# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 21:18:13 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (2R,3R)-4-(6-amino-9H-purin-9-yl)-2,3-dihydroxybutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(C[C@@H](O)[C@@H](O)C(O)=O)cnc12
#
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
 DEA  DEA  '(2R,3R)-4-(6-amino-9H-purin-9-yl)-2,3-dihydroxybutanoic acid'  ligand  28  18  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DEA
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
 DEA  N9    N  NR5    0  -0.487  -0.9774  -0.4107   0.6376
 DEA  C8    C  CR15   0   0.104  -1.9940   0.3596   1.1213
 DEA  N7    N  N      0  -0.456  -1.7929   0.7924   2.3333
 DEA  C5    C  CR56   0  -0.004  -0.5657   0.2835   2.6684
 DEA  C6    C  CR6    0   0.447   0.2182   0.3651   3.8329
 DEA  N6    N  NH2    0  -0.818  -0.1563   1.0661   4.9077
 DEA  N1    N  N      0  -0.476   1.3919  -0.2750   3.8466
 DEA  C2    C  CR16   0   0.035   1.7686  -0.9584   2.7668
 DEA  N3    N  N      0  -0.458   1.1274  -1.1057   1.6225
 DEA  C4    C  CR56   0   0.487  -0.0393  -0.4614   1.6226
 DEA  C1'   C  CH2    0  -0.343  -0.8614  -0.9634  -0.6932
 DEA  C2'   C  CH1    0   0.013  -0.2422   0.0432  -1.6690
 DEA  O2'   O  OH1    0  -0.647   0.9391   0.5887  -1.1469
 DEA  C3'   C  CH1    0  -0.117  -0.0568  -0.6154  -3.0472
 DEA  O3'   O  OH1    0  -0.693  -1.2945  -1.0992  -3.5044
 DEA  C4'   C  C      0   0.396   0.5116   0.3892  -4.0762
 DEA  O     O  O      0  -0.611  -0.3409   0.8221  -4.8865
 DEA  OXT   O  OC    -1  -0.583   1.7147   0.6729  -4.0191
 DEA  H8    H  HCR5   0   0.291  -2.8732   0.5611   0.5262
 DEA  HN61  H  HNH2   0   0.401   0.3778   1.0033   5.7574
 DEA  HN62  H  HNH2   0   0.408  -1.0739   1.4729   4.9597
 DEA  H2    H  HCR6   0   0.248   2.7288  -1.4576   2.8452
 DEA  H1'1  H  HCH2   0   0.264  -0.2424  -1.8607  -0.6286
 DEA  H1'2  H  HCH2   0   0.281  -1.8502  -1.2683  -1.0303
 DEA  H2'   H  HCH1   0   0.236  -0.9371   0.8841  -1.7781
 DEA  HO'2  H  HOH1   0   0.440   1.6195  -0.0931  -1.1319
 DEA  H3'   H  HCH1   0   0.211   0.6477  -1.4531  -2.9374
 DEA  HO'3  H  HOH1   0   0.430  -1.5115  -0.4658  -4.2144

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
 DEA  N9   C8    aromatic  1.364  0.020  1.364
 DEA  N9   C4    aromatic  1.361  0.020  1.361
 DEA  N9   C1'   single    1.446  0.020  1.446
 DEA  C8   N7    aromatic  1.303  0.020  1.303
 DEA  C8   H8    single    0.930  0.020  1.080
 DEA  N7   C5    aromatic  1.370  0.020  1.370
 DEA  C5   C6    aromatic  1.406  0.020  1.406
 DEA  C5   C4    aromatic  1.388  0.020  1.388
 DEA  C6   N6    single    1.337  0.020  1.337
 DEA  C6   N1    aromatic  1.337  0.020  1.337
 DEA  N6   HN61  single    0.860  0.020  1.020
 DEA  N6   HN62  single    0.860  0.020  1.020
 DEA  N1   C2    aromatic  1.332  0.020  1.332
 DEA  C2   N3    aromatic  1.320  0.020  1.320
 DEA  C2   H2    single    0.930  0.020  1.080
 DEA  N3   C4    aromatic  1.333  0.020  1.333
 DEA  C1'  C2'   single    1.533  0.020  1.533
 DEA  C1'  H1'1  single    0.970  0.020  1.090
 DEA  C1'  H1'2  single    0.970  0.020  1.090
 DEA  C2'  O2'   single    1.402  0.020  1.402
 DEA  C2'  C3'   single    1.539  0.020  1.539
 DEA  C2'  H2'   single    0.970  0.020  1.090
 DEA  O2'  HO'2  single    0.850  0.020  0.980
 DEA  C3'  O3'   single    1.405  0.020  1.405
 DEA  C3'  C4'   single    1.546  0.020  1.546
 DEA  C3'  H3'   single    0.970  0.020  1.090
 DEA  O3'  HO'3  single    0.850  0.020  0.980
 DEA  C4'  O     deloc     1.253  0.020  1.253
 DEA  C4'  OXT   deloc     1.237  0.020  1.237

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
 DEA  C1'   N9   C4    126.62  3.000
 DEA  C1'   N9   C8    127.02  3.000
 DEA  C4    N9   C8    106.15  3.000
 DEA  H8    C8   N7    125.17  3.000
 DEA  H8    C8   N9    121.09  3.000
 DEA  N7    C8   N9    113.74  3.000
 DEA  C5    N7   C8    104.03  3.000
 DEA  C4    C5   C6    116.34  3.000
 DEA  C4    C5   N7    110.79  3.000
 DEA  C6    C5   N7    132.87  3.000
 DEA  N1    C6   N6    119.26  3.000
 DEA  N1    C6   C5    118.04  3.000
 DEA  N6    C6   C5    122.69  3.000
 DEA  HN62  N6   HN61  117.81  3.000
 DEA  HN62  N6   C6    120.64  3.000
 DEA  HN61  N6   C6    119.85  3.000
 DEA  C2    N1   C6    119.04  3.000
 DEA  H2    C2   N3    116.17  3.000
 DEA  H2    C2   N1    115.32  3.000
 DEA  N3    C2   N1    128.51  3.000
 DEA  C4    N3   C2    111.79  3.000
 DEA  N3    C4   C5    126.28  3.000
 DEA  N3    C4   N9    128.41  3.000
 DEA  C5    C4   N9    105.30  3.000
 DEA  H1'2  C1'  H1'1  107.64  3.000
 DEA  H1'2  C1'  C2'   110.73  3.000
 DEA  H1'1  C1'  C2'   110.38  3.000
 DEA  H1'2  C1'  N9    108.62  3.000
 DEA  H1'1  C1'  N9    107.77  3.000
 DEA  C2'   C1'  N9    111.56  3.000
 DEA  H2'   C2'  C3'   108.40  3.000
 DEA  H2'   C2'  O2'   105.83  3.000
 DEA  C3'   C2'  O2'   113.49  3.000
 DEA  H2'   C2'  C1'   108.12  3.000
 DEA  C3'   C2'  C1'   109.75  3.000
 DEA  O2'   C2'  C1'   111.03  3.000
 DEA  HO'2  O2'  C2'   109.00  3.000
 DEA  H3'   C3'  C4'   109.01  3.000
 DEA  H3'   C3'  O3'   109.53  3.000
 DEA  C4'   C3'  O3'   109.32  3.000
 DEA  H3'   C3'  C2'   108.28  3.000
 DEA  C4'   C3'  C2'   111.24  3.000
 DEA  O3'   C3'  C2'   109.43  3.000
 DEA  HO'3  O3'  C3'   102.07  3.000
 DEA  OXT   C4'  O     127.74  3.000
 DEA  OXT   C4'  C3'   118.40  3.000
 DEA  O     C4'  C3'   113.87  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
 DEA  CONST_01  C5    N7   C8  N9    0.00   0.0  0
 DEA  CONST_02  N7    C5   C4  N9    0.00   0.0  0
 DEA  CONST_03  C6    C5   C4  N9  180.00   0.0  0
 DEA  CONST_04  C2    N3   C4  N9  180.00   0.0  0
 DEA  CONST_05  C5    C4   N9  C8    0.00   0.0  0
 DEA  CONST_06  N3    C4   N9  C8  180.00   0.0  0
 DEA  CONST_07  C6    C5   N7  C8  180.00   0.0  0
 DEA  CONST_08  C4    C5   N7  C8    0.00   0.0  0
 DEA  CONST_09  C4    N9   C8  N7    0.00   0.0  0
 DEA  CONST_10  N1    C6   C5  N7  180.00   0.0  0
 DEA  CONST_11  N3    C4   C5  N7  180.00   0.0  0
 DEA  CONST_12  C2    N1   C6  C5    0.00   0.0  0
 DEA  CONST_13  C2    N3   C4  C5    0.00   0.0  0
 DEA  CONST_14  N3    C4   C5  C6    0.00   0.0  0
 DEA  CONST_15  N3    C2   N1  C6    0.00   0.0  0
 DEA  CONST_16  C4    C5   C6  N1    0.00   0.0  0
 DEA  CONST_17  C4    N3   C2  N1    0.00   0.0  0
 DEA  CONST_18  C1'   N9   C8  N7  180.00   0.0  0
 DEA  CONST_19  N6    C6   C5  N7    0.00   0.0  0
 DEA  CONST_20  C1'   N9   C4  C5  180.00   0.0  0
 DEA  CONST_21  C4    C5   C6  N6  180.00   0.0  0
 DEA  CONST_22  C2    N1   C6  N6  180.00   0.0  0
 DEA  CONST_23  C1'   N9   C4  N3    0.00   0.0  0
 DEA  CONST_24  H8    C8   N7  C5  180.00   0.0  0
 DEA  CONST_25  H2    C2   N1  C6  180.00   0.0  0
 DEA  CONST_26  HN61  N6   C6  C5  180.00   0.0  0
 DEA  CONST_27  HN62  N6   C6  C5    0.00   0.0  0
 DEA  Var_01    C2'   C1'  N9  C8   84.97  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
 DEA  chir_01  C2'  C1'  O2'  C3'  negativ
 DEA  chir_02  C3'  O3'  C2'  C4'  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
 DEA  plan-1  N9    0.020
 DEA  plan-1  C8    0.020
 DEA  plan-1  N7    0.020
 DEA  plan-1  C5    0.020
 DEA  plan-1  C6    0.020
 DEA  plan-1  N6    0.020
 DEA  plan-1  N1    0.020
 DEA  plan-1  C2    0.020
 DEA  plan-1  N3    0.020
 DEA  plan-1  C4    0.020
 DEA  plan-1  C1'   0.020
 DEA  plan-1  H8    0.020
 DEA  plan-1  H2    0.020
 DEA  plan-2  C6    0.020
 DEA  plan-2  N6    0.020
 DEA  plan-2  HN61  0.020
 DEA  plan-2  HN62  0.020
 DEA  plan-3  C3'   0.020
 DEA  plan-3  C4'   0.020
 DEA  plan-3  O     0.020
 DEA  plan-3  OXT   0.020

