# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:03:55 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  29  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  -0.493  -1.0178  -0.4387   0.6300
 DEA  C8    C  CR15  0   0.109  -2.1052   0.1732   1.1846
 DEA  N7    N  N     0  -0.453  -1.9083   0.5788   2.4056
 DEA  C5    C  CR56  0   0.002  -0.6132   0.2191   2.6736
 DEA  C6    C  CR6   0   0.454   0.2084   0.3644   3.8067
 DEA  N6    N  NH2   0  -0.817  -0.2121   0.9441   4.9326
 DEA  N1    N  N     0  -0.475   1.4565  -0.1130   3.7421
 DEA  C2    C  CR16  0   0.041   1.8701  -0.6996   2.6213
 DEA  N3    N  N     0  -0.471   1.1995  -0.8897   1.4990
 DEA  C4    C  CR56  0   0.492  -0.0410  -0.4096   1.5792
 DEA  C1'   C  CH2   0  -0.359  -0.8902  -0.9630  -0.7089
 DEA  C2'   C  CH1   0  -0.002  -0.2882   0.0652  -1.6656
 DEA  O2'   O  OH1   0  -0.649   0.9096   0.6114  -1.1877
 DEA  C3'   C  CH1   0  -0.093  -0.1073  -0.5633  -3.0612
 DEA  O3'   O  OH1   0  -0.649  -1.3289  -0.9494  -3.6208
 DEA  C4'   C  C     0   0.518   0.6023   0.4438  -3.9546
 DEA  O     O  O     0  -0.441   0.0119   1.3232  -4.5302
 DEA  OXT   O  OH1   0  -0.577   1.9064   0.2530  -4.0191
 DEA  H8    H  HCR5  0   0.294  -3.0271   0.2808   0.6317
 DEA  HN61  H  HNH2  0   0.403   0.4274   1.0916   5.6943
 DEA  HN62  H  HNH2  0   0.411  -1.1159   1.3805   4.9823
 DEA  H2    H  HCR6  0   0.252   2.8917  -1.0642   2.6361
 DEA  H1'1  H  HCH2  0   0.279  -0.2635  -1.8565  -0.6637
 DEA  H1'2  H  HCH2  0   0.295  -1.8739  -1.2737  -1.0561
 DEA  H2'   H  HCH1  0   0.260  -0.9847   0.9063  -1.7576
 DEA  HO'2  H  HOH1  0   0.452   1.4991  -0.0941  -0.8936
 DEA  H3'   H  HCH1  0   0.280   0.5030  -1.4674  -2.9747
 DEA  HO'3  H  HOH1  0   0.452  -1.8617  -0.1620  -3.7851
 DEA  HXT   H  HOH1  0   0.486   2.3218   0.9392  -4.5644

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  1.365  0.020  1.365
 DEA  N9   C4    aromatic  1.362  0.020  1.362
 DEA  N9   C1'   single    1.444  0.020  1.444
 DEA  C8   N7    aromatic  1.302  0.020  1.302
 DEA  C8   H8    single    0.930  0.020  1.080
 DEA  N7   C5    aromatic  1.371  0.020  1.371
 DEA  C5   C6    aromatic  1.407  0.020  1.407
 DEA  C5   C4    aromatic  1.386  0.020  1.386
 DEA  C6   N6    single    1.334  0.020  1.334
 DEA  C6   N1    aromatic  1.338  0.020  1.338
 DEA  N6   HN61  single    0.860  0.020  1.020
 DEA  N6   HN62  single    0.860  0.020  1.020
 DEA  N1   C2    aromatic  1.331  0.020  1.331
 DEA  C2   N3    aromatic  1.321  0.020  1.321
 DEA  C2   H2    single    0.930  0.020  1.080
 DEA  N3   C4    aromatic  1.333  0.020  1.333
 DEA  C1'  C2'   single    1.528  0.020  1.528
 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    1.400  0.020  1.400
 DEA  C2'  C3'   single    1.541  0.020  1.541
 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    1.398  0.020  1.398
 DEA  C3'  C4'   single    1.522  0.020  1.522
 DEA  C3'  H3'   single    0.970  0.020  1.090
 DEA  O3'  HO'3  single    0.850  0.020  0.980
 DEA  C4'  O     double    1.206  0.020  1.206
 DEA  C4'  OXT   single    1.320  0.020  1.320
 DEA  OXT  HXT   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
 DEA  C1'   N9   C4    126.20  3.000
 DEA  C1'   N9   C8    127.58  3.000
 DEA  C4    N9   C8    106.17  3.000
 DEA  H8    C8   N7    125.32  3.000
 DEA  H8    C8   N9    121.08  3.000
 DEA  N7    C8   N9    113.59  3.000
 DEA  C5    N7   C8    104.16  3.000
 DEA  C4    C5   C6    116.21  3.000
 DEA  C4    C5   N7    110.78  3.000
 DEA  C6    C5   N7    133.01  3.000
 DEA  N1    C6   N6    119.32  3.000
 DEA  N1    C6   C5    117.97  3.000
 DEA  N6    C6   C5    122.70  3.000
 DEA  HN62  N6   HN61  118.09  3.000
 DEA  HN62  N6   C6    120.92  3.000
 DEA  HN61  N6   C6    120.17  3.000
 DEA  C2    N1   C6    119.20  3.000
 DEA  H2    C2   N3    116.18  3.000
 DEA  H2    C2   N1    115.43  3.000
 DEA  N3    C2   N1    128.39  3.000
 DEA  C4    N3   C2    111.69  3.000
 DEA  N3    C4   C5    126.54  3.000
 DEA  N3    C4   N9    128.16  3.000
 DEA  C5    C4   N9    105.30  3.000
 DEA  H1'2  C1'  H1'1  107.35  3.000
 DEA  H1'2  C1'  C2'   110.39  3.000
 DEA  H1'1  C1'  C2'   110.51  3.000
 DEA  H1'2  C1'  N9    108.64  3.000
 DEA  H1'1  C1'  N9    108.02  3.000
 DEA  C2'   C1'  N9    111.79  3.000
 DEA  H2'   C2'  C3'   108.15  3.000
 DEA  H2'   C2'  O2'   105.84  3.000
 DEA  C3'   C2'  O2'   111.57  3.000
 DEA  H2'   C2'  C1'   108.58  3.000
 DEA  C3'   C2'  C1'   109.80  3.000
 DEA  O2'   C2'  C1'   112.69  3.000
 DEA  HO'2  O2'  C2'   109.95  3.000
 DEA  H3'   C3'  C4'   109.46  3.000
 DEA  H3'   C3'  O3'   106.90  3.000
 DEA  C4'   C3'  O3'   110.81  3.000
 DEA  H3'   C3'  C2'   109.32  3.000
 DEA  C4'   C3'  C2'   108.44  3.000
 DEA  O3'   C3'  C2'   111.88  3.000
 DEA  HO'3  O3'  C3'   108.98  3.000
 DEA  OXT   C4'  O     124.48  3.000
 DEA  OXT   C4'  C3'   113.19  3.000
 DEA  O     C4'  C3'   122.32  3.000
 DEA  HXT   OXT  C4'   110.39  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  CONST_28  HXT   OXT  C4'  C3'  180.00   0.0  0
 DEA  Var_01    C2'   C1'  N9   C8    93.13  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
 DEA  plan-3  HXT   0.020

