# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 22:53:49 2021
#   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  49  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_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  -0.492  -4.1944  27.3299  24.8815
 2JW  C2   C  CR6    0   0.730  -3.5330  26.4958  25.4715
 2JW  N3   N  NR16   0  -0.731  -3.0139  25.3942  24.8466
 2JW  C4   C  CR6    0   0.553  -2.2533  24.3839  25.4084
 2JW  O4   O  O      0  -0.461  -1.8653  23.4509  24.7267
 2JW  C5   C  CR6    0  -0.176  -1.9836  24.5567  26.8180
 2JW  CAR  C  CH3    0  -0.704  -1.1597  23.5309  27.5230
 2JW  C6   C  CR16   0   0.060  -2.4952  25.6356  27.4396
 2JW  N1   N  NR6    0  -0.562  -3.2512  26.5842  26.8105
 2JW  CAJ  C  CR15   0   0.220  -3.7946  27.7745  27.5060
 2JW  OAF  O  O      0  -0.500  -3.1841  27.9009  28.7515
 2JW  CAI  C  CH2    0  -0.529  -5.2995  27.6790  27.7701
 2JW  CAG  C  CR15   0  -0.042  -5.3613  27.1773  29.1949
 2JW  OAH  O  O2     0  -0.501  -5.1915  25.7611  29.1500
 2JW  CAE  C  CR15   0   0.012  -4.1476  27.8541  29.8052
 2JW  CAC  C  CH2    0  -0.236  -3.6015  27.1194  31.0038
 2JW  OAD  O  O2     0  -0.487  -3.5359  25.7190  30.7743
 2JW  CAB  C  CT     0   0.273  -4.6841  25.1195  30.2773
 2JW  PAA  P  P      0   1.363  -6.0456  25.0443  31.5673
 2JW  OBA  O  OH1    0  -0.733  -7.1487  24.0810  30.9128
 2JW  OBC  O  O      0  -0.691  -6.5589  26.3604  32.0224
 2JW  OBB  O  OH1    0  -0.730  -5.3674  24.1079  32.6643
 2JW  CAU  C  CR6    0   0.007  -4.3117  23.7104  29.8648
 2JW  CAV  C  CR16   0  -0.248  -4.9474  23.1002  28.7883
 2JW  CAW  C  CR16   0  -0.256  -4.6154  21.8105  28.4141
 2JW  CAX  C  CR6    0   0.240  -3.6463  21.1310  29.1352
 2JW  NCA  N  N      1   0.328  -3.2899  19.7749  28.7452
 2JW  OCA  O  O     -1  -0.376  -3.8866  19.2743  27.8214
 2JW  OCB  O  O      0  -0.376  -2.4136  19.2179  29.3633
 2JW  CAY  C  CR16   0  -0.255  -3.0035  21.7164  30.2142
 2JW  CAZ  C  CR16   0  -0.249  -3.3421  23.0082  30.5748
 2JW  H1   H  HNR6   0   0.424  -3.2150  25.3180  23.8568
 2JW  H2   H  HCH3   0   0.244  -0.9947  23.8115  28.5616
 2JW  H3   H  HCH3   0   0.240  -1.6490  22.5562  27.5160
 2JW  H4   H  HCH3   0   0.246  -0.1850  23.4055  27.0496
 2JW  H5   H  HCR6   0   0.307  -2.3069  25.8027  28.4885
 2JW  H6   H  HCR5   0   0.278  -3.5451  28.6344  26.8829
 2JW  H7   H  HCH2   0   0.281  -5.7362  28.6775  27.7249
 2JW  H8   H  HCH2   0   0.291  -5.8375  27.0490  27.0648
 2JW  H9   H  HCR5   0   0.282  -6.2866  27.4509  29.7043
 2JW  H10  H  HCR5   0   0.272  -4.4118  28.8729  30.1083
 2JW  H11  H  HCH2   0   0.277  -2.5832  27.4374  31.2242
 2JW  H12  H  HCH2   0   0.254  -4.2185  27.3561  31.8740
 2JW  H13  H  HOH1   0   0.499  -7.8680  24.5448  30.4641
 2JW  H14  H  HOH1   0   0.504  -5.8132  24.1018  33.5235
 2JW  H15  H  HCR6   0   0.274  -5.7017  23.6233  28.2199
 2JW  H16  H  HCR6   0   0.299  -5.1136  21.3544  27.5715
 2JW  H17  H  HCR6   0   0.299  -2.2470  21.1865  30.7736
 2JW  H18  H  HCR6   0   0.276  -2.8323  23.4574  31.4142

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    1.219  0.020  1.219
 2JW  CAR  C5   single    1.493  0.020  1.493
 2JW  C4   C5   single    1.445  0.020  1.445
 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    1.366  0.020  1.366
 2JW  C2   N1   single    1.371  0.020  1.371
 2JW  C2   O2   double    1.217  0.020  1.217
 2JW  N1   CAJ  single    1.482  0.020  1.482
 2JW  CAJ  CAI  single    1.531  0.020  1.531
 2JW  CAJ  OAF  single    1.393  0.020  1.393
 2JW  CAI  CAG  single    1.512  0.020  1.512
 2JW  OAF  CAE  single    1.429  0.020  1.429
 2JW  CAG  OAH  single    1.427  0.020  1.427
 2JW  CAG  CAE  single    1.518  0.020  1.518
 2JW  OAH  CAB  single    1.393  0.020  1.393
 2JW  CAV  CAW  aromatic  1.383  0.020  1.383
 2JW  CAV  CAU  aromatic  1.391  0.020  1.391
 2JW  CAW  CAX  aromatic  1.386  0.020  1.386
 2JW  CAE  CAC  single    1.508  0.020  1.508
 2JW  OCA  NCA  single    1.208  0.020  1.208
 2JW  CAU  CAB  single    1.515  0.020  1.515
 2JW  CAU  CAZ  aromatic  1.392  0.020  1.392
 2JW  CAX  NCA  single    1.455  0.020  1.455
 2JW  CAX  CAY  aromatic  1.386  0.020  1.386
 2JW  CAB  OAD  single    1.387  0.020  1.387
 2JW  CAB  PAA  single    1.877  0.020  1.877
 2JW  NCA  OCB  double    1.208  0.020  1.208
 2JW  OAD  CAC  single    1.421  0.020  1.421
 2JW  CAZ  CAY  aromatic  1.383  0.020  1.383
 2JW  OBC  PAA  double    1.484  0.020  1.484
 2JW  OBA  PAA  single    1.604  0.020  1.604
 2JW  PAA  OBB  single    1.594  0.020  1.594
 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  OBA  H13  single    0.850  0.020  0.980
 2JW  OBB  H14  single    0.850  0.020  0.980
 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   114.82  3.000
 2JW  N1   C2   O2   122.75  3.000
 2JW  N3   C2   O2   122.43  3.000
 2JW  H1   N3   C4   116.81  3.000
 2JW  H1   N3   C2   115.56  3.000
 2JW  C4   N3   C2   127.63  3.000
 2JW  C5   C4   O4   125.28  3.000
 2JW  C5   C4   N3   114.28  3.000
 2JW  O4   C4   N3   120.44  3.000
 2JW  C6   C5   CAR  122.85  3.000
 2JW  C6   C5   C4   118.37  3.000
 2JW  CAR  C5   C4   118.78  3.000
 2JW  H4   CAR  H3   107.18  3.000
 2JW  H4   CAR  H2   107.96  3.000
 2JW  H3   CAR  H2   107.73  3.000
 2JW  H4   CAR  C5   111.55  3.000
 2JW  H3   CAR  C5   111.31  3.000
 2JW  H2   CAR  C5   110.93  3.000
 2JW  H5   C6   N1   115.90  3.000
 2JW  H5   C6   C5   120.45  3.000
 2JW  N1   C6   C5   123.64  3.000
 2JW  CAJ  N1   C6   122.98  3.000
 2JW  CAJ  N1   C2   115.77  3.000
 2JW  C6   N1   C2   121.24  3.000
 2JW  H6   CAJ  CAI  111.87  3.000
 2JW  H6   CAJ  OAF  109.82  3.000
 2JW  CAI  CAJ  OAF  106.40  3.000
 2JW  H6   CAJ  N1   106.33  3.000
 2JW  OAF  CAJ  N1   109.38  3.000
 2JW  CAI  CAJ  N1   113.04  3.000
 2JW  CAE  OAF  CAJ  111.16  3.000
 2JW  H8   CAI  H7   107.77  3.000
 2JW  H8   CAI  CAG  113.49  3.000
 2JW  H7   CAI  CAG  109.05  3.000
 2JW  H8   CAI  CAJ  114.23  3.000
 2JW  H7   CAI  CAJ  109.23  3.000
 2JW  CAG  CAI  CAJ  102.91  3.000
 2JW  H9   CAG  CAE  112.25  3.000
 2JW  H9   CAG  OAH  111.37  3.000
 2JW  CAE  CAG  OAH  111.10  3.000
 2JW  H9   CAG  CAI  113.04  3.000
 2JW  CAE  CAG  CAI  101.44  3.000
 2JW  OAH  CAG  CAI  107.15  3.000
 2JW  CAB  OAH  CAG  118.36  3.000
 2JW  H10  CAE  CAC  108.69  3.000
 2JW  H10  CAE  CAG  109.46  3.000
 2JW  CAC  CAE  CAG  113.07  3.000
 2JW  H10  CAE  OAF  109.66  3.000
 2JW  CAC  CAE  OAF  110.97  3.000
 2JW  CAG  CAE  OAF  104.91  3.000
 2JW  H12  CAC  H11  107.66  3.000
 2JW  H12  CAC  OAD  111.61  3.000
 2JW  H11  CAC  OAD  106.10  3.000
 2JW  H12  CAC  CAE  108.84  3.000
 2JW  H11  CAC  CAE  110.92  3.000
 2JW  OAD  CAC  CAE  111.63  3.000
 2JW  CAB  OAD  CAC  116.46  3.000
 2JW  CAU  CAB  PAA  109.16  3.000
 2JW  PAA  CAB  OAD  111.80  3.000
 2JW  CAU  CAB  OAD  107.22  3.000
 2JW  PAA  CAB  OAH  108.09  3.000
 2JW  OAD  CAB  OAH  113.11  3.000
 2JW  CAU  CAB  OAH  107.32  3.000
 2JW  OBB  PAA  OBC  117.20  3.000
 2JW  OBB  PAA  OBA  102.75  3.000
 2JW  OBC  PAA  OBA  114.82  3.000
 2JW  OBB  PAA  CAB  100.83  3.000
 2JW  OBA  PAA  CAB  104.03  3.000
 2JW  OBC  PAA  CAB  115.22  3.000
 2JW  H13  OBA  PAA  114.41  3.000
 2JW  H14  OBB  PAA  114.74  3.000
 2JW  CAZ  CAU  CAV  119.45  3.000
 2JW  CAZ  CAU  CAB  120.11  3.000
 2JW  CAV  CAU  CAB  120.43  3.000
 2JW  H15  CAV  CAW  118.49  3.000
 2JW  H15  CAV  CAU  120.93  3.000
 2JW  CAW  CAV  CAU  120.57  3.000
 2JW  H16  CAW  CAX  121.43  3.000
 2JW  H16  CAW  CAV  119.61  3.000
 2JW  CAX  CAW  CAV  118.96  3.000
 2JW  CAY  CAX  NCA  119.26  3.000
 2JW  CAY  CAX  CAW  121.49  3.000
 2JW  NCA  CAX  CAW  119.25  3.000
 2JW  OCB  NCA  OCA  123.93  3.000
 2JW  OCB  NCA  CAX  118.03  3.000
 2JW  OCA  NCA  CAX  118.04  3.000
 2JW  H17  CAY  CAZ  119.66  3.000
 2JW  H17  CAY  CAX  121.40  3.000
 2JW  CAZ  CAY  CAX  118.95  3.000
 2JW  H18  CAZ  CAY  118.39  3.000
 2JW  H18  CAZ  CAU  121.03  3.000
 2JW  CAY  CAZ  CAU  120.58  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     0.00   0.0  0
 2JW  CONST_23  OCB  NCA  CAX  CAW   180.00   0.0  0
 2JW  CONST_24  CAY  CAX  NCA  OCA   180.00   0.0  0
 2JW  CONST_25  CAY  CAX  NCA  OCB     0.00   0.0  0
 2JW  Var_01    H11  CAC  OAD  CAB  -170.66  30.0  1
 2JW  Var_02    H2   CAR  C5   C4    177.14  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

