# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 28 22:26:29 2021
#   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  50  31  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.491  -28.6738  1.3709  -27.8281
 2E2  C2   C  CR6   0   0.731  -27.9820  2.2252  -28.3502
 2E2  N3   N  NR16  0  -0.731  -27.8508  2.3343  -29.7077
 2E2  C4   C  CR6   0   0.554  -27.0747  3.2383  -30.4115
 2E2  O4   O  O     0  -0.461  -27.0526  3.2158  -31.6300
 2E2  C5   C  CR6   0  -0.177  -26.3321  4.1597  -29.5802
 2E2  CAR  C  CH3   0  -0.706  -25.4480  5.1662  -30.2382
 2E2  C6   C  CR16  0   0.066  -26.4675  4.0666  -28.2440
 2E2  N1   N  NR6   0  -0.563  -27.2714  3.1494  -27.6268
 2E2  CAJ  C  CH1   0   0.215  -27.4156  3.0639  -26.1581
 2E2  OAF  O  O2    0  -0.499  -27.0106  4.2673  -25.5823
 2E2  CAI  C  CH2   0  -0.530  -26.5508  1.9658  -25.5293
 2E2  CAG  C  CH1   0  -0.032  -25.3552  2.7291  -25.0020
 2E2  OAH  O  O2    0  -0.500  -24.4494  2.9110  -26.0864
 2E2  CAE  C  CH1   0   0.008  -25.9961  4.0459  -24.6032
 2E2  CAC  C  CH2   0  -0.230  -25.0185  5.1928  -24.5770
 2E2  OAD  O  O2    0  -0.484  -24.1722  5.1853  -25.7151
 2E2  CAB  C  CT    0   0.273  -23.5605  3.9821  -26.0390
 2E2  PAA  P  P     0   1.369  -22.1028  3.5491  -24.9366
 2E2  OBB  O  OH1   0  -0.738  -21.3152  4.9398  -24.8326
 2E2  OBA  O  O     0  -0.690  -21.3408  2.3811  -25.4338
 2E2  OBC  O  OH1   0  -0.740  -22.6891  3.4113  -23.4477
 2E2  CAU  C  CR6   0  -0.029  -22.9655  4.1491  -27.4240
 2E2  CAV  C  CR16  0  -0.241  -22.9184  3.0795  -28.3126
 2E2  CAW  C  CR16  0  -0.240  -22.3598  3.2424  -29.5676
 2E2  CAX  C  CR6   0  -0.086  -21.8250  4.4690  -29.9514
 2E2  CCA  C  C     0   0.531  -21.2458  4.5930  -31.3120
 2E2  OCB  O  OH1   0  -0.592  -20.7560  5.7992  -31.5595
 2E2  OCA  O  O     0  -0.436  -21.2220  3.6913  -32.1153
 2E2  CAY  C  CR16  0  -0.244  -21.8615  5.5355  -29.0575
 2E2  CAZ  C  CR16  0  -0.251  -22.4258  5.3750  -27.8029
 2E2  H1   H  HNR6  0   0.424  -28.3727  1.6573  -30.2508
 2E2  H2   H  HCH3  0   0.245  -24.8943  5.7425  -29.4991
 2E2  H3   H  HCH3  0   0.241  -24.7182  4.6823  -30.8877
 2E2  H4   H  HCH3  0   0.246  -26.0194  5.8633  -30.8531
 2E2  H5   H  HCR6  0   0.302  -25.9378  4.7438  -27.5928
 2E2  H6   H  HCH1  0   0.277  -28.4760  2.8971  -25.9662
 2E2  H7   H  HCH2  0   0.281  -27.0855  1.5231  -24.6880
 2E2  H8   H  HCH2  0   0.291  -26.2882  1.1633  -26.2166
 2E2  H9   H  HCH1  0   0.274  -24.8756  2.2271  -24.1598
 2E2  H10  H  HCH1  0   0.272  -26.4505  3.9481  -23.6108
 2E2  H11  H  HCH2  0   0.250  -24.4487  5.1509  -23.6452
 2E2  H12  H  HCH2  0   0.276  -25.5412  6.1488  -24.5947
 2E2  H13  H  HOH1  0   0.502  -20.4201  4.9177  -25.1958
 2E2  H14  H  HOH1  0   0.503  -22.5682  2.5333  -23.0603
 2E2  H15  H  HCR6  0   0.265  -23.3264  2.1174  -28.0404
 2E2  H16  H  HCR6  0   0.268  -22.3427  2.4057  -30.2526
 2E2  H17  H  HOH1  0   0.489  -20.3889  5.8294  -32.4556
 2E2  H18  H  HCR6  0   0.270  -21.4587  6.5016  -29.3274
 2E2  H19  H  HCR6  0   0.269  -22.4455  6.2207  -27.1308

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  double    1.208  0.020  1.208
 2E2  OCB  CCA  single    1.325  0.020  1.325
 2E2  O4   C4   double    1.219  0.020  1.219
 2E2  CCA  CAX  single    1.484  0.020  1.484
 2E2  C4   N3   single    1.384  0.020  1.384
 2E2  C4   C5   single    1.446  0.020  1.446
 2E2  CAR  C5   single    1.493  0.020  1.493
 2E2  CAX  CAW  aromatic  1.392  0.020  1.392
 2E2  CAX  CAY  aromatic  1.392  0.020  1.392
 2E2  N3   C2   single    1.368  0.020  1.368
 2E2  C5   C6   double    1.346  0.020  1.346
 2E2  CAW  CAV  aromatic  1.383  0.020  1.383
 2E2  CAY  CAZ  aromatic  1.385  0.020  1.385
 2E2  C2   O2   double    1.217  0.020  1.217
 2E2  C2   N1   single    1.372  0.020  1.372
 2E2  C6   N1   single    1.367  0.020  1.367
 2E2  CAV  CAU  aromatic  1.391  0.020  1.391
 2E2  CAZ  CAU  aromatic  1.392  0.020  1.392
 2E2  N1   CAJ  single    1.478  0.020  1.478
 2E2  CAU  CAB  single    1.517  0.020  1.517
 2E2  CAJ  CAI  single    1.533  0.020  1.533
 2E2  CAJ  OAF  single    1.394  0.020  1.394
 2E2  OAH  CAB  single    1.393  0.020  1.393
 2E2  OAH  CAG  single    1.425  0.020  1.425
 2E2  CAB  OAD  single    1.388  0.020  1.388
 2E2  CAB  PAA  single    1.878  0.020  1.878
 2E2  OAD  CAC  single    1.418  0.020  1.418
 2E2  CAI  CAG  single    1.513  0.020  1.513
 2E2  OAF  CAE  single    1.427  0.020  1.427
 2E2  OBA  PAA  double    1.481  0.020  1.481
 2E2  CAG  CAE  single    1.518  0.020  1.518
 2E2  CAC  CAE  single    1.507  0.020  1.507
 2E2  PAA  OBB  single    1.602  0.020  1.602
 2E2  PAA  OBC  single    1.606  0.020  1.606
 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  OBB  H13  single    0.850  0.020  0.980
 2E2  OBC  H14  single    0.850  0.020  0.980
 2E2  CAV  H15  single    0.930  0.020  1.080
 2E2  CAW  H16  single    0.930  0.020  1.080
 2E2  OCB  H17  single    0.850  0.020  0.980
 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   114.82  3.000
 2E2  N1   C2   O2   122.76  3.000
 2E2  N3   C2   O2   122.42  3.000
 2E2  H1   N3   C4   116.94  3.000
 2E2  H1   N3   C2   115.43  3.000
 2E2  C4   N3   C2   127.63  3.000
 2E2  C5   C4   O4   125.25  3.000
 2E2  C5   C4   N3   114.32  3.000
 2E2  O4   C4   N3   120.44  3.000
 2E2  C6   C5   CAR  122.94  3.000
 2E2  C6   C5   C4   118.35  3.000
 2E2  CAR  C5   C4   118.71  3.000
 2E2  H4   CAR  H3   107.35  3.000
 2E2  H4   CAR  H2   108.10  3.000
 2E2  H3   CAR  H2   107.39  3.000
 2E2  H4   CAR  C5   111.66  3.000
 2E2  H3   CAR  C5   111.10  3.000
 2E2  H2   CAR  C5   111.04  3.000
 2E2  H5   C6   N1   115.95  3.000
 2E2  H5   C6   C5   120.43  3.000
 2E2  N1   C6   C5   123.62  3.000
 2E2  CAJ  N1   C6   123.01  3.000
 2E2  CAJ  N1   C2   115.75  3.000
 2E2  C6   N1   C2   121.24  3.000
 2E2  H6   CAJ  CAI  111.52  3.000
 2E2  H6   CAJ  OAF  109.99  3.000
 2E2  CAI  CAJ  OAF  106.56  3.000
 2E2  H6   CAJ  N1   106.17  3.000
 2E2  OAF  CAJ  N1   109.39  3.000
 2E2  CAI  CAJ  N1   113.21  3.000
 2E2  CAE  OAF  CAJ  110.85  3.000
 2E2  H8   CAI  H7   107.82  3.000
 2E2  H8   CAI  CAG  113.65  3.000
 2E2  H7   CAI  CAG  108.86  3.000
 2E2  H8   CAI  CAJ  113.90  3.000
 2E2  H7   CAI  CAJ  109.31  3.000
 2E2  CAG  CAI  CAJ  103.14  3.000
 2E2  H9   CAG  CAE  112.45  3.000
 2E2  H9   CAG  OAH  111.51  3.000
 2E2  CAE  CAG  OAH  110.96  3.000
 2E2  H9   CAG  CAI  112.58  3.000
 2E2  CAE  CAG  CAI  101.28  3.000
 2E2  OAH  CAG  CAI  107.55  3.000
 2E2  CAB  OAH  CAG  118.57  3.000
 2E2  H10  CAE  CAC  108.73  3.000
 2E2  H10  CAE  CAG  109.61  3.000
 2E2  CAC  CAE  CAG  113.01  3.000
 2E2  H10  CAE  OAF  109.90  3.000
 2E2  CAC  CAE  OAF  110.79  3.000
 2E2  CAG  CAE  OAF  104.74  3.000
 2E2  H12  CAC  H11  107.31  3.000
 2E2  H12  CAC  OAD  106.13  3.000
 2E2  H11  CAC  OAD  111.89  3.000
 2E2  H12  CAC  CAE  110.86  3.000
 2E2  H11  CAC  CAE  108.89  3.000
 2E2  OAD  CAC  CAE  111.65  3.000
 2E2  CAB  OAD  CAC  117.05  3.000
 2E2  CAU  CAB  PAA  104.89  3.000
 2E2  PAA  CAB  OAD  113.88  3.000
 2E2  CAU  CAB  OAD  106.89  3.000
 2E2  PAA  CAB  OAH  109.76  3.000
 2E2  OAD  CAB  OAH  113.16  3.000
 2E2  CAU  CAB  OAH  107.70  3.000
 2E2  OBC  PAA  OBA  115.56  3.000
 2E2  OBC  PAA  OBB  101.18  3.000
 2E2  OBA  PAA  OBB  116.98  3.000
 2E2  OBC  PAA  CAB  106.29  3.000
 2E2  OBB  PAA  CAB  102.69  3.000
 2E2  OBA  PAA  CAB  112.59  3.000
 2E2  H13  OBB  PAA  114.29  3.000
 2E2  H14  OBC  PAA  113.80  3.000
 2E2  CAZ  CAU  CAV  119.35  3.000
 2E2  CAZ  CAU  CAB  119.84  3.000
 2E2  CAV  CAU  CAB  120.79  3.000
 2E2  H15  CAV  CAW  119.09  3.000
 2E2  H15  CAV  CAU  120.74  3.000
 2E2  CAW  CAV  CAU  120.17  3.000
 2E2  H16  CAW  CAX  120.07  3.000
 2E2  H16  CAW  CAV  119.34  3.000
 2E2  CAX  CAW  CAV  120.59  3.000
 2E2  CAY  CAX  CCA  122.34  3.000
 2E2  CAY  CAX  CAW  119.21  3.000
 2E2  CCA  CAX  CAW  118.45  3.000
 2E2  OCA  CCA  OCB  123.24  3.000
 2E2  OCB  CCA  CAX  113.05  3.000
 2E2  OCA  CCA  CAX  123.72  3.000
 2E2  H17  OCB  CCA  109.94  3.000
 2E2  H18  CAY  CAZ  118.79  3.000
 2E2  H18  CAY  CAX  120.97  3.000
 2E2  CAZ  CAY  CAX  120.24  3.000
 2E2  H19  CAZ  CAY  118.70  3.000
 2E2  H19  CAZ  CAU  120.86  3.000
 2E2  CAY  CAZ  CAU  120.43  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  CONST_22  H17  OCB  CCA  CAX   180.00   0.0  0
 2E2  Var_01    H11  CAC  OAD  CAB    73.58  30.0  1
 2E2  Var_02    OCA  CCA  CAX  CAW     0.73  30.0  3
 2E2  Var_03    H2   CAR  C5   C4   -175.72  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
 2E2  plan-3  H17  0.020

