# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 21 05:29:27 2020
#   Inital geometry file: a 139 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,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl methanediylbis[hydrogen (R,S)-phosphonate] (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)C[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
 ADV  ADV  '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl methanediylbis[hydrogen (R,S)-phosphonate] (non-preferred name)'  ligand  59  36  .  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_ADV
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
 ADV  PA    P  P      0   1.276  -0.8598   0.7077  -0.1097
 ADV  O5'   O  O2     0  -0.631  -1.6531  -0.5090   0.7086
 ADV  C5'   C  CH2    0  -0.148  -2.1822  -0.1755   1.9691
 ADV  C4'   C  CH1    0   0.006  -1.9039  -1.2778   2.9648
 ADV  O4'   O  O2     0  -0.488  -0.4987  -1.4751   3.1307
 ADV  C3'   C  CH1    0  -0.048  -2.4394  -0.9478   4.3583
 ADV  O3'   O  OH1    0  -0.658  -3.7442  -1.4378   4.5027
 ADV  C2'   C  CH1    0  -0.038  -1.4189  -1.6320   5.2732
 ADV  O2'   O  OH1    0  -0.667  -1.6552  -3.0117   5.3450
 ADV  C1'   C  CH1    0   0.175  -0.1356  -1.4345   4.4715
 ADV  N9    N  NR5    0  -0.546   0.4920  -0.1432   4.7634
 ADV  C8    C  CR15   0   0.062   0.8075   0.8551   3.8780
 ADV  N7    N  N      0  -0.458   1.4446   1.8472   4.4339
 ADV  C5    C  CR56   0  -0.003   1.5744   1.4821   5.7467
 ADV  C6    C  CR6    0   0.446   2.1771   2.1000   6.8570
 ADV  N6    N  NH2    0  -0.817   2.7494   3.3061   6.7888
 ADV  N1    N  N      0  -0.474   2.1566   1.4512   8.0258
 ADV  C2    C  CR16   0   0.037   1.5714   0.2577   8.0932
 ADV  N3    N  N      0  -0.459   0.9732  -0.4192   7.1290
 ADV  C4    C  CR56   0   0.485   0.9986   0.2410   5.9710
 ADV  CX    C  CH2    0  -0.998  -0.4954  -0.2306  -1.6295
 ADV  PB    P  P      0   1.273   0.8205   0.5706  -2.6114
 ADV  O1B   O  O      0  -0.810   2.1866   0.1261  -2.1643
 ADV  OR5   O  O2     0  -0.634   0.4829  -0.1810  -4.0604
 ADV  CR5   C  CH2    0  -0.139   1.3266   0.1225  -5.1475
 ADV  CR4   C  CH1    0   0.005   0.7495  -0.4659  -6.4125
 ADV  OR4   O  O2     0  -0.513  -0.4851   0.1566  -6.7321
 ADV  CR3   C  CH1    0   0.005   1.6330  -0.2210  -7.6359
 ADV  OR3   O  OH1    0  -0.661   2.6661  -1.1579  -7.6933
 ADV  CR2   C  CH1    0  -0.090   0.6138  -0.2753  -8.7689
 ADV  OR2   O  OH1    0  -0.667   0.3322  -1.6206  -9.0448
 ADV  CR1   C  CH1    0   0.277  -0.5687   0.4434  -8.1172
 ADV  OR1   O  OH1    0  -0.665  -1.7588  -0.0167  -8.6505
 ADV  O2A   O  OP    -1  -0.802  -1.8468   1.8147  -0.3614
 ADV  O2B   O  OP    -1  -0.806   0.5376   2.0411  -2.7607
 ADV  O1A   O  O      0  -0.784   0.4172   1.0208   0.6307
 ADV  H5'1  H  HCH2   0   0.224  -3.2694  -0.0434   1.9090
 ADV  H5'2  H  HCH2   0   0.200  -1.7752   0.7653   2.3592
 ADV  H'4   H  HCH1   0   0.244  -2.3441  -2.2175   2.6101
 ADV  H'3   H  HCH1   0   0.246  -2.4010   0.1365   4.5276
 ADV  HO'3  H  HOH1   0   0.468  -4.1681  -0.9815   5.2367
 ADV  H'2   H  HCH1   0   0.261  -1.3693  -1.1760   6.2674
 ADV  HO'2  H  HOH1   0   0.451  -2.6112  -3.1438   5.3640
 ADV  H'1   H  HCH1   0   0.284   0.6002  -2.2160   4.6812
 ADV  H8    H  HCR5   0   0.327   0.5605   0.7987   2.8239
 ADV  H61   H  HNH2   0   0.401   3.2757   3.6518   7.5727
 ADV  H62   H  HNH2   0   0.409   2.8841   3.7568   5.9005
 ADV  H2    H  HCR6   0   0.250   1.5924  -0.2171   9.0686
 ADV  HX1   H  HCH2   0   0.261  -0.1849  -1.2466  -1.3763
 ADV  HX2   H  HCH2   0   0.262  -1.4098  -0.3044  -2.2222
 ADV  H5R1  H  HCH2   0   0.196   1.4391   1.2069  -5.2766
 ADV  H5R2  H  HCH2   0   0.205   2.3310  -0.2933  -4.9997
 ADV  HR4   H  HCH1   0   0.218   0.6052  -1.5471  -6.2770
 ADV  HR3   H  HCH1   0   0.226   2.0247   0.8062  -7.5884
 ADV  HOR3  H  HOH1   0   0.458   3.3242  -0.8516  -8.3243
 ADV  HR2   H  HCH1   0   0.239   0.9496   0.2617  -9.6658
 ADV  HOR2  H  HOH1   0   0.451  -0.4700  -1.6577  -9.5766
 ADV  HR1   H  HCH1   0   0.206  -0.4745   1.5286  -8.2533
 ADV  HOR1  H  HOH1   0   0.469  -2.4564   0.6272  -8.4924

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
 ADV  PA   O5'   single    1.667  0.020  1.667
 ADV  PA   CX    single    1.823  0.020  1.823
 ADV  PA   O2A   deloc     1.504  0.020  1.504
 ADV  PA   O1A   deloc     1.509  0.020  1.509
 ADV  O5'  C5'   single    1.407  0.020  1.407
 ADV  C5'  C4'   single    1.511  0.020  1.511
 ADV  C5'  H5'1  single    0.970  0.020  1.090
 ADV  C5'  H5'2  single    0.970  0.020  1.090
 ADV  C4'  O4'   single    1.429  0.020  1.429
 ADV  C4'  C3'   single    1.529  0.020  1.529
 ADV  C4'  H'4   single    0.970  0.020  1.090
 ADV  O4'  C1'   single    1.390  0.020  1.390
 ADV  C3'  O3'   single    1.401  0.020  1.401
 ADV  C3'  C2'   single    1.532  0.020  1.532
 ADV  C3'  H'3   single    0.970  0.020  1.090
 ADV  O3'  HO'3  single    0.850  0.020  0.980
 ADV  C2'  O2'   single    1.402  0.020  1.402
 ADV  C2'  C1'   single    1.526  0.020  1.526
 ADV  C2'  H'2   single    0.970  0.020  1.090
 ADV  O2'  HO'2  single    0.850  0.020  0.980
 ADV  C1'  N9    single    1.465  0.020  1.465
 ADV  C1'  H'1   single    0.970  0.020  1.090
 ADV  N9   C8    aromatic  1.371  0.020  1.371
 ADV  N9   C4    aromatic  1.365  0.020  1.365
 ADV  C8   N7    aromatic  1.304  0.020  1.304
 ADV  C8   H8    single    0.930  0.020  1.080
 ADV  N7   C5    aromatic  1.369  0.020  1.369
 ADV  C5   C6    aromatic  1.406  0.020  1.406
 ADV  C5   C4    aromatic  1.386  0.020  1.386
 ADV  C6   N6    single    1.337  0.020  1.337
 ADV  C6   N1    aromatic  1.337  0.020  1.337
 ADV  N6   H61   single    0.860  0.020  1.020
 ADV  N6   H62   single    0.860  0.020  1.020
 ADV  N1   C2    aromatic  1.331  0.020  1.331
 ADV  C2   N3    aromatic  1.321  0.020  1.321
 ADV  C2   H2    single    0.930  0.020  1.080
 ADV  N3   C4    aromatic  1.333  0.020  1.333
 ADV  CX   PB    single    1.827  0.020  1.827
 ADV  CX   HX1   single    0.970  0.020  1.090
 ADV  CX   HX2   single    0.970  0.020  1.090
 ADV  PB   O1B   deloc     1.505  0.020  1.505
 ADV  PB   OR5   single    1.667  0.020  1.667
 ADV  PB   O2B   deloc     1.505  0.020  1.505
 ADV  OR5  CR5   single    1.409  0.020  1.409
 ADV  CR5  CR4   single    1.510  0.020  1.510
 ADV  CR5  H5R1  single    0.970  0.020  1.090
 ADV  CR5  H5R2  single    0.970  0.020  1.090
 ADV  CR4  OR4   single    1.419  0.020  1.419
 ADV  CR4  CR3   single    1.529  0.020  1.529
 ADV  CR4  HR4   single    0.970  0.020  1.090
 ADV  OR4  CR1   single    1.417  0.020  1.417
 ADV  CR3  OR3   single    1.396  0.020  1.396
 ADV  CR3  CR2   single    1.525  0.020  1.525
 ADV  CR3  HR3   single    0.970  0.020  1.090
 ADV  OR3  HOR3  single    0.850  0.020  0.980
 ADV  CR2  OR2   single    1.402  0.020  1.402
 ADV  CR2  CR1   single    1.530  0.020  1.530
 ADV  CR2  HR2   single    0.970  0.020  1.090
 ADV  OR2  HOR2  single    0.850  0.020  0.980
 ADV  CR1  OR1   single    1.383  0.020  1.383
 ADV  CR1  HR1   single    0.970  0.020  1.090
 ADV  OR1  HOR1  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
 ADV  O1A   PA   O2A   118.99  3.000
 ADV  O1A   PA   CX    110.28  3.000
 ADV  O2A   PA   CX    111.74  3.000
 ADV  O1A   PA   O5'   108.26  3.000
 ADV  O2A   PA   O5'   107.88  3.000
 ADV  CX    PA   O5'    97.39  3.000
 ADV  C5'   O5'  PA    116.46  3.000
 ADV  H5'2  C5'  H5'1  106.50  3.000
 ADV  H5'2  C5'  C4'   108.84  3.000
 ADV  H5'1  C5'  C4'   107.85  3.000
 ADV  H5'2  C5'  O5'   112.48  3.000
 ADV  H5'1  C5'  O5'   110.62  3.000
 ADV  C4'   C5'  O5'   110.37  3.000
 ADV  H'4   C4'  C3'   109.82  3.000
 ADV  H'4   C4'  O4'   108.31  3.000
 ADV  C3'   C4'  O4'   105.58  3.000
 ADV  H'4   C4'  C5'   109.75  3.000
 ADV  C3'   C4'  C5'   112.24  3.000
 ADV  O4'   C4'  C5'   111.00  3.000
 ADV  C1'   O4'  C4'   111.41  3.000
 ADV  H'3   C3'  C2'   109.00  3.000
 ADV  H'3   C3'  O3'   111.23  3.000
 ADV  C2'   C3'  O3'   113.74  3.000
 ADV  H'3   C3'  C4'   109.96  3.000
 ADV  C2'   C3'  C4'   102.39  3.000
 ADV  O3'   C3'  C4'   110.16  3.000
 ADV  HO'3  O3'  C3'   108.83  3.000
 ADV  H'2   C2'  C1'   112.65  3.000
 ADV  H'2   C2'  O2'   111.78  3.000
 ADV  C1'   C2'  O2'   107.22  3.000
 ADV  H'2   C2'  C3'   112.73  3.000
 ADV  C1'   C2'  C3'   100.88  3.000
 ADV  O2'   C2'  C3'   110.97  3.000
 ADV  HO'2  O2'  C2'   107.62  3.000
 ADV  H'1   C1'  N9    107.66  3.000
 ADV  H'1   C1'  C2'   111.88  3.000
 ADV  N9    C1'  C2'   111.69  3.000
 ADV  H'1   C1'  O4'   109.88  3.000
 ADV  N9    C1'  O4'   109.26  3.000
 ADV  C2'   C1'  O4'   106.46  3.000
 ADV  C4    N9   C8    106.32  3.000
 ADV  C4    N9   C1'   125.69  3.000
 ADV  C8    N9   C1'   127.70  3.000
 ADV  H8    C8   N7    124.44  3.000
 ADV  H8    C8   N9    122.52  3.000
 ADV  N7    C8   N9    113.03  3.000
 ADV  C5    N7   C8    104.62  3.000
 ADV  C4    C5   C6    116.33  3.000
 ADV  C4    C5   N7    110.77  3.000
 ADV  C6    C5   N7    132.89  3.000
 ADV  N1    C6   N6    119.28  3.000
 ADV  N1    C6   C5    118.06  3.000
 ADV  N6    C6   C5    122.66  3.000
 ADV  H62   N6   H61   117.69  3.000
 ADV  H62   N6   C6    120.46  3.000
 ADV  H61   N6   C6    119.64  3.000
 ADV  C2    N1   C6    119.09  3.000
 ADV  H2    C2   N3    116.15  3.000
 ADV  H2    C2   N1    115.43  3.000
 ADV  N3    C2   N1    128.43  3.000
 ADV  C4    N3   C2    111.81  3.000
 ADV  N3    C4   C5    126.28  3.000
 ADV  N3    C4   N9    128.47  3.000
 ADV  C5    C4   N9    105.25  3.000
 ADV  HX2   CX   HX1   107.51  3.000
 ADV  HX2   CX   PB    109.94  3.000
 ADV  HX1   CX   PB    109.13  3.000
 ADV  HX2   CX   PA    108.66  3.000
 ADV  HX1   CX   PA    110.03  3.000
 ADV  PB    CX   PA    111.49  3.000
 ADV  O2B   PB   OR5   108.44  3.000
 ADV  O2B   PB   O1B   119.27  3.000
 ADV  OR5   PB   O1B   108.00  3.000
 ADV  O2B   PB   CX    110.27  3.000
 ADV  OR5   PB   CX     97.10  3.000
 ADV  O1B   PB   CX    111.39  3.000
 ADV  CR5   OR5  PB    116.89  3.000
 ADV  H5R2  CR5  H5R1  107.24  3.000
 ADV  H5R2  CR5  CR4   108.36  3.000
 ADV  H5R1  CR5  CR4   109.00  3.000
 ADV  H5R2  CR5  OR5   111.26  3.000
 ADV  H5R1  CR5  OR5   111.40  3.000
 ADV  CR4   CR5  OR5   109.49  3.000
 ADV  HR4   CR4  CR3   109.40  3.000
 ADV  HR4   CR4  OR4   110.18  3.000
 ADV  CR3   CR4  OR4   104.61  3.000
 ADV  HR4   CR4  CR5   109.29  3.000
 ADV  CR3   CR4  CR5   112.78  3.000
 ADV  OR4   CR4  CR5   110.50  3.000
 ADV  CR1   OR4  CR4   111.11  3.000
 ADV  HR3   CR3  CR2   107.65  3.000
 ADV  HR3   CR3  OR3   111.40  3.000
 ADV  CR2   CR3  OR3   116.12  3.000
 ADV  HR3   CR3  CR4   108.71  3.000
 ADV  CR2   CR3  CR4   101.69  3.000
 ADV  OR3   CR3  CR4   110.67  3.000
 ADV  HOR3  OR3  CR3   108.64  3.000
 ADV  HR2   CR2  CR1   110.77  3.000
 ADV  HR2   CR2  OR2   111.72  3.000
 ADV  CR1   CR2  OR2   112.30  3.000
 ADV  HR2   CR2  CR3   112.65  3.000
 ADV  CR1   CR2  CR3   100.57  3.000
 ADV  OR2   CR2  CR3   108.34  3.000
 ADV  HOR2  OR2  CR2   108.24  3.000
 ADV  HR1   CR1  OR1   110.79  3.000
 ADV  HR1   CR1  CR2   110.20  3.000
 ADV  OR1   CR1  CR2   110.16  3.000
 ADV  HR1   CR1  OR4   108.43  3.000
 ADV  OR1   CR1  OR4   111.12  3.000
 ADV  CR2   CR1  OR4   106.01  3.000
 ADV  HOR1  OR1  CR1   109.75  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
 ADV  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 ADV  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 ADV  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 ADV  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 ADV  CONST_05  C5   C4   N9   C8      0.00   0.0  0
 ADV  CONST_06  N3   C4   N9   C8    180.00   0.0  0
 ADV  CONST_07  C6   C5   N7   C8    180.00   0.0  0
 ADV  CONST_08  C4   C5   N7   C8      0.00   0.0  0
 ADV  CONST_09  C4   N9   C8   N7      0.00   0.0  0
 ADV  CONST_10  N1   C6   C5   N7    180.00   0.0  0
 ADV  CONST_11  N3   C4   C5   N7    180.00   0.0  0
 ADV  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 ADV  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 ADV  CONST_14  N3   C4   C5   C6      0.00   0.0  0
 ADV  CONST_15  N3   C2   N1   C6      0.00   0.0  0
 ADV  CONST_16  C4   C5   C6   N1      0.00   0.0  0
 ADV  CONST_17  C4   N3   C2   N1      0.00   0.0  0
 ADV  CONST_18  N7   C8   N9   C1'   180.00   0.0  0
 ADV  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 ADV  CONST_20  N3   C4   N9   C1'     0.00   0.0  0
 ADV  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 ADV  CONST_22  C4   C5   C6   N6    180.00   0.0  0
 ADV  CONST_23  C2   N1   C6   N6    180.00   0.0  0
 ADV  CONST_24  H8   C8   N9   C1'     0.00   0.0  0
 ADV  CONST_25  H2   C2   N1   C6    180.00   0.0  0
 ADV  CONST_26  H61  N6   C6   C5    180.00   0.0  0
 ADV  CONST_27  H62  N6   C6   C5      0.00   0.0  0
 ADV  Var_01    C4'  C5'  O5'  PA   -136.92  30.0  3
 ADV  Var_02    CR4  CR5  OR5  PB   -171.08  30.0  3
 ADV  Var_03    O1B  PB   CX   PA     86.84  30.0  3
 ADV  Var_04    PB   CX   PA   O5'  -162.38  30.0  3
 ADV  Var_05    CX   PA   O5'  C5'  -177.13  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
 ADV  chir_02  C4'  C5'  O4'  C3'  negativ
 ADV  chir_03  C3'  O3'  C4'  C2'  positiv
 ADV  chir_04  C2'  O2'  C3'  C1'  positiv
 ADV  chir_05  C1'  O4'  N9   C2'  negativ
 ADV  chir_07  CR4  CR5  OR4  CR3  negativ
 ADV  chir_08  CR3  OR3  CR4  CR2  positiv
 ADV  chir_09  CR2  OR2  CR3  CR1  positiv
 ADV  chir_10  CR1  OR4  OR1  CR2  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
 ADV  plan-1  C6   0.020
 ADV  plan-1  N6   0.020
 ADV  plan-1  H61  0.020
 ADV  plan-1  H62  0.020
 ADV  plan-2  C1'  0.020
 ADV  plan-2  N9   0.020
 ADV  plan-2  C8   0.020
 ADV  plan-2  N7   0.020
 ADV  plan-2  C5   0.020
 ADV  plan-2  C6   0.020
 ADV  plan-2  N6   0.020
 ADV  plan-2  N1   0.020
 ADV  plan-2  C2   0.020
 ADV  plan-2  N3   0.020
 ADV  plan-2  C4   0.020
 ADV  plan-2  H8   0.020
 ADV  plan-2  H2   0.020

