# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:17:08 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  45  29  .  2021-08-17  2021-08-17  
;
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   1.153   2.6725   2.4773   0.8798
 O02  O1B   O  OP    -1  -0.915   4.1253   2.8088   0.5153
 O02  O2B   O  OP    -1  -0.928   2.3033   2.8656   2.3226
 O02  O3B   O  O      0  -0.885   1.6504   2.9553  -0.1522
 O02  PA    P  P      0   1.271   3.1675  -0.2498  -0.5768
 O02  O1A   O  OP    -1  -0.817   4.6734  -0.3040  -0.5971
 O02  O2A   O  O      0  -0.811   2.4295   0.1663  -1.8287
 O02  C3A   C  CH2    0  -0.995   2.5649   0.6089   0.8925
 O02  O5'   O  O2     0  -0.637   2.7204  -1.8452  -0.2446
 O02  C5'   C  CH2    0  -0.146   1.6787  -2.4903  -0.9183
 O02  C4'   C  CH1    0  -0.030   0.5376  -2.8579   0.0141
 O02  O4'   O  O2     0  -0.493  -0.0755  -1.6912   0.5801
 O02  C3'   C  CH1    0  -0.038  -0.5747  -3.5948  -0.7222
 O02  O3'   O  OH1    0  -0.671  -1.2351  -4.4510   0.1759
 O02  C2'   C  CH1    0  -0.048  -1.4753  -2.4287  -1.1310
 O02  O2'   O  OH1    0  -0.654  -2.8062  -2.7670  -1.3868
 O02  C1'   C  CH1    0   0.237  -1.3836  -1.5441   0.1107
 O02  N9    N  NR5    0  -0.557  -1.6657  -0.1541  -0.1384
 O02  C8    C  CR15   0   0.078  -0.8715   0.7800  -0.7742
 O02  N7    N  N      0  -0.447  -1.4684   1.9220  -0.9248
 O02  C5    C  CR5    0  -0.053  -2.7104   1.7478  -0.3635
 O02  C6    C  C      0   0.433  -3.8131   2.5974  -0.1787
 O02  N6    N  NH2    0  -0.821  -3.8255   3.8608  -0.6336
 O02  N1    N  N      0  -0.503  -4.8925   2.1304   0.4455
 O02  C2    C  C      0   0.564  -4.8933   0.8655   0.8781
 O02  N3    N  N      0  -0.530  -3.9137  -0.0346   0.7554
 O02  C4    C  CR5    0   0.498  -2.8523   0.4635   0.1365
 O02  N4    N  NH1    0  -0.545  -5.9883   0.4156   1.5468
 O02  N5    N  NH2    0  -0.641  -7.1624   1.1399   1.6006
 O02  H3A2  H  HCH2   0   0.196   3.1261   0.2248   1.7514
 O02  H3A1  H  HCH2   0   0.225   1.5215   0.3292   1.0543
 O02  H5'1  H  HCH2   0   0.202   1.3085  -1.8866  -1.7535
 O02  H5'2  H  HCH2   0   0.204   2.0537  -3.4284  -1.3479
 O02  H4'   H  HCH1   0   0.246   0.9260  -3.4690   0.8356
 O02  H3'   H  HCH1   0   0.245  -0.1921  -4.1425  -1.5937
 O02  HO3'  H  HOH1   0   0.447  -2.1085  -4.6427  -0.1849
 O02  H2'   H  HCH1   0   0.245  -1.0195  -1.9057  -1.9821
 O02  HO2'  H  HOH1   0   0.467  -2.8786  -3.0641  -2.2991
 O02  H1'   H  HCH1   0   0.245  -2.1201  -1.8726   0.8541
 O02  H5    H  HCR5   0   0.310   0.1460   0.5639  -1.0755
 O02  H61   H  HNH2   0   0.402  -2.9648   4.2848  -0.9342
 O02  H62   H  HNH2   0   0.394  -4.5535   4.4815  -0.3230
 O02  H4    H  HNH1   0   0.379  -6.0136  -0.5785   1.7208
 O02  H12   H  HNH2   0   0.359  -7.8634   0.7122   1.0079
 O02  H11   H  HNH2   0   0.365  -7.5119   1.1259   2.5488

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    1.381  0.020  1.381
 O02  N4   C2    single    1.360  0.020  1.360
 O02  C2   N3    aromatic  1.336  0.020  1.336
 O02  C2   N1    aromatic  1.337  0.020  1.337
 O02  N3   C4    aromatic  1.326  0.020  1.326
 O02  O2'  C2'   single    1.397  0.020  1.397
 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    1.527  0.020  1.527
 O02  C2'  C3'   single    1.529  0.020  1.529
 O02  C6   C5    aromatic  1.404  0.020  1.404
 O02  C6   N6    single    1.343  0.020  1.343
 O02  C1'  N9    single    1.440  0.020  1.440
 O02  C1'  O4'   single    1.398  0.020  1.398
 O02  N9   C8    aromatic  1.381  0.020  1.381
 O02  C5   N7    aromatic  1.374  0.020  1.374
 O02  O3'  C3'   single    1.406  0.020  1.406
 O02  C3'  C4'   single    1.524  0.020  1.524
 O02  O4'  C4'   single    1.434  0.020  1.434
 O02  C4'  C5'   single    1.519  0.020  1.519
 O02  C8   N7    aromatic  1.297  0.020  1.297
 O02  C5'  O5'   single    1.398  0.020  1.398
 O02  O5'  PA    single    1.690  0.020  1.690
 O02  O2A  PA    deloc     1.512  0.020  1.512
 O02  PA   O1A   deloc     1.507  0.020  1.507
 O02  PA   C3A   single    1.805  0.020  1.805
 O02  O3B  PB    deloc     1.529  0.020  1.529
 O02  C3A  PB    single    1.872  0.020  1.872
 O02  PB   O1B   deloc     1.534  0.020  1.534
 O02  PB   O2B   deloc     1.539  0.020  1.539
 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    0.890  0.020  1.040
 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   106.15  3.000
 O02  C3A   PB   O2B   103.39  3.000
 O02  O3B   PB   O2B   113.17  3.000
 O02  O2B   PB   O1B   113.29  3.000
 O02  C3A   PB   O1B   105.77  3.000
 O02  O3B   PB   O1B   113.90  3.000
 O02  O5'   PA   C3A   101.58  3.000
 O02  C3A   PA   O2A   112.34  3.000
 O02  O5'   PA   O2A   107.07  3.000
 O02  C3A   PA   O1A   111.20  3.000
 O02  O2A   PA   O1A   119.12  3.000
 O02  O5'   PA   O1A   103.48  3.000
 O02  H3A1  C3A  H3A2  106.47  3.000
 O02  H3A1  C3A  PA    108.51  3.000
 O02  H3A2  C3A  PA    107.47  3.000
 O02  H3A1  C3A  PB    108.16  3.000
 O02  H3A2  C3A  PB    109.02  3.000
 O02  PA    C3A  PB    116.75  3.000
 O02  C5'   O5'  PA    122.55  3.000
 O02  H5'2  C5'  H5'1  106.74  3.000
 O02  H5'2  C5'  C4'   106.86  3.000
 O02  H5'1  C5'  C4'   110.35  3.000
 O02  H5'2  C5'  O5'   109.16  3.000
 O02  H5'1  C5'  O5'   111.41  3.000
 O02  C4'   C5'  O5'   112.06  3.000
 O02  H4'   C4'  C3'   110.58  3.000
 O02  H4'   C4'  O4'   108.03  3.000
 O02  C3'   C4'  O4'   105.78  3.000
 O02  H4'   C4'  C5'   109.22  3.000
 O02  O4'   C4'  C5'   111.50  3.000
 O02  C3'   C4'  C5'   111.64  3.000
 O02  C1'   O4'  C4'   110.68  3.000
 O02  H3'   C3'  C2'   111.93  3.000
 O02  H3'   C3'  O3'   111.53  3.000
 O02  C2'   C3'  O3'   111.02  3.000
 O02  H3'   C3'  C4'   111.74  3.000
 O02  O3'   C3'  C4'   109.19  3.000
 O02  C2'   C3'  C4'   100.97  3.000
 O02  HO3'  O3'  C3'   107.91  3.000
 O02  H2'   C2'  C1'   109.24  3.000
 O02  H2'   C2'  O2'   111.65  3.000
 O02  C1'   C2'  O2'   110.26  3.000
 O02  H2'   C2'  C3'   109.02  3.000
 O02  C1'   C2'  C3'   100.90  3.000
 O02  O2'   C2'  C3'   115.18  3.000
 O02  HO2'  O2'  C2'   108.67  3.000
 O02  H1'   C1'  N9    105.95  3.000
 O02  H1'   C1'  C2'   109.71  3.000
 O02  N9    C1'  C2'   113.99  3.000
 O02  H1'   C1'  O4'   111.68  3.000
 O02  N9    C1'  O4'   110.06  3.000
 O02  C2'   C1'  O4'   105.56  3.000
 O02  C4    N9   C8    106.65  3.000
 O02  C8    N9   C1'   128.30  3.000
 O02  C4    N9   C1'   124.88  3.000
 O02  H5    C8   N7    125.14  3.000
 O02  H5    C8   N9    122.24  3.000
 O02  N7    C8   N9    112.59  3.000
 O02  C5    N7   C8    104.88  3.000
 O02  C4    C5   C6    115.65  3.000
 O02  C6    C5   N7    133.39  3.000
 O02  C4    C5   N7    110.95  3.000
 O02  N1    C6   N6    118.77  3.000
 O02  N6    C6   C5    122.13  3.000
 O02  N1    C6   C5    119.09  3.000
 O02  H62   N6   H61   116.85  3.000
 O02  H62   N6   C6    118.86  3.000
 O02  H61   N6   C6    119.35  3.000
 O02  C2    N1   C6    118.95  3.000
 O02  N4    C2   N3    114.38  3.000
 O02  N3    C2   N1    127.40  3.000
 O02  N4    C2   N1    118.21  3.000
 O02  C4    N3   C2    112.13  3.000
 O02  N3    C4   C5    126.78  3.000
 O02  C5    C4   N9    104.93  3.000
 O02  N3    C4   N9    128.29  3.000
 O02  H4    N4   N5    119.25  3.000
 O02  H4    N4   C2    115.51  3.000
 O02  N5    N4   C2    122.03  3.000
 O02  H11   N5   H12   107.68  3.000
 O02  H11   N5   N4    108.87  3.000
 O02  H12   N5   N4    110.14  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   -116.28  30.0  2
 O02  Var_02    O5'  PA   C3A  PB   -173.24  30.0  2
 O02  Var_03    PA   C3A  PB   O1B   -52.00  30.0  3

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

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

