5AD  5AD  '5'-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_5AD
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
 5AD  N1    N  N     0  -0.474  -0.8278   0.3092   3.7864
 5AD  C2    C  CR16  0   0.039  -1.7418  -0.0225   2.8779
 5AD  N3    N  N     0  -0.458  -1.5609  -0.3383   1.6075
 5AD  C4    C  CR56  0   0.485  -0.2724  -0.2987   1.2710
 5AD  N9    N  NR5   0  -0.536   0.2883  -0.5602   0.0559
 5AD  C8    C  CR15  0   0.101   1.6367  -0.3953   0.2142
 5AD  N7    N  N     0  -0.452   1.9754  -0.0430   1.4208
 5AD  C5    C  CR56  0  -0.002   0.7891   0.0240   2.1017
 5AD  C6    C  CR6   0   0.457   0.4619   0.3428   3.4330
 5AD  N6    N  NH2   0  -0.816   1.3814   0.6634   4.3448
 5AD  C1'   C  CH1   0   0.177  -0.4449  -0.9718  -1.1387
 5AD  C2'   C  CH1   0  -0.044  -1.2431   0.1898  -1.7307
 5AD  C3'   C  CH1   0  -0.008  -0.2071   0.7887  -2.6775
 5AD  C4'   C  CH1   0   0.026   0.4853  -0.4663  -3.2169
 5AD  C5'   C  CH3   0  -0.687   1.9017  -0.2531  -3.6949
 5AD  O4'   O  O2    0  -0.498   0.4652  -1.3800  -2.1111
 5AD  O2'   O  OH1   0  -0.664  -2.3262  -0.3720  -2.4217
 5AD  O3'   O  OH1   0  -0.662  -0.8278   1.5778  -3.6492
 5AD  H2    H  HCR6  0   0.252  -2.7675  -0.0318   3.2310
 5AD  H8    H  HCR5  0   0.296   2.3299  -0.5571  -0.5955
 5AD  HN61  H  HNH2  0   0.403   1.1018   0.9395   5.2703
 5AD  HN62  H  HNH2  0   0.411   2.3501   0.7532   4.0938
 5AD  H1'   H  HCH1  0   0.284  -1.0990  -1.7994  -0.8492
 5AD  H2'   H  HCH1  0   0.262  -1.5728   0.8993  -0.9631
 5AD  H3'   H  HCH1  0   0.229   0.5120   1.3730  -2.0843
 5AD  H4'   H  HCH1  0   0.237  -0.1174  -0.8846  -4.0314
 5AD  H5'1  H  HCH3  0   0.251   2.3636  -1.1880  -4.0118
 5AD  H5'2  H  HCH3  0   0.240   1.9001   0.4160  -4.5571
 5AD  H5'3  H  HCH3  0   0.229   2.5245   0.1991  -2.9211
 5AD  HO2'  H  HOH1  0   0.458  -2.6757   0.2862  -3.0323
 5AD  HO3'  H  HOH1  0   0.465  -0.1582   2.0566  -4.1470

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
 5AD  N1   C2    aromatic  1.331  0.020  1.331
 5AD  N1   C6    aromatic  1.338  0.020  1.338
 5AD  C2   N3    aromatic  1.322  0.020  1.322
 5AD  C2   H2    single    0.930  0.020  1.080
 5AD  N3   C4    aromatic  1.332  0.020  1.332
 5AD  C4   N9    aromatic  1.364  0.020  1.364
 5AD  C4   C5    aromatic  1.386  0.020  1.386
 5AD  N9   C8    aromatic  1.368  0.020  1.368
 5AD  N9   C1'   single    1.461  0.020  1.461
 5AD  C8   N7    aromatic  1.302  0.020  1.302
 5AD  C8   H8    single    0.930  0.020  1.080
 5AD  N7   C5    aromatic  1.370  0.020  1.370
 5AD  C5   C6    aromatic  1.408  0.020  1.408
 5AD  C6   N6    single    1.334  0.020  1.334
 5AD  N6   HN61  single    0.860  0.020  1.020
 5AD  N6   HN62  single    0.860  0.020  1.020
 5AD  C1'  C2'   single    1.529  0.020  1.529
 5AD  C1'  O4'   single    1.393  0.020  1.393
 5AD  C1'  H1'   single    0.970  0.020  1.090
 5AD  C2'  C3'   single    1.526  0.020  1.526
 5AD  C2'  O2'   single    1.402  0.020  1.402
 5AD  C2'  H2'   single    0.970  0.020  1.090
 5AD  C3'  C4'   single    1.531  0.020  1.531
 5AD  C3'  O3'   single    1.397  0.020  1.397
 5AD  C3'  H3'   single    0.970  0.020  1.090
 5AD  C4'  C5'   single    1.510  0.020  1.510
 5AD  C4'  O4'   single    1.435  0.020  1.435
 5AD  C4'  H4'   single    0.970  0.020  1.090
 5AD  C5'  H5'1  single    0.970  0.020  1.090
 5AD  C5'  H5'2  single    0.970  0.020  1.090
 5AD  C5'  H5'3  single    0.970  0.020  1.090
 5AD  O2'  HO2'  single    0.850  0.020  0.980
 5AD  O3'  HO3'  single    0.850  0.020  0.980

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
 5AD  C6    N1   C2    119.22  3.000
 5AD  H2    C2   N3    116.12  3.000
 5AD  H2    C2   N1    115.43  3.000
 5AD  N3    C2   N1    128.45  3.000
 5AD  C4    N3   C2    111.59  3.000
 5AD  C5    C4   N9    105.30  3.000
 5AD  C5    C4   N3    126.60  3.000
 5AD  N9    C4   N3    128.10  3.000
 5AD  C1'   N9   C8    128.57  3.000
 5AD  C1'   N9   C4    125.20  3.000
 5AD  C8    N9   C4    106.21  3.000
 5AD  H8    C8   N7    124.71  3.000
 5AD  H8    C8   N9    121.93  3.000
 5AD  N7    C8   N9    113.36  3.000
 5AD  C5    N7   C8    104.40  3.000
 5AD  C6    C5   N7    133.06  3.000
 5AD  C6    C5   C4    116.21  3.000
 5AD  N7    C5   C4    110.74  3.000
 5AD  N6    C6   C5    122.73  3.000
 5AD  N6    C6   N1    119.34  3.000
 5AD  C5    C6   N1    117.92  3.000
 5AD  HN62  N6   HN61  118.26  3.000
 5AD  HN62  N6   C6    121.01  3.000
 5AD  HN61  N6   C6    120.23  3.000
 5AD  H1'   C1'  O4'   110.72  3.000
 5AD  H1'   C1'  C2'   111.42  3.000
 5AD  O4'   C1'  C2'   107.07  3.000
 5AD  H1'   C1'  N9    107.27  3.000
 5AD  O4'   C1'  N9    109.00  3.000
 5AD  C2'   C1'  N9    111.38  3.000
 5AD  H2'   C2'  O2'   111.85  3.000
 5AD  H2'   C2'  C3'   112.63  3.000
 5AD  O2'   C2'  C3'   112.08  3.000
 5AD  H2'   C2'  C1'   112.19  3.000
 5AD  O2'   C2'  C1'   106.84  3.000
 5AD  C3'   C2'  C1'   100.60  3.000
 5AD  H3'   C3'  O3'   111.43  3.000
 5AD  H3'   C3'  C4'   109.25  3.000
 5AD  O3'   C3'  C4'   114.75  3.000
 5AD  H3'   C3'  C2'   108.52  3.000
 5AD  O3'   C3'  C2'   110.58  3.000
 5AD  C4'   C3'  C2'   101.76  3.000
 5AD  H4'   C4'  O4'   108.79  3.000
 5AD  H4'   C4'  C5'   109.54  3.000
 5AD  O4'   C4'  C5'   110.31  3.000
 5AD  H4'   C4'  C3'   109.01  3.000
 5AD  O4'   C4'  C3'   104.13  3.000
 5AD  C5'   C4'  C3'   114.82  3.000
 5AD  H5'3  C5'  H5'2  107.87  3.000
 5AD  H5'3  C5'  H5'1  108.64  3.000
 5AD  H5'2  C5'  H5'1  107.27  3.000
 5AD  H5'3  C5'  C4'   111.68  3.000
 5AD  H5'2  C5'  C4'   109.59  3.000
 5AD  H5'1  C5'  C4'   111.62  3.000
 5AD  C4'   O4'  C1'   111.14  3.000
 5AD  HO2'  O2'  C2'   108.59  3.000
 5AD  HO3'  O3'  C3'   109.37  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
 5AD  CONST_01  C4    N3  C2  N1    0.00  0.0  0
 5AD  CONST_02  C4    C5  C6  N1    0.00  0.0  0
 5AD  CONST_03  N7    C5  C6  N1  180.00  0.0  0
 5AD  CONST_04  C5    C6  N1  C2    0.00  0.0  0
 5AD  CONST_05  N9    C4  N3  C2  180.00  0.0  0
 5AD  CONST_06  C5    C4  N3  C2    0.00  0.0  0
 5AD  CONST_07  C6    N1  C2  N3    0.00  0.0  0
 5AD  CONST_08  C8    N9  C4  N3  180.00  0.0  0
 5AD  CONST_09  N7    C5  C4  N3  180.00  0.0  0
 5AD  CONST_10  C6    C5  C4  N3    0.00  0.0  0
 5AD  CONST_11  N7    C8  N9  C4    0.00  0.0  0
 5AD  CONST_12  C8    N7  C5  C4    0.00  0.0  0
 5AD  CONST_13  N7    C5  C4  N9    0.00  0.0  0
 5AD  CONST_14  C6    C5  C4  N9  180.00  0.0  0
 5AD  CONST_15  C5    N7  C8  N9    0.00  0.0  0
 5AD  CONST_16  C5    C4  N9  C8    0.00  0.0  0
 5AD  CONST_17  C6    C5  N7  C8  180.00  0.0  0
 5AD  CONST_18  C1'   N9  C4  N3    0.00  0.0  0
 5AD  CONST_19  C1'   N9  C8  N7  180.00  0.0  0
 5AD  CONST_20  C1'   N9  C4  C5  180.00  0.0  0
 5AD  CONST_21  N6    C6  N1  C2  180.00  0.0  0
 5AD  CONST_22  N6    C6  C5  C4  180.00  0.0  0
 5AD  CONST_23  N6    C6  C5  N7    0.00  0.0  0
 5AD  CONST_24  H2    C2  N3  C4  180.00  0.0  0
 5AD  CONST_25  H8    C8  N9  C4  180.00  0.0  0
 5AD  CONST_26  HN61  N6  C6  N1    0.00  0.0  0
 5AD  CONST_27  HN62  N6  C6  N1  180.00  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
 5AD  chir_01  C1'  N9   C2'  O4'  negativ
 5AD  chir_02  C2'  O2'  C3'  C1'  positiv
 5AD  chir_03  C3'  O3'  C4'  C2'  positiv
 5AD  chir_04  C4'  O4'  C3'  C5'  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
 5AD  plan-1  N1    0.020
 5AD  plan-1  C2    0.020
 5AD  plan-1  N3    0.020
 5AD  plan-1  C4    0.020
 5AD  plan-1  N9    0.020
 5AD  plan-1  C8    0.020
 5AD  plan-1  N7    0.020
 5AD  plan-1  C5    0.020
 5AD  plan-1  C6    0.020
 5AD  plan-1  N6    0.020
 5AD  plan-1  C1'   0.020
 5AD  plan-1  H2    0.020
 5AD  plan-1  H8    0.020
 5AD  plan-2  C6    0.020
 5AD  plan-2  N6    0.020
 5AD  plan-2  HN61  0.020
 5AD  plan-2  HN62  0.020

