# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 10:07:53 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: [(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(6-aminopurin-9-yl)-2-oxidanyl-2-oxidanylidene-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H]4O[P](O)(=O)O[C@@H]34
#
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
 ACK  ACK  '[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(6-aminopurin-9-yl)-2-oxidanyl-2-oxidanylidene-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol'  ligand  34  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ACK
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
 ACK  O3P  O  OH1   0  -0.699  -3.5511   2.5379  -1.5886
 ACK  P    P  P     0   1.455  -2.9079   1.8740  -0.2978
 ACK  O1P  O  O     0  -0.658  -3.0794   2.6260   0.9535
 ACK  O2'  O  O2    0  -0.575  -1.3910   1.5396  -0.7321
 ACK  O3'  O  O2    0  -0.576  -3.4511   0.3601  -0.3052
 ACK  C3'  C  CH1   0  -0.018  -2.4760  -0.5951  -0.6903
 ACK  C4'  C  CH1   0   0.004  -2.1418  -1.5793   0.4394
 ACK  O4'  O  O2    0  -0.472  -0.7293  -1.6965   0.4022
 ACK  C5'  C  CH2   0  -0.141  -2.7794  -2.9328   0.2532
 ACK  O5'  O  OH1   0  -0.643  -2.4545  -3.7423   1.3521
 ACK  C1'  C  CH1   0   0.204  -0.2112  -0.4249   0.1367
 ACK  N9   N  NR5   0  -0.562   1.1510  -0.5599  -0.2746
 ACK  C8   C  CR15  0   0.143   1.6349  -1.3156  -1.3126
 ACK  N7   N  N     0  -0.438   2.9266  -1.2638  -1.4234
 ACK  C5   C  CR56  0   0.002   3.3273  -0.4338  -0.4066
 ACK  C6   C  CR6   0   0.483   4.5891   0.0269   0.0141
 ACK  N6   N  NH2   0  -0.794   5.7239  -0.3233  -0.5905
 ACK  N1   N  N     0  -0.477   4.6352   0.8441   1.0729
 ACK  C2   C  CR16  0   0.043   3.5025   1.1854   1.6797
 ACK  N3   N  N     0  -0.434   2.2672   0.8226   1.3772
 ACK  C4   C  CR56  0   0.494   2.2396   0.0114   0.3247
 ACK  C2'  C  CH1   0  -0.036  -1.1520   0.1610  -0.9298
 ACK  H1   H  HOH1  0   0.482  -3.9870   3.3845  -1.4197
 ACK  H2   H  HCH1  0   0.279  -2.8210  -1.1035  -1.5920
 ACK  H3   H  HCH1  0   0.252  -2.4601  -1.1429   1.3970
 ACK  H4   H  HCH2  0   0.208  -3.8617  -2.7746   0.1598
 ACK  H5   H  HCH2  0   0.193  -2.4357  -3.3624  -0.6974
 ACK  H6   H  HOH1  0   0.441  -2.8650  -4.6021   1.2240
 ACK  H7   H  HCH1  0   0.275  -0.2146   0.2201   1.0254
 ACK  H8   H  HCR5  0   0.271   0.9802  -1.8898  -1.9514
 ACK  H9   H  HNH2  0   0.392   5.7177  -0.8917  -1.4191
 ACK  H10  H  HNH2  0   0.382   6.5999   0.0663  -0.2877
 ACK  H11  H  HCR6  0   0.236   3.6102   1.8473   2.5320
 ACK  H12  H  HCH1  0   0.285  -0.7676   0.0083  -1.9394

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
 ACK  C5'  C4'  single    1.508  0.020  1.508
 ACK  C5'  O5'  single    1.403  0.020  1.403
 ACK  C4'  O4'  single    1.418  0.020  1.418
 ACK  C4'  C3'  single    1.535  0.020  1.535
 ACK  O4'  C1'  single    1.399  0.020  1.399
 ACK  C3'  O3'  single    1.418  0.020  1.418
 ACK  C3'  C2'  single    1.543  0.020  1.543
 ACK  O3'  P    single    1.608  0.020  1.608
 ACK  C1'  N9   single    1.429  0.020  1.429
 ACK  C1'  C2'  single    1.538  0.020  1.538
 ACK  C8   N9   aromatic  1.372  0.020  1.372
 ACK  C8   N7   aromatic  1.297  0.020  1.297
 ACK  N9   C4   aromatic  1.368  0.020  1.368
 ACK  C2'  O2'  single    1.413  0.020  1.413
 ACK  O1P  P    double    1.470  0.020  1.470
 ACK  P    O2'  single    1.613  0.020  1.613
 ACK  P    O3P  single    1.588  0.020  1.588
 ACK  N7   C5   aromatic  1.372  0.020  1.372
 ACK  C4   N3   aromatic  1.329  0.020  1.329
 ACK  C4   C5   aromatic  1.384  0.020  1.384
 ACK  N3   C2   aromatic  1.323  0.020  1.323
 ACK  C5   C6   aromatic  1.408  0.020  1.408
 ACK  C2   N1   aromatic  1.329  0.020  1.329
 ACK  C6   N1   aromatic  1.338  0.020  1.338
 ACK  C6   N6   single    1.333  0.020  1.333
 ACK  O3P  H1   single    0.850  0.020  0.980
 ACK  C3'  H2   single    0.970  0.020  1.090
 ACK  C4'  H3   single    0.970  0.020  1.090
 ACK  C5'  H4   single    0.970  0.020  1.090
 ACK  C5'  H5   single    0.970  0.020  1.090
 ACK  O5'  H6   single    0.850  0.020  0.980
 ACK  C1'  H7   single    0.970  0.020  1.090
 ACK  C8   H8   single    0.930  0.020  1.080
 ACK  N6   H9   single    0.860  0.020  1.020
 ACK  N6   H10  single    0.860  0.020  1.020
 ACK  C2   H11  single    0.930  0.020  1.080
 ACK  C2'  H12  single    0.970  0.020  1.090

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
 ACK  H1   O3P  P    114.00  3.000
 ACK  O3'  P    O2'   96.97  3.000
 ACK  O2'  P    O1P  116.43  3.000
 ACK  O3'  P    O1P  116.49  3.000
 ACK  O2'  P    O3P  104.41  3.000
 ACK  O1P  P    O3P  115.52  3.000
 ACK  O3'  P    O3P  104.65  3.000
 ACK  C2'  O2'  P    113.52  3.000
 ACK  C3'  O3'  P    113.76  3.000
 ACK  H2   C3'  C2'  111.79  3.000
 ACK  H2   C3'  C4'  112.22  3.000
 ACK  C2'  C3'  C4'  103.98  3.000
 ACK  H2   C3'  O3'  108.71  3.000
 ACK  C2'  C3'  O3'  107.58  3.000
 ACK  C4'  C3'  O3'  112.44  3.000
 ACK  H3   C4'  C5'  109.97  3.000
 ACK  H3   C4'  O4'  110.12  3.000
 ACK  C5'  C4'  O4'  110.11  3.000
 ACK  H3   C4'  C3'  108.87  3.000
 ACK  O4'  C4'  C3'  104.51  3.000
 ACK  C5'  C4'  C3'  113.12  3.000
 ACK  C1'  O4'  C4'  107.39  3.000
 ACK  H5   C5'  H4   106.93  3.000
 ACK  H5   C5'  O5'  112.32  3.000
 ACK  H4   C5'  O5'  112.22  3.000
 ACK  H5   C5'  C4'  109.01  3.000
 ACK  H4   C5'  C4'  107.34  3.000
 ACK  O5'  C5'  C4'  108.86  3.000
 ACK  H6   O5'  C5'  108.22  3.000
 ACK  H7   C1'  C2'  109.61  3.000
 ACK  H7   C1'  N9   106.94  3.000
 ACK  C2'  C1'  N9   114.79  3.000
 ACK  H7   C1'  O4'  112.29  3.000
 ACK  C2'  C1'  O4'  104.56  3.000
 ACK  N9   C1'  O4'  108.77  3.000
 ACK  C4   N9   C8   106.31  3.000
 ACK  C4   N9   C1'  126.37  3.000
 ACK  C8   N9   C1'  127.29  3.000
 ACK  H8   C8   N7   125.05  3.000
 ACK  H8   C8   N9   121.76  3.000
 ACK  N7   C8   N9   113.19  3.000
 ACK  C5   N7   C8   104.57  3.000
 ACK  C4   C5   C6   116.18  3.000
 ACK  C6   C5   N7   132.93  3.000
 ACK  C4   C5   N7   110.89  3.000
 ACK  N1   C6   N6   119.35  3.000
 ACK  N6   C6   C5   122.80  3.000
 ACK  N1   C6   C5   117.85  3.000
 ACK  H10  N6   H9   118.22  3.000
 ACK  H10  N6   C6   120.23  3.000
 ACK  H9   N6   C6   121.17  3.000
 ACK  C2   N1   C6   119.25  3.000
 ACK  H11  C2   N3   116.10  3.000
 ACK  H11  C2   N1   115.52  3.000
 ACK  N3   C2   N1   128.38  3.000
 ACK  C4   N3   C2   111.59  3.000
 ACK  N3   C4   C5   126.75  3.000
 ACK  C5   C4   N9   105.04  3.000
 ACK  N3   C4   N9   128.20  3.000
 ACK  H12  C2'  C1'  111.90  3.000
 ACK  H12  C2'  C3'  112.17  3.000
 ACK  C1'  C2'  C3'  103.33  3.000
 ACK  H12  C2'  O2'  109.00  3.000
 ACK  C1'  C2'  O2'  112.21  3.000
 ACK  C3'  C2'  O2'  108.12  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
 ACK  CONST_01  C5   N7  C8  N9     0.00  0.0  0
 ACK  CONST_02  C2   N3  C4  N9   180.00  0.0  0
 ACK  CONST_03  N7   C5  C4  N9     0.00  0.0  0
 ACK  CONST_04  C6   C5  C4  N9   180.00  0.0  0
 ACK  CONST_05  N3   C4  N9  C8   180.00  0.0  0
 ACK  CONST_06  C5   C4  N9  C8     0.00  0.0  0
 ACK  CONST_07  C4   C5  N7  C8     0.00  0.0  0
 ACK  CONST_08  C6   C5  N7  C8   180.00  0.0  0
 ACK  CONST_09  C4   N9  C8  N7     0.00  0.0  0
 ACK  CONST_10  N3   C4  C5  N7   180.00  0.0  0
 ACK  CONST_11  N1   C6  C5  N7   180.00  0.0  0
 ACK  CONST_12  C2   N3  C4  C5     0.00  0.0  0
 ACK  CONST_13  C2   N1  C6  C5     0.00  0.0  0
 ACK  CONST_14  N3   C4  C5  C6     0.00  0.0  0
 ACK  CONST_15  N3   C2  N1  C6     0.00  0.0  0
 ACK  CONST_16  C4   N3  C2  N1     0.00  0.0  0
 ACK  CONST_17  C4   C5  C6  N1     0.00  0.0  0
 ACK  CONST_18  N7   C8  N9  C1'  180.00  0.0  0
 ACK  CONST_19  N3   C4  N9  C1'    0.00  0.0  0
 ACK  CONST_20  C5   C4  N9  C1'  180.00  0.0  0
 ACK  CONST_21  N6   C6  C5  N7     0.00  0.0  0
 ACK  CONST_22  C4   C5  C6  N6   180.00  0.0  0
 ACK  CONST_23  C2   N1  C6  N6   180.00  0.0  0
 ACK  CONST_24  H8   C8  N9  C1'    0.00  0.0  0
 ACK  CONST_25  H11  C2  N1  C6   180.00  0.0  0
 ACK  CONST_26  H9   N6  C6  C5     0.00  0.0  0
 ACK  CONST_27  H10  N6  C6  C5   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
 ACK  chir_02  C3'  C4'  O3'  C2'  negativ
 ACK  chir_03  C4'  O4'  C5'  C3'  positiv
 ACK  chir_04  C1'  O4'  N9   C2'  negativ
 ACK  chir_05  C2'  O2'  C3'  C1'  positiv
 ACK  chir_06  P    O1P  O2'  O3P  both

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
 ACK  plan-1  C1'  0.020
 ACK  plan-1  N9   0.020
 ACK  plan-1  C8   0.020
 ACK  plan-1  N7   0.020
 ACK  plan-1  C5   0.020
 ACK  plan-1  C6   0.020
 ACK  plan-1  N6   0.020
 ACK  plan-1  N1   0.020
 ACK  plan-1  C2   0.020
 ACK  plan-1  N3   0.020
 ACK  plan-1  C4   0.020
 ACK  plan-1  H8   0.020
 ACK  plan-1  H11  0.020
 ACK  plan-2  C6   0.020
 ACK  plan-2  N6   0.020
 ACK  plan-2  H9   0.020
 ACK  plan-2  H10  0.020

