# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat May 23 08:47:36 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 1-{2-deoxy-3,5-O-[(4-nitrophenyl)(phosphono)methylidene]-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)[N+]([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
 2JW  2JW  1-{2-deoxy-3,5-O-[(4-nitrophenyl)(phosphono)methylidene]-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_2JW
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
 2JW  O2   O  O      0  -0.487  -2.9511   1.8205   2.8059
 2JW  C2   C  CR6    0   0.737  -3.1480   1.8844   1.6079
 2JW  N3   N  NR16   0  -0.733  -4.3578   1.5802   1.0438
 2JW  C4   C  CR6    0   0.558  -4.6934   1.5863  -0.2989
 2JW  O4   O  O      0  -0.457  -5.8149   1.2743  -0.6578
 2JW  C5   C  CR6    0  -0.176  -3.6177   1.9901  -1.1793
 2JW  CAR  C  CH3    0  -0.707  -3.8692   2.0512  -2.6503
 2JW  C6   C  CR16   0   0.046  -2.4310   2.3073  -0.6285
 2JW  N1   N  NR6    0  -0.569  -2.1778   2.2631   0.7140
 2JW  CAJ  C  CR15   0   0.233  -0.8509   2.5799   1.2817
 2JW  OAF  O  O      0  -0.498  -0.0914   3.2667   0.3240
 2JW  CAI  C  CH2    0  -0.566  -0.0564   1.3382   1.6802
 2JW  CAG  C  CR15   0  -0.001   1.3764   1.7714   1.3556
 2JW  OAH  O  O2     0  -0.502   2.3492   0.7705   1.2065
 2JW  CAE  C  CR15   0  -0.022   1.1574   2.6249   0.1089
 2JW  CAC  C  CH2    0  -0.224   1.1458   1.7276  -1.1171
 2JW  OAD  O  O2     0  -0.493   2.3293   0.9609  -1.1111
 2JW  CAB  C  CT     0   0.163   2.4448   0.0853  -0.0238
 2JW  PAA  P  P      0   1.184   4.2200  -0.6522  -0.1002
 2JW  OBA  O  OP    -1  -0.872   4.2838  -1.5419   1.1366
 2JW  OBC  O  O      0  -0.873   4.2240  -1.3933  -1.4337
 2JW  OBB  O  OP    -1  -0.879   5.1172   0.5811  -0.0504
 2JW  CAU  C  CR6    0   0.043   1.4775  -1.0578  -0.1136
 2JW  CAV  C  CR16   0  -0.259   1.0526  -1.5369  -1.3541
 2JW  CAW  C  CR16   0  -0.267   0.2351  -2.6461  -1.4525
 2JW  CAX  C  CR6    0   0.227  -0.1417  -3.3124  -0.2934
 2JW  NCA  N  N      1   0.326  -0.9927  -4.4774  -0.3869
 2JW  OCA  O  O     -1  -0.392  -1.2976  -5.0501   0.6359
 2JW  OCB  O  O      0  -0.392  -1.3636  -4.8320  -1.4842
 2JW  CAY  C  CR16   0  -0.266   0.2895  -2.8768   0.9540
 2JW  CAZ  C  CR16   0  -0.261   1.1007  -1.7620   1.0319
 2JW  H1   H  HNR6   0   0.425  -5.0816   1.3010   1.6951
 2JW  H2   H  HCH3   0   0.247  -4.1645   1.0782  -3.0453
 2JW  H3   H  HCH3   0   0.246  -4.6687   2.7535  -2.8903
 2JW  H4   H  HCH3   0   0.246  -2.9743   2.3690  -3.1833
 2JW  H5   H  HCR6   0   0.311  -1.6094   2.6358  -1.2465
 2JW  H6   H  HCR5   0   0.273  -1.0278   3.2377   2.1353
 2JW  H7   H  HCH2   0   0.284  -0.1963   1.0830   2.7284
 2JW  H8   H  HCH2   0   0.266  -0.3699   0.4787   1.0852
 2JW  H9   H  HCR5   0   0.267   1.7397   2.4073   2.1683
 2JW  H10  H  HCR5   0   0.266   1.9186   3.3999  -0.0024
 2JW  H11  H  HCH2   0   0.202   0.2505   1.0879  -1.1243
 2JW  H12  H  HCH2   0   0.262   1.1341   2.3122  -2.0388
 2JW  H15  H  HCR6   0   0.258   1.3542  -1.0337  -2.2610
 2JW  H16  H  HCR6   0   0.286  -0.0919  -2.9862  -2.4244
 2JW  H17  H  HCR6   0   0.285   0.0045  -3.3967   1.8572
 2JW  H18  H  HCR6   0   0.257   1.4335  -1.4265   2.0028

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
 2JW  O4   C4   double    1.218  0.020  1.218
 2JW  CAR  C5   single    1.494  0.020  1.494
 2JW  C4   C5   single    1.447  0.020  1.447
 2JW  C4   N3   single    1.384  0.020  1.384
 2JW  C5   C6   double    1.346  0.020  1.346
 2JW  N3   C2   single    1.369  0.020  1.369
 2JW  C6   N1   single    1.367  0.020  1.367
 2JW  C2   N1   single    1.373  0.020  1.373
 2JW  C2   O2   double    1.216  0.020  1.216
 2JW  N1   CAJ  single    1.478  0.020  1.478
 2JW  CAJ  CAI  single    1.527  0.020  1.527
 2JW  CAJ  OAF  single    1.402  0.020  1.402
 2JW  CAI  CAG  single    1.532  0.020  1.532
 2JW  OAF  CAE  single    1.420  0.020  1.420
 2JW  CAG  OAH  single    1.404  0.020  1.404
 2JW  CAG  CAE  single    1.527  0.020  1.527
 2JW  OAH  CAB  single    1.411  0.020  1.411
 2JW  CAV  CAW  aromatic  1.381  0.020  1.381
 2JW  CAV  CAU  aromatic  1.396  0.020  1.396
 2JW  CAW  CAX  aromatic  1.389  0.020  1.389
 2JW  CAE  CAC  single    1.519  0.020  1.519
 2JW  OCA  NCA  single    1.211  0.020  1.211
 2JW  CAU  CAB  single    1.500  0.020  1.500
 2JW  CAU  CAZ  aromatic  1.396  0.020  1.396
 2JW  CAX  NCA  single    1.446  0.020  1.446
 2JW  CAX  CAY  aromatic  1.390  0.020  1.390
 2JW  CAB  OAD  single    1.401  0.020  1.401
 2JW  CAB  PAA  single    1.924  0.020  1.924
 2JW  NCA  OCB  double    1.211  0.020  1.211
 2JW  OAD  CAC  single    1.410  0.020  1.410
 2JW  CAZ  CAY  aromatic  1.381  0.020  1.381
 2JW  OBC  PAA  deloc     1.526  0.020  1.526
 2JW  OBA  PAA  deloc     1.525  0.020  1.525
 2JW  PAA  OBB  deloc     1.526  0.020  1.526
 2JW  N3   H1   single    0.860  0.020  1.020
 2JW  CAR  H2   single    0.970  0.020  1.090
 2JW  CAR  H3   single    0.970  0.020  1.090
 2JW  CAR  H4   single    0.970  0.020  1.090
 2JW  C6   H5   single    0.930  0.020  1.080
 2JW  CAJ  H6   single    0.970  0.020  1.090
 2JW  CAI  H7   single    0.970  0.020  1.090
 2JW  CAI  H8   single    0.970  0.020  1.090
 2JW  CAG  H9   single    0.970  0.020  1.090
 2JW  CAE  H10  single    0.970  0.020  1.090
 2JW  CAC  H11  single    0.970  0.020  1.090
 2JW  CAC  H12  single    0.970  0.020  1.090
 2JW  CAV  H15  single    0.930  0.020  1.080
 2JW  CAW  H16  single    0.930  0.020  1.080
 2JW  CAY  H17  single    0.930  0.020  1.080
 2JW  CAZ  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
 2JW  N1   C2   N3   114.68  3.000
 2JW  N1   C2   O2   122.81  3.000
 2JW  N3   C2   O2   122.51  3.000
 2JW  H1   N3   C4   116.86  3.000
 2JW  H1   N3   C2   115.32  3.000
 2JW  C4   N3   C2   127.81  3.000
 2JW  C5   C4   O4   125.20  3.000
 2JW  C5   C4   N3   114.28  3.000
 2JW  O4   C4   N3   120.53  3.000
 2JW  C6   C5   CAR  122.80  3.000
 2JW  C6   C5   C4   118.16  3.000
 2JW  CAR  C5   C4   119.03  3.000
 2JW  H4   CAR  H3   107.86  3.000
 2JW  H4   CAR  H2   107.79  3.000
 2JW  H3   CAR  H2   107.23  3.000
 2JW  H4   CAR  C5   110.83  3.000
 2JW  H3   CAR  C5   111.50  3.000
 2JW  H2   CAR  C5   111.45  3.000
 2JW  H5   C6   N1   115.55  3.000
 2JW  H5   C6   C5   120.56  3.000
 2JW  N1   C6   C5   123.88  3.000
 2JW  CAJ  N1   C6   122.46  3.000
 2JW  CAJ  N1   C2   116.34  3.000
 2JW  C6   N1   C2   121.18  3.000
 2JW  H6   CAJ  CAI  111.72  3.000
 2JW  H6   CAJ  OAF  109.06  3.000
 2JW  CAI  CAJ  OAF  107.14  3.000
 2JW  H6   CAJ  N1   106.50  3.000
 2JW  OAF  CAJ  N1   109.21  3.000
 2JW  CAI  CAJ  N1   113.15  3.000
 2JW  CAE  OAF  CAJ  111.00  3.000
 2JW  H8   CAI  H7   107.68  3.000
 2JW  H8   CAI  CAG  112.08  3.000
 2JW  H7   CAI  CAG  113.01  3.000
 2JW  H8   CAI  CAJ  110.40  3.000
 2JW  H7   CAI  CAJ  112.04  3.000
 2JW  CAG  CAI  CAJ  101.62  3.000
 2JW  H9   CAG  CAE  109.23  3.000
 2JW  H9   CAG  OAH  105.26  3.000
 2JW  CAE  CAG  OAH  114.29  3.000
 2JW  H9   CAG  CAI  108.52  3.000
 2JW  CAE  CAG  CAI  101.36  3.000
 2JW  OAH  CAG  CAI  117.98  3.000
 2JW  CAB  OAH  CAG  119.05  3.000
 2JW  H10  CAE  CAC  110.01  3.000
 2JW  H10  CAE  CAG  112.34  3.000
 2JW  CAC  CAE  CAG  109.26  3.000
 2JW  H10  CAE  OAF  107.91  3.000
 2JW  CAC  CAE  OAF  112.48  3.000
 2JW  CAG  CAE  OAF  104.77  3.000
 2JW  H12  CAC  H11  107.28  3.000
 2JW  H12  CAC  OAD  107.68  3.000
 2JW  H11  CAC  OAD  111.52  3.000
 2JW  H12  CAC  CAE  111.42  3.000
 2JW  H11  CAC  CAE  110.78  3.000
 2JW  OAD  CAC  CAE  108.13  3.000
 2JW  CAB  OAD  CAC  114.35  3.000
 2JW  CAU  CAB  PAA  107.49  3.000
 2JW  PAA  CAB  OAD  106.55  3.000
 2JW  CAU  CAB  OAD  112.12  3.000
 2JW  PAA  CAB  OAH  106.45  3.000
 2JW  OAD  CAB  OAH  111.56  3.000
 2JW  CAU  CAB  OAH  112.24  3.000
 2JW  OBB  PAA  OBC  114.81  3.000
 2JW  OBB  PAA  OBA  114.87  3.000
 2JW  OBC  PAA  OBA  115.18  3.000
 2JW  OBB  PAA  CAB  103.38  3.000
 2JW  OBA  PAA  CAB  103.30  3.000
 2JW  OBC  PAA  CAB  102.90  3.000
 2JW  CAZ  CAU  CAV  118.28  3.000
 2JW  CAZ  CAU  CAB  120.60  3.000
 2JW  CAV  CAU  CAB  120.73  3.000
 2JW  H15  CAV  CAW  118.65  3.000
 2JW  H15  CAV  CAU  120.08  3.000
 2JW  CAW  CAV  CAU  121.26  3.000
 2JW  H16  CAW  CAX  121.17  3.000
 2JW  H16  CAW  CAV  119.73  3.000
 2JW  CAX  CAW  CAV  119.09  3.000
 2JW  CAY  CAX  NCA  119.55  3.000
 2JW  CAY  CAX  CAW  120.96  3.000
 2JW  NCA  CAX  CAW  119.49  3.000
 2JW  OCB  NCA  OCA  123.32  3.000
 2JW  OCB  NCA  CAX  118.34  3.000
 2JW  OCA  NCA  CAX  118.33  3.000
 2JW  H17  CAY  CAZ  119.75  3.000
 2JW  H17  CAY  CAX  121.18  3.000
 2JW  CAZ  CAY  CAX  119.07  3.000
 2JW  H18  CAZ  CAY  118.86  3.000
 2JW  H18  CAZ  CAU  119.85  3.000
 2JW  CAY  CAZ  CAU  121.29  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
 2JW  CONST_01  CAX  CAW  CAV  CAU    0.00   0.0  0
 2JW  CONST_02  CAX  CAY  CAZ  CAU    0.00   0.0  0
 2JW  CONST_03  CAY  CAX  CAW  CAV    0.00   0.0  0
 2JW  CONST_04  CAY  CAZ  CAU  CAV    0.00   0.0  0
 2JW  CONST_05  CAZ  CAU  CAV  CAW    0.00   0.0  0
 2JW  CONST_06  CAZ  CAY  CAX  CAW    0.00   0.0  0
 2JW  CONST_07  CAW  CAV  CAU  CAB  180.00   0.0  0
 2JW  CONST_08  CAY  CAZ  CAU  CAB  180.00   0.0  0
 2JW  CONST_09  C6   N1   C2   N3     0.00   0.0  0
 2JW  CONST_10  CAJ  N1   C2   N3   180.00   0.0  0
 2JW  CONST_11  N1   C2   N3   C4     0.00   0.0  0
 2JW  CONST_12  NCA  CAX  CAW  CAV  180.00   0.0  0
 2JW  CONST_13  CAZ  CAY  CAX  NCA  180.00   0.0  0
 2JW  CONST_14  C4   N3   C2   O2   180.00   0.0  0
 2JW  CONST_15  C6   N1   C2   O2   180.00   0.0  0
 2JW  CONST_16  CAJ  N1   C2   O2     0.00   0.0  0
 2JW  CONST_17  H15  CAV  CAU  CAB    0.00   0.0  0
 2JW  CONST_18  H18  CAZ  CAU  CAB    0.00   0.0  0
 2JW  CONST_19  H16  CAW  CAV  CAU  180.00   0.0  0
 2JW  CONST_20  H17  CAY  CAZ  CAU  180.00   0.0  0
 2JW  CONST_21  H1   N3   C2   N1   180.00   0.0  0
 2JW  CONST_22  OCA  NCA  CAX  CAW  180.00   0.0  0
 2JW  CONST_23  OCB  NCA  CAX  CAW    0.00   0.0  0
 2JW  CONST_24  CAY  CAX  NCA  OCA    0.00   0.0  0
 2JW  CONST_25  CAY  CAX  NCA  OCB  180.00   0.0  0
 2JW  Var_01    H11  CAC  OAD  CAB  -58.53  30.0  1
 2JW  Var_02    H2   CAR  C5   C4   -59.97  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
 2JW  chir_01  CAJ  N1   CAI  OAF  negativ
 2JW  chir_02  CAG  OAH  CAE  CAI  negativ
 2JW  chir_03  CAE  OAF  CAG  CAC  negativ
 2JW  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
 2JW  plan-1  O2   0.020
 2JW  plan-1  C2   0.020
 2JW  plan-1  N3   0.020
 2JW  plan-1  C4   0.020
 2JW  plan-1  O4   0.020
 2JW  plan-1  C5   0.020
 2JW  plan-1  CAR  0.020
 2JW  plan-1  C6   0.020
 2JW  plan-1  N1   0.020
 2JW  plan-1  CAJ  0.020
 2JW  plan-1  H1   0.020
 2JW  plan-1  H5   0.020
 2JW  plan-2  CAB  0.020
 2JW  plan-2  CAU  0.020
 2JW  plan-2  CAV  0.020
 2JW  plan-2  CAW  0.020
 2JW  plan-2  CAX  0.020
 2JW  plan-2  NCA  0.020
 2JW  plan-2  CAY  0.020
 2JW  plan-2  CAZ  0.020
 2JW  plan-2  H15  0.020
 2JW  plan-2  H16  0.020
 2JW  plan-2  H17  0.020
 2JW  plan-2  H18  0.020
 2JW  plan-3  CAX  0.020
 2JW  plan-3  NCA  0.020
 2JW  plan-3  OCA  0.020
 2JW  plan-3  OCB  0.020

