# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 24 02:53:38 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)/C=C/C1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
#
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
 2O2  2O2  1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione  ligand  49  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2O2
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
 2O2  CAV  C  CR16   0  -0.273  -1.7529   1.3632   1.7006
 2O2  CAW  C  CR16   0  -0.253  -1.2098   1.1608   2.9627
 2O2  CAX  C  CR16   0  -0.277  -1.5567   0.0396   3.7041
 2O2  CAY  C  CR16   0  -0.255  -2.4545  -0.8750   3.1672
 2O2  CAZ  C  CR16   0  -0.263  -2.9911  -0.6716   1.9043
 2O2  CAU  C  CR6    0   0.027  -2.6304   0.4377   1.1399
 2O2  CAB  C  CT     0   0.170  -3.2809   0.6927  -0.1968
 2O2  PAA  P  P      0   1.172  -4.9223   1.6261   0.0792
 2O2  OBB  O  OP    -1  -0.883  -4.4829   2.9111   0.7785
 2O2  OBC  O  OP    -1  -0.891  -5.4721   1.8295  -1.3322
 2O2  OBA  O  O      0  -0.881  -5.7411   0.6729   0.9466
 2O2  OAH  O  O2     0  -0.505  -3.6135  -0.5141  -0.8595
 2O2  OAD  O  O2     0  -0.499  -2.4892   1.5119  -1.0190
 2O2  CAC  C  CH2    0  -0.219  -1.2994   0.9111  -1.4780
 2O2  CAE  C  CH1    0  -0.021  -1.6676  -0.2792  -2.3481
 2O2  OAF  O  O2     0  -0.499  -0.5421  -1.0944  -2.6491
 2O2  CAG  C  CH1    0  -0.002  -2.6176  -1.1925  -1.5752
 2O2  CAI  C  CH2    0  -0.565  -1.6243  -2.0577  -0.7918
 2O2  CAJ  C  CH1    0   0.235  -0.4976  -2.2146  -1.8073
 2O2  N1   N  NR6    0  -0.569   0.8386  -2.3026  -1.1835
 2O2  C6   C  CR16   0   0.029   1.7028  -1.2510  -1.1493
 2O2  C2   C  CR6    0   0.734   1.1603  -3.5023  -0.5992
 2O2  O2   O  O      0  -0.487   0.4094  -4.4585  -0.5959
 2O2  N3   N  NR16   0  -0.731   2.3960  -3.5311  -0.0162
 2O2  C4   C  CR6    0   0.534   3.3335  -2.5129   0.0756
 2O2  O4   O  O      0  -0.450   4.3840  -2.7252   0.6525
 2O2  C5   C  CR6    0  -0.125   2.9242  -1.2705  -0.5597
 2O2  CAR  C  C1     0  -0.273   3.7481  -0.0633  -0.6087
 2O2  CAS  C  C1     0  -0.592   4.9507   0.1769  -0.0737
 2O2  PBD  P  P      0   1.142   5.8462   1.7785  -0.2251
 2O2  OBF  O  OP    -1  -0.895   4.9578   2.6788  -1.0904
 2O2  OBG  O  O      0  -0.902   5.9966   2.2543   1.2249
 2O2  OBE  O  OP    -1  -0.903   7.1777   1.3960  -0.8826
 2O2  H1   H  HCR6   0   0.238  -1.4781   2.2505   1.1465
 2O2  H2   H  HCR6   0   0.242  -0.5183   1.8872   3.3715
 2O2  H3   H  HCR6   0   0.244  -1.1358  -0.1196   4.6888
 2O2  H4   H  HCR6   0   0.241  -2.7434  -1.7494   3.7376
 2O2  H5   H  HCR6   0   0.233  -3.6875  -1.3930   1.5008
 2O2  H8   H  HCH2   0   0.256  -0.7456   1.6627  -2.0441
 2O2  H9   H  HCH2   0   0.202  -0.6588   0.5962  -0.6418
 2O2  H10  H  HCH1   0   0.261  -2.0966   0.0623  -3.2925
 2O2  H11  H  HCH1   0   0.262  -3.1530  -1.8342  -2.2819
 2O2  H12  H  HCH2   0   0.271  -1.2692  -1.5482   0.1050
 2O2  H13  H  HCH2   0   0.280  -2.0387  -3.0168  -0.4890
 2O2  H14  H  HCH1   0   0.270  -0.6168  -3.1192  -2.4075
 2O2  H15  H  HCR6   0   0.311   1.3628  -0.3575  -1.6514
 2O2  H16  H  HNR6   0   0.424   2.6471  -4.4097   0.4208
 2O2  H17  H  H      0   0.215   3.2873   0.7492  -1.1676
 2O2  H18  H  H      0   0.219   5.4373  -0.6103   0.4924

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
 2O2  OBG  PBD  deloc     1.533  0.020  1.533
 2O2  O4   C4   double    1.217  0.020  1.217
 2O2  PBD  OBF  deloc     1.532  0.020  1.532
 2O2  PBD  OBE  deloc     1.534  0.020  1.534
 2O2  PBD  CAS  single    1.841  0.020  1.841
 2O2  CAR  C5   single    1.462  0.020  1.462
 2O2  CAR  CAS  double    1.338  0.020  1.338
 2O2  C4   C5   single    1.454  0.020  1.454
 2O2  C4   N3   single    1.387  0.020  1.387
 2O2  C5   C6   double    1.356  0.020  1.356
 2O2  N3   C2   single    1.367  0.020  1.367
 2O2  C6   N1   single    1.362  0.020  1.362
 2O2  C2   O2   double    1.216  0.020  1.216
 2O2  C2   N1   single    1.373  0.020  1.373
 2O2  N1   CAJ  single    1.477  0.020  1.477
 2O2  CAJ  CAI  single    1.525  0.020  1.525
 2O2  CAJ  OAF  single    1.402  0.020  1.402
 2O2  CAI  CAG  single    1.533  0.020  1.533
 2O2  CAW  CAV  aromatic  1.389  0.020  1.389
 2O2  CAW  CAX  aromatic  1.388  0.020  1.388
 2O2  OAF  CAE  single    1.422  0.020  1.422
 2O2  CAV  CAU  aromatic  1.393  0.020  1.393
 2O2  CAG  OAH  single    1.401  0.020  1.401
 2O2  CAG  CAE  single    1.528  0.020  1.528
 2O2  CAX  CAY  aromatic  1.390  0.020  1.390
 2O2  OAH  CAB  single    1.416  0.020  1.416
 2O2  CAE  CAC  single    1.520  0.020  1.520
 2O2  CAU  CAB  single    1.508  0.020  1.508
 2O2  CAU  CAZ  aromatic  1.395  0.020  1.395
 2O2  CAY  CAZ  aromatic  1.387  0.020  1.387
 2O2  CAB  OAD  single    1.405  0.020  1.405
 2O2  CAB  PAA  single    1.908  0.020  1.908
 2O2  OAD  CAC  single    1.410  0.020  1.410
 2O2  OBA  PAA  deloc     1.527  0.020  1.527
 2O2  PAA  OBC  deloc     1.528  0.020  1.528
 2O2  PAA  OBB  deloc     1.527  0.020  1.527
 2O2  CAV  H1   single    0.930  0.020  1.080
 2O2  CAW  H2   single    0.930  0.020  1.080
 2O2  CAX  H3   single    0.930  0.020  1.080
 2O2  CAY  H4   single    0.930  0.020  1.080
 2O2  CAZ  H5   single    0.930  0.020  1.080
 2O2  CAC  H8   single    0.970  0.020  1.090
 2O2  CAC  H9   single    0.970  0.020  1.090
 2O2  CAE  H10  single    0.970  0.020  1.090
 2O2  CAG  H11  single    0.970  0.020  1.090
 2O2  CAI  H12  single    0.970  0.020  1.090
 2O2  CAI  H13  single    0.970  0.020  1.090
 2O2  CAJ  H14  single    0.970  0.020  1.090
 2O2  C6   H15  single    0.930  0.020  1.080
 2O2  N3   H16  single    0.860  0.020  1.020
 2O2  CAR  H17  single    0.930  0.020  1.080
 2O2  CAS  H18  single    0.930  0.020  1.080

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
 2O2  H1   CAV  CAU  119.92  3.000
 2O2  H1   CAV  CAW  119.06  3.000
 2O2  CAU  CAV  CAW  121.01  3.000
 2O2  H2   CAW  CAX  119.98  3.000
 2O2  H2   CAW  CAV  119.67  3.000
 2O2  CAX  CAW  CAV  120.36  3.000
 2O2  H3   CAX  CAY  120.39  3.000
 2O2  H3   CAX  CAW  120.49  3.000
 2O2  CAY  CAX  CAW  119.12  3.000
 2O2  H4   CAY  CAZ  119.64  3.000
 2O2  H4   CAY  CAX  120.01  3.000
 2O2  CAZ  CAY  CAX  120.35  3.000
 2O2  H5   CAZ  CAU  119.53  3.000
 2O2  H5   CAZ  CAY  119.42  3.000
 2O2  CAU  CAZ  CAY  121.04  3.000
 2O2  CAB  CAU  CAZ  120.58  3.000
 2O2  CAZ  CAU  CAV  118.08  3.000
 2O2  CAB  CAU  CAV  121.07  3.000
 2O2  OAD  CAB  OAH  110.81  3.000
 2O2  OAD  CAB  PAA  106.51  3.000
 2O2  OAH  CAB  PAA  106.41  3.000
 2O2  PAA  CAB  CAU  108.99  3.000
 2O2  OAD  CAB  CAU  111.97  3.000
 2O2  OAH  CAB  CAU  111.83  3.000
 2O2  OBA  PAA  OBC  114.51  3.000
 2O2  OBC  PAA  OBB  114.47  3.000
 2O2  OBA  PAA  OBB  114.80  3.000
 2O2  OBB  PAA  CAB  103.32  3.000
 2O2  OBC  PAA  CAB  103.94  3.000
 2O2  OBA  PAA  CAB  103.77  3.000
 2O2  CAG  OAH  CAB  118.98  3.000
 2O2  CAC  OAD  CAB  114.69  3.000
 2O2  H9   CAC  H8   107.22  3.000
 2O2  H9   CAC  CAE  110.63  3.000
 2O2  H8   CAC  CAE  111.42  3.000
 2O2  H9   CAC  OAD  111.49  3.000
 2O2  H8   CAC  OAD  107.67  3.000
 2O2  CAE  CAC  OAD  108.40  3.000
 2O2  H10  CAE  CAG  112.34  3.000
 2O2  H10  CAE  OAF  107.89  3.000
 2O2  CAG  CAE  OAF  104.87  3.000
 2O2  H10  CAE  CAC  110.21  3.000
 2O2  CAG  CAE  CAC  109.22  3.000
 2O2  OAF  CAE  CAC  112.24  3.000
 2O2  CAJ  OAF  CAE  110.86  3.000
 2O2  H11  CAG  CAI  108.43  3.000
 2O2  H11  CAG  CAE  109.15  3.000
 2O2  CAI  CAG  CAE  101.13  3.000
 2O2  H11  CAG  OAH  105.43  3.000
 2O2  CAE  CAG  OAH  114.26  3.000
 2O2  CAI  CAG  OAH  118.21  3.000
 2O2  H13  CAI  H12  107.88  3.000
 2O2  H13  CAI  CAJ  112.10  3.000
 2O2  H12  CAI  CAJ  110.80  3.000
 2O2  H13  CAI  CAG  113.14  3.000
 2O2  H12  CAI  CAG  111.56  3.000
 2O2  CAJ  CAI  CAG  101.33  3.000
 2O2  H14  CAJ  N1   106.35  3.000
 2O2  H14  CAJ  CAI  111.75  3.000
 2O2  N1   CAJ  CAI  113.15  3.000
 2O2  H14  CAJ  OAF  109.17  3.000
 2O2  CAI  CAJ  OAF  107.11  3.000
 2O2  N1   CAJ  OAF  109.26  3.000
 2O2  C2   N1   C6   121.04  3.000
 2O2  C2   N1   CAJ  116.34  3.000
 2O2  C6   N1   CAJ  122.60  3.000
 2O2  H15  C6   C5   119.83  3.000
 2O2  H15  C6   N1   115.31  3.000
 2O2  C5   C6   N1   124.84  3.000
 2O2  N3   C2   O2   122.73  3.000
 2O2  O2   C2   N1   122.94  3.000
 2O2  N3   C2   N1   114.33  3.000
 2O2  H16  N3   C4   116.15  3.000
 2O2  H16  N3   C2   115.24  3.000
 2O2  C4   N3   C2   128.60  3.000
 2O2  C5   C4   O4   126.80  3.000
 2O2  C5   C4   N3   114.08  3.000
 2O2  O4   C4   N3   119.12  3.000
 2O2  CAR  C5   C4   124.15  3.000
 2O2  C4   C5   C6   117.10  3.000
 2O2  CAR  C5   C6   118.75  3.000
 2O2  H17  CAR  CAS  116.87  3.000
 2O2  H17  CAR  C5   113.26  3.000
 2O2  CAS  CAR  C5   129.88  3.000
 2O2  H18  CAS  PBD  117.13  3.000
 2O2  H18  CAS  CAR  118.79  3.000
 2O2  PBD  CAS  CAR  124.08  3.000
 2O2  OBE  PBD  OBG  113.43  3.000
 2O2  OBE  PBD  OBF  114.07  3.000
 2O2  OBG  PBD  OBF  114.11  3.000
 2O2  OBE  PBD  CAS  103.92  3.000
 2O2  OBF  PBD  CAS  105.99  3.000
 2O2  OBG  PBD  CAS  103.87  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
 2O2  CONST_01  CAY  CAX  CAW  CAV    0.00   0.0  0
 2O2  CONST_02  CAY  CAZ  CAU  CAV    0.00   0.0  0
 2O2  CONST_03  CAZ  CAU  CAV  CAW    0.00   0.0  0
 2O2  CONST_04  CAZ  CAY  CAX  CAW    0.00   0.0  0
 2O2  CONST_05  CAU  CAV  CAW  CAX    0.00   0.0  0
 2O2  CONST_06  CAU  CAZ  CAY  CAX    0.00   0.0  0
 2O2  CONST_07  CAB  CAU  CAV  CAW  180.00   0.0  0
 2O2  CONST_08  CAB  CAU  CAZ  CAY  180.00   0.0  0
 2O2  CONST_09  N3   C2   N1   CAJ  180.00   0.0  0
 2O2  CONST_10  C4   N3   C2   N1     0.00   0.0  0
 2O2  CONST_11  N3   C2   N1   C6     0.00   0.0  0
 2O2  CONST_12  C5   C4   N3   C2     0.00   0.0  0
 2O2  CONST_13  O2   C2   N1   CAJ    0.00   0.0  0
 2O2  CONST_14  O2   C2   N1   C6   180.00   0.0  0
 2O2  CONST_15  O4   C4   N3   C2   180.00   0.0  0
 2O2  CONST_16  C4   N3   C2   O2   180.00   0.0  0
 2O2  CONST_17  H3   CAX  CAW  CAV  180.00   0.0  0
 2O2  CONST_18  H5   CAZ  CAU  CAV  180.00   0.0  0
 2O2  CONST_19  H4   CAY  CAX  CAW  180.00   0.0  0
 2O2  CONST_20  H1   CAV  CAW  CAX  180.00   0.0  0
 2O2  CONST_21  H2   CAW  CAX  CAY  180.00   0.0  0
 2O2  CONST_22  H16  N3   C2   N1   180.00   0.0  0
 2O2  CONST_23  PBD  CAS  CAR  C5   180.00   0.0  0
 2O2  CONST_24  H18  CAS  CAR  C5     0.00   0.0  0
 2O2  CONST_25  H17  CAR  CAS  PBD    0.00   0.0  0
 2O2  Var_01    CAE  CAC  OAD  CAB   63.10  30.0  1
 2O2  Var_02    CAS  CAR  C5   C6   177.63  30.0  3
 2O2  Var_03    OBG  PBD  CAS  CAR  118.82  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
 2O2  chir_01  CAB  CAU  OAD  OAH  negativ
 2O2  chir_02  CAE  OAF  CAG  CAC  negativ
 2O2  chir_03  CAG  OAH  CAI  CAE  positiv
 2O2  chir_04  CAJ  OAF  N1   CAI  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
 2O2  plan-1  CAV  0.020
 2O2  plan-1  CAW  0.020
 2O2  plan-1  CAX  0.020
 2O2  plan-1  CAY  0.020
 2O2  plan-1  CAZ  0.020
 2O2  plan-1  CAU  0.020
 2O2  plan-1  CAB  0.020
 2O2  plan-1  H1   0.020
 2O2  plan-1  H2   0.020
 2O2  plan-1  H3   0.020
 2O2  plan-1  H4   0.020
 2O2  plan-1  H5   0.020
 2O2  plan-2  CAJ  0.020
 2O2  plan-2  N1   0.020
 2O2  plan-2  C6   0.020
 2O2  plan-2  C2   0.020
 2O2  plan-2  O2   0.020
 2O2  plan-2  N3   0.020
 2O2  plan-2  C4   0.020
 2O2  plan-2  O4   0.020
 2O2  plan-2  C5   0.020
 2O2  plan-2  CAR  0.020
 2O2  plan-2  H15  0.020
 2O2  plan-2  H16  0.020
 2O2  plan-3  C5   0.020
 2O2  plan-3  CAR  0.020
 2O2  plan-3  CAS  0.020
 2O2  plan-3  PBD  0.020
 2O2  plan-3  H17  0.020
 2O2  plan-3  H18  0.020

