# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 04:19:52 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC(=O)Nc23
#
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
 CZF  CZF  '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  47  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CZF
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
 CZF  C1   C  CH1   0   0.198  50.7278  49.4001  -22.4743
 CZF  C2   C  CR6   0   0.683  55.0163  49.1654  -21.4009
 CZF  C3   C  CH1   0   0.040  50.5917  50.7084  -23.2415
 CZF  C4   C  CH1   0  -0.081  49.1600  51.1057  -22.8759
 CZF  C5   C  CR56  0   0.582  53.0652  48.5467  -22.5886
 CZF  C6   C  CH1   0  -0.013  48.4718  49.7276  -22.8431
 CZF  C7   C  CR56  0   0.054  53.7025  47.5837  -23.3274
 CZF  C8   C  CH2   0  -0.226  47.7511  49.4141  -24.1347
 CZF  C9   C  CR6   0   0.498  55.0983  47.3293  -23.1159
 CZF  C10  C  CR15  0   0.064  51.6816  47.5749  -23.9655
 CZF  N1   N  NR16  0  -0.700  55.6277  48.1630  -22.1314
 CZF  N2   N  NR16  0  -0.840  53.6701  49.3233  -21.6553
 CZF  N3   N  N     0  -0.395  52.8153  46.9873  -24.1823
 CZF  N4   N  NR5   0  -0.550  51.7724  48.5375  -22.9801
 CZF  O2   O  OH1   0  -0.654  51.6061  51.5725  -22.8500
 CZF  O3   O  OH1   0  -0.660  49.1910  51.7193  -21.6185
 CZF  O4   O  O2    0  -0.519  49.5003  48.7580  -22.6092
 CZF  O5   O  O2    0  -0.599  47.0078  48.1931  -24.0278
 CZF  O6   O  O     0  -0.489  55.7927  46.5098  -23.6848
 CZF  O7   O  O2    0  -0.673  46.2279  46.0478  -24.7996
 CZF  O8   O  O     0  -0.737  48.6845  46.6766  -25.3594
 CZF  O9   O  OH1   0  -0.698  47.9079  46.1648  -22.9142
 CZF  O10  O  O2    0  -0.610  46.3016  44.9230  -27.0629
 CZF  O11  O  OH1   0  -0.701  44.6631  44.1721  -25.3886
 CZF  O12  O  O     0  -0.635  47.2128  43.6714  -25.0208
 CZF  O13  O  OH1   0  -0.805  44.3977  46.6004  -27.4058
 CZF  O14  O  OH1   0  -0.645  46.6645  47.3965  -27.5179
 CZF  O15  O  O     0  -0.640  45.8644  45.7478  -29.4065
 CZF  P1   P  P     0   1.430  47.6173  46.7722  -24.3445
 CZF  P2   P  P     0   1.474  46.1783  44.5944  -25.5007
 CZF  P3   P  P     0   1.437  45.7981  46.1628  -28.0004
 CZF  H1   H  HCH1  0   0.323  50.9632  49.6028  -21.4207
 CZF  H2   H  HCH1  0   0.318  50.6278  50.4894  -24.3175
 CZF  H3   H  HCH1  0   0.266  48.7093  51.7564  -23.6357
 CZF  H4   H  HCH1  0   0.297  47.7512  49.6800  -22.0173
 CZF  H5   H  HCH2  0   0.281  48.4364  49.3776  -24.9854
 CZF  H6   H  HCH2  0   0.307  47.0120  50.1891  -24.3306
 CZF  H7   H  HCR5  0   0.300  50.7521  47.3591  -24.4684
 CZF  H8   H  HNR6  0   0.443  56.6127  48.0412  -21.9293
 CZF  H9   H  HNR6  0   0.405  53.2080  50.1094  -21.2190
 CZF  H10  H  HOH1  0   0.423  51.6929  52.2824  -23.4945
 CZF  H11  H  HOH1  0   0.465  48.2944  51.9731  -21.3769
 CZF  H12  H  HOH1  0   0.505  48.5166  45.4089  -22.9026
 CZF  H13  H  HOH1  0   0.538  44.4608  43.6468  -24.5952
 CZF  H14  H  HOH1  0   0.480  43.6354  46.2533  -27.8880
 CZF  H15  H  HOH1  0   0.517  47.6188  47.2639  -27.6076
 CZF  O1   O  O     0  -0.458  55.6113  49.8448  -20.5995

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
 CZF  O15  P3   double    1.467  0.020  1.467
 CZF  P3   O10  single    1.634  0.020  1.634
 CZF  P3   O14  single    1.583  0.020  1.583
 CZF  P3   O13  single    1.583  0.020  1.583
 CZF  O10  P2   single    1.601  0.020  1.601
 CZF  O12  P2   double    1.467  0.020  1.467
 CZF  P2   O11  single    1.577  0.020  1.577
 CZF  P2   O7   single    1.614  0.020  1.614
 CZF  O8   P1   double    1.476  0.020  1.476
 CZF  O7   P1   single    1.632  0.020  1.632
 CZF  P1   O9   single    1.581  0.020  1.581
 CZF  P1   O5   single    1.578  0.020  1.578
 CZF  O5   C8   single    1.433  0.020  1.433
 CZF  C8   C6   single    1.512  0.020  1.512
 CZF  C4   C3   single    1.530  0.020  1.530
 CZF  C4   C6   single    1.541  0.020  1.541
 CZF  C4   O3   single    1.399  0.020  1.399
 CZF  C3   O2   single    1.389  0.020  1.389
 CZF  C3   C1   single    1.523  0.020  1.523
 CZF  O4   C6   single    1.433  0.020  1.433
 CZF  O4   C1   single    1.392  0.020  1.392
 CZF  C1   N4   single    1.446  0.020  1.446
 CZF  N4   C10  aromatic  1.381  0.020  1.381
 CZF  N4   C5   aromatic  1.351  0.020  1.351
 CZF  C10  N3   aromatic  1.295  0.020  1.295
 CZF  C5   N2   single    1.357  0.020  1.357
 CZF  C5   C7   aromatic  1.371  0.020  1.371
 CZF  N3   C7   aromatic  1.369  0.020  1.369
 CZF  N2   C2   single    1.379  0.020  1.379
 CZF  C7   C9   single    1.434  0.020  1.434
 CZF  C2   O1   double    1.207  0.020  1.207
 CZF  C2   N1   single    1.383  0.020  1.383
 CZF  C9   N1   single    1.394  0.020  1.394
 CZF  C9   O6   double    1.215  0.020  1.215
 CZF  C1   H1   single    0.970  0.020  1.090
 CZF  C3   H2   single    0.970  0.020  1.090
 CZF  C4   H3   single    0.970  0.020  1.090
 CZF  C6   H4   single    0.970  0.020  1.090
 CZF  C8   H5   single    0.970  0.020  1.090
 CZF  C8   H6   single    0.970  0.020  1.090
 CZF  C10  H7   single    0.930  0.020  1.080
 CZF  N1   H8   single    0.860  0.020  1.020
 CZF  N2   H9   single    0.860  0.020  1.020
 CZF  O2   H10  single    0.850  0.020  0.980
 CZF  O3   H11  single    0.850  0.020  0.980
 CZF  O9   H12  single    0.850  0.020  0.980
 CZF  O11  H13  single    0.850  0.020  0.980
 CZF  O13  H14  single    0.850  0.020  0.980
 CZF  O14  H15  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
 CZF  H1   C1   O4   111.54  3.000
 CZF  H1   C1   N4   106.90  3.000
 CZF  O4   C1   N4   109.15  3.000
 CZF  H1   C1   C3   110.11  3.000
 CZF  N4   C1   C3   113.63  3.000
 CZF  O4   C1   C3   105.59  3.000
 CZF  O1   C2   N2   122.61  3.000
 CZF  O1   C2   N1   122.73  3.000
 CZF  N2   C2   N1   114.66  3.000
 CZF  H2   C3   O2   112.09  3.000
 CZF  H2   C3   C4   108.45  3.000
 CZF  O2   C3   C4   117.03  3.000
 CZF  H2   C3   C1   108.62  3.000
 CZF  O2   C3   C1   109.11  3.000
 CZF  C4   C3   C1   100.74  3.000
 CZF  H3   C4   O3   111.79  3.000
 CZF  H3   C4   C6   111.21  3.000
 CZF  O3   C4   C6   112.52  3.000
 CZF  H3   C4   C3   111.89  3.000
 CZF  O3   C4   C3   107.92  3.000
 CZF  C6   C4   C3   101.00  3.000
 CZF  N4   C5   N2   129.05  3.000
 CZF  N2   C5   C7   124.44  3.000
 CZF  N4   C5   C7   106.50  3.000
 CZF  H4   C6   O4   108.62  3.000
 CZF  H4   C6   C8   108.72  3.000
 CZF  O4   C6   C8   109.95  3.000
 CZF  H4   C6   C4   110.38  3.000
 CZF  O4   C6   C4   106.75  3.000
 CZF  C8   C6   C4   112.35  3.000
 CZF  N3   C7   C9   130.20  3.000
 CZF  C9   C7   C5   119.84  3.000
 CZF  N3   C7   C5   109.96  3.000
 CZF  H6   C8   H5   108.02  3.000
 CZF  H6   C8   O5   105.53  3.000
 CZF  H5   C8   O5   110.78  3.000
 CZF  H6   C8   C6   109.25  3.000
 CZF  H5   C8   C6   111.90  3.000
 CZF  O5   C8   C6   111.11  3.000
 CZF  O6   C9   N1   121.11  3.000
 CZF  O6   C9   C7   127.34  3.000
 CZF  N1   C9   C7   111.56  3.000
 CZF  H7   C10  N4   121.94  3.000
 CZF  H7   C10  N3   125.84  3.000
 CZF  N4   C10  N3   112.22  3.000
 CZF  H8   N1   C9   115.99  3.000
 CZF  H8   N1   C2   114.31  3.000
 CZF  C9   N1   C2   129.68  3.000
 CZF  H9   N2   C5   122.57  3.000
 CZF  H9   N2   C2   117.11  3.000
 CZF  C5   N2   C2   119.78  3.000
 CZF  C10  N3   C7   105.37  3.000
 CZF  C10  N4   C5   105.94  3.000
 CZF  C5   N4   C1   125.87  3.000
 CZF  C10  N4   C1   128.17  3.000
 CZF  H10  O2   C3   109.63  3.000
 CZF  H11  O3   C4   108.69  3.000
 CZF  C6   O4   C1   109.68  3.000
 CZF  P1   O5   C8   123.48  3.000
 CZF  P2   O7   P1   123.16  3.000
 CZF  H12  O9   P1   115.18  3.000
 CZF  P3   O10  P2   133.78  3.000
 CZF  H13  O11  P2   113.73  3.000
 CZF  H14  O13  P3   114.27  3.000
 CZF  H15  O14  P3   113.88  3.000
 CZF  O9   P1   O8   117.67  3.000
 CZF  O9   P1   O7   103.79  3.000
 CZF  O8   P1   O7   113.28  3.000
 CZF  O9   P1   O5   103.61  3.000
 CZF  O7   P1   O5    97.29  3.000
 CZF  O8   P1   O5   118.40  3.000
 CZF  O12  P2   O11  119.06  3.000
 CZF  O11  P2   O10  101.44  3.000
 CZF  O12  P2   O10  113.20  3.000
 CZF  O11  P2   O7   103.87  3.000
 CZF  O12  P2   O7   113.74  3.000
 CZF  O10  P2   O7   103.69  3.000
 CZF  O15  P3   O14  119.19  3.000
 CZF  O14  P3   O13   98.87  3.000
 CZF  O15  P3   O13  118.56  3.000
 CZF  O13  P3   O10  105.47  3.000
 CZF  O14  P3   O10  104.35  3.000
 CZF  O15  P3   O10  108.74  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
 CZF  CONST_01  N3   C10  N4  C5    0.00   0.0  0
 CZF  CONST_02  C10  N3   C7  C5    0.00   0.0  0
 CZF  CONST_03  C10  N4   C5  C7    0.00   0.0  0
 CZF  CONST_04  N4   C10  N3  C7    0.00   0.0  0
 CZF  CONST_05  N4   C5   C7  N3    0.00   0.0  0
 CZF  CONST_06  N3   C10  N4  C1  180.00   0.0  0
 CZF  CONST_07  N2   C5   N4  C1    0.00   0.0  0
 CZF  CONST_08  C7   C5   N4  C1  180.00   0.0  0
 CZF  CONST_09  N1   C2   N2  C5    0.00   0.0  0
 CZF  CONST_10  N2   C2   N1  C9    0.00   0.0  0
 CZF  CONST_11  O1   C2   N2  C5  180.00   0.0  0
 CZF  CONST_12  O1   C2   N1  C9  180.00   0.0  0
 CZF  CONST_13  H7   C10  N4  C1    0.00   0.0  0
 CZF  CONST_14  H9   N2   C2  N1  180.00   0.0  0
 CZF  CONST_15  H8   N1   C2  N2  180.00   0.0  0
 CZF  Var_01    O8   P1   O5  C8  -30.30  30.0  1
 CZF  Var_02    H5   C8   O5  P1   36.84  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
 CZF  chir_01  C1  C3   O4   N4   negativ
 CZF  chir_02  C3  O2   C4   C1   positiv
 CZF  chir_03  C4  O3   C6   C3   positiv
 CZF  chir_04  C6  O4   C4   C8   negativ
 CZF  chir_05  P1  O7   O9   O5   both
 CZF  chir_06  P2  O11  O12  O10  both

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
 CZF  plan-1  C1   0.020
 CZF  plan-1  C2   0.020
 CZF  plan-1  C5   0.020
 CZF  plan-1  C7   0.020
 CZF  plan-1  C9   0.020
 CZF  plan-1  C10  0.020
 CZF  plan-1  N1   0.020
 CZF  plan-1  N2   0.020
 CZF  plan-1  N3   0.020
 CZF  plan-1  N4   0.020
 CZF  plan-1  O6   0.020
 CZF  plan-1  H7   0.020
 CZF  plan-1  H8   0.020
 CZF  plan-1  H9   0.020
 CZF  plan-1  O1   0.020

