# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  8 16:36:46 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (2S)-4-(6-amino-9H-purin-9-yl)-2-hydroxybutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CC[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
 ZD2  ZD2  '(2S)-4-(6-amino-9H-purin-9-yl)-2-hydroxybutanoic acid'  ligand  27  17  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ZD2
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
 ZD2  O    O  O     -1  -0.608  -5.0109  -0.0426  -0.8434
 ZD2  C4'  C  C      0   0.399  -4.0056   0.6263  -0.5109
 ZD2  OXT  O  OC     0  -0.593  -3.6772   1.7520  -0.9129
 ZD2  C3'  C  CH1    0  -0.088  -3.0846  -0.0675   0.5191
 ZD2  O3'  O  OH1    0  -0.700  -3.6366  -1.3100   0.8788
 ZD2  C2'  C  CH2    0  -0.454  -1.6762  -0.2284  -0.0433
 ZD2  C1'  C  CH2    0  -0.302  -0.7448  -0.9113   0.9486
 ZD2  N9   N  NR5    0  -0.494   0.6101  -1.0141   0.4412
 ZD2  C4   C  CR56   0   0.478   1.5496  -0.0286   0.4369
 ZD2  C5   C  CR56   0  -0.003   2.6479  -0.5713  -0.2147
 ZD2  N7   N  N      0  -0.457   2.3916  -1.8579  -0.6094
 ZD2  C8   C  CR15   0   0.106   1.1727  -2.0756  -0.2033
 ZD2  N3   N  N      0  -0.456   1.4597   1.1985   0.9494
 ZD2  C2   C  CR16   0   0.036   2.5734   1.8851   0.7696
 ZD2  N1   N  N      0  -0.475   3.6963   1.4999   0.1661
 ZD2  C6   C  CR6    0   0.450   3.7715   0.2655  -0.3430
 ZD2  N6   N  NH2    0  -0.818   4.9016  -0.1291  -0.9360
 ZD2  H2   H  HCH1   0   0.204  -3.0244   0.5813   1.4068
 ZD2  H3   H  HOH1   0   0.428  -4.4245  -1.3549   0.3042
 ZD2  H4   H  HCH2   0   0.230  -1.7089  -0.8107  -0.9699
 ZD2  H5   H  HCH2   0   0.239  -1.2803   0.7578  -0.2935
 ZD2  H6   H  HCH2   0   0.259  -0.7080  -0.3544   1.8862
 ZD2  H7   H  HCH2   0   0.270  -1.0888  -1.9183   1.1800
 ZD2  H8   H  HCR5   0   0.291   0.6266  -2.9980  -0.3390
 ZD2  H9   H  HCR6   0   0.249   2.5803   2.8969   1.1616
 ZD2  H10  H  HNH2   0   0.409   4.9525  -1.0152  -1.4074
 ZD2  H11  H  HNH2   0   0.401   5.6462   0.5294  -1.0876

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
 ZD2  N6   C6   single    1.336  0.020  1.336
 ZD2  N7   C8   aromatic  1.303  0.020  1.303
 ZD2  N7   C5   aromatic  1.370  0.020  1.370
 ZD2  C8   N9   aromatic  1.363  0.020  1.363
 ZD2  C6   C5   aromatic  1.407  0.020  1.407
 ZD2  C6   N1   aromatic  1.337  0.020  1.337
 ZD2  C5   C4   aromatic  1.388  0.020  1.388
 ZD2  N9   C4   aromatic  1.362  0.020  1.362
 ZD2  N9   C1'  single    1.450  0.020  1.450
 ZD2  N1   C2   aromatic  1.332  0.020  1.332
 ZD2  C4   N3   aromatic  1.333  0.020  1.333
 ZD2  C1'  C2'  single    1.522  0.020  1.522
 ZD2  C2   N3   aromatic  1.321  0.020  1.321
 ZD2  C3'  C2'  single    1.525  0.020  1.525
 ZD2  C3'  C4'  single    1.546  0.020  1.546
 ZD2  C3'  O3'  single    1.406  0.020  1.406
 ZD2  O    C4'  deloc     1.252  0.020  1.252
 ZD2  C4'  OXT  deloc     1.240  0.020  1.240
 ZD2  C3'  H2   single    0.970  0.020  1.090
 ZD2  O3'  H3   single    0.850  0.020  0.980
 ZD2  C2'  H4   single    0.970  0.020  1.090
 ZD2  C2'  H5   single    0.970  0.020  1.090
 ZD2  C1'  H6   single    0.970  0.020  1.090
 ZD2  C1'  H7   single    0.970  0.020  1.090
 ZD2  C8   H8   single    0.930  0.020  1.080
 ZD2  C2   H9   single    0.930  0.020  1.080
 ZD2  N6   H10  single    0.860  0.020  1.020
 ZD2  N6   H11  single    0.860  0.020  1.020

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
 ZD2  C3'  C4'  OXT  117.76  3.000
 ZD2  OXT  C4'  O    127.70  3.000
 ZD2  C3'  C4'  O    114.54  3.000
 ZD2  H2   C3'  C2'  108.00  3.000
 ZD2  H2   C3'  O3'  109.62  3.000
 ZD2  C2'  C3'  O3'  111.32  3.000
 ZD2  H2   C3'  C4'  107.77  3.000
 ZD2  O3'  C3'  C4'  109.45  3.000
 ZD2  C2'  C3'  C4'  110.59  3.000
 ZD2  H3   O3'  C3'  101.94  3.000
 ZD2  H5   C2'  H4   107.30  3.000
 ZD2  H5   C2'  C1'  109.43  3.000
 ZD2  H4   C2'  C1'  109.33  3.000
 ZD2  H5   C2'  C3'  108.91  3.000
 ZD2  H4   C2'  C3'  109.92  3.000
 ZD2  C1'  C2'  C3'  111.84  3.000
 ZD2  H7   C1'  H6   107.46  3.000
 ZD2  H7   C1'  N9   107.69  3.000
 ZD2  H6   C1'  N9   107.77  3.000
 ZD2  H7   C1'  C2'  111.10  3.000
 ZD2  H6   C1'  C2'  110.58  3.000
 ZD2  N9   C1'  C2'  112.05  3.000
 ZD2  C8   N9   C4   106.10  3.000
 ZD2  C4   N9   C1'  126.47  3.000
 ZD2  C8   N9   C1'  127.31  3.000
 ZD2  N3   C4   C5   126.44  3.000
 ZD2  N3   C4   N9   128.21  3.000
 ZD2  C5   C4   N9   105.34  3.000
 ZD2  C6   C5   N7   132.98  3.000
 ZD2  C6   C5   C4   116.26  3.000
 ZD2  N7   C5   C4   110.76  3.000
 ZD2  C8   N7   C5   104.01  3.000
 ZD2  H8   C8   N7   125.18  3.000
 ZD2  H8   C8   N9   121.03  3.000
 ZD2  N7   C8   N9   113.79  3.000
 ZD2  C2   N3   C4   111.68  3.000
 ZD2  H9   C2   N1   115.35  3.000
 ZD2  H9   C2   N3   116.16  3.000
 ZD2  N1   C2   N3   128.49  3.000
 ZD2  C6   N1   C2   119.14  3.000
 ZD2  N6   C6   N1   119.29  3.000
 ZD2  N1   C6   C5   118.00  3.000
 ZD2  N6   C6   C5   122.71  3.000
 ZD2  H11  N6   H10  117.98  3.000
 ZD2  H11  N6   C6   120.00  3.000
 ZD2  H10  N6   C6   120.77  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
 ZD2  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 ZD2  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 ZD2  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 ZD2  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 ZD2  CONST_05  C8   N7   C5   C4      0.00   0.0  0
 ZD2  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 ZD2  CONST_07  N7   C8   N9   C4      0.00   0.0  0
 ZD2  CONST_08  N1   C2   N3   C4      0.00   0.0  0
 ZD2  CONST_09  C2   N1   C6   C5      0.00   0.0  0
 ZD2  CONST_10  C8   N9   C4   C5      0.00   0.0  0
 ZD2  CONST_11  C2   N3   C4   C5      0.00   0.0  0
 ZD2  CONST_12  N1   C6   C5   N7    180.00   0.0  0
 ZD2  CONST_13  N3   C4   C5   N7    180.00   0.0  0
 ZD2  CONST_14  C6   C5   N7   C8    180.00   0.0  0
 ZD2  CONST_15  N3   C4   N9   C8    180.00   0.0  0
 ZD2  CONST_16  C6   C5   C4   N3      0.00   0.0  0
 ZD2  CONST_17  C6   N1   C2   N3      0.00   0.0  0
 ZD2  CONST_18  N7   C8   N9   C1'   180.00   0.0  0
 ZD2  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 ZD2  CONST_20  N3   C4   N9   C1'     0.00   0.0  0
 ZD2  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 ZD2  CONST_22  N6   C6   C5   N7      0.00   0.0  0
 ZD2  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 ZD2  CONST_24  H8   C8   N9   C4    180.00   0.0  0
 ZD2  CONST_25  H9   C2   N3   C4    180.00   0.0  0
 ZD2  CONST_26  H10  N6   C6   C5      0.00   0.0  0
 ZD2  CONST_27  H11  N6   C6   C5    180.00   0.0  0
 ZD2  Var_01    C8   N9   C1'  C2'   -95.16  30.0  2
 ZD2  Var_02    N9   C1'  C2'  C3'  -177.48  30.0  1

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
 ZD2  chir_01  C3'  C2'  C4'  O3'  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
 ZD2  plan-1  C1'  0.020
 ZD2  plan-1  N9   0.020
 ZD2  plan-1  C4   0.020
 ZD2  plan-1  C5   0.020
 ZD2  plan-1  N7   0.020
 ZD2  plan-1  C8   0.020
 ZD2  plan-1  N3   0.020
 ZD2  plan-1  C2   0.020
 ZD2  plan-1  N1   0.020
 ZD2  plan-1  C6   0.020
 ZD2  plan-1  N6   0.020
 ZD2  plan-1  H8   0.020
 ZD2  plan-1  H9   0.020
 ZD2  plan-2  C6   0.020
 ZD2  plan-2  N6   0.020
 ZD2  plan-2  H10  0.020
 ZD2  plan-2  H11  0.020
 ZD2  plan-3  O    0.020
 ZD2  plan-3  C4'  0.020
 ZD2  plan-3  OXT  0.020
 ZD2  plan-3  C3'  0.020

