# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:49:02 2020
#   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  44  30  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.098   3.1716   0.1549  -0.8827
 FCJ  PA   P  P      0   1.322  -2.0958   2.2311  -1.0454
 FCJ  O1A  O  OP    -1  -0.930  -1.4815   1.8051  -2.3442
 FCJ  O2A  O  O      0  -0.750  -3.0550   3.3870  -1.0181
 FCJ  O3A  O  O2     0  -0.777  -2.8035   1.0234  -0.2437
 FCJ  PB   P  P      0   1.237  -2.6337  -0.6645  -0.3825
 FCJ  O2B  O  O      0  -0.811  -3.0726  -1.0290  -1.7760
 FCJ  O1B  O  OP    -1  -0.842  -3.4554  -1.1444   0.7867
 FCJ  C3B  C  CH2    0  -0.978  -0.8659  -0.9281  -0.1320
 FCJ  PG   P  P      0   1.125  -0.4070  -2.6883   0.3247
 FCJ  O1G  O  OP    -1  -0.996   1.1052  -2.7782   0.0972
 FCJ  O2G  O  OP    -1  -0.937  -0.8223  -2.8597   1.7909
 FCJ  O3G  O  O      0  -0.850  -1.2185  -3.5701  -0.6401
 FCJ  C5'  C  CH2    0  -0.157   0.3900   2.9208  -0.4307
 FCJ  C4'  C  CH1    0  -0.014   1.3724   2.9137   0.7169
 FCJ  O4'  O  O2     0  -0.515   1.4954   1.6042   1.2566
 FCJ  C1'  C  CH1    0   0.246   2.8348   1.2187   1.3980
 FCJ  N9   N  NR5    0  -0.516   3.1587   0.1393   0.4846
 FCJ  C4   C  CR5    0   0.370   3.5123  -1.1288   0.8458
 FCJ  N3   N  N      0  -0.386   3.6265  -1.6309   2.0712
 FCJ  C2   C  C1     0   0.052   3.9720  -2.9038   2.0456
 FCJ  N1   N  N      0  -0.454   4.2186  -3.6746   0.9893
 FCJ  C6   C  C      0   0.421   4.0932  -3.1501  -0.2320
 FCJ  N6   N  NH2    0  -0.832   4.2942  -3.9361  -1.3008
 FCJ  C5   C  CR5    0   0.040   3.7451  -1.7983  -0.3404
 FCJ  N7   N  N      0  -0.431   3.5251  -0.9779  -1.4129
 FCJ  C2'  C  CH2    0  -0.613   3.6636   2.4806   1.1816
 FCJ  C3'  C  CH1    0   0.088   2.7776   3.3352   0.2805
 FCJ  O3'  O  OH1    0  -0.661   2.9249   4.7204   0.4355
 FCJ  H1   H  HCR5   0   0.307   2.9208   1.0398  -1.4477
 FCJ  H4   H  HCH2   0   0.226  -0.3513  -0.6341  -1.0502
 FCJ  H5   H  HCH2   0   0.236  -0.4822  -0.2508   0.6333
 FCJ  H8   H  HCH2   0   0.197   0.7371   2.2315  -1.2071
 FCJ  H9   H  HCH2   0   0.245   0.3953   3.9284  -0.8697
 FCJ  H10  H  HCH1   0   0.208   1.0294   3.5940   1.5084
 FCJ  H11  H  HCH1   0   0.262   2.9927   0.8015   2.3937
 FCJ  H12  H  H      0   0.273   4.0872  -3.3874   3.0109
 FCJ  H13  H  HNH2   0   0.380   4.7049  -4.8448  -1.1721
 FCJ  H14  H  HNH2   0   0.400   4.3568  -3.5295  -2.2175
 FCJ  H15  H  HCH2   0   0.283   3.7884   2.9888   2.1404
 FCJ  H16  H  HCH2   0   0.289   4.6533   2.2765   0.7749
 FCJ  H17  H  HCH1   0   0.207   2.9342   3.0530  -0.7706
 FCJ  H18  H  HOH1   0   0.455   3.7484   4.9871   0.0158
 FCJ  O5'  O  O2     0  -0.520  -0.8855   2.5679   0.0374

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  1.319  0.020  1.319
 FCJ  C2   N1   aromatic  1.331  0.020  1.331
 FCJ  N3   C4   aromatic  1.329  0.020  1.329
 FCJ  N1   C6   aromatic  1.335  0.020  1.335
 FCJ  C4   C5   aromatic  1.382  0.020  1.382
 FCJ  C4   N9   aromatic  1.365  0.020  1.365
 FCJ  C6   N6   single    1.342  0.020  1.342
 FCJ  C6   C5   aromatic  1.400  0.020  1.400
 FCJ  C2'  C1'  single    1.525  0.020  1.525
 FCJ  C2'  C3'  single    1.526  0.020  1.526
 FCJ  C1'  N9   single    1.451  0.020  1.451
 FCJ  C1'  O4'  single    1.401  0.020  1.401
 FCJ  C5   N7   aromatic  1.368  0.020  1.368
 FCJ  N9   C8   aromatic  1.368  0.020  1.368
 FCJ  O3'  C3'  single    1.402  0.020  1.402
 FCJ  C3'  C4'  single    1.531  0.020  1.531
 FCJ  O4'  C4'  single    1.422  0.020  1.422
 FCJ  N7   C8   aromatic  1.300  0.020  1.300
 FCJ  C4'  C5'  single    1.511  0.020  1.511
 FCJ  O2B  PB   deloc     1.506  0.020  1.506
 FCJ  C5'  O5'  single    1.404  0.020  1.404
 FCJ  O5'  PA   single    1.659  0.020  1.659
 FCJ  O3A  PB   single    1.702  0.020  1.702
 FCJ  O3A  PA   single    1.613  0.020  1.613
 FCJ  PB   O1B  deloc     1.508  0.020  1.508
 FCJ  PB   C3B  single    1.805  0.020  1.805
 FCJ  PA   O2A  deloc     1.502  0.020  1.502
 FCJ  PA   O1A  deloc     1.499  0.020  1.499
 FCJ  C3B  PG   single    1.875  0.020  1.875
 FCJ  PG   O3G  deloc     1.539  0.020  1.539
 FCJ  PG   O1G  deloc     1.532  0.020  1.532
 FCJ  PG   O2G  deloc     1.534  0.020  1.534
 FCJ  C8   H1   single    0.930  0.020  1.080
 FCJ  C3B  H4   single    0.970  0.020  1.090
 FCJ  C3B  H5   single    0.970  0.020  1.090
 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    0.890  0.020  1.040
 FCJ  N6   H14  single    0.890  0.020  1.040
 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   124.35  3.000
 FCJ  H1   C8   N9   122.04  3.000
 FCJ  N7   C8   N9   113.61  3.000
 FCJ  O5'  PA   O3A   98.50  3.000
 FCJ  O3A  PA   O2A  106.68  3.000
 FCJ  O5'  PA   O2A  107.33  3.000
 FCJ  O2A  PA   O1A  119.74  3.000
 FCJ  O3A  PA   O1A  113.44  3.000
 FCJ  O5'  PA   O1A  108.93  3.000
 FCJ  PB   O3A  PA   131.16  3.000
 FCJ  C3B  PB   O1B  112.32  3.000
 FCJ  C3B  PB   O2B  112.25  3.000
 FCJ  O1B  PB   O2B  118.81  3.000
 FCJ  C3B  PB   O3A  103.37  3.000
 FCJ  O1B  PB   O3A  101.42  3.000
 FCJ  O2B  PB   O3A  106.64  3.000
 FCJ  H5   C3B  H4   104.86  3.000
 FCJ  H5   C3B  PG   109.00  3.000
 FCJ  H4   C3B  PG   109.99  3.000
 FCJ  H5   C3B  PB   110.55  3.000
 FCJ  H4   C3B  PB   107.78  3.000
 FCJ  PG   C3B  PB   114.24  3.000
 FCJ  O3G  PG   O2G  113.12  3.000
 FCJ  O2G  PG   O1G  113.76  3.000
 FCJ  O3G  PG   O1G  113.20  3.000
 FCJ  O2G  PG   C3B  105.75  3.000
 FCJ  O1G  PG   C3B  105.10  3.000
 FCJ  O3G  PG   C3B  104.84  3.000
 FCJ  H9   C5'  H8   107.00  3.000
 FCJ  H9   C5'  C4'  107.73  3.000
 FCJ  H8   C5'  C4'  109.24  3.000
 FCJ  H9   C5'  O5'  111.60  3.000
 FCJ  H8   C5'  O5'  111.49  3.000
 FCJ  C4'  C5'  O5'  109.66  3.000
 FCJ  H10  C4'  C3'  108.76  3.000
 FCJ  H10  C4'  O4'  108.90  3.000
 FCJ  C3'  C4'  O4'  106.41  3.000
 FCJ  H10  C4'  C5'  109.96  3.000
 FCJ  O4'  C4'  C5'  110.42  3.000
 FCJ  C3'  C4'  C5'  112.28  3.000
 FCJ  C1'  O4'  C4'  111.99  3.000
 FCJ  H11  C1'  C2'  111.54  3.000
 FCJ  H11  C1'  N9   104.93  3.000
 FCJ  C2'  C1'  N9   113.89  3.000
 FCJ  H11  C1'  O4'  109.62  3.000
 FCJ  N9   C1'  O4'  110.78  3.000
 FCJ  C2'  C1'  O4'  106.12  3.000
 FCJ  C4   N9   C1'  125.63  3.000
 FCJ  C1'  N9   C8   128.55  3.000
 FCJ  C4   N9   C8   105.83  3.000
 FCJ  C5   C4   N3   126.44  3.000
 FCJ  C5   C4   N9   105.46  3.000
 FCJ  N3   C4   N9   128.10  3.000
 FCJ  C2   N3   C4   111.66  3.000
 FCJ  H12  C2   N1   115.34  3.000
 FCJ  H12  C2   N3   116.12  3.000
 FCJ  N1   C2   N3   128.52  3.000
 FCJ  C6   N1   C2   118.76  3.000
 FCJ  C5   C6   N6   122.76  3.000
 FCJ  C5   C6   N1   118.26  3.000
 FCJ  N6   C6   N1   118.97  3.000
 FCJ  H14  N6   H13  117.20  3.000
 FCJ  H14  N6   C6   119.93  3.000
 FCJ  H13  N6   C6   119.25  3.000
 FCJ  N7   C5   C6   132.82  3.000
 FCJ  N7   C5   C4   110.82  3.000
 FCJ  C6   C5   C4   116.30  3.000
 FCJ  C5   N7   C8   104.28  3.000
 FCJ  H16  C2'  H15  108.13  3.000
 FCJ  H16  C2'  C3'  114.33  3.000
 FCJ  H15  C2'  C3'  108.91  3.000
 FCJ  H16  C2'  C1'  113.06  3.000
 FCJ  H15  C2'  C1'  108.82  3.000
 FCJ  C3'  C2'  C1'  103.40  3.000
 FCJ  H17  C3'  O3'  110.14  3.000
 FCJ  H17  C3'  C2'  109.77  3.000
 FCJ  O3'  C3'  C2'  115.30  3.000
 FCJ  H17  C3'  C4'  109.43  3.000
 FCJ  O3'  C3'  C4'  109.70  3.000
 FCJ  C2'  C3'  C4'  102.15  3.000
 FCJ  H18  O3'  C3'  108.41  3.000
 FCJ  C5'  O5'  PA   119.76  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   -169.04  30.0  1
 FCJ  Var_02    O2B  PB   O3A  PA    -61.94  30.0  3
 FCJ  Var_03    PG   C3B  PB   O3A   161.31  30.0  3
 FCJ  Var_04    O3G  PG   C3B  PB     44.82  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

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

