# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 11:42:21 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-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](O)[C@H](CN3CCCC3)O2)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
 TXS  TXS  1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione  ligand  42  21  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TXS
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
 TXS  C21   C  CH2   0  -0.274  -4.6041  -1.1677   0.4888
 TXS  C22   C  CH2   0  -0.464  -5.3311  -1.8710  -0.6531
 TXS  C23   C  CH2   0  -0.468  -4.2317  -2.0958  -1.7120
 TXS  C24   C  CH2   0  -0.273  -2.9916  -1.4019  -1.1375
 TXS  N25   N  NT    0  -0.437  -3.5312  -0.4489  -0.1783
 TXS  C5'   C  CH2   0  -0.281  -2.5775   0.1175   0.7434
 TXS  C4'   C  CR15  0   0.035  -1.6213   1.1132   0.1201
 TXS  O4'   O  O     0  -0.487  -0.6105   0.4507  -0.6230
 TXS  C3'   C  CR15  0   0.029  -0.8525   1.9422   1.1462
 TXS  O3'   O  OH1   0  -0.663  -1.6515   3.0032   1.5896
 TXS  C2'   C  CH2   0  -0.577   0.3922   2.3506   0.3575
 TXS  C1'   C  CR15  0   0.181   0.5477   1.2469  -0.6963
 TXS  N1    N  NR6   0  -0.562   1.6995   0.3787  -0.4911
 TXS  C6    C  CR16  0   0.077   1.8532  -0.2504   0.7173
 TXS  C5    C  CR6   0  -0.185   2.8378  -1.1180   1.0006
 TXS  C5M   C  CH3   0  -0.707   2.9861  -1.7831   2.3292
 TXS  C4    C  CR6   0   0.561   3.7938  -1.4202  -0.0475
 TXS  O4    O  O     0  -0.451   4.7326  -2.1865   0.0641
 TXS  N3    N  NR16  0  -0.736   3.5610  -0.7605  -1.2407
 TXS  C2    C  CR6   0   0.733   2.5508   0.1159  -1.5408
 TXS  O2    O  O     0  -0.483   2.4410   0.6136  -2.6429
 TXS  H21   H  HCH2  0   0.232  -5.2424  -0.4820   1.0502
 TXS  H21A  H  HCH2  0   0.190  -4.2128  -1.9109   1.2047
 TXS  H22   H  HCH2  0   0.233  -5.7944  -2.8005  -0.3236
 TXS  H22A  H  HCH2  0   0.233  -6.1251  -1.2376  -1.0499
 TXS  H23   H  HCH2  0   0.233  -4.0398  -3.1529  -1.8937
 TXS  H23A  H  HCH2  0   0.234  -4.5173  -1.6566  -2.6679
 TXS  H24   H  HCH2  0   0.189  -2.3350  -2.1367  -0.6425
 TXS  H24A  H  HCH2  0   0.233  -2.3986  -0.9037  -1.9035
 TXS  H5'   H  HCH2  0   0.244  -3.1391   0.6615   1.5092
 TXS  H5'A  H  HCH2  0   0.195  -1.9920  -0.6578   1.2710
 TXS  H4'   H  HCR5  0   0.226  -2.1859   1.7982  -0.5298
 TXS  H3'   H  HCR5  0   0.219  -0.5691   1.2968   1.9902
 TXS  HO3'  H  HOH1  0   0.460  -1.2456   3.3871   2.3724
 TXS  H2'   H  HCH2  0   0.279   0.1989   3.3006  -0.1433
 TXS  H2'A  H  HCH2  0   0.282   1.2821   2.4782   0.9739
 TXS  H1'   H  HCR5  0   0.273   0.6648   1.6710  -1.6919
 TXS  H6    H  HCR6  0   0.307   1.1186   0.0014   1.4696
 TXS  H5M   H  HCH3  0   0.248   2.8992  -2.8670   2.2433
 TXS  H5MA  H  HCH3  0   0.248   3.9600  -1.5708   2.7717
 TXS  H5MB  H  HCH3  0   0.247   2.2210  -1.4387   3.0230
 TXS  HN3   H  HNR6  0   0.426   4.1994  -0.9593  -2.0015

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
 TXS  C21  C22   single  1.525  0.020  1.525
 TXS  C21  N25   single  1.454  0.020  1.454
 TXS  C22  C23   single  1.543  0.020  1.543
 TXS  C23  C24   single  1.533  0.020  1.533
 TXS  C24  N25   single  1.456  0.020  1.456
 TXS  N25  C5'   single  1.442  0.020  1.442
 TXS  C5'  C4'   single  1.515  0.020  1.515
 TXS  C4'  O4'   single  1.419  0.020  1.419
 TXS  C4'  C3'   single  1.527  0.020  1.527
 TXS  O4'  C1'   single  1.407  0.020  1.407
 TXS  C3'  O3'   single  1.400  0.020  1.400
 TXS  C3'  C2'   single  1.529  0.020  1.529
 TXS  C2'  C1'   single  1.534  0.020  1.534
 TXS  C1'  N1    single  1.457  0.020  1.457
 TXS  N1   C6    single  1.371  0.020  1.371
 TXS  N1   C2    single  1.377  0.020  1.377
 TXS  C6   C5    double  1.343  0.020  1.343
 TXS  C5   C5M   single  1.493  0.020  1.493
 TXS  C5   C4    single  1.450  0.020  1.450
 TXS  C4   O4    double  1.217  0.020  1.217
 TXS  C4   N3    single  1.383  0.020  1.383
 TXS  N3   C2    single  1.371  0.020  1.371
 TXS  C2   O2    double  1.214  0.020  1.214
 TXS  C21  H21   single  0.970  0.020  1.090
 TXS  C21  H21A  single  0.970  0.020  1.090
 TXS  C22  H22   single  0.970  0.020  1.090
 TXS  C22  H22A  single  0.970  0.020  1.090
 TXS  C23  H23   single  0.970  0.020  1.090
 TXS  C23  H23A  single  0.970  0.020  1.090
 TXS  C24  H24   single  0.970  0.020  1.090
 TXS  C24  H24A  single  0.970  0.020  1.090
 TXS  C5'  H5'   single  0.970  0.020  1.090
 TXS  C5'  H5'A  single  0.970  0.020  1.090
 TXS  C4'  H4'   single  0.970  0.020  1.090
 TXS  C3'  H3'   single  0.970  0.020  1.090
 TXS  O3'  HO3'  single  0.850  0.020  0.980
 TXS  C2'  H2'   single  0.970  0.020  1.090
 TXS  C2'  H2'A  single  0.970  0.020  1.090
 TXS  C1'  H1'   single  0.970  0.020  1.090
 TXS  C6   H6    single  0.930  0.020  1.080
 TXS  C5M  H5M   single  0.970  0.020  1.090
 TXS  C5M  H5MA  single  0.970  0.020  1.090
 TXS  C5M  H5MB  single  0.970  0.020  1.090
 TXS  N3   HN3   single  0.860  0.020  1.020

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
 TXS  H21A  C21  H21   107.25  3.000
 TXS  H21A  C21  N25   111.66  3.000
 TXS  H21   C21  N25   110.90  3.000
 TXS  H21A  C21  C22   110.13  3.000
 TXS  H21   C21  C22   113.31  3.000
 TXS  N25   C21  C22   103.66  3.000
 TXS  H22A  C22  H22   107.21  3.000
 TXS  H22A  C22  C23   110.72  3.000
 TXS  H22   C22  C23   112.72  3.000
 TXS  H22A  C22  C21   110.58  3.000
 TXS  H22   C22  C21   111.68  3.000
 TXS  C23   C22  C21   103.97  3.000
 TXS  H23A  C23  H23   106.90  3.000
 TXS  H23A  C23  C24   110.99  3.000
 TXS  H23   C23  C24   111.06  3.000
 TXS  H23A  C23  C22   110.88  3.000
 TXS  H23   C23  C22   112.41  3.000
 TXS  C24   C23  C22   104.68  3.000
 TXS  H24A  C24  H24   107.23  3.000
 TXS  H24A  C24  N25   111.45  3.000
 TXS  H24   C24  N25   111.17  3.000
 TXS  H24A  C24  C23   112.58  3.000
 TXS  H24   C24  C23   110.39  3.000
 TXS  N25   C24  C23   104.09  3.000
 TXS  C5'   N25  C24   115.67  3.000
 TXS  C5'   N25  C21   112.90  3.000
 TXS  C24   N25  C21   104.61  3.000
 TXS  H5'A  C5'  H5'   106.64  3.000
 TXS  H5'A  C5'  C4'   108.85  3.000
 TXS  H5'   C5'  C4'   106.56  3.000
 TXS  H5'A  C5'  N25   112.32  3.000
 TXS  H5'   C5'  N25   107.64  3.000
 TXS  C4'   C5'  N25   114.38  3.000
 TXS  H4'   C4'  C3'   108.51  3.000
 TXS  H4'   C4'  O4'   110.30  3.000
 TXS  C3'   C4'  O4'   104.29  3.000
 TXS  H4'   C4'  C5'   109.17  3.000
 TXS  C3'   C4'  C5'   113.47  3.000
 TXS  O4'   C4'  C5'   111.00  3.000
 TXS  C1'   O4'  C4'   110.45  3.000
 TXS  H3'   C3'  C2'   110.05  3.000
 TXS  H3'   C3'  O3'   110.41  3.000
 TXS  C2'   C3'  O3'   115.18  3.000
 TXS  H3'   C3'  C4'   109.08  3.000
 TXS  C2'   C3'  C4'   102.02  3.000
 TXS  O3'   C3'  C4'   109.69  3.000
 TXS  HO3'  O3'  C3'   108.63  3.000
 TXS  H2'A  C2'  H2'   107.59  3.000
 TXS  H2'A  C2'  C1'   112.95  3.000
 TXS  H2'   C2'  C1'   109.22  3.000
 TXS  H2'A  C2'  C3'   113.84  3.000
 TXS  H2'   C2'  C3'   108.97  3.000
 TXS  C1'   C2'  C3'   104.16  3.000
 TXS  H1'   C1'  N1    106.02  3.000
 TXS  H1'   C1'  C2'   111.03  3.000
 TXS  N1    C1'  C2'   114.34  3.000
 TXS  H1'   C1'  O4'   110.89  3.000
 TXS  N1    C1'  O4'   107.83  3.000
 TXS  C2'   C1'  O4'   106.73  3.000
 TXS  C2    N1   C6    121.00  3.000
 TXS  C2    N1   C1'   119.68  3.000
 TXS  C6    N1   C1'   119.09  3.000
 TXS  H6    C6   C5    120.13  3.000
 TXS  H6    C6   N1    115.48  3.000
 TXS  C5    C6   N1    124.39  3.000
 TXS  C4    C5   C5M   118.99  3.000
 TXS  C4    C5   C6    117.75  3.000
 TXS  C5M   C5   C6    123.26  3.000
 TXS  H5MB  C5M  H5MA  107.90  3.000
 TXS  H5MB  C5M  H5M   107.97  3.000
 TXS  H5MA  C5M  H5M   107.25  3.000
 TXS  H5MB  C5M  C5    110.87  3.000
 TXS  H5MA  C5M  C5    111.29  3.000
 TXS  H5M   C5M  C5    111.39  3.000
 TXS  N3    C4   O4    120.62  3.000
 TXS  N3    C4   C5    114.40  3.000
 TXS  O4    C4   C5    124.99  3.000
 TXS  HN3   N3   C2    115.18  3.000
 TXS  HN3   N3   C4    116.64  3.000
 TXS  C2    N3   C4    128.16  3.000
 TXS  O2    C2   N3    121.84  3.000
 TXS  O2    C2   N1    123.90  3.000
 TXS  N3    C2   N1    114.26  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
 TXS  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 TXS  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 TXS  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 TXS  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 TXS  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 TXS  CONST_06  O2   C2   N1   C6    180.00   0.0  0
 TXS  CONST_07  O2   C2   N3   C4    180.00   0.0  0
 TXS  CONST_08  C2   N3   C4   O4    180.00   0.0  0
 TXS  CONST_09  HN3  N3   C2   N1    180.00   0.0  0
 TXS  Var_01    C24  C23  C22  C21    -4.44  30.0  1
 TXS  Var_02    C23  C24  N25  C21    40.80  30.0  1
 TXS  Var_03    C24  N25  C21  C22   -43.86  30.0  1
 TXS  Var_04    N25  C24  C23  C22   -21.44  30.0  1
 TXS  Var_05    N25  C21  C22  C23    28.86  30.0  1
 TXS  Var_06    C4'  C5'  N25  C21  -167.54  30.0  3
 TXS  Var_07    H5M  C5M  C5   C6    118.13  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
 TXS  chir_01  C4'  C5'  O4'  C3'  positiv
 TXS  chir_02  C3'  O3'  C4'  C2'  negativ
 TXS  chir_03  C1'  O4'  N1   C2'  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
 TXS  plan-1  C1'  0.020
 TXS  plan-1  N1   0.020
 TXS  plan-1  C6   0.020
 TXS  plan-1  C5   0.020
 TXS  plan-1  C5M  0.020
 TXS  plan-1  C4   0.020
 TXS  plan-1  O4   0.020
 TXS  plan-1  N3   0.020
 TXS  plan-1  C2   0.020
 TXS  plan-1  O2   0.020
 TXS  plan-1  H6   0.020
 TXS  plan-1  HN3  0.020

