# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat May 23 10:19:28 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 1-{3,5-O-[(4-carboxyphenyl)(phosphono)methylidene]-2-deoxy-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccc(cc4)C(O)=O)[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
 2E2  2E2  1-{3,5-O-[(4-carboxyphenyl)(phosphono)methylidene]-2-deoxy-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione  ligand  47  31  .  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_2E2
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
 2E2  O2   O  O      0  -0.487   3.0045  -1.8957   2.7618
 2E2  C2   C  C      0   0.737   3.1864  -1.9190   1.5599
 2E2  N3   N  NH1    0  -0.733   4.3934  -1.6080   0.9932
 2E2  C4   C  C      0   0.558   4.7139  -1.5693  -0.3524
 2E2  O4   O  O      0  -0.458   5.8360  -1.2605  -0.7127
 2E2  C5   C  C      0  -0.177   3.6224  -1.9235  -1.2347
 2E2  CAR  C  CH3    0  -0.707   3.8569  -1.9292  -2.7097
 2E2  C6   C  C1     0   0.047   2.4381  -2.2470  -0.6823
 2E2  N1   N  NT     0  -0.569   2.2023  -2.2547   0.6639
 2E2  CAJ  C  CR15   0   0.233   0.8784  -2.5778   1.2334
 2E2  OAF  O  O      0  -0.500   0.1136  -3.2488   0.2685
 2E2  CAI  C  CH2    0  -0.563   0.0868  -1.3438   1.6553
 2E2  CAG  C  CR15   0   0.002  -1.3493  -1.7899   1.3655
 2E2  OAH  O  O2     0  -0.507  -2.3384  -0.8037   1.2585
 2E2  CAE  C  CR15   0  -0.021  -1.1552  -2.6291   0.1040
 2E2  CAC  C  CH2    0  -0.220  -1.2050  -1.7225  -1.1131
 2E2  OAD  O  O2     0  -0.498  -2.4049  -0.9856  -1.0588
 2E2  CAB  C  CT     0   0.170  -2.4982  -0.1080   0.0346
 2E2  PAA  P  P      0   1.171  -4.2860   0.5595   0.0433
 2E2  OBB  O  OP    -1  -0.891  -5.1479  -0.6955   0.1774
 2E2  OBA  O  O      0  -0.883  -4.3216   1.4815   1.2600
 2E2  OBC  O  OP    -1  -0.883  -4.4092   1.2691  -1.3036
 2E2  CAU  C  CR6    0   0.026  -1.5330   1.0432  -0.0868
 2E2  CAV  C  CR16   0  -0.259  -1.1477   1.5313  -1.3340
 2E2  CAW  C  CR16   0  -0.290  -0.3160   2.6360  -1.4449
 2E2  CAX  C  CR6    0  -0.115   0.1396   3.3134  -0.3169
 2E2  CCA  C  C      0   0.386   1.0500   4.5244  -0.4372
 2E2  OCB  O  OC    -1  -0.600   1.3932   5.0779   0.6270
 2E2  OCA  O  O      0  -0.600   1.3823   4.8682  -1.5895
 2E2  CAY  C  CR16   0  -0.290  -0.2705   2.8419   0.9283
 2E2  CAZ  C  CR16   0  -0.258  -1.0967   1.7349   1.0421
 2E2  H1   H  HNH1   0   0.425   5.1281  -1.3634   1.6460
 2E2  H2   H  HCH3   0   0.246   4.6479  -2.6280  -2.9857
 2E2  H3   H  HCH3   0   0.246   2.9535  -2.2187  -3.2444
 2E2  H4   H  HCH3   0   0.247   4.1563  -0.9440  -3.0697
 2E2  H5   H  H      0   0.310   1.6045  -2.5390  -1.3026
 2E2  H6   H  HCR5   0   0.269   1.0608  -3.2487   2.0757
 2E2  H7   H  HCH2   0   0.279   0.2504  -1.0927   2.7013
 2E2  H8   H  HCH2   0   0.271   0.3745  -0.4779   1.0567
 2E2  H9   H  HCR5   0   0.259  -1.6777  -2.4423   2.1810
 2E2  H10  H  HCR5   0   0.261  -1.9047  -3.4184   0.0130
 2E2  H11  H  HCH2   0   0.202  -0.3252  -1.0629  -1.1425
 2E2  H12  H  HCH2   0   0.255  -1.2103  -2.2996  -2.0401
 2E2  H15  H  HCR6   0   0.229  -1.4929   1.0404  -2.2341
 2E2  H16  H  HCR6   0   0.229  -0.0229   2.9829  -2.4276
 2E2  H18  H  HCR6   0   0.229   0.0608   3.3530   1.8232
 2E2  H19  H  HCR6   0   0.226  -1.3947   1.3968   2.0250

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
 2E2  OCA  CCA  deloc     1.248  0.020  1.248
 2E2  OCB  CCA  deloc     1.248  0.020  1.248
 2E2  O4   C4   double    1.218  0.020  1.218
 2E2  CCA  CAX  single    1.520  0.020  1.520
 2E2  C4   N3   single    1.384  0.020  1.384
 2E2  C4   C5   single    1.447  0.020  1.447
 2E2  CAR  C5   single    1.494  0.020  1.494
 2E2  CAX  CAW  aromatic  1.392  0.020  1.392
 2E2  CAX  CAY  aromatic  1.393  0.020  1.393
 2E2  N3   C2   single    1.369  0.020  1.369
 2E2  C5   C6   double    1.346  0.020  1.346
 2E2  CAW  CAV  aromatic  1.387  0.020  1.387
 2E2  CAY  CAZ  aromatic  1.386  0.020  1.386
 2E2  C2   O2   double    1.216  0.020  1.216
 2E2  C2   N1   single    1.372  0.020  1.372
 2E2  C6   N1   single    1.367  0.020  1.367
 2E2  CAV  CAU  aromatic  1.394  0.020  1.394
 2E2  CAZ  CAU  aromatic  1.394  0.020  1.394
 2E2  N1   CAJ  single    1.477  0.020  1.477
 2E2  CAU  CAB  single    1.507  0.020  1.507
 2E2  CAJ  CAI  single    1.526  0.020  1.526
 2E2  CAJ  OAF  single    1.402  0.020  1.402
 2E2  OAH  CAB  single    1.417  0.020  1.417
 2E2  OAH  CAG  single    1.401  0.020  1.401
 2E2  CAB  OAD  single    1.405  0.020  1.405
 2E2  CAB  PAA  single    1.908  0.020  1.908
 2E2  OAD  CAC  single    1.409  0.020  1.409
 2E2  CAI  CAG  single    1.531  0.020  1.531
 2E2  OAF  CAE  single    1.422  0.020  1.422
 2E2  OBA  PAA  deloc     1.527  0.020  1.527
 2E2  CAG  CAE  single    1.527  0.020  1.527
 2E2  CAC  CAE  single    1.519  0.020  1.519
 2E2  PAA  OBB  deloc     1.528  0.020  1.528
 2E2  PAA  OBC  deloc     1.527  0.020  1.527
 2E2  N3   H1   single    0.860  0.020  1.020
 2E2  CAR  H2   single    0.970  0.020  1.090
 2E2  CAR  H3   single    0.970  0.020  1.090
 2E2  CAR  H4   single    0.970  0.020  1.090
 2E2  C6   H5   single    0.930  0.020  1.080
 2E2  CAJ  H6   single    0.970  0.020  1.090
 2E2  CAI  H7   single    0.970  0.020  1.090
 2E2  CAI  H8   single    0.970  0.020  1.090
 2E2  CAG  H9   single    0.970  0.020  1.090
 2E2  CAE  H10  single    0.970  0.020  1.090
 2E2  CAC  H11  single    0.970  0.020  1.090
 2E2  CAC  H12  single    0.970  0.020  1.090
 2E2  CAV  H15  single    0.930  0.020  1.080
 2E2  CAW  H16  single    0.930  0.020  1.080
 2E2  CAY  H18  single    0.930  0.020  1.080
 2E2  CAZ  H19  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
 2E2  N1   C2   N3   114.67  3.000
 2E2  N1   C2   O2   122.87  3.000
 2E2  N3   C2   O2   122.46  3.000
 2E2  H1   N3   C4   116.87  3.000
 2E2  H1   N3   C2   115.31  3.000
 2E2  C4   N3   C2   127.81  3.000
 2E2  C5   C4   O4   125.19  3.000
 2E2  C5   C4   N3   114.28  3.000
 2E2  O4   C4   N3   120.53  3.000
 2E2  C6   C5   CAR  122.85  3.000
 2E2  C6   C5   C4   118.17  3.000
 2E2  CAR  C5   C4   118.98  3.000
 2E2  H4   CAR  H3   107.80  3.000
 2E2  H4   CAR  H2   107.22  3.000
 2E2  H3   CAR  H2   107.89  3.000
 2E2  H4   CAR  C5   111.44  3.000
 2E2  H3   CAR  C5   110.84  3.000
 2E2  H2   CAR  C5   111.48  3.000
 2E2  H5   C6   N1   115.55  3.000
 2E2  H5   C6   C5   120.57  3.000
 2E2  N1   C6   C5   123.87  3.000
 2E2  CAJ  N1   C6   122.39  3.000
 2E2  CAJ  N1   C2   116.39  3.000
 2E2  C6   N1   C2   121.19  3.000
 2E2  H6   CAJ  CAI  111.73  3.000
 2E2  H6   CAJ  OAF  109.14  3.000
 2E2  CAI  CAJ  OAF  107.12  3.000
 2E2  H6   CAJ  N1   106.38  3.000
 2E2  OAF  CAJ  N1   109.16  3.000
 2E2  CAI  CAJ  N1   113.25  3.000
 2E2  CAE  OAF  CAJ  110.97  3.000
 2E2  H8   CAI  H7   107.74  3.000
 2E2  H8   CAI  CAG  111.99  3.000
 2E2  H7   CAI  CAG  112.96  3.000
 2E2  H8   CAI  CAJ  110.69  3.000
 2E2  H7   CAI  CAJ  111.99  3.000
 2E2  CAG  CAI  CAJ  101.46  3.000
 2E2  H9   CAG  CAE  109.02  3.000
 2E2  H9   CAG  OAH  105.34  3.000
 2E2  CAE  CAG  OAH  114.42  3.000
 2E2  H9   CAG  CAI  108.30  3.000
 2E2  CAE  CAG  CAI  101.37  3.000
 2E2  OAH  CAG  CAI  118.13  3.000
 2E2  CAB  OAH  CAG  119.43  3.000
 2E2  H10  CAE  CAC  110.01  3.000
 2E2  H10  CAE  CAG  112.25  3.000
 2E2  CAC  CAE  CAG  109.25  3.000
 2E2  H10  CAE  OAF  107.89  3.000
 2E2  CAC  CAE  OAF  112.47  3.000
 2E2  CAG  CAE  OAF  104.91  3.000
 2E2  H12  CAC  H11  107.35  3.000
 2E2  H12  CAC  OAD  107.75  3.000
 2E2  H11  CAC  OAD  111.63  3.000
 2E2  H12  CAC  CAE  111.41  3.000
 2E2  H11  CAC  CAE  110.68  3.000
 2E2  OAD  CAC  CAE  108.01  3.000
 2E2  CAB  OAD  CAC  114.40  3.000
 2E2  CAU  CAB  PAA  109.46  3.000
 2E2  PAA  CAB  OAD  106.51  3.000
 2E2  CAU  CAB  OAD  111.83  3.000
 2E2  PAA  CAB  OAH  105.88  3.000
 2E2  OAD  CAB  OAH  110.98  3.000
 2E2  CAU  CAB  OAH  111.86  3.000
 2E2  OBC  PAA  OBA  114.85  3.000
 2E2  OBC  PAA  OBB  114.42  3.000
 2E2  OBA  PAA  OBB  114.38  3.000
 2E2  OBC  PAA  CAB  103.54  3.000
 2E2  OBB  PAA  CAB  103.97  3.000
 2E2  OBA  PAA  CAB  103.69  3.000
 2E2  CAZ  CAU  CAV  117.67  3.000
 2E2  CAZ  CAU  CAB  120.95  3.000
 2E2  CAV  CAU  CAB  121.11  3.000
 2E2  H15  CAV  CAW  119.09  3.000
 2E2  H15  CAV  CAU  119.83  3.000
 2E2  CAW  CAV  CAU  121.08  3.000
 2E2  H16  CAW  CAX  119.40  3.000
 2E2  H16  CAW  CAV  119.35  3.000
 2E2  CAX  CAW  CAV  121.25  3.000
 2E2  CAY  CAX  CCA  121.11  3.000
 2E2  CAY  CAX  CAW  117.59  3.000
 2E2  CCA  CAX  CAW  121.30  3.000
 2E2  OCA  CCA  OCB  126.32  3.000
 2E2  OCB  CCA  CAX  116.79  3.000
 2E2  OCA  CCA  CAX  116.88  3.000
 2E2  H18  CAY  CAZ  119.45  3.000
 2E2  H18  CAY  CAX  119.28  3.000
 2E2  CAZ  CAY  CAX  121.28  3.000
 2E2  H19  CAZ  CAY  119.26  3.000
 2E2  H19  CAZ  CAU  119.65  3.000
 2E2  CAY  CAZ  CAU  121.09  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
 2E2  CONST_01  CAX  CAW  CAV  CAU    0.00   0.0  0
 2E2  CONST_02  CAX  CAY  CAZ  CAU    0.00   0.0  0
 2E2  CONST_03  CAY  CAX  CAW  CAV    0.00   0.0  0
 2E2  CONST_04  CAY  CAZ  CAU  CAV    0.00   0.0  0
 2E2  CONST_05  CAZ  CAY  CAX  CAW    0.00   0.0  0
 2E2  CONST_06  CAZ  CAU  CAV  CAW    0.00   0.0  0
 2E2  CONST_07  CAW  CAV  CAU  CAB  180.00   0.0  0
 2E2  CONST_08  CAY  CAZ  CAU  CAB  180.00   0.0  0
 2E2  CONST_09  C6   N1   C2   N3     0.00   0.0  0
 2E2  CONST_10  CAJ  N1   C2   N3   180.00   0.0  0
 2E2  CONST_11  N1   C2   N3   C4     0.00   0.0  0
 2E2  CONST_12  CCA  CAX  CAW  CAV  180.00   0.0  0
 2E2  CONST_13  CAZ  CAY  CAX  CCA  180.00   0.0  0
 2E2  CONST_14  C4   N3   C2   O2   180.00   0.0  0
 2E2  CONST_15  C6   N1   C2   O2   180.00   0.0  0
 2E2  CONST_16  CAJ  N1   C2   O2     0.00   0.0  0
 2E2  CONST_17  H15  CAV  CAU  CAB    0.00   0.0  0
 2E2  CONST_18  H19  CAZ  CAU  CAB    0.00   0.0  0
 2E2  CONST_19  H16  CAW  CAV  CAU  180.00   0.0  0
 2E2  CONST_20  H18  CAY  CAZ  CAU  180.00   0.0  0
 2E2  CONST_21  H1   N3   C2   N1   180.00   0.0  0
 2E2  Var_01    H11  CAC  OAD  CAB  -57.66  30.0  1
 2E2  Var_02    OCA  CCA  CAX  CAW   -0.98  30.0  3
 2E2  Var_03    H2   CAR  C5   C4    59.49  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
 2E2  chir_01  CAJ  N1   CAI  OAF  negativ
 2E2  chir_02  CAG  OAH  CAI  CAE  positiv
 2E2  chir_03  CAE  OAF  CAG  CAC  negativ
 2E2  chir_04  CAB  OAH  OAD  CAU  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
 2E2  plan-1  O2   0.020
 2E2  plan-1  C2   0.020
 2E2  plan-1  N3   0.020
 2E2  plan-1  C4   0.020
 2E2  plan-1  O4   0.020
 2E2  plan-1  C5   0.020
 2E2  plan-1  CAR  0.020
 2E2  plan-1  C6   0.020
 2E2  plan-1  N1   0.020
 2E2  plan-1  CAJ  0.020
 2E2  plan-1  H1   0.020
 2E2  plan-1  H5   0.020
 2E2  plan-2  CAB  0.020
 2E2  plan-2  CAU  0.020
 2E2  plan-2  CAV  0.020
 2E2  plan-2  CAW  0.020
 2E2  plan-2  CAX  0.020
 2E2  plan-2  CCA  0.020
 2E2  plan-2  CAY  0.020
 2E2  plan-2  CAZ  0.020
 2E2  plan-2  H15  0.020
 2E2  plan-2  H16  0.020
 2E2  plan-2  H18  0.020
 2E2  plan-2  H19  0.020
 2E2  plan-3  CAX  0.020
 2E2  plan-3  CCA  0.020
 2E2  plan-3  OCB  0.020
 2E2  plan-3  OCA  0.020

