# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 16:59:03 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-diazanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NNc1nc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1
#
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
 O02  O02  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-diazanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  48  29  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O02
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
 O02  PB    P  P     0   1.374   4.8757   1.9577   0.7243
 O02  O1B   O  OH1   0  -0.741   6.2450   1.1520   0.5044
 O02  O2B   O  OH1   0  -0.737   4.9675   2.6567   2.1618
 O02  O3B   O  O     0  -0.698   4.6180   2.8311  -0.4403
 O02  PA    P  P     0   1.393   3.0015  -0.0820  -0.4534
 O02  O1A   O  OH1   0  -0.740   4.2910  -0.5733  -1.2693
 O02  O2A   O  O     0  -0.685   2.1368   0.7315  -1.3366
 O02  C3A   C  CH2   0  -1.040   3.5937   0.7239   1.0506
 O02  O5'   O  O2    0  -0.588   2.3193  -1.3895   0.1751
 O02  C5'   C  CH2   0  -0.175   1.5343  -2.2632  -0.6384
 O02  C4'   C  CH1   0  -0.035   0.3554  -2.7515   0.1781
 O02  O4'   O  O2    0  -0.490  -0.4087  -1.6489   0.6674
 O02  C3'   C  CH1   0  -0.036  -0.5970  -3.5880  -0.6680
 O02  O3'   O  OH1   0  -0.667  -1.2563  -4.5032   0.1661
 O02  C2'   C  CH1   0  -0.048  -1.5609  -2.5097  -1.1702
 O02  O2'   O  OH1   0  -0.651  -2.8221  -2.9758  -1.5425
 O02  C1'   C  CH1   0   0.222  -1.6752  -1.6190   0.0663
 O02  N9    N  NR5   0  -0.551  -2.0339  -0.2566  -0.2173
 O02  C8    C  CR15  0   0.076  -1.2498   0.7057  -0.8125
 O02  N7    N  N     0  -0.452  -1.8588   1.8426  -0.9485
 O02  C5    C  CR56  0  -0.054  -3.1117   1.6300  -0.4234
 O02  C6    C  CR6   0   0.443  -4.2404   2.4505  -0.2528
 O02  N6    N  NH2   0  -0.819  -4.2663   3.7244  -0.6688
 O02  N1    N  N     0  -0.503  -5.3275   1.9399   0.3199
 O02  C2    C  CR6   0   0.574  -5.3145   0.6637   0.7189
 O02  N3    N  N     0  -0.532  -4.3046  -0.2078   0.6164
 O02  C4    C  CR56  0   0.506  -3.2406   0.3302   0.0408
 O02  N4    N  NH1   0  -0.546  -6.4395   0.1564   1.2788
 O02  N5    N  NH2   0  -0.637  -7.5333   0.9383   1.5865
 O02  H1    H  HOH1  0   0.494   6.5695   0.6480   1.2621
 O02  H2    H  HOH1  0   0.500   5.5561   3.4246   2.1963
 O02  H3    H  HOH1  0   0.493   4.9117  -1.1375  -0.7886
 O02  H3A2  H  HCH2  0   0.341   3.9611  -0.0231   1.7581
 O02  H3A1  H  HCH2  0   0.344   2.7397   1.2199   1.5180
 O02  H5'1  H  HCH2  0   0.235   1.2010  -1.7554  -1.5481
 O02  H5'2  H  HCH2  0   0.263   2.1437  -3.1188  -0.9370
 O02  H4'   H  HCH1  0   0.273   0.7246  -3.3260   1.0333
 O02  H3'   H  HCH1  0   0.256  -0.0784  -4.0923  -1.4943
 O02  HO3'  H  HOH1  0   0.450  -2.0784  -4.7604  -0.2681
 O02  H2'   H  HCH1  0   0.249  -1.0808  -1.9482  -1.9825
 O02  HO2'  H  HOH1  0   0.470  -2.7880  -3.2681  -2.4589
 O02  H1'   H  HCH1  0   0.258  -2.4499  -2.0088   0.7361
 O02  H5    H  HCR5  0   0.296  -0.2257   0.5146  -1.0998
 O02  H61   H  HNH2  0   0.404  -3.4132   4.1763  -0.9492
 O02  H62   H  HNH2  0   0.396  -5.0282   4.3169  -0.3858
 O02  H4    H  HNH1  0   0.383  -6.3730  -0.7811   1.6467
 O02  H12   H  HNH2  0   0.365  -8.3611   0.5288   1.1749
 O02  H11   H  HNH2  0   0.363  -7.6678   0.9575   2.5895

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
 O02  N5   N4    single    1.379  0.020  1.379
 O02  N4   C2    single    1.355  0.020  1.355
 O02  C2   N3    aromatic  1.338  0.020  1.338
 O02  C2   N1    aromatic  1.337  0.020  1.337
 O02  N3   C4    aromatic  1.324  0.020  1.324
 O02  O2'  C2'   single    1.395  0.020  1.395
 O02  N1   C6    aromatic  1.331  0.020  1.331
 O02  C4   N9    aromatic  1.366  0.020  1.366
 O02  C4   C5    aromatic  1.386  0.020  1.386
 O02  C2'  C1'   single    1.528  0.020  1.528
 O02  C2'  C3'   single    1.531  0.020  1.531
 O02  C6   C5    aromatic  1.406  0.020  1.406
 O02  C6   N6    single    1.340  0.020  1.340
 O02  C1'  N9    single    1.437  0.020  1.437
 O02  C1'  O4'   single    1.402  0.020  1.402
 O02  N9   C8    aromatic  1.377  0.020  1.377
 O02  C5   N7    aromatic  1.375  0.020  1.375
 O02  O3'  C3'   single    1.403  0.020  1.403
 O02  C3'  C4'   single    1.524  0.020  1.524
 O02  O4'  C4'   single    1.428  0.020  1.428
 O02  C4'  C5'   single    1.515  0.020  1.515
 O02  C8   N7    aromatic  1.297  0.020  1.297
 O02  C5'  O5'   single    1.429  0.020  1.429
 O02  O5'  PA    single    1.603  0.020  1.603
 O02  O2A  PA    double    1.480  0.020  1.480
 O02  PA   O1A   single    1.603  0.020  1.603
 O02  PA   C3A   single    1.806  0.020  1.806
 O02  O3B  PB    double    1.478  0.020  1.478
 O02  C3A  PB    single    1.809  0.020  1.809
 O02  PB   O1B   single    1.604  0.020  1.604
 O02  PB   O2B   single    1.601  0.020  1.601
 O02  O1B  H1    single    0.850  0.020  0.980
 O02  O2B  H2    single    0.850  0.020  0.980
 O02  O1A  H3    single    0.850  0.020  0.980
 O02  C3A  H3A2  single    0.970  0.020  1.090
 O02  C3A  H3A1  single    0.970  0.020  1.090
 O02  C5'  H5'1  single    0.970  0.020  1.090
 O02  C5'  H5'2  single    0.970  0.020  1.090
 O02  C4'  H4'   single    0.970  0.020  1.090
 O02  C3'  H3'   single    0.970  0.020  1.090
 O02  O3'  HO3'  single    0.850  0.020  0.980
 O02  C2'  H2'   single    0.970  0.020  1.090
 O02  O2'  HO2'  single    0.850  0.020  0.980
 O02  C1'  H1'   single    0.970  0.020  1.090
 O02  C8   H5    single    0.930  0.020  1.080
 O02  N6   H61   single    0.890  0.020  1.040
 O02  N6   H62   single    0.890  0.020  1.040
 O02  N4   H4    single    0.860  0.020  1.020
 O02  N5   H12   single    0.890  0.020  1.040
 O02  N5   H11   single    0.890  0.020  1.040

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
 O02  C3A   PB   O3B   114.93  3.000
 O02  C3A   PB   O2B   100.16  3.000
 O02  O3B   PB   O2B   117.35  3.000
 O02  O2B   PB   O1B   107.07  3.000
 O02  C3A   PB   O1B   106.69  3.000
 O02  O3B   PB   O1B   109.73  3.000
 O02  H1    O1B  PB    116.18  3.000
 O02  H2    O2B  PB    114.40  3.000
 O02  O5'   PA   C3A   100.20  3.000
 O02  C3A   PA   O2A   116.31  3.000
 O02  O5'   PA   O2A   115.70  3.000
 O02  C3A   PA   O1A   107.27  3.000
 O02  O2A   PA   O1A   109.56  3.000
 O02  O5'   PA   O1A   106.97  3.000
 O02  H3    O1A  PA    116.25  3.000
 O02  H3A1  C3A  H3A2  107.22  3.000
 O02  H3A1  C3A  PA    107.61  3.000
 O02  H3A2  C3A  PA    110.14  3.000
 O02  H3A1  C3A  PB    108.76  3.000
 O02  H3A2  C3A  PB    110.17  3.000
 O02  PA    C3A  PB    112.74  3.000
 O02  C5'   O5'  PA    120.62  3.000
 O02  H5'2  C5'  H5'1  107.84  3.000
 O02  H5'2  C5'  C4'   109.22  3.000
 O02  H5'1  C5'  C4'   111.15  3.000
 O02  H5'2  C5'  O5'   109.16  3.000
 O02  H5'1  C5'  O5'   110.92  3.000
 O02  C4'   C5'  O5'   108.53  3.000
 O02  H4'   C4'  C3'   110.89  3.000
 O02  H4'   C4'  O4'   108.55  3.000
 O02  C3'   C4'  O4'   106.24  3.000
 O02  H4'   C4'  C5'   109.14  3.000
 O02  O4'   C4'  C5'   110.63  3.000
 O02  C3'   C4'  C5'   111.34  3.000
 O02  C1'   O4'  C4'   110.67  3.000
 O02  H3'   C3'  C2'   111.96  3.000
 O02  H3'   C3'  O3'   111.70  3.000
 O02  C2'   C3'  O3'   111.01  3.000
 O02  H3'   C3'  C4'   112.01  3.000
 O02  O3'   C3'  C4'   108.76  3.000
 O02  C2'   C3'  C4'   100.90  3.000
 O02  HO3'  O3'  C3'   107.87  3.000
 O02  H2'   C2'  C1'   109.46  3.000
 O02  H2'   C2'  O2'   111.64  3.000
 O02  C1'   C2'  O2'   110.06  3.000
 O02  H2'   C2'  C3'   109.12  3.000
 O02  C1'   C2'  C3'   101.08  3.000
 O02  O2'   C2'  C3'   114.92  3.000
 O02  HO2'  O2'  C2'   108.87  3.000
 O02  H1'   C1'  N9    106.35  3.000
 O02  H1'   C1'  C2'   109.88  3.000
 O02  N9    C1'  C2'   114.30  3.000
 O02  H1'   C1'  O4'   111.65  3.000
 O02  N9    C1'  O4'   109.28  3.000
 O02  C2'   C1'  O4'   105.48  3.000
 O02  C4    N9   C8    106.53  3.000
 O02  C8    N9   C1'   127.29  3.000
 O02  C4    N9   C1'   126.17  3.000
 O02  H5    C8   N7    124.90  3.000
 O02  H5    C8   N9    122.08  3.000
 O02  N7    C8   N9    113.00  3.000
 O02  C5    N7   C8    104.61  3.000
 O02  C4    C5   C6    115.59  3.000
 O02  C6    C5   N7    133.45  3.000
 O02  C4    C5   N7    110.95  3.000
 O02  N1    C6   N6    118.85  3.000
 O02  N6    C6   C5    122.18  3.000
 O02  N1    C6   C5    118.96  3.000
 O02  H62   N6   H61   117.16  3.000
 O02  H62   N6   C6    119.16  3.000
 O02  H61   N6   C6    119.82  3.000
 O02  C2    N1   C6    119.13  3.000
 O02  N4    C2   N3    114.48  3.000
 O02  N3    C2   N1    127.31  3.000
 O02  N4    C2   N1    118.20  3.000
 O02  C4    N3   C2    112.04  3.000
 O02  N3    C4   C5    126.97  3.000
 O02  C5    C4   N9    104.91  3.000
 O02  N3    C4   N9    128.12  3.000
 O02  H4    N4   N5    119.83  3.000
 O02  H4    N4   C2    116.34  3.000
 O02  N5    N4   C2    122.57  3.000
 O02  H11   N5   H12   107.60  3.000
 O02  H11   N5   N4    109.70  3.000
 O02  H12   N5   N4    109.19  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
 O02  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 O02  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 O02  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 O02  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 O02  CONST_05  N3   C4   N9   C8    180.00   0.0  0
 O02  CONST_06  C5   C4   N9   C8      0.00   0.0  0
 O02  CONST_07  C4   C5   N7   C8      0.00   0.0  0
 O02  CONST_08  C6   C5   N7   C8    180.00   0.0  0
 O02  CONST_09  N3   C4   C5   N7    180.00   0.0  0
 O02  CONST_10  N1   C6   C5   N7    180.00   0.0  0
 O02  CONST_11  C4   N9   C8   N7      0.00   0.0  0
 O02  CONST_12  C2   N3   C4   C5      0.00   0.0  0
 O02  CONST_13  C2   N1   C6   C5      0.00   0.0  0
 O02  CONST_14  N3   C2   N1   C6      0.00   0.0  0
 O02  CONST_15  N3   C4   C5   C6      0.00   0.0  0
 O02  CONST_16  C4   N3   C2   N1      0.00   0.0  0
 O02  CONST_17  C4   C5   C6   N1      0.00   0.0  0
 O02  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 O02  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 O02  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 O02  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 O02  CONST_22  N4   C2   N1   C6    180.00   0.0  0
 O02  CONST_23  C2   N1   C6   N6    180.00   0.0  0
 O02  CONST_24  C4   C5   C6   N6    180.00   0.0  0
 O02  CONST_25  N4   C2   N3   C4    180.00   0.0  0
 O02  CONST_26  H5   C8   N9   C1'     0.00   0.0  0
 O02  CONST_27  N5   N4   C2   N1      0.00   0.0  0
 O02  CONST_28  N5   N4   C2   N3    180.00   0.0  0
 O02  CONST_29  H61  N6   C6   C5      0.00   0.0  0
 O02  CONST_30  H62  N6   C6   C5    180.00   0.0  0
 O02  CONST_31  H4   N4   C2   N1    180.00   0.0  0
 O02  Var_01    C4'  C5'  O5'  PA   -142.06  30.0  2
 O02  Var_02    O5'  PA   C3A  PB    161.37  30.0  1
 O02  Var_03    PA   C3A  PB   O1B   -78.94  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
 O02  chir_02  C4'  C3'  O4'  C5'  positiv
 O02  chir_03  C3'  O3'  C2'  C4'  negativ
 O02  chir_04  C2'  O2'  C1'  C3'  negativ
 O02  chir_05  C1'  O4'  N9   C2'  negativ
 O02  chir_06  PA   O2A  O1A  C3A  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
 O02  plan-1  C1'  0.020
 O02  plan-1  N9   0.020
 O02  plan-1  C8   0.020
 O02  plan-1  N7   0.020
 O02  plan-1  C5   0.020
 O02  plan-1  C6   0.020
 O02  plan-1  N6   0.020
 O02  plan-1  N1   0.020
 O02  plan-1  C2   0.020
 O02  plan-1  N3   0.020
 O02  plan-1  C4   0.020
 O02  plan-1  N4   0.020
 O02  plan-1  H5   0.020
 O02  plan-2  C6   0.020
 O02  plan-2  N6   0.020
 O02  plan-2  H61  0.020
 O02  plan-2  H62  0.020
 O02  plan-3  C2   0.020
 O02  plan-3  N4   0.020
 O02  plan-3  N5   0.020
 O02  plan-3  H4   0.020

