# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 17:12:26 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: (1R)-1-[6-amino-5-(dihydroxyamino)-2-hydroxypyridin-3-yl]-1,4-anhydro-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-erythro-pentitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(O)c(cc1N(O)O)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
#
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
 A5J  A5J  (1R)-1-[6-amino-5-(dihydroxyamino)-2-hydroxypyridin-3-yl]-1,4-anhydro-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-erythro-pentitol  ligand  49  31  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A5J
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
 A5J  N     N  NT    0  -0.047  20.3716  -16.5763   -6.6855
 A5J  C1    C  CR6   0  -0.101  18.8694  -19.9333   -7.3861
 A5J  C2    C  CR6   0   0.449  18.5365  -20.2233   -6.0630
 A5J  O2    O  OH1   0  -0.613  17.9012  -21.3713   -5.8086
 A5J  N3    N  N     0  -0.507  18.8146  -19.4400   -5.0404
 A5J  C4    C  CR6   0   0.430  19.4238  -18.2738   -5.2434
 A5J  N4    N  NH2   0  -0.821  19.6532  -17.4908   -4.1562
 A5J  C5    C  CR6   0   0.145  19.7706  -17.8636   -6.5409
 A5J  C6    C  CR16  0  -0.239  19.5017  -18.7190   -7.5893
 A5J  C1'   C  CH1   0  -0.016  18.5104  -20.8595   -8.5210
 A5J  C2'   C  CH2   0  -0.519  17.0641  -20.6757   -8.9971
 A5J  C3'   C  CH1   0   0.020  17.2333  -19.6386  -10.0967
 A5J  O3'   O  OH1   0  -0.692  16.1537  -19.5160  -10.9936
 A5J  C4'   C  CH1   0   0.020  18.5385  -20.1161  -10.7410
 A5J  O4'   O  O2    0  -0.499  19.3230  -20.5733   -9.6600
 A5J  C5'   C  CH2   0  -0.239  19.3197  -19.1420  -11.5929
 A5J  O5'   O  O2    0  -0.583  19.6512  -17.9429  -10.8638
 A5J  ON1   O  OH1   0  -0.559  19.3407  -15.6405   -6.6576
 A5J  ON2   O  OH1   0  -0.567  20.9678  -16.5020   -7.9472
 A5J  O1A   O  O     0  -0.709  19.6835  -15.9582  -12.5618
 A5J  O1B   O  OH1   0  -0.723  15.2546  -17.1737  -11.8326
 A5J  O1G   O  O     0  -0.682  16.7676  -14.8572  -15.4021
 A5J  O2A   O  OH1   0  -0.736  19.5291  -15.6154  -10.0053
 A5J  O2B   O  O     0  -0.672  17.1721  -17.4884  -13.6091
 A5J  O2G   O  OH1   0  -0.765  18.3497  -13.9387  -13.5210
 A5J  O3A   O  O2    0  -0.698  17.5745  -16.5183  -11.2404
 A5J  O3B   O  O2    0  -0.680  16.2162  -15.1858  -12.8893
 A5J  O3G   O  OH1   0  -0.714  16.1931  -12.8738  -13.7995
 A5J  PA    P  P     0   1.527  19.1962  -16.4826  -11.2576
 A5J  PB    P  P     0   1.460  16.5791  -16.6977  -12.5208
 A5J  PG    P  P     0   1.451  16.9118  -14.2591  -14.0667
 A5J  H21   H  HOH1  0   0.474  17.7603  -21.4473   -4.8554
 A5J  H41   H  HNH2  0   0.389  19.6190  -17.9594   -3.2654
 A5J  H42   H  HNH2  0   0.391  20.3799  -16.7974   -4.2291
 A5J  H61   H  HCR6  0   0.281  19.8065  -18.4586   -8.5891
 A5J  H1'1  H  HCH1  0   0.261  18.6886  -21.8965   -8.2237
 A5J  H2'1  H  HCH2  0   0.276  16.3914  -20.3578   -8.2021
 A5J  H2'2  H  HCH2  0   0.262  16.6785  -21.6081   -9.4201
 A5J  H3'1  H  HCH1  0   0.261  17.3591  -18.6482   -9.6526
 A5J  H3'2  H  HOH1  0   0.476  15.9929  -20.3489  -11.4541
 A5J  H4'1  H  HCH1  0   0.246  18.3024  -20.9509  -11.4220
 A5J  H5'1  H  HCH2  0   0.267  18.7478  -18.9164  -12.4929
 A5J  H5'2  H  HCH2  0   0.288  20.2619  -19.5917  -11.9043
 A5J  HN11  H  HOH1  0   0.473  19.7127  -14.8794   -6.1930
 A5J  HN21  H  HOH1  0   0.501  21.7769  -15.9880   -7.8175
 A5J  H1    H  HOH1  0   0.518  15.3683  -18.0922  -11.4687
 A5J  H2    H  HOH1  0   0.505  20.0557  -15.9775   -9.2407
 A5J  H3    H  HOH1  0   0.500  18.9391  -14.7010  -13.2509
 A5J  H4    H  HOH1  0   0.510  15.4572  -12.6926  -14.4001

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
 A5J  O1G  PG    double    1.470  0.020  1.470
 A5J  O2G  PG    single    1.571  0.020  1.571
 A5J  PG   O3G   single    1.583  0.020  1.583
 A5J  PG   O3B   single    1.652  0.020  1.652
 A5J  O2B  PB    double    1.470  0.020  1.470
 A5J  O1A  PA    double    1.488  0.020  1.488
 A5J  O3B  PB    single    1.598  0.020  1.598
 A5J  PB   O1B   single    1.567  0.020  1.567
 A5J  PB   O3A   single    1.632  0.020  1.632
 A5J  PA   O3A   single    1.622  0.020  1.622
 A5J  PA   O2A   single    1.559  0.020  1.559
 A5J  PA   O5'   single    1.579  0.020  1.579
 A5J  C5'  O5'   single    1.442  0.020  1.442
 A5J  C5'  C4'   single    1.512  0.020  1.512
 A5J  O3'  C3'   single    1.409  0.020  1.409
 A5J  C4'  C3'   single    1.532  0.020  1.532
 A5J  C4'  O4'   single    1.412  0.020  1.412
 A5J  C3'  C2'   single    1.521  0.020  1.521
 A5J  O4'  C1'   single    1.428  0.020  1.428
 A5J  C2'  C1'   single    1.534  0.020  1.534
 A5J  C1'  C1    single    1.508  0.020  1.508
 A5J  ON2  N     single    1.397  0.020  1.397
 A5J  C6   C1    aromatic  1.384  0.020  1.384
 A5J  C6   C5    aromatic  1.380  0.020  1.380
 A5J  C1   C2    aromatic  1.395  0.020  1.395
 A5J  N    C5    single    1.428  0.020  1.428
 A5J  N    ON1   single    1.393  0.020  1.393
 A5J  C5   C4    aromatic  1.404  0.020  1.404
 A5J  C2   O2    single    1.337  0.020  1.337
 A5J  C2   N3    aromatic  1.318  0.020  1.318
 A5J  C4   N3    aromatic  1.331  0.020  1.331
 A5J  C4   N4    single    1.359  0.020  1.359
 A5J  O2   H21   single    0.850  0.020  0.980
 A5J  N4   H41   single    0.890  0.020  1.040
 A5J  N4   H42   single    0.890  0.020  1.040
 A5J  C6   H61   single    0.930  0.020  1.080
 A5J  C1'  H1'1  single    0.970  0.020  1.090
 A5J  C2'  H2'1  single    0.970  0.020  1.090
 A5J  C2'  H2'2  single    0.970  0.020  1.090
 A5J  C3'  H3'1  single    0.970  0.020  1.090
 A5J  O3'  H3'2  single    0.850  0.020  0.980
 A5J  C4'  H4'1  single    0.970  0.020  1.090
 A5J  C5'  H5'1  single    0.970  0.020  1.090
 A5J  C5'  H5'2  single    0.970  0.020  1.090
 A5J  ON1  HN11  single    0.850  0.020  0.980
 A5J  ON2  HN21  single    0.850  0.020  0.980
 A5J  O1B  H1    single    0.850  0.020  0.980
 A5J  O2A  H2    single    0.850  0.020  0.980
 A5J  O2G  H3    single    0.850  0.020  0.980
 A5J  O3G  H4    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
 A5J  ON2   N    ON1   107.35  3.000
 A5J  ON1   N    C5    106.99  3.000
 A5J  ON2   N    C5    108.59  3.000
 A5J  C1'   C1   C6    122.49  3.000
 A5J  C6    C1   C2    115.51  3.000
 A5J  C1'   C1   C2    121.96  3.000
 A5J  N3    C2   O2    117.59  3.000
 A5J  N3    C2   C1    124.21  3.000
 A5J  O2    C2   C1    118.20  3.000
 A5J  H21   O2   C2    108.93  3.000
 A5J  C4    N3   C2    119.93  3.000
 A5J  C5    C4   N4    121.95  3.000
 A5J  N4    C4   N3    117.38  3.000
 A5J  C5    C4   N3    120.65  3.000
 A5J  H42   N4   H41   114.14  3.000
 A5J  H42   N4   C4    117.41  3.000
 A5J  H41   N4   C4    115.70  3.000
 A5J  C6    C5   C4    118.22  3.000
 A5J  C4    C5   N     117.43  3.000
 A5J  C6    C5   N     124.34  3.000
 A5J  H61   C6   C5    120.02  3.000
 A5J  H61   C6   C1    118.53  3.000
 A5J  C5    C6   C1    121.43  3.000
 A5J  H1'1  C1'  O4'   108.32  3.000
 A5J  H1'1  C1'  C2'   110.59  3.000
 A5J  O4'   C1'  C2'   105.36  3.000
 A5J  H1'1  C1'  C1    109.82  3.000
 A5J  C2'   C1'  C1    112.61  3.000
 A5J  O4'   C1'  C1    109.97  3.000
 A5J  H2'2  C2'  H2'1  108.27  3.000
 A5J  H2'2  C2'  C3'   109.93  3.000
 A5J  H2'1  C2'  C3'   113.42  3.000
 A5J  H2'2  C2'  C1'   110.50  3.000
 A5J  H2'1  C2'  C1'   113.01  3.000
 A5J  C3'   C2'  C1'   101.61  3.000
 A5J  H3'1  C3'  C4'   110.82  3.000
 A5J  H3'1  C3'  O3'   105.55  3.000
 A5J  C4'   C3'  O3'   114.35  3.000
 A5J  H3'1  C3'  C2'   109.69  3.000
 A5J  C4'   C3'  C2'   100.74  3.000
 A5J  O3'   C3'  C2'   115.74  3.000
 A5J  H3'2  O3'  C3'   110.87  3.000
 A5J  H4'1  C4'  C5'   104.50  3.000
 A5J  H4'1  C4'  O4'   110.29  3.000
 A5J  C5'   C4'  O4'   110.68  3.000
 A5J  H4'1  C4'  C3'   108.25  3.000
 A5J  O4'   C4'  C3'   104.62  3.000
 A5J  C5'   C4'  C3'   118.45  3.000
 A5J  C4'   O4'  C1'   111.07  3.000
 A5J  H5'2  C5'  H5'1  107.65  3.000
 A5J  H5'2  C5'  O5'   106.79  3.000
 A5J  H5'1  C5'  O5'   111.47  3.000
 A5J  H5'2  C5'  C4'   110.00  3.000
 A5J  H5'1  C5'  C4'   109.12  3.000
 A5J  O5'   C5'  C4'   111.70  3.000
 A5J  PA    O5'  C5'   125.21  3.000
 A5J  HN11  ON1  N     104.71  3.000
 A5J  HN21  ON2  N     105.31  3.000
 A5J  H1    O1B  PB    110.16  3.000
 A5J  H2    O2A  PA    121.80  3.000
 A5J  H3    O2G  PG    118.52  3.000
 A5J  PB    O3A  PA    127.15  3.000
 A5J  PG    O3B  PB    126.84  3.000
 A5J  H4    O3G  PG    113.85  3.000
 A5J  O3A   PA   O2A   102.54  3.000
 A5J  O2A   PA   O1A   115.98  3.000
 A5J  O3A   PA   O1A   110.15  3.000
 A5J  O2A   PA   O5'   104.63  3.000
 A5J  O3A   PA   O5'   105.37  3.000
 A5J  O1A   PA   O5'   116.75  3.000
 A5J  O3B   PB   O3A   102.44  3.000
 A5J  O3A   PB   O2B   113.20  3.000
 A5J  O3B   PB   O2B   115.46  3.000
 A5J  O3A   PB   O1B   101.80  3.000
 A5J  O3B   PB   O1B   101.35  3.000
 A5J  O2B   PB   O1B   120.18  3.000
 A5J  O3G   PG   O3B   100.33  3.000
 A5J  O3B   PG   O2G   104.61  3.000
 A5J  O3G   PG   O2G   100.27  3.000
 A5J  O3B   PG   O1G   112.20  3.000
 A5J  O3G   PG   O1G   117.69  3.000
 A5J  O2G   PG   O1G   119.22  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
 A5J  CONST_01  C4    C5   C6   C1     0.00   0.0  0
 A5J  CONST_02  C4    N3   C2   C1     0.00   0.0  0
 A5J  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 A5J  CONST_04  C5    C4   N3   C2     0.00   0.0  0
 A5J  CONST_05  C6    C1   C2   N3     0.00   0.0  0
 A5J  CONST_06  C6    C5   C4   N3     0.00   0.0  0
 A5J  CONST_07  C1'   C1   C2   N3   180.00   0.0  0
 A5J  CONST_08  C1'   C1   C6   C5   180.00   0.0  0
 A5J  CONST_09  C1    C6   C5   N    180.00   0.0  0
 A5J  CONST_10  N3    C4   C5   N    180.00   0.0  0
 A5J  CONST_11  N4    C4   N3   C2   180.00   0.0  0
 A5J  CONST_12  C1'   C1   C2   O2     0.00   0.0  0
 A5J  CONST_13  C6    C1   C2   O2   180.00   0.0  0
 A5J  CONST_14  C4    N3   C2   O2   180.00   0.0  0
 A5J  CONST_15  C6    C5   C4   N4   180.00   0.0  0
 A5J  CONST_16  H61   C6   C1   C2   180.00   0.0  0
 A5J  Var_01    O1A   PA   O5'  C5'  -62.73  30.0  1
 A5J  Var_02    H5'1  C5'  O5'  PA     2.84  30.0  1

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
 A5J  chir_01  C1'  O4'  C2'  C1   positiv
 A5J  chir_02  C3'  O3'  C4'  C2'  positiv
 A5J  chir_03  C4'  O4'  C5'  C3'  positiv
 A5J  chir_04  PA   O3A  O2A  O5'  both
 A5J  chir_05  PB   O1B  O3B  O2B  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
 A5J  plan-1  N    0.020
 A5J  plan-1  C1   0.020
 A5J  plan-1  C2   0.020
 A5J  plan-1  O2   0.020
 A5J  plan-1  N3   0.020
 A5J  plan-1  C4   0.020
 A5J  plan-1  N4   0.020
 A5J  plan-1  C5   0.020
 A5J  plan-1  C6   0.020
 A5J  plan-1  C1'  0.020
 A5J  plan-1  H61  0.020
 A5J  plan-2  N    0.020
 A5J  plan-2  C5   0.020
 A5J  plan-2  ON1  0.020
 A5J  plan-2  ON2  0.020
 A5J  plan-3  C4   0.020
 A5J  plan-3  N4   0.020
 A5J  plan-3  H41  0.020
 A5J  plan-3  H42  0.020

