# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 01:18:52 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]oxy}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 ACQ  ACQ  5'-O-[(R)-hydroxy{[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]oxy}phosphoryl]adenosine  ligand  54  35  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ACQ
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
 ACQ  PG    P  P     0   1.409  15.8982   1.9212  15.6159
 ACQ  O1G   O  O     0  -0.674  15.5560   3.0898  16.4453
 ACQ  O2G   O  OH1   0  -0.757  15.3835   0.5433  16.1665
 ACQ  O3G   O  O2    0  -0.694  15.2098   1.9458  14.1263
 ACQ  PB    P  P     0   1.411  18.7822   1.2640  16.5068
 ACQ  O1B   O  O     0  -0.658  18.1834   1.2637  17.8518
 ACQ  O2B   O  OH1   0  -0.738  20.1047   2.1100  16.3808
 ACQ  C3B   C  CH2   0  -1.142  17.6538   1.7574  15.1705
 ACQ  PA    P  P     0   1.538  18.4853  -1.5756  15.8299
 ACQ  O1A   O  O     0  -0.716  17.0154  -1.3933  15.9070
 ACQ  O2A   O  OH1   0  -0.695  18.9826  -2.5668  16.9461
 ACQ  O3A   O  O2    0  -0.695  19.3203  -0.2193  16.0280
 ACQ  O5'   O  O2    0  -0.574  19.0519  -2.0582  14.4374
 ACQ  C5'   C  CH2   0  -0.217  18.2449  -2.6997  13.4340
 ACQ  C4'   C  CH1   0   0.025  18.4176  -1.9922  12.1152
 ACQ  O4'   O  O2    0  -0.491  18.0300  -0.6317  12.2399
 ACQ  C3'   C  CH1   0   0.007  19.8381  -1.9461  11.5601
 ACQ  O3'   O  OH1   0  -0.654  20.1511  -3.1614  10.9618
 ACQ  C2'   C  CH1   0  -0.065  19.7590  -0.7386  10.6175
 ACQ  O2'   O  OH1   0  -0.653  19.1968  -1.1693   9.4138
 ACQ  C1'   C  CH1   0   0.143  18.7799   0.1811  11.3757
 ACQ  N9    N  NR5   0  -0.526  19.4285   1.2224  12.1503
 ACQ  C8    C  CR15  0   0.133  20.3378   1.0679  13.1537
 ACQ  N7    N  N     0  -0.528  20.6858   2.1974  13.7051
 ACQ  C5    C  CR56  0   0.027  19.9859   3.1571  13.0147
 ACQ  C6    C  CR6   0   0.495  19.9458   4.5642  13.0956
 ACQ  N6    N  NH2   0  -0.805  20.6649   5.2604  13.9650
 ACQ  N1    N  N     0  -0.461  19.1357   5.2109  12.2474
 ACQ  C2    C  CR16  0   0.099  18.3751   4.5179  11.4192
 ACQ  N3    N  N     0  -0.555  18.3265   3.1987  11.2568
 ACQ  C4    C  CR56  0   0.533  19.1817   2.5661  12.0601
 ACQ  PD    P  P     0   1.447  15.2964   3.1457  13.0433
 ACQ  O1D   O  O     0  -0.692  16.1739   4.2549  13.4662
 ACQ  O2D   O  OH1   0  -0.757  15.7147   2.4093  11.7050
 ACQ  O3D   O  OH1   0  -0.716  13.7411   3.4190  12.8907
 ACQ  HOG2  H  HOH1  0   0.501  15.9775  -0.2530  16.0416
 ACQ  HOB2  H  HOH1  0   0.501  20.5179   2.1704  15.4772
 ACQ  H3B1  H  HCH2  0   0.325  17.7363   1.0734  14.3242
 ACQ  H3B2  H  HCH2  0   0.355  17.9532   2.7475  14.8165
 ACQ  HOA2  H  HOH1  0   0.516  19.9111  -2.8408  16.9160
 ACQ  H5'1  H  HCH2  0   0.279  18.5759  -3.7334  13.3358
 ACQ  H5'2  H  HCH2  0   0.277  17.1940  -2.7046  13.7258
 ACQ  H4'   H  HCH1  0   0.265  17.7707  -2.5135  11.3972
 ACQ  H3'   H  HCH1  0   0.242  20.5447  -1.7119  12.3668
 ACQ  HO3'  H  HOH1  0   0.465  21.0997  -3.1947  10.8040
 ACQ  H2'   H  HCH1  0   0.275  20.7281  -0.2493  10.4670
 ACQ  HO2'  H  HOH1  0   0.465  19.2258  -0.4433   8.7823
 ACQ  H1'   H  HCH1  0   0.285  18.1281   0.7016  10.6700
 ACQ  H8    H  HCR5  0   0.320  20.7091   0.1039  13.4622
 ACQ  HN61  H  HNH2  0   0.415  20.6162   6.2658  13.9687
 ACQ  HN62  H  HNH2  0   0.421  21.3286   4.8192  14.5783
 ACQ  H2    H  HCR6  0   0.274  17.7080   5.0952  10.7909
 ACQ  HOD2  H  HOH1  0   0.508  16.6178   2.6568  11.3741
 ACQ  HOD3  H  HOH1  0   0.508  13.5168   4.1083  12.2501

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
 ACQ  PG   O1G   double    1.473  0.020  1.473
 ACQ  PG   O2G   single    1.571  0.020  1.571
 ACQ  PG   O3G   single    1.641  0.020  1.641
 ACQ  PG   C3B   single    1.819  0.020  1.819
 ACQ  O2G  HOG2  single    0.850  0.020  0.980
 ACQ  O3G  PD    single    1.619  0.020  1.619
 ACQ  PB   O1B   double    1.472  0.020  1.472
 ACQ  PB   O2B   single    1.575  0.020  1.575
 ACQ  PB   C3B   single    1.817  0.020  1.817
 ACQ  PB   O3A   single    1.649  0.020  1.649
 ACQ  O2B  HOB2  single    0.850  0.020  0.980
 ACQ  C3B  H3B1  single    0.970  0.020  1.090
 ACQ  C3B  H3B2  single    0.970  0.020  1.090
 ACQ  PA   O1A   double    1.483  0.020  1.483
 ACQ  PA   O2A   single    1.573  0.020  1.573
 ACQ  PA   O3A   single    1.605  0.020  1.605
 ACQ  PA   O5'   single    1.579  0.020  1.579
 ACQ  O2A  HOA2  single    0.850  0.020  0.980
 ACQ  O5'  C5'   single    1.439  0.020  1.439
 ACQ  C5'  C4'   single    1.506  0.020  1.506
 ACQ  C5'  H5'1  single    0.970  0.020  1.090
 ACQ  C5'  H5'2  single    0.970  0.020  1.090
 ACQ  C4'  O4'   single    1.420  0.020  1.420
 ACQ  C4'  C3'   single    1.526  0.020  1.526
 ACQ  C4'  H4'   single    0.970  0.020  1.090
 ACQ  O4'  C1'   single    1.404  0.020  1.404
 ACQ  C3'  O3'   single    1.390  0.020  1.390
 ACQ  C3'  C2'   single    1.534  0.020  1.534
 ACQ  C3'  H3'   single    0.970  0.020  1.090
 ACQ  O3'  HO3'  single    0.850  0.020  0.980
 ACQ  C2'  O2'   single    1.397  0.020  1.397
 ACQ  C2'  C1'   single    1.543  0.020  1.543
 ACQ  C2'  H2'   single    0.970  0.020  1.090
 ACQ  O2'  HO2'  single    0.850  0.020  0.980
 ACQ  C1'  N9    single    1.451  0.020  1.451
 ACQ  C1'  H1'   single    0.970  0.020  1.090
 ACQ  N9   C8    aromatic  1.363  0.020  1.363
 ACQ  N9   C4    aromatic  1.369  0.020  1.369
 ACQ  C8   N7    aromatic  1.304  0.020  1.304
 ACQ  C8   H8    single    0.930  0.020  1.080
 ACQ  N7   C5    aromatic  1.374  0.020  1.374
 ACQ  C5   C6    aromatic  1.410  0.020  1.410
 ACQ  C5   C4    aromatic  1.381  0.020  1.381
 ACQ  C6   N6    single    1.326  0.020  1.326
 ACQ  C6   N1    aromatic  1.339  0.020  1.339
 ACQ  N6   HN61  single    0.860  0.020  1.020
 ACQ  N6   HN62  single    0.860  0.020  1.020
 ACQ  N1   C2    aromatic  1.321  0.020  1.321
 ACQ  C2   N3    aromatic  1.330  0.020  1.330
 ACQ  C2   H2    single    0.930  0.020  1.080
 ACQ  N3   C4    aromatic  1.333  0.020  1.333
 ACQ  PD   O1D   double    1.476  0.020  1.476
 ACQ  PD   O2D   single    1.584  0.020  1.584
 ACQ  PD   O3D   single    1.587  0.020  1.587
 ACQ  O2D  HOD2  single    0.850  0.020  0.980
 ACQ  O3D  HOD3  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
 ACQ  C3B   PG   O3G   100.60  3.000
 ACQ  C3B   PG   O2G   108.86  3.000
 ACQ  O3G   PG   O2G   101.18  3.000
 ACQ  C3B   PG   O1G   115.69  3.000
 ACQ  O3G   PG   O1G   113.68  3.000
 ACQ  O2G   PG   O1G   114.99  3.000
 ACQ  HOG2  O2G  PG    117.36  3.000
 ACQ  PD    O3G  PG    126.58  3.000
 ACQ  O3A   PB   C3B   103.50  3.000
 ACQ  O3A   PB   O2B   100.72  3.000
 ACQ  C3B   PB   O2B   108.47  3.000
 ACQ  O3A   PB   O1B   113.44  3.000
 ACQ  C3B   PB   O1B   114.79  3.000
 ACQ  O2B   PB   O1B   114.50  3.000
 ACQ  HOB2  O2B  PB    116.98  3.000
 ACQ  H3B2  C3B  H3B1  107.21  3.000
 ACQ  H3B2  C3B  PB    108.30  3.000
 ACQ  H3B1  C3B  PB    110.68  3.000
 ACQ  H3B2  C3B  PG    105.19  3.000
 ACQ  H3B1  C3B  PG    108.62  3.000
 ACQ  PB    C3B  PG    116.34  3.000
 ACQ  O5'   PA   O3A   100.40  3.000
 ACQ  O5'   PA   O2A   108.64  3.000
 ACQ  O3A   PA   O2A   106.28  3.000
 ACQ  O5'   PA   O1A   116.05  3.000
 ACQ  O3A   PA   O1A   113.91  3.000
 ACQ  O2A   PA   O1A   110.72  3.000
 ACQ  HOA2  O2A  PA    117.34  3.000
 ACQ  PA    O3A  PB    128.77  3.000
 ACQ  C5'   O5'  PA    123.37  3.000
 ACQ  H5'2  C5'  H5'1  108.21  3.000
 ACQ  H5'2  C5'  C4'   110.29  3.000
 ACQ  H5'1  C5'  C4'   109.37  3.000
 ACQ  H5'2  C5'  O5'   110.85  3.000
 ACQ  H5'1  C5'  O5'   108.38  3.000
 ACQ  C4'   C5'  O5'   109.69  3.000
 ACQ  H4'   C4'  C3'   108.96  3.000
 ACQ  H4'   C4'  O4'   110.57  3.000
 ACQ  C3'   C4'  O4'   104.89  3.000
 ACQ  H4'   C4'  C5'   106.38  3.000
 ACQ  C3'   C4'  C5'   116.07  3.000
 ACQ  O4'   C4'  C5'   109.98  3.000
 ACQ  C1'   O4'  C4'   110.79  3.000
 ACQ  H3'   C3'  C2'   108.47  3.000
 ACQ  H3'   C3'  O3'   110.97  3.000
 ACQ  C2'   C3'  O3'   115.80  3.000
 ACQ  H3'   C3'  C4'   109.78  3.000
 ACQ  C2'   C3'  C4'   101.50  3.000
 ACQ  O3'   C3'  C4'   109.86  3.000
 ACQ  HO3'  O3'  C3'   108.83  3.000
 ACQ  H2'   C2'  C1'   111.25  3.000
 ACQ  H2'   C2'  O2'   112.04  3.000
 ACQ  C1'   C2'  O2'   110.61  3.000
 ACQ  H2'   C2'  C3'   112.97  3.000
 ACQ  C1'   C2'  C3'   101.54  3.000
 ACQ  O2'   C2'  C3'   107.92  3.000
 ACQ  HO2'  O2'  C2'   108.71  3.000
 ACQ  H1'   C1'  N9    105.64  3.000
 ACQ  H1'   C1'  C2'   110.20  3.000
 ACQ  N9    C1'  C2'   113.99  3.000
 ACQ  H1'   C1'  O4'   110.78  3.000
 ACQ  N9    C1'  O4'   109.01  3.000
 ACQ  C2'   C1'  O4'   107.25  3.000
 ACQ  C4    N9   C8    106.26  3.000
 ACQ  C4    N9   C1'   126.06  3.000
 ACQ  C8    N9   C1'   127.59  3.000
 ACQ  H8    C8   N7    124.16  3.000
 ACQ  H8    C8   N9    122.81  3.000
 ACQ  N7    C8   N9    113.03  3.000
 ACQ  C5    N7   C8    104.86  3.000
 ACQ  C4    C5   C6    116.75  3.000
 ACQ  C4    C5   N7    110.19  3.000
 ACQ  C6    C5   N7    133.06  3.000
 ACQ  N1    C6   N6    119.32  3.000
 ACQ  N1    C6   C5    117.57  3.000
 ACQ  N6    C6   C5    123.11  3.000
 ACQ  HN62  N6   HN61  117.90  3.000
 ACQ  HN62  N6   C6    121.84  3.000
 ACQ  HN61  N6   C6    120.05  3.000
 ACQ  C2    N1   C6    119.47  3.000
 ACQ  H2    C2   N3    115.81  3.000
 ACQ  H2    C2   N1    116.02  3.000
 ACQ  N3    C2   N1    128.17  3.000
 ACQ  C4    N3   C2    111.94  3.000
 ACQ  N3    C4   C5    125.95  3.000
 ACQ  N3    C4   N9    128.40  3.000
 ACQ  C5    C4   N9    105.63  3.000
 ACQ  O3D   PD   O2D   104.93  3.000
 ACQ  O3D   PD   O1D   118.74  3.000
 ACQ  O2D   PD   O1D   115.75  3.000
 ACQ  O3D   PD   O3G    98.03  3.000
 ACQ  O2D   PD   O3G   103.58  3.000
 ACQ  O1D   PD   O3G   113.40  3.000
 ACQ  HOD2  O2D  PD    113.95  3.000
 ACQ  HOD3  O3D  PD    114.44  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
 ACQ  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 ACQ  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 ACQ  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 ACQ  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 ACQ  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 ACQ  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 ACQ  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 ACQ  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 ACQ  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 ACQ  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 ACQ  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 ACQ  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 ACQ  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 ACQ  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 ACQ  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 ACQ  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 ACQ  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 ACQ  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 ACQ  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 ACQ  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 ACQ  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 ACQ  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 ACQ  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 ACQ  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 ACQ  CONST_25  H2    C2   N1   C6   180.00   0.0  0
 ACQ  CONST_26  HN61  N6   C6   C5   180.00   0.0  0
 ACQ  CONST_27  HN62  N6   C6   C5     0.00   0.0  0
 ACQ  Var_01    C4'   C5'  O5'  PA   128.02  30.0  3
 ACQ  Var_02    O1D   PD   O3G  PG     4.46  30.0  3
 ACQ  Var_03    O1B   PB   C3B  PG    -9.50  30.0  1
 ACQ  Var_04    PB    C3B  PG   O1G   72.21  30.0  3
 ACQ  Var_05    O1A   PA   O3A  PB     9.53  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
 ACQ  chir_04  C4'  C5'  O4'  C3'  negativ
 ACQ  chir_05  C3'  O3'  C4'  C2'  positiv
 ACQ  chir_06  C2'  O2'  C3'  C1'  positiv
 ACQ  chir_07  C1'  O4'  N9   C2'  negativ
 ACQ  chir_08  PG   O2G  O3G  C3B  both
 ACQ  chir_09  PB   O2B  O1B  C3B  both
 ACQ  chir_10  PA   O2A  O3A  O5'  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
 ACQ  plan-1  C1'   0.020
 ACQ  plan-1  N9    0.020
 ACQ  plan-1  C8    0.020
 ACQ  plan-1  N7    0.020
 ACQ  plan-1  C5    0.020
 ACQ  plan-1  C6    0.020
 ACQ  plan-1  N6    0.020
 ACQ  plan-1  N1    0.020
 ACQ  plan-1  C2    0.020
 ACQ  plan-1  N3    0.020
 ACQ  plan-1  C4    0.020
 ACQ  plan-1  H8    0.020
 ACQ  plan-1  H2    0.020
 ACQ  plan-2  C6    0.020
 ACQ  plan-2  N6    0.020
 ACQ  plan-2  HN61  0.020
 ACQ  plan-2  HN62  0.020

