# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 10:51:07 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)O3
#
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
 FCJ  FCJ  2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]adenosine  ligand  48  30  .  2021-08-09  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FCJ
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
 FCJ  C8   C  CR15  0   0.094   6.9973   7.5885  11.7903
 FCJ  PA   P  P     0   1.514   4.6192   5.4678  14.8602
 FCJ  O1A  O  OH1   0  -0.736   3.2985   5.3989  15.7356
 FCJ  O2A  O  O     0  -0.664   5.9038   5.7188  15.5218
 FCJ  O3A  O  O2    0  -0.706   4.5485   4.0612  14.0852
 FCJ  PB   P  P     0   1.433   3.6804   2.7228  13.8181
 FCJ  O2B  O  O     0  -0.677   3.4431   2.5780  12.3598
 FCJ  O1B  O  OH1   0  -0.717   2.3931   2.8013  14.7395
 FCJ  C3B  C  CH2   0  -1.040   4.6573   1.4199  14.5645
 FCJ  PG   P  P     0   1.391   4.6642   1.3110  16.3745
 FCJ  O1G  O  OH1   0  -0.735   5.1332   2.7937  16.7389
 FCJ  O2G  O  OH1   0  -0.736   5.9614   0.4239  16.6971
 FCJ  O3G  O  O     0  -0.695   3.4111   0.8213  16.9885
 FCJ  C5'  C  CH2   0  -0.224   3.1433   6.6518  12.9716
 FCJ  C4'  C  CH1   0   0.019   3.4137   6.7747  11.4943
 FCJ  O4'  O  O2    0  -0.497   4.2569   7.8902  11.2338
 FCJ  C1'  C  CH1   0   0.192   5.0641   7.6414  10.1177
 FCJ  N9   N  NR5   0  -0.529   6.4644   7.6813  10.5346
 FCJ  C4   C  CR56  0   0.484   7.5192   7.7996   9.6801
 FCJ  N3   N  N     0  -0.459   7.4918   7.9167   8.3531
 FCJ  C2   C  CR16  0   0.038   8.7091   8.0126   7.8479
 FCJ  N1   N  N     0  -0.474   9.8745   8.0005   8.4907
 FCJ  C6   C  CR6   0   0.453   9.8846   7.8781   9.8227
 FCJ  N6   N  NH2   0  -0.816  11.0536   7.8457  10.4666
 FCJ  C5   C  CR56  0  -0.001   8.6477   7.7707  10.4846
 FCJ  N7   N  N     0  -0.455   8.2992   7.6395  11.8024
 FCJ  C2'  C  CH2   0  -0.539   4.6591   6.2764   9.5740
 FCJ  C3'  C  CH1   0   0.005   4.0895   5.5842  10.8046
 FCJ  O3'  O  OH1   0  -0.695   3.1974   4.5633  10.4781
 FCJ  H1   H  HCR5  0   0.295   6.3783   7.4926  12.6673
 FCJ  H2   H  HOH1  0   0.511   3.2160   6.0955  16.4023
 FCJ  H3   H  HOH1  0   0.508   1.6140   3.2267  14.3532
 FCJ  H4   H  HCH2  0   0.348   4.2762   0.4715  14.1770
 FCJ  H5   H  HCH2  0   0.349   5.6795   1.5239  14.1930
 FCJ  H6   H  HOH1  0   0.502   5.0928   3.0164  17.6797
 FCJ  H7   H  HOH1  0   0.499   5.7520  -0.4625  17.0201
 FCJ  H8   H  HCH2  0   0.280   2.6200   7.5330  13.3455
 FCJ  H9   H  HCH2  0   0.238   2.4773   5.7958  13.1158
 FCJ  H10  H  HCH1  0   0.247   2.4339   6.9292  11.0206
 FCJ  H11  H  HCH1  0   0.275   4.9415   8.4329   9.3750
 FCJ  H12  H  HCR6  0   0.251   8.7734   8.1135   6.7697
 FCJ  H13  H  HNH2  0   0.402  11.9093   8.0088   9.9644
 FCJ  H14  H  HNH2  0   0.410  11.0881   7.8462  11.4708
 FCJ  H15  H  HCH2  0   0.266   3.8699   6.4054   8.8293
 FCJ  H16  H  HCH2  0   0.280   5.4852   5.7447   9.1043
 FCJ  H17  H  HCH1  0   0.226   4.9159   5.2127  11.4251
 FCJ  H18  H  HOH1  0   0.460   3.2550   3.8600  11.1489
 FCJ  O5'  O  O2    0  -0.575   4.3680   6.5242  13.6981

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
 FCJ  C2   N3   aromatic  1.321  0.020  1.321
 FCJ  C2   N1   aromatic  1.331  0.020  1.331
 FCJ  N3   C4   aromatic  1.333  0.020  1.333
 FCJ  N1   C6   aromatic  1.338  0.020  1.338
 FCJ  C4   C5   aromatic  1.386  0.020  1.386
 FCJ  C4   N9   aromatic  1.363  0.020  1.363
 FCJ  C6   N6   single    1.335  0.020  1.335
 FCJ  C6   C5   aromatic  1.407  0.020  1.407
 FCJ  C2'  C1'  single    1.524  0.020  1.524
 FCJ  C2'  C3'  single    1.522  0.020  1.522
 FCJ  C1'  N9   single    1.462  0.020  1.462
 FCJ  C1'  O4'  single    1.400  0.020  1.400
 FCJ  C5   N7   aromatic  1.369  0.020  1.369
 FCJ  N9   C8   aromatic  1.367  0.020  1.367
 FCJ  O3'  C3'  single    1.395  0.020  1.395
 FCJ  C3'  C4'  single    1.533  0.020  1.533
 FCJ  O4'  C4'  single    1.422  0.020  1.422
 FCJ  N7   C8   aromatic  1.303  0.020  1.303
 FCJ  C4'  C5'  single    1.507  0.020  1.507
 FCJ  O2B  PB   double    1.485  0.020  1.485
 FCJ  C5'  O5'  single    1.430  0.020  1.430
 FCJ  O5'  PA   single    1.590  0.020  1.590
 FCJ  O3A  PB   single    1.617  0.020  1.617
 FCJ  O3A  PA   single    1.607  0.020  1.607
 FCJ  PB   O1B  single    1.585  0.020  1.585
 FCJ  PB   C3B  single    1.791  0.020  1.791
 FCJ  PA   O2A  double    1.467  0.020  1.467
 FCJ  PA   O1A  single    1.586  0.020  1.586
 FCJ  C3B  PG   single    1.813  0.020  1.813
 FCJ  PG   O3G  double    1.479  0.020  1.479
 FCJ  PG   O1G  single    1.597  0.020  1.597
 FCJ  PG   O2G  single    1.604  0.020  1.604
 FCJ  C8   H1   single    0.930  0.020  1.080
 FCJ  O1A  H2   single    0.850  0.020  0.980
 FCJ  O1B  H3   single    0.850  0.020  0.980
 FCJ  C3B  H4   single    0.970  0.020  1.090
 FCJ  C3B  H5   single    0.970  0.020  1.090
 FCJ  O1G  H6   single    0.850  0.020  0.980
 FCJ  O2G  H7   single    0.850  0.020  0.980
 FCJ  C5'  H8   single    0.970  0.020  1.090
 FCJ  C5'  H9   single    0.970  0.020  1.090
 FCJ  C4'  H10  single    0.970  0.020  1.090
 FCJ  C1'  H11  single    0.970  0.020  1.090
 FCJ  C2   H12  single    0.930  0.020  1.080
 FCJ  N6   H13  single    0.860  0.020  1.020
 FCJ  N6   H14  single    0.860  0.020  1.020
 FCJ  C2'  H15  single    0.970  0.020  1.090
 FCJ  C2'  H16  single    0.970  0.020  1.090
 FCJ  C3'  H17  single    0.970  0.020  1.090
 FCJ  O3'  H18  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
 FCJ  H1   C8   N7   124.73  3.000
 FCJ  H1   C8   N9   121.98  3.000
 FCJ  N7   C8   N9   113.29  3.000
 FCJ  O5'  PA   O3A  102.83  3.000
 FCJ  O3A  PA   O2A  113.94  3.000
 FCJ  O5'  PA   O2A  110.75  3.000
 FCJ  O2A  PA   O1A  119.20  3.000
 FCJ  O3A  PA   O1A  101.04  3.000
 FCJ  O5'  PA   O1A  107.50  3.000
 FCJ  H2   O1A  PA   114.84  3.000
 FCJ  PB   O3A  PA   145.82  3.000
 FCJ  C3B  PB   O1B  103.69  3.000
 FCJ  C3B  PB   O2B  115.18  3.000
 FCJ  O1B  PB   O2B  116.49  3.000
 FCJ  C3B  PB   O3A  103.91  3.000
 FCJ  O1B  PB   O3A  107.39  3.000
 FCJ  O2B  PB   O3A  109.19  3.000
 FCJ  H3   O1B  PB   116.32  3.000
 FCJ  H5   C3B  H4   106.75  3.000
 FCJ  H5   C3B  PG   109.97  3.000
 FCJ  H4   C3B  PG   107.65  3.000
 FCJ  H5   C3B  PB   107.42  3.000
 FCJ  H4   C3B  PB   107.05  3.000
 FCJ  PG   C3B  PB   117.49  3.000
 FCJ  O3G  PG   O2G  114.74  3.000
 FCJ  O2G  PG   O1G  103.29  3.000
 FCJ  O3G  PG   O1G  117.49  3.000
 FCJ  O2G  PG   C3B  103.71  3.000
 FCJ  O1G  PG   C3B   99.97  3.000
 FCJ  O3G  PG   C3B  115.54  3.000
 FCJ  H6   O1G  PG   115.03  3.000
 FCJ  H7   O2G  PG   113.53  3.000
 FCJ  H9   C5'  H8   107.14  3.000
 FCJ  H9   C5'  C4'  107.59  3.000
 FCJ  H8   C5'  C4'  110.86  3.000
 FCJ  H9   C5'  O5'  112.62  3.000
 FCJ  H8   C5'  O5'  107.99  3.000
 FCJ  C4'  C5'  O5'  110.59  3.000
 FCJ  H10  C4'  C3'  107.95  3.000
 FCJ  H10  C4'  O4'  109.83  3.000
 FCJ  C3'  C4'  O4'  105.38  3.000
 FCJ  H10  C4'  C5'  105.91  3.000
 FCJ  O4'  C4'  C5'  110.48  3.000
 FCJ  C3'  C4'  C5'  117.18  3.000
 FCJ  C1'  O4'  C4'  110.40  3.000
 FCJ  H11  C1'  C2'  112.13  3.000
 FCJ  H11  C1'  N9   106.36  3.000
 FCJ  C2'  C1'  N9   112.38  3.000
 FCJ  H11  C1'  O4'  110.41  3.000
 FCJ  N9   C1'  O4'  108.67  3.000
 FCJ  C2'  C1'  O4'  106.88  3.000
 FCJ  C4   N9   C1'  124.41  3.000
 FCJ  C1'  N9   C8   129.31  3.000
 FCJ  C4   N9   C8   106.26  3.000
 FCJ  C5   C4   N3   126.63  3.000
 FCJ  C5   C4   N9   105.34  3.000
 FCJ  N3   C4   N9   128.04  3.000
 FCJ  C2   N3   C4   111.60  3.000
 FCJ  H12  C2   N1   115.40  3.000
 FCJ  H12  C2   N3   116.18  3.000
 FCJ  N1   C2   N3   128.41  3.000
 FCJ  C6   N1   C2   119.23  3.000
 FCJ  C5   C6   N6   122.76  3.000
 FCJ  C5   C6   N1   117.96  3.000
 FCJ  N6   C6   N1   119.28  3.000
 FCJ  H14  N6   H13  118.03  3.000
 FCJ  H14  N6   C6   120.80  3.000
 FCJ  H13  N6   C6   120.02  3.000
 FCJ  N7   C5   C6   133.14  3.000
 FCJ  N7   C5   C4   110.69  3.000
 FCJ  C6   C5   C4   116.17  3.000
 FCJ  C5   N7   C8   104.42  3.000
 FCJ  H16  C2'  H15  108.15  3.000
 FCJ  H16  C2'  C3'  114.24  3.000
 FCJ  H15  C2'  C3'  109.53  3.000
 FCJ  H16  C2'  C1'  112.93  3.000
 FCJ  H15  C2'  C1'  109.22  3.000
 FCJ  C3'  C2'  C1'  102.61  3.000
 FCJ  H17  C3'  O3'  111.47  3.000
 FCJ  H17  C3'  C2'  109.21  3.000
 FCJ  O3'  C3'  C2'  112.51  3.000
 FCJ  H17  C3'  C4'  109.89  3.000
 FCJ  O3'  C3'  C4'  113.07  3.000
 FCJ  C2'  C3'  C4'  100.11  3.000
 FCJ  H18  O3'  C3'  109.25  3.000
 FCJ  C5'  O5'  PA   124.46  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
 FCJ  CONST_01  N3   C4   N9   C8    180.00   0.0  0
 FCJ  CONST_02  C5   C4   N9   C8      0.00   0.0  0
 FCJ  CONST_03  C4   C5   N7   C8      0.00   0.0  0
 FCJ  CONST_04  C6   C5   N7   C8    180.00   0.0  0
 FCJ  CONST_05  C2   N3   C4   N9    180.00   0.0  0
 FCJ  CONST_06  C6   C5   C4   N9    180.00   0.0  0
 FCJ  CONST_07  N7   C5   C4   N9      0.00   0.0  0
 FCJ  CONST_08  C5   N7   C8   N9      0.00   0.0  0
 FCJ  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 FCJ  CONST_10  N1   C6   C5   C4      0.00   0.0  0
 FCJ  CONST_11  N7   C8   N9   C4      0.00   0.0  0
 FCJ  CONST_12  C6   N1   C2   N3      0.00   0.0  0
 FCJ  CONST_13  C6   C5   C4   N3      0.00   0.0  0
 FCJ  CONST_14  N7   C5   C4   N3    180.00   0.0  0
 FCJ  CONST_15  C5   C4   N3   C2      0.00   0.0  0
 FCJ  CONST_16  C5   C6   N1   C2      0.00   0.0  0
 FCJ  CONST_17  N7   C5   C6   N1    180.00   0.0  0
 FCJ  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 FCJ  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 FCJ  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 FCJ  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 FCJ  CONST_22  N6   C6   N1   C2    180.00   0.0  0
 FCJ  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 FCJ  CONST_24  H1   C8   N9   C1'     0.00   0.0  0
 FCJ  CONST_25  H12  C2   N3   C4    180.00   0.0  0
 FCJ  CONST_26  H13  N6   C6   N1      0.00   0.0  0
 FCJ  CONST_27  H14  N6   C6   N1    180.00   0.0  0
 FCJ  Var_01    C4'  C5'  O5'  PA   -134.73  30.0  2
 FCJ  Var_02    O2B  PB   O3A  PA    123.65  30.0  3
 FCJ  Var_03    PG   C3B  PB   O3A    74.63  30.0  3
 FCJ  Var_04    O3G  PG   C3B  PB     72.01  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
 FCJ  chir_03  C4'  C3'  O4'  C5'  positiv
 FCJ  chir_04  C1'  O4'  N9   C2'  negativ
 FCJ  chir_05  C3'  O3'  C4'  C2'  positiv
 FCJ  chir_06  PA   O3A  O2A  O1A  both
 FCJ  chir_07  PB   O3A  O1B  C3B  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
 FCJ  plan-1  C8   0.020
 FCJ  plan-1  C1'  0.020
 FCJ  plan-1  N9   0.020
 FCJ  plan-1  C4   0.020
 FCJ  plan-1  N3   0.020
 FCJ  plan-1  C2   0.020
 FCJ  plan-1  N1   0.020
 FCJ  plan-1  C6   0.020
 FCJ  plan-1  N6   0.020
 FCJ  plan-1  C5   0.020
 FCJ  plan-1  N7   0.020
 FCJ  plan-1  H1   0.020
 FCJ  plan-1  H12  0.020
 FCJ  plan-2  C6   0.020
 FCJ  plan-2  N6   0.020
 FCJ  plan-2  H13  0.020
 FCJ  plan-2  H14  0.020

