# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:28:28 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: 2'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO)O3
#
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
 3D1  3D1  '2'-deoxyadenosine        '  ligand  31  18  .  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_3D1
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
 3D1  O5'   O  OH1   0  -0.667   4.3329   1.8001   0.9371
 3D1  C5'   C  CH2   0  -0.158   3.7815   1.1580  -0.1858
 3D1  C4'   C  CH1   0   0.007   3.1222  -0.1261   0.2498
 3D1  O4'   O  O2    0  -0.496   2.0102   0.1463   1.1031
 3D1  C1'   C  CH1   0   0.181   0.9444  -0.7164   0.8297
 3D1  N9    N  NR5   0  -0.526  -0.1820   0.0729   0.3339
 3D1  C4    C  CR56  0   0.486  -1.4876  -0.3150   0.3809
 3D1  N3    N  N     0  -0.460  -1.9952  -1.4314   0.9025
 3D1  C2    C  CR16  0   0.040  -3.3095  -1.4753   0.7718
 3D1  N1    N  N     0  -0.474  -4.1155  -0.5802   0.2063
 3D1  C6    C  CR6   0   0.455  -3.5905   0.5346  -0.3154
 3D1  N6    N  NH2   0  -0.817  -4.3977   1.4345  -0.8780
 3D1  C5    C  CR56  0  -0.004  -2.1952   0.7039  -0.2382
 3D1  N7    N  N     0  -0.453  -1.3488   1.6954  -0.6580
 3D1  C8    C  CR15  0   0.099  -0.1660   1.2820  -0.3027
 3D1  C2'   C  CH2   0  -0.538   1.4483  -1.7239  -0.1951
 3D1  C3'   C  CH1   0   0.012   2.5469  -0.9399  -0.9053
 3D1  O3'   O  OH1   0  -0.661   3.5560  -1.7114  -1.4927
 3D1  H5'   H  HOH1  0   0.459   4.7462   2.6168   0.6430
 3D1  H5'1  H  HCH2  0   0.201   3.0443   1.7890  -0.7011
 3D1  H5'2  H  HCH2  0   0.212   4.5480   0.8988  -0.9277
 3D1  H4'   H  HCH1  0   0.240   3.8497  -0.7460   0.7918
 3D1  H1'   H  HCH1  0   0.274   0.5958  -1.1979   1.7456
 3D1  H2    H  HCR6  0   0.251  -3.8007  -2.3545   1.1749
 3D1  HN61  H  HNH2  0   0.403  -5.3850   1.2570  -0.9469
 3D1  HN62  H  HNH2  0   0.411  -4.0307   2.2621  -1.3138
 3D1  H8    H  HCR5  0   0.295   0.7487   1.8280  -0.4726
 3D1  H2'1  H  HCH2  0   0.266   1.8891  -2.5775   0.3250
 3D1  H2'2  H  HCH2  0   0.280   0.6609  -2.0927  -0.8514
 3D1  H3'   H  HCH1  0   0.220   2.0951  -0.2596  -1.6422
 3D1  H1    H  HOH1  0   0.462   3.2178  -2.0816  -2.3138

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
 3D1  O5'  C5'   single    1.406  0.020  1.406
 3D1  O5'  H5'   single    0.850  0.020  0.980
 3D1  C5'  C4'   single    1.508  0.020  1.508
 3D1  C5'  H5'1  single    0.970  0.020  1.090
 3D1  C5'  H5'2  single    0.970  0.020  1.090
 3D1  C4'  O4'   single    1.428  0.020  1.428
 3D1  C4'  C3'   single    1.526  0.020  1.526
 3D1  C4'  H4'   single    0.970  0.020  1.090
 3D1  O4'  C1'   single    1.398  0.020  1.398
 3D1  C1'  N9    single    1.462  0.020  1.462
 3D1  C1'  C2'   single    1.523  0.020  1.523
 3D1  C1'  H1'   single    0.970  0.020  1.090
 3D1  N9   C4    aromatic  1.363  0.020  1.363
 3D1  N9   C8    aromatic  1.367  0.020  1.367
 3D1  C4   N3    aromatic  1.333  0.020  1.333
 3D1  C4   C5    aromatic  1.386  0.020  1.386
 3D1  N3   C2    aromatic  1.322  0.020  1.322
 3D1  C2   N1    aromatic  1.331  0.020  1.331
 3D1  C2   H2    single    0.930  0.020  1.080
 3D1  N1   C6    aromatic  1.338  0.020  1.338
 3D1  C6   N6    single    1.333  0.020  1.333
 3D1  C6   C5    aromatic  1.408  0.020  1.408
 3D1  N6   HN61  single    0.860  0.020  1.020
 3D1  N6   HN62  single    0.860  0.020  1.020
 3D1  C5   N7    aromatic  1.370  0.020  1.370
 3D1  N7   C8    aromatic  1.302  0.020  1.302
 3D1  C8   H8    single    0.930  0.020  1.080
 3D1  C2'  C3'   single    1.525  0.020  1.525
 3D1  C2'  H2'1  single    0.970  0.020  1.090
 3D1  C2'  H2'2  single    0.970  0.020  1.090
 3D1  C3'  O3'   single    1.399  0.020  1.399
 3D1  C3'  H3'   single    0.970  0.020  1.090
 3D1  O3'  H1    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
 3D1  H5'   O5'  C5'   108.19  3.000
 3D1  H5'2  C5'  H5'1  106.69  3.000
 3D1  H5'2  C5'  C4'   107.43  3.000
 3D1  H5'1  C5'  C4'   109.34  3.000
 3D1  H5'2  C5'  O5'   111.95  3.000
 3D1  H5'1  C5'  O5'   112.05  3.000
 3D1  C4'   C5'  O5'   109.25  3.000
 3D1  H4'   C4'  C3'   108.80  3.000
 3D1  H4'   C4'  O4'   109.18  3.000
 3D1  C3'   C4'  O4'   105.11  3.000
 3D1  H4'   C4'  C5'   109.48  3.000
 3D1  C3'   C4'  C5'   113.60  3.000
 3D1  O4'   C4'  C5'   110.53  3.000
 3D1  C1'   O4'  C4'   111.04  3.000
 3D1  H1'   C1'  C2'   112.23  3.000
 3D1  H1'   C1'  N9    106.06  3.000
 3D1  C2'   C1'  N9    112.57  3.000
 3D1  H1'   C1'  O4'   110.58  3.000
 3D1  C2'   C1'  O4'   106.71  3.000
 3D1  N9    C1'  O4'   108.70  3.000
 3D1  C8    N9   C4    106.21  3.000
 3D1  C8    N9   C1'   128.80  3.000
 3D1  C4    N9   C1'   124.94  3.000
 3D1  C5    C4   N3    126.58  3.000
 3D1  C5    C4   N9    105.33  3.000
 3D1  N3    C4   N9    128.08  3.000
 3D1  C2    N3   C4    111.59  3.000
 3D1  H2    C2   N1    115.39  3.000
 3D1  H2    C2   N3    116.14  3.000
 3D1  N1    C2   N3    128.47  3.000
 3D1  C6    N1   C2    119.24  3.000
 3D1  C5    C6   N6    122.82  3.000
 3D1  C5    C6   N1    117.89  3.000
 3D1  N6    C6   N1    119.29  3.000
 3D1  HN62  N6   HN61  118.32  3.000
 3D1  HN62  N6   C6    121.18  3.000
 3D1  HN61  N6   C6    120.27  3.000
 3D1  N7    C5   C6    133.07  3.000
 3D1  N7    C5   C4    110.70  3.000
 3D1  C6    C5   C4    116.23  3.000
 3D1  C8    N7   C5    104.35  3.000
 3D1  H8    C8   N7    124.50  3.000
 3D1  H8    C8   N9    122.08  3.000
 3D1  N7    C8   N9    113.41  3.000
 3D1  H2'2  C2'  H2'1  108.30  3.000
 3D1  H2'2  C2'  C3'   114.47  3.000
 3D1  H2'1  C2'  C3'   109.44  3.000
 3D1  H2'2  C2'  C1'   112.97  3.000
 3D1  H2'1  C2'  C1'   109.27  3.000
 3D1  C3'   C2'  C1'   102.22  3.000
 3D1  H3'   C3'  O3'   110.85  3.000
 3D1  H3'   C3'  C2'   109.51  3.000
 3D1  O3'   C3'  C2'   115.56  3.000
 3D1  H3'   C3'  C4'   109.40  3.000
 3D1  O3'   C3'  C4'   109.88  3.000
 3D1  C2'   C3'  C4'   101.14  3.000
 3D1  H1    O3'  C3'   108.48  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
 3D1  CONST_01  C2    N3  C4  N9   180.00  0.0  0
 3D1  CONST_02  C6    C5  C4  N9   180.00  0.0  0
 3D1  CONST_03  N7    C5  C4  N9     0.00  0.0  0
 3D1  CONST_04  C5    N7  C8  N9     0.00  0.0  0
 3D1  CONST_05  N7    C8  N9  C4     0.00  0.0  0
 3D1  CONST_06  N1    C2  N3  C4     0.00  0.0  0
 3D1  CONST_07  N1    C6  C5  C4     0.00  0.0  0
 3D1  CONST_08  C8    N7  C5  C4     0.00  0.0  0
 3D1  CONST_09  C8    N9  C4  N3   180.00  0.0  0
 3D1  CONST_10  C6    C5  C4  N3     0.00  0.0  0
 3D1  CONST_11  N7    C5  C4  N3   180.00  0.0  0
 3D1  CONST_12  C6    N1  C2  N3     0.00  0.0  0
 3D1  CONST_13  C5    C4  N3  C2     0.00  0.0  0
 3D1  CONST_14  C5    C6  N1  C2     0.00  0.0  0
 3D1  CONST_15  N7    C5  C6  N1   180.00  0.0  0
 3D1  CONST_16  C8    N7  C5  C6   180.00  0.0  0
 3D1  CONST_17  C8    N9  C4  C5     0.00  0.0  0
 3D1  CONST_18  N3    C4  N9  C1'    0.00  0.0  0
 3D1  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 3D1  CONST_20  N7    C8  N9  C1'  180.00  0.0  0
 3D1  CONST_21  N6    C6  C5  C4   180.00  0.0  0
 3D1  CONST_22  N6    C6  N1  C2   180.00  0.0  0
 3D1  CONST_23  N7    C5  C6  N6     0.00  0.0  0
 3D1  CONST_24  H8    C8  N9  C1'    0.00  0.0  0
 3D1  CONST_25  H2    C2  N3  C4   180.00  0.0  0
 3D1  CONST_26  HN61  N6  C6  N1     0.00  0.0  0
 3D1  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
 3D1  chir_01  C4'  C5'  O4'  C3'  negativ
 3D1  chir_02  C1'  O4'  N9   C2'  negativ
 3D1  chir_03  C3'  O3'  C4'  C2'  positiv

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
 3D1  plan-1  C1'   0.020
 3D1  plan-1  N9    0.020
 3D1  plan-1  C4    0.020
 3D1  plan-1  N3    0.020
 3D1  plan-1  C2    0.020
 3D1  plan-1  N1    0.020
 3D1  plan-1  C6    0.020
 3D1  plan-1  N6    0.020
 3D1  plan-1  C5    0.020
 3D1  plan-1  N7    0.020
 3D1  plan-1  C8    0.020
 3D1  plan-1  H2    0.020
 3D1  plan-1  H8    0.020
 3D1  plan-2  C6    0.020
 3D1  plan-2  N6    0.020
 3D1  plan-2  HN61  0.020
 3D1  plan-2  HN62  0.020

