# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:57:59 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   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)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[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
 APR  APR  '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  57  36  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_APR
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
 APR  N1    N  N      0  -0.472  58.6922  22.6486   4.1296
 APR  C2    C  CR16   0   0.036  59.4270  21.6636   3.6196
 APR  N3    N  N      0  -0.459  59.5355  20.4159   4.0415
 APR  C4    C  CR56   0   0.482  58.7788  20.1935   5.1159
 APR  C5    C  CR56   0  -0.003  57.9593  21.1115   5.7538
 APR  C6    C  CR6    0   0.451  57.9389  22.4088   5.2092
 APR  N6    N  NH2    0  -0.817  57.2048  23.3975   5.7235
 APR  N7    N  N      0  -0.458  57.3147  20.5301   6.8131
 APR  C8    C  CR15   0   0.069  57.7344  19.2960   6.8166
 APR  N9    N  NR5    0  -0.539  58.6329  19.0332   5.8171
 APR  C1'   C  CH1    0   0.188  59.2741  17.7667   5.4749
 APR  C2'   C  CH1    0  -0.051  60.7770  17.7984   5.7504
 APR  O2'   O  OH1    0  -0.660  61.3699  16.9002   4.8520
 APR  C3'   C  CH1    0  -0.013  60.8240  17.2802   7.1856
 APR  O3'   O  OH1    0  -0.660  62.0945  16.7797   7.4835
 APR  O4'   O  O2     0  -0.492  58.7351  16.7521   6.2618
 APR  C4'   C  CH1    0  -0.010  59.7054  16.2327   7.1745
 APR  C5'   C  CH2    0  -0.152  59.0893  16.0106   8.5357
 APR  O5'   O  O2     0  -0.618  58.0142  15.1119   8.4252
 APR  PA    P  P      0   1.353  57.2334  14.5261   9.7493
 APR  O1A   O  O      0  -0.789  58.1644  13.6834  10.5617
 APR  O2A   O  OP    -1  -0.790  55.9382  13.9908   9.2335
 APR  O3A   O  O2     0  -0.753  57.0026  15.8848  10.6525
 APR  PB    P  P      0   1.376  56.1023  17.2265  10.3436
 APR  O1B   O  O      0  -0.770  55.9982  17.4598   8.8689
 APR  O2B   O  OP    -1  -0.785  56.6148  18.2724  11.2829
 APR  O5D   O  O2     0  -0.614  54.6100  16.7271  10.8094
 APR  C5D   C  CH2    0  -0.172  54.1608  16.9063  12.1346
 APR  O4D   O  O2     0  -0.503  52.3566  18.3735  11.3918
 APR  C1D   C  CH1    0   0.289  51.1317  18.1042  12.0309
 APR  O2D   O  OH1    0  -0.659  50.4457  18.1575  14.3280
 APR  C2D   C  CH1    0  -0.044  51.4772  17.7515  13.4781
 APR  O3D   O  OH1    0  -0.664  52.6124  19.7792  13.9912
 APR  C3D   C  CH1    0  -0.017  52.8330  18.4264  13.6823
 APR  C4D   C  CH1    0  -0.060  53.4471  18.2410  12.2954
 APR  H2    H  HCR6   0   0.247  60.0120  21.9250   2.7439
 APR  H61   H  HNH2   0   0.410  56.6276  23.2503   6.5325
 APR  H62   H  HNH2   0   0.401  57.2158  24.3104   5.3025
 APR  H8    H  HCR5   0   0.318  57.3966  18.5386   7.5113
 APR  H'1   H  HCH1   0   0.277  59.0745  17.5804   4.4153
 APR  H'2   H  HCH1   0   0.261  61.1933  18.8076   5.6557
 APR  HO'2  H  HOH1   0   0.456  62.2682  16.7181   5.1492
 APR  H'3   H  HCH1   0   0.237  60.5462  18.1014   7.8617
 APR  HO'3  H  HOH1   0   0.465  62.1936  16.7068   8.4376
 APR  H'4   H  HCH1   0   0.235  60.0931  15.2844   6.7830
 APR  H5'1  H  HCH2   0   0.210  59.8780  15.6292   9.1978
 APR  H5'2  H  HCH2   0   0.209  58.7629  16.9743   8.9405
 APR  H5R1  H  HCH2   0   0.224  53.4873  16.0742  12.3593
 APR  H5R2  H  HCH2   0   0.212  54.9786  16.8593  12.8611
 APR  HOR2  H  HOH1   0   0.455  50.6138  17.8046  15.2070
 APR  HOR3  H  HOH1   0   0.451  53.4668  20.2192  14.0453
 APR  HR'3  H  HCH1   0   0.233  53.4277  17.9290  14.4604
 APR  HR'4  H  HCH1   0   0.247  54.1674  19.0354  12.0759
 APR  HR'1  H  HCH1   0   0.202  50.5157  19.0131  11.9892
 APR  O1D   O  OH1    0  -0.659  50.4647  17.0381  11.4417
 APR  HOR1  H  HOH1   0   0.457  50.0460  17.3355  10.6272
 APR  HR'2  H  HCH1   0   0.231  51.6356  16.6653  13.5350

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
 APR  N1   C2    aromatic  1.331  0.020  1.331
 APR  N1   C6    aromatic  1.338  0.020  1.338
 APR  C2   N3    aromatic  1.322  0.020  1.322
 APR  C2   H2    single    0.930  0.020  1.080
 APR  N3   C4    aromatic  1.333  0.020  1.333
 APR  C4   C5    aromatic  1.386  0.020  1.386
 APR  C4   N9    aromatic  1.364  0.020  1.364
 APR  C5   C6    aromatic  1.407  0.020  1.407
 APR  C5   N7    aromatic  1.370  0.020  1.370
 APR  C6   N6    single    1.335  0.020  1.335
 APR  N6   H61   single    0.860  0.020  1.020
 APR  N6   H62   single    0.860  0.020  1.020
 APR  N7   C8    aromatic  1.304  0.020  1.304
 APR  C8   N9    aromatic  1.369  0.020  1.369
 APR  C8   H8    single    0.930  0.020  1.080
 APR  N9   C1'   single    1.460  0.020  1.460
 APR  C1'  C2'   single    1.528  0.020  1.528
 APR  C1'  O4'   single    1.393  0.020  1.393
 APR  C1'  H'1   single    0.970  0.020  1.090
 APR  C2'  O2'   single    1.402  0.020  1.402
 APR  C2'  C3'   single    1.527  0.020  1.527
 APR  C2'  H'2   single    0.970  0.020  1.090
 APR  O2'  HO'2  single    0.850  0.020  0.980
 APR  C3'  O3'   single    1.398  0.020  1.398
 APR  C3'  C4'   single    1.533  0.020  1.533
 APR  C3'  H'3   single    0.970  0.020  1.090
 APR  O3'  HO'3  single    0.850  0.020  0.980
 APR  O4'  C4'   single    1.430  0.020  1.430
 APR  C4'  C5'   single    1.511  0.020  1.511
 APR  C4'  H'4   single    0.970  0.020  1.090
 APR  C5'  O5'   single    1.406  0.020  1.406
 APR  C5'  H5'1  single    0.970  0.020  1.090
 APR  C5'  H5'2  single    0.970  0.020  1.090
 APR  O5'  PA    single    1.645  0.020  1.645
 APR  PA   O1A   deloc     1.496  0.020  1.496
 APR  PA   O2A   deloc     1.493  0.020  1.493
 APR  PA   O3A   single    1.648  0.020  1.648
 APR  O3A  PB    single    1.645  0.020  1.645
 APR  PB   O1B   deloc     1.497  0.020  1.497
 APR  PB   O2B   deloc     1.496  0.020  1.496
 APR  PB   O5D   single    1.641  0.020  1.641
 APR  O5D  C5D   single    1.411  0.020  1.411
 APR  C5D  C4D   single    1.522  0.020  1.522
 APR  C5D  H5R1  single    0.970  0.020  1.090
 APR  C5D  H5R2  single    0.970  0.020  1.090
 APR  O4D  C1D   single    1.408  0.020  1.408
 APR  O4D  C4D   single    1.422  0.020  1.422
 APR  O1D  C1D   single    1.389  0.020  1.389
 APR  O1D  HOR1  single    0.850  0.020  0.980
 APR  C1D  C2D   single    1.529  0.020  1.529
 APR  C1D  HR'1  single    0.970  0.020  1.090
 APR  O2D  C2D   single    1.397  0.020  1.397
 APR  O2D  HOR2  single    0.850  0.020  0.980
 APR  C2D  C3D   single    1.528  0.020  1.528
 APR  C2D  HR'2  single    0.970  0.020  1.090
 APR  O3D  C3D   single    1.405  0.020  1.405
 APR  O3D  HOR3  single    0.850  0.020  0.980
 APR  C3D  C4D   single    1.528  0.020  1.528
 APR  C3D  HR'3  single    0.970  0.020  1.090
 APR  C4D  HR'4  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
 APR  C6    N1   C2    119.18  3.000
 APR  H2    C2   N3    116.15  3.000
 APR  H2    C2   N1    115.39  3.000
 APR  N3    C2   N1    128.45  3.000
 APR  C4    N3   C2    111.61  3.000
 APR  N9    C4   C5    105.28  3.000
 APR  N9    C4   N3    128.12  3.000
 APR  C5    C4   N3    126.60  3.000
 APR  N7    C5   C6    133.15  3.000
 APR  N7    C5   C4    110.68  3.000
 APR  C6    C5   C4    116.17  3.000
 APR  N6    C6   C5    122.81  3.000
 APR  N6    C6   N1    119.20  3.000
 APR  C5    C6   N1    117.99  3.000
 APR  H62   N6   H61   118.46  3.000
 APR  H62   N6   C6    120.35  3.000
 APR  H61   N6   C6    121.19  3.000
 APR  C8    N7   C5    104.62  3.000
 APR  H8    C8   N9    122.63  3.000
 APR  H8    C8   N7    124.33  3.000
 APR  N9    C8   N7    113.01  3.000
 APR  C1'   N9   C8    128.73  3.000
 APR  C1'   N9   C4    124.79  3.000
 APR  C8    N9   C4    106.40  3.000
 APR  H'1   C1'  O4'   110.64  3.000
 APR  H'1   C1'  C2'   110.94  3.000
 APR  O4'   C1'  C2'   107.09  3.000
 APR  H'1   C1'  N9    107.13  3.000
 APR  O4'   C1'  N9    109.24  3.000
 APR  C2'   C1'  N9    111.82  3.000
 APR  H'2   C2'  C3'   112.47  3.000
 APR  H'2   C2'  O2'   111.96  3.000
 APR  C3'   C2'  O2'   111.84  3.000
 APR  H'2   C2'  C1'   112.16  3.000
 APR  C3'   C2'  C1'   101.11  3.000
 APR  O2'   C2'  C1'   106.69  3.000
 APR  HO'2  O2'  C2'   108.52  3.000
 APR  H'3   C3'  C4'   109.30  3.000
 APR  H'3   C3'  O3'   111.47  3.000
 APR  C4'   C3'  O3'   114.85  3.000
 APR  H'3   C3'  C2'   108.47  3.000
 APR  C4'   C3'  C2'   101.70  3.000
 APR  O3'   C3'  C2'   110.49  3.000
 APR  HO'3  O3'  C3'   109.41  3.000
 APR  C4'   O4'  C1'   111.27  3.000
 APR  H'4   C4'  C5'   109.80  3.000
 APR  H'4   C4'  O4'   109.03  3.000
 APR  C5'   C4'  O4'   110.60  3.000
 APR  H'4   C4'  C3'   109.61  3.000
 APR  C5'   C4'  C3'   113.06  3.000
 APR  O4'   C4'  C3'   104.58  3.000
 APR  H5'2  C5'  H5'1  107.27  3.000
 APR  H5'2  C5'  O5'   111.33  3.000
 APR  H5'1  C5'  O5'   112.00  3.000
 APR  H5'2  C5'  C4'   108.98  3.000
 APR  H5'1  C5'  C4'   107.55  3.000
 APR  O5'   C5'  C4'   109.58  3.000
 APR  PA    O5'  C5'   121.84  3.000
 APR  O3A   PA   O2A   111.31  3.000
 APR  O3A   PA   O1A   104.72  3.000
 APR  O2A   PA   O1A   121.71  3.000
 APR  O3A   PA   O5'   102.36  3.000
 APR  O2A   PA   O5'   105.14  3.000
 APR  O1A   PA   O5'   110.02  3.000
 APR  PB    O3A  PA    130.26  3.000
 APR  O5D   PB   O2B   110.25  3.000
 APR  O5D   PB   O1B   105.30  3.000
 APR  O2B   PB   O1B   122.24  3.000
 APR  O5D   PB   O3A   101.31  3.000
 APR  O2B   PB   O3A   105.36  3.000
 APR  O1B   PB   O3A   110.50  3.000
 APR  C5D   O5D  PB    121.16  3.000
 APR  H5R2  C5D  H5R1  106.92  3.000
 APR  H5R2  C5D  C4D   108.53  3.000
 APR  H5R1  C5D  C4D   110.90  3.000
 APR  H5R2  C5D  O5D   112.33  3.000
 APR  H5R1  C5D  O5D   107.00  3.000
 APR  C4D   C5D  O5D   111.10  3.000
 APR  C4D   O4D  C1D   111.16  3.000
 APR  HR'1  C1D  C2D   110.69  3.000
 APR  HR'1  C1D  O1D   110.47  3.000
 APR  C2D   C1D  O1D   109.45  3.000
 APR  HR'1  C1D  O4D   108.20  3.000
 APR  C2D   C1D  O4D   106.09  3.000
 APR  O1D   C1D  O4D   111.85  3.000
 APR  HOR2  O2D  C2D   108.68  3.000
 APR  HR'2  C2D  C3D   107.55  3.000
 APR  HR'2  C2D  O2D   111.23  3.000
 APR  C3D   C2D  O2D   116.45  3.000
 APR  HR'2  C2D  C1D   108.03  3.000
 APR  C3D   C2D  C1D   103.01  3.000
 APR  O2D   C2D  C1D   110.00  3.000
 APR  HOR3  O3D  C3D   108.24  3.000
 APR  HR'3  C3D  C4D   111.74  3.000
 APR  HR'3  C3D  O3D   111.42  3.000
 APR  C4D   C3D  O3D   112.30  3.000
 APR  HR'3  C3D  C2D   112.03  3.000
 APR  C4D   C3D  C2D   100.47  3.000
 APR  O3D   C3D  C2D   108.38  3.000
 APR  HR'4  C4D  C3D   111.00  3.000
 APR  HR'4  C4D  O4D   108.03  3.000
 APR  C3D   C4D  O4D   104.90  3.000
 APR  HR'4  C4D  C5D   107.86  3.000
 APR  C3D   C4D  C5D   113.00  3.000
 APR  O4D   C4D  C5D   111.97  3.000
 APR  HOR1  O1D  C1D   109.30  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
 APR  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 APR  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 APR  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 APR  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 APR  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 APR  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 APR  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 APR  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 APR  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 APR  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 APR  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 APR  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 APR  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 APR  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 APR  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 APR  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 APR  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 APR  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 APR  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 APR  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 APR  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 APR  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 APR  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 APR  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 APR  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 APR  CONST_26  H61   N6   C6   N1   180.00   0.0  0
 APR  CONST_27  H62   N6   C6   N1     0.00   0.0  0
 APR  Var_01    C4D   C5D  O5D  PB    90.23  30.0  3
 APR  Var_02    O1A   PA   O5'  C5'  -64.85  30.0  3
 APR  Var_03    O1B   PB   O3A  PA   -28.50  30.0  3
 APR  Var_04    H5'1  C5'  O5'  PA    53.75  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
 APR  chir_01  C1'  N9   C2'  O4'  negativ
 APR  chir_02  C2'  O2'  C3'  C1'  positiv
 APR  chir_03  C3'  O3'  C4'  C2'  positiv
 APR  chir_04  C4'  O4'  C3'  C5'  negativ
 APR  chir_07  C1D  O4D  O1D  C2D  negativ
 APR  chir_08  C2D  O2D  C1D  C3D  negativ
 APR  chir_09  C3D  O3D  C2D  C4D  negativ
 APR  chir_10  C4D  O4D  C3D  C5D  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
 APR  plan-1  C6   0.020
 APR  plan-1  N6   0.020
 APR  plan-1  H61  0.020
 APR  plan-1  H62  0.020
 APR  plan-2  N1   0.020
 APR  plan-2  C2   0.020
 APR  plan-2  N3   0.020
 APR  plan-2  C4   0.020
 APR  plan-2  C5   0.020
 APR  plan-2  C6   0.020
 APR  plan-2  N6   0.020
 APR  plan-2  N7   0.020
 APR  plan-2  C8   0.020
 APR  plan-2  N9   0.020
 APR  plan-2  C1'  0.020
 APR  plan-2  H2   0.020
 APR  plan-2  H8   0.020

