# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 20:08:11 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 3-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-7-[(3-chlorophenyl)methyl]-6-oxidanylidene-1~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(c[n+](Cc3cccc(Cl)c3)c2C(=O)N1)[C@@H]4O[C@H](CNC5=C(O)C(=O)C5=O)[C@@H](O)[C@H]4O
#
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
 5NX  5NX  3-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-7-[(3-chlorophenyl)methyl]-6-oxidanylidene-1~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione  ligand  55  35  .  2022-07-23  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_5NX
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
 5NX  C4   C   CR56  0   0.526   1.6257  -1.9445  -0.0304
 5NX  C5   C   CR56  0   0.076   2.3031  -0.9977   0.7024
 5NX  C6   C   CR6   0   0.584   3.7237  -1.0849   0.8225
 5NX  C8   C   CR15  0   0.271   0.1710  -0.5693   0.8809
 5NX  N1   N   NR16  0  -0.732   4.1975  -2.1585   0.0730
 5NX  N3   N   N     0  -0.505   2.1295  -2.9583  -0.7194
 5NX  CAL  C   CR16  0  -0.252   3.0479   2.5909   0.6767
 5NX  CAU  C   CR6   0  -0.020   3.1837   3.6925  -0.1525
 5NX  CL   CL  CL    0  -0.123   4.7559   4.1071  -0.7511
 5NX  CAJ  C   CR16  0  -0.213   2.0933   4.4715  -0.5067
 5NX  CAI  C   CR16  0  -0.249   0.8430   4.1375  -0.0079
 5NX  CAK  C   CR16  0  -0.298   0.6896   3.0398   0.8257
 5NX  CAV  C   CR6   0   0.130   1.7891   2.2594   1.1648
 5NX  N7   N   NR5   1  -0.470   1.3603  -0.1575   1.2592
 5NX  O6   O   O     0  -0.446   4.4748  -0.3778   1.4654
 5NX  C2   C   CR6   0   0.731   3.4430  -3.0355  -0.6544
 5NX  N9   N   NR5   0  -0.556   0.2904  -1.6485   0.0972
 5NX  CBG  C   CH1   0   0.216  -0.7996  -2.4309  -0.4568
 5NX  OAS  O   O2    0  -0.493  -1.7679  -1.5656  -0.9583
 5NX  CBE  C   CH1   0  -0.026  -1.5219  -3.2787   0.5837
 5NX  OAG  O   OH1   0  -0.647  -0.7838  -4.4223   0.8726
 5NX  CBD  C   CH1   0  -0.052  -2.8512  -3.5215  -0.1378
 5NX  OAF  O   OH1   0  -0.663  -2.7271  -4.5376  -1.0958
 5NX  CBF  C   CH1   0   0.005  -3.0586  -2.1906  -0.8642
 5NX  CAN  C   CH2   0  -0.323  -4.0259  -1.2630  -0.1490
 5NX  NAQ  N   NH1   0  -0.634  -4.2671  -0.0519  -0.9030
 5NX  CAX  C   C     0   0.254  -3.7796   1.1332  -0.6047
 5NX  CBA  C   C     0   0.265  -2.9495   1.6773   0.4843
 5NX  OAD  O   O     0  -0.431  -2.3976   1.2232   1.4619
 5NX  CAZ  C   C     0   0.235  -3.0725   3.0379  -0.1559
 5NX  OAC  O   O     0  -0.427  -2.6754   4.1558   0.0846
 5NX  CAW  C   C     0   0.189  -3.8769   2.3982  -1.1816
 5NX  OAE  O   OH1   0  -0.556  -4.4950   2.7798  -2.2698
 5NX  H1   H   HCR5  0   0.371  -0.7625  -0.1027   1.1607
 5NX  H2   H   HNR6  0   0.441   5.2013  -2.2936   0.1003
 5NX  H3   H   HNH2  0   0.428   5.0784  -4.1148  -1.2664
 5NX  H4   H   HNH2  0   0.428   3.5470  -4.6760  -1.8232
 5NX  H6   H   HCR6  0   0.285   2.2164   5.3282  -1.1551
 5NX  H7   H   HCR6  0   0.272  -0.0157   4.7404  -0.2689
 5NX  H8   H   HCR6  0   0.263  -0.2884   2.7987   1.2221
 5NX  H11  H   HCH1  0   0.283  -0.3484  -3.0602  -1.2313
 5NX  H12  H   HCH1  0   0.258  -1.7074  -2.6684   1.4780
 5NX  H13  H   HOH1  0   0.474  -1.0494  -4.7611   1.7334
 5NX  H14  H   HCH1  0   0.262  -3.6642  -3.7260   0.5708
 5NX  H15  H   HOH1  0   0.453  -2.3022  -5.2954  -0.6770
 5NX  H16  H   HCH1  0   0.275  -3.4320  -2.3790  -1.8758
 5NX  H17  H   HCH2  0   0.288  -4.9760  -1.7844  -0.0247
 5NX  H18  H   HCH2  0   0.274  -3.6675  -1.0054   0.8473
 5NX  H19  H   HNH1  0   0.421  -4.8339  -0.1365  -1.7345
 5NX  H20  H   HOH1  0   0.505  -4.3838   3.7286  -2.4203
 5NX  N2   N   NH2   0  -0.821   4.0811  -3.9939  -1.3116
 5NX  CAO  C   CH2   0  -0.459   1.6069   1.0544   2.0484
 5NX  H5   H   HCR6  0   0.286   3.9140   2.0028   0.9478
 5NX  H9   H   HCH2  0   0.324   2.4780   0.8699   2.6715
 5NX  H10  H   HCH2  0   0.323   0.7518   1.1822   2.7098

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
 5NX  OAC  CAZ  double    1.211  0.020  1.211
 5NX  CAK  CAI  aromatic  1.387  0.020  1.387
 5NX  CAK  CAV  aromatic  1.390  0.020  1.390
 5NX  CAI  CAJ  aromatic  1.387  0.020  1.387
 5NX  CAZ  CBA  single    1.509  0.020  1.509
 5NX  CAZ  CAW  single    1.452  0.020  1.452
 5NX  OAD  CBA  double    1.211  0.020  1.211
 5NX  CAO  CAV  single    1.505  0.020  1.505
 5NX  CAO  N7   single    1.467  0.020  1.467
 5NX  CBA  CAX  single    1.473  0.020  1.473
 5NX  CAV  CAL  aromatic  1.390  0.020  1.390
 5NX  CAJ  CAU  aromatic  1.386  0.020  1.386
 5NX  CAW  OAE  single    1.308  0.020  1.308
 5NX  CAW  CAX  double    1.394  0.020  1.394
 5NX  O6   C6   double    1.215  0.020  1.215
 5NX  CAX  NAQ  single    1.316  0.020  1.316
 5NX  N7   C8   aromatic  1.314  0.020  1.314
 5NX  N7   C5   aromatic  1.380  0.020  1.380
 5NX  CAL  CAU  aromatic  1.385  0.020  1.385
 5NX  CAU  CL   single    1.733  0.020  1.733
 5NX  C6   C5   single    1.428  0.020  1.428
 5NX  C6   N1   single    1.392  0.020  1.392
 5NX  C8   N9   aromatic  1.339  0.020  1.339
 5NX  NAQ  CAN  single    1.447  0.020  1.447
 5NX  C5   C4   aromatic  1.376  0.020  1.376
 5NX  N1   C2   single    1.366  0.020  1.366
 5NX  N9   C4   aromatic  1.374  0.020  1.374
 5NX  N9   CBG  single    1.452  0.020  1.452
 5NX  C4   N3   single    1.325  0.020  1.325
 5NX  CAN  CBF  single    1.519  0.020  1.519
 5NX  OAS  CBG  single    1.392  0.020  1.392
 5NX  OAS  CBF  single    1.437  0.020  1.437
 5NX  C2   N3   double    1.317  0.020  1.317
 5NX  C2   N2   single    1.326  0.020  1.326
 5NX  CBG  CBE  single    1.524  0.020  1.524
 5NX  CBF  CBD  single    1.530  0.020  1.530
 5NX  CBD  CBE  single    1.532  0.020  1.532
 5NX  CBD  OAF  single    1.402  0.020  1.402
 5NX  CBE  OAG  single    1.391  0.020  1.391
 5NX  C8   H1   single    0.930  0.020  1.080
 5NX  N1   H2   single    0.860  0.020  1.020
 5NX  N2   H3   single    0.860  0.020  1.020
 5NX  N2   H4   single    0.860  0.020  1.020
 5NX  CAL  H5   single    0.930  0.020  1.080
 5NX  CAJ  H6   single    0.930  0.020  1.080
 5NX  CAI  H7   single    0.930  0.020  1.080
 5NX  CAK  H8   single    0.930  0.020  1.080
 5NX  CAO  H9   single    0.970  0.020  1.090
 5NX  CAO  H10  single    0.970  0.020  1.090
 5NX  CBG  H11  single    0.970  0.020  1.090
 5NX  CBE  H12  single    0.970  0.020  1.090
 5NX  OAG  H13  single    0.850  0.020  0.980
 5NX  CBD  H14  single    0.970  0.020  1.090
 5NX  OAF  H15  single    0.850  0.020  0.980
 5NX  CBF  H16  single    0.970  0.020  1.090
 5NX  CAN  H17  single    0.970  0.020  1.090
 5NX  CAN  H18  single    0.970  0.020  1.090
 5NX  NAQ  H19  single    0.860  0.020  1.020
 5NX  OAE  H20  single    0.850  0.020  0.980

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
 5NX  N9   C4   N3   125.64  3.000
 5NX  N3   C4   C5   128.04  3.000
 5NX  N9   C4   C5   106.31  3.000
 5NX  N7   C5   C6   133.05  3.000
 5NX  C6   C5   C4   119.51  3.000
 5NX  N7   C5   C4   107.31  3.000
 5NX  O6   C6   N1   121.53  3.000
 5NX  N1   C6   C5   109.89  3.000
 5NX  O6   C6   C5   128.58  3.000
 5NX  H1   C8   N9   125.21  3.000
 5NX  H1   C8   N7   124.89  3.000
 5NX  N9   C8   N7   109.89  3.000
 5NX  H2   N1   C2   118.41  3.000
 5NX  H2   N1   C6   115.18  3.000
 5NX  C2   N1   C6   126.40  3.000
 5NX  C2   N3   C4   113.46  3.000
 5NX  H5   CAL  CAV  120.50  3.000
 5NX  H5   CAL  CAU  120.26  3.000
 5NX  CAV  CAL  CAU  119.24  3.000
 5NX  CAJ  CAU  CL   119.41  3.000
 5NX  CL   CAU  CAL  119.07  3.000
 5NX  CAJ  CAU  CAL  121.52  3.000
 5NX  H6   CAJ  CAI  120.60  3.000
 5NX  H6   CAJ  CAU  120.59  3.000
 5NX  CAI  CAJ  CAU  118.81  3.000
 5NX  H7   CAI  CAK  119.91  3.000
 5NX  H7   CAI  CAJ  119.66  3.000
 5NX  CAK  CAI  CAJ  120.43  3.000
 5NX  H8   CAK  CAV  120.01  3.000
 5NX  H8   CAK  CAI  119.76  3.000
 5NX  CAV  CAK  CAI  120.23  3.000
 5NX  CAO  CAV  CAK  119.79  3.000
 5NX  CAO  CAV  CAL  120.43  3.000
 5NX  CAK  CAV  CAL  119.77  3.000
 5NX  CAO  N7   C8   124.46  3.000
 5NX  C8   N7   C5   108.14  3.000
 5NX  CAO  N7   C5   127.24  3.000
 5NX  N3   C2   N2   119.85  3.000
 5NX  N2   C2   N1   117.52  3.000
 5NX  N3   C2   N1   122.63  3.000
 5NX  CBG  N9   C8   126.22  3.000
 5NX  CBG  N9   C4   125.33  3.000
 5NX  C8   N9   C4   108.34  3.000
 5NX  H11  CBG  CBE  111.00  3.000
 5NX  H11  CBG  OAS  112.89  3.000
 5NX  CBE  CBG  OAS  105.19  3.000
 5NX  H11  CBG  N9   105.68  3.000
 5NX  CBE  CBG  N9   113.27  3.000
 5NX  OAS  CBG  N9   108.95  3.000
 5NX  CBF  OAS  CBG  109.31  3.000
 5NX  H12  CBE  CBD  108.97  3.000
 5NX  H12  CBE  OAG  112.16  3.000
 5NX  CBD  CBE  OAG  115.33  3.000
 5NX  H12  CBE  CBG  109.08  3.000
 5NX  OAG  CBE  CBG  110.33  3.000
 5NX  CBD  CBE  CBG  100.24  3.000
 5NX  H13  OAG  CBE  109.18  3.000
 5NX  H14  CBD  CBF  111.60  3.000
 5NX  H14  CBD  OAF  111.82  3.000
 5NX  CBF  CBD  OAF  108.54  3.000
 5NX  H14  CBD  CBE  111.60  3.000
 5NX  OAF  CBD  CBE  111.10  3.000
 5NX  CBF  CBD  CBE  101.73  3.000
 5NX  H15  OAF  CBD  108.16  3.000
 5NX  H16  CBF  CAN  108.84  3.000
 5NX  H16  CBF  CBD  109.58  3.000
 5NX  CAN  CBF  CBD  113.20  3.000
 5NX  H16  CBF  OAS  108.70  3.000
 5NX  CBD  CBF  OAS  106.72  3.000
 5NX  CAN  CBF  OAS  109.70  3.000
 5NX  H18  CAN  H17  107.17  3.000
 5NX  H18  CAN  NAQ  109.48  3.000
 5NX  H17  CAN  NAQ  108.32  3.000
 5NX  H18  CAN  CBF  111.43  3.000
 5NX  H17  CAN  CBF  108.44  3.000
 5NX  NAQ  CAN  CBF  111.83  3.000
 5NX  H19  NAQ  CAX  118.04  3.000
 5NX  H19  NAQ  CAN  116.91  3.000
 5NX  CAX  NAQ  CAN  125.03  3.000
 5NX  CAW  CAX  CBA   90.57  3.000
 5NX  CAW  CAX  NAQ  134.26  3.000
 5NX  CBA  CAX  NAQ  135.14  3.000
 5NX  CAZ  CBA  OAD  135.88  3.000
 5NX  OAD  CBA  CAX  135.64  3.000
 5NX  CAZ  CBA  CAX   88.48  3.000
 5NX  CAW  CAZ  OAC  136.80  3.000
 5NX  CAW  CAZ  CBA   87.00  3.000
 5NX  OAC  CAZ  CBA  136.20  3.000
 5NX  OAE  CAW  CAZ  136.11  3.000
 5NX  OAE  CAW  CAX  129.94  3.000
 5NX  CAZ  CAW  CAX   93.95  3.000
 5NX  H20  OAE  CAW  111.18  3.000
 5NX  H4   N2   H3   117.89  3.000
 5NX  H4   N2   C2   119.13  3.000
 5NX  H3   N2   C2   122.81  3.000
 5NX  H10  CAO  H9   107.53  3.000
 5NX  H10  CAO  N7   106.96  3.000
 5NX  H9   CAO  N7   107.63  3.000
 5NX  H10  CAO  CAV  110.96  3.000
 5NX  H9   CAO  CAV  112.05  3.000
 5NX  N7   CAO  CAV  111.46  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
 5NX  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 5NX  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 5NX  CONST_03  N9   C8   N7   C5      0.00   0.0  0
 5NX  CONST_04  C8   N9   C4   C5      0.00   0.0  0
 5NX  CONST_05  CAI  CAK  CAV  CAL     0.00   0.0  0
 5NX  CONST_06  CAI  CAJ  CAU  CAL     0.00   0.0  0
 5NX  CONST_07  CAK  CAI  CAJ  CAU     0.00   0.0  0
 5NX  CONST_08  CAK  CAV  CAL  CAU     0.00   0.0  0
 5NX  CONST_09  CAV  CAK  CAI  CAJ     0.00   0.0  0
 5NX  CONST_10  CAV  CAL  CAU  CAJ     0.00   0.0  0
 5NX  CONST_11  N9   C4   C5   N7      0.00   0.0  0
 5NX  CONST_12  CBG  N9   C4   C5    180.00   0.0  0
 5NX  CONST_13  CBG  N9   C4   N3      0.00   0.0  0
 5NX  CONST_14  CBG  N9   C8   N7    180.00   0.0  0
 5NX  CONST_15  N1   C2   N3   C4      0.00   0.0  0
 5NX  CONST_16  C2   N1   C6   C5      0.00   0.0  0
 5NX  CONST_17  N3   C2   N1   C6      0.00   0.0  0
 5NX  CONST_18  CAO  N7   C5   C4    180.00   0.0  0
 5NX  CONST_19  CAO  N7   C5   C6      0.00   0.0  0
 5NX  CONST_20  CAO  CAV  CAL  CAU   180.00   0.0  0
 5NX  CONST_21  CAI  CAJ  CAU  CL    180.00   0.0  0
 5NX  CONST_22  CAV  CAL  CAU  CL    180.00   0.0  0
 5NX  CONST_23  CAO  CAV  CAK  CAI   180.00   0.0  0
 5NX  CONST_24  N9   C8   N7   CAO   180.00   0.0  0
 5NX  CONST_25  N2   C2   N3   C4    180.00   0.0  0
 5NX  CONST_26  N2   C2   N1   C6    180.00   0.0  0
 5NX  CONST_27  C2   N1   C6   O6    180.00   0.0  0
 5NX  CONST_28  H1   C8   N9   C4    180.00   0.0  0
 5NX  CONST_29  H8   CAK  CAV  CAL   180.00   0.0  0
 5NX  CONST_30  H6   CAJ  CAU  CAL   180.00   0.0  0
 5NX  CONST_31  H7   CAI  CAJ  CAU   180.00   0.0  0
 5NX  CONST_32  H5   CAL  CAU  CAJ   180.00   0.0  0
 5NX  CONST_33  H2   N1   C6   C5    180.00   0.0  0
 5NX  CONST_34  H3   N2   C2   N1      0.00   0.0  0
 5NX  CONST_35  H4   N2   C2   N1    180.00   0.0  0
 5NX  Var_01    CAW  CAZ  CBA  CAX    -0.16  30.0  1
 5NX  Var_02    CAV  CAO  N7   C5     85.86  30.0  2
 5NX  Var_03    N7   CAO  CAV  CAL   -88.22  30.0  1
 5NX  Var_04    CAX  NAQ  CAN  CBF  -105.83  30.0  1
 5NX  Var_05    CBA  CAX  NAQ  CAN    -2.60  30.0  2

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
 5NX  chir_01  CBG  N9   OAS  CBE  positiv
 5NX  chir_02  CBE  OAG  CBG  CBD  negativ
 5NX  chir_03  CBD  OAF  CBE  CBF  negativ
 5NX  chir_04  CBF  OAS  CBD  CAN  negativ

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
 5NX  plan-1  CAL  0.020
 5NX  plan-1  CAU  0.020
 5NX  plan-1  CL   0.020
 5NX  plan-1  CAJ  0.020
 5NX  plan-1  CAI  0.020
 5NX  plan-1  CAK  0.020
 5NX  plan-1  CAV  0.020
 5NX  plan-1  H6   0.020
 5NX  plan-1  H7   0.020
 5NX  plan-1  H8   0.020
 5NX  plan-1  CAO  0.020
 5NX  plan-1  H5   0.020
 5NX  plan-2  C4   0.020
 5NX  plan-2  C5   0.020
 5NX  plan-2  C6   0.020
 5NX  plan-2  C8   0.020
 5NX  plan-2  N1   0.020
 5NX  plan-2  N3   0.020
 5NX  plan-2  N7   0.020
 5NX  plan-2  O6   0.020
 5NX  plan-2  C2   0.020
 5NX  plan-2  N9   0.020
 5NX  plan-2  CBG  0.020
 5NX  plan-2  H1   0.020
 5NX  plan-2  H2   0.020
 5NX  plan-2  H3   0.020
 5NX  plan-2  H4   0.020
 5NX  plan-2  N2   0.020
 5NX  plan-2  CAO  0.020
 5NX  plan-3  CAX  0.020
 5NX  plan-3  CBA  0.020
 5NX  plan-3  OAD  0.020
 5NX  plan-3  CAZ  0.020
 5NX  plan-4  CBA  0.020
 5NX  plan-4  CAZ  0.020
 5NX  plan-4  OAC  0.020
 5NX  plan-4  CAW  0.020

