# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 20 01:42:02 2020
#   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  45  31  .  2021-08-06  2021-08-06  
;
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  -0.054   1.6260   2.0869   1.0528
 A5J  C1    C  C      0  -0.089   3.7415  -0.3917  -0.7542
 A5J  C2    C  C      0   0.402   3.8894   0.3394  -1.9292
 A5J  O2    O  OH1    0  -0.620   4.5511  -0.1157  -3.0161
 A5J  N3    N  N      0  -0.489   3.3680   1.5374  -2.1178
 A5J  C4    C  C      0   0.379   2.6303   2.1143  -1.1730
 A5J  N4    N  NH2    0  -0.858   2.0470   3.2957  -1.4958
 A5J  C5    C  C      0   0.205   2.4848   1.5093   0.1024
 A5J  C6    C  C1     0  -0.274   3.0406   0.2630   0.2614
 A5J  C1'   C  CH1    0  -0.051   4.0695  -1.8617  -0.6907
 A5J  C2'   C  CH2    0  -0.554   4.2331  -2.4682   0.7105
 A5J  C3'   C  CH1    0   0.022   3.4644  -3.7839   0.6312
 A5J  O3'   O  OH1    0  -0.676   4.2337  -4.8291   0.0782
 A5J  C4'   C  CH1    0  -0.049   2.3727  -3.4363  -0.3730
 A5J  O4'   O  O2     0  -0.488   3.0141  -2.6047  -1.3179
 A5J  C5'   C  CH2    0  -0.134   1.1713  -2.7706   0.2827
 A5J  O5'   O  O2     0  -0.620   0.2366  -2.4443  -0.7213
 A5J  ON1   O  OH1    0  -0.629   1.5441   1.3478   2.2083
 A5J  ON2   O  OH1    0  -0.643   1.9815   3.3896   1.3666
 A5J  O1A   O  O      0  -0.817  -1.6757  -2.3663   0.9906
 A5J  O1B   O  OP    -1  -0.819  -0.9583   0.9270   2.1334
 A5J  O1G   O  O      0  -0.867  -2.1833   3.8239   1.5511
 A5J  O2A   O  OP    -1  -0.801  -2.0501  -1.9265  -1.5576
 A5J  O2B   O  O      0  -0.814  -3.0642   0.5707   0.6929
 A5J  O2G   O  OP    -1  -0.844  -0.0477   4.3876   0.2445
 A5J  O3A   O  O2     0  -0.739  -0.7636  -0.2352  -0.1320
 A5J  O3B   O  O2     0  -0.752  -1.2277   2.1461  -0.1514
 A5J  O3G   O  OP    -1  -0.871  -2.2682   4.2870  -0.9834
 A5J  PA    P  P      0   1.359  -1.2218  -1.7967  -0.3179
 A5J  PB    P  P      0   1.414  -1.5988   0.8777   0.7595
 A5J  PG    P  P      0   1.290  -1.4801   3.7884   0.2118
 A5J  H21   H  HOH1   0   0.472   4.9594  -0.9694  -2.8402
 A5J  H41   H  HNH2   0   0.365   2.0309   3.5028  -2.4807
 A5J  H42   H  HNH2   0   0.406   1.2444   3.6332  -0.9631
 A5J  H61   H  H      0   0.245   2.8783  -0.2280   1.2081
 A5J  H1'1  H  HCH1   0   0.219   4.9851  -2.0743  -1.2571
 A5J  H2'1  H  HCH2   0   0.272   5.2833  -2.6107   0.9684
 A5J  H2'2  H  HCH2   0   0.260   3.8032  -1.8464   1.4936
 A5J  H3'1  H  HCH1   0   0.231   3.0530  -4.0693   1.6078
 A5J  H3'2  H  HOH1   0   0.450   5.0095  -4.9530   0.6333
 A5J  H4'1  H  HCH1   0   0.240   2.0252  -4.3343  -0.8963
 A5J  H5'1  H  HCH2   0   0.206   0.7436  -3.4724   1.0070
 A5J  H5'2  H  HCH2   0   0.206   1.4744  -1.8772   0.8391
 A5J  HN11  H  HOH1   0   0.460   0.5574   1.1376   2.2377
 A5J  HN21  H  HOH1   0   0.448   1.1544   3.8787   1.0443

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    deloc     1.513  0.020  1.513
 A5J  O2G  PG    deloc     1.553  0.020  1.553
 A5J  PG   O3G   deloc     1.516  0.020  1.516
 A5J  PG   O3B   single    1.701  0.020  1.701
 A5J  O2B  PB    deloc     1.499  0.020  1.499
 A5J  O1A  PA    deloc     1.498  0.020  1.498
 A5J  O3B  PB    single    1.605  0.020  1.605
 A5J  PB   O1B   deloc     1.517  0.020  1.517
 A5J  PB   O3A   single    1.652  0.020  1.652
 A5J  PA   O3A   single    1.638  0.020  1.638
 A5J  PA   O2A   deloc     1.497  0.020  1.497
 A5J  PA   O5'   single    1.646  0.020  1.646
 A5J  C5'  O5'   single    1.410  0.020  1.410
 A5J  C5'  C4'   single    1.522  0.020  1.522
 A5J  O3'  C3'   single    1.411  0.020  1.411
 A5J  C4'  C3'   single    1.523  0.020  1.523
 A5J  C4'  O4'   single    1.413  0.020  1.413
 A5J  C3'  C2'   single    1.526  0.020  1.526
 A5J  O4'  C1'   single    1.435  0.020  1.435
 A5J  C2'  C1'   single    1.536  0.020  1.536
 A5J  C1'  C1    single    1.507  0.020  1.507
 A5J  ON2  N     single    1.386  0.020  1.386
 A5J  C6   C1    aromatic  1.397  0.020  1.397
 A5J  C6   C5    aromatic  1.374  0.020  1.374
 A5J  C1   C2    aromatic  1.392  0.020  1.392
 A5J  N    C5    single    1.405  0.020  1.405
 A5J  N    ON1   single    1.374  0.020  1.374
 A5J  C5   C4    aromatic  1.419  0.020  1.419
 A5J  C2   O2    single    1.351  0.020  1.351
 A5J  C2   N3    aromatic  1.320  0.020  1.320
 A5J  C4   N3    aromatic  1.330  0.020  1.330
 A5J  C4   N4    single    1.357  0.020  1.357
 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

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   109.29  3.000
 A5J  ON1   N    C5    112.59  3.000
 A5J  ON2   N    C5    112.50  3.000
 A5J  C1'   C1   C6    122.38  3.000
 A5J  C6    C1   C2    114.89  3.000
 A5J  C1'   C1   C2    121.65  3.000
 A5J  N3    C2   O2    112.59  3.000
 A5J  N3    C2   C1    123.73  3.000
 A5J  O2    C2   C1    123.65  3.000
 A5J  H21   O2   C2    111.06  3.000
 A5J  C4    N3   C2    120.74  3.000
 A5J  C5    C4   N4    122.76  3.000
 A5J  N4    C4   N3    116.56  3.000
 A5J  C5    C4   N3    120.68  3.000
 A5J  H42   N4   H41   115.47  3.000
 A5J  H42   N4   C4    120.13  3.000
 A5J  H41   N4   C4    114.77  3.000
 A5J  C6    C5   C4    116.70  3.000
 A5J  C4    C5   N     119.69  3.000
 A5J  C6    C5   N     122.81  3.000
 A5J  H61   C6   C5    116.98  3.000
 A5J  H61   C6   C1    120.02  3.000
 A5J  C5    C6   C1    122.95  3.000
 A5J  H1'1  C1'  O4'   106.72  3.000
 A5J  H1'1  C1'  C2'   107.79  3.000
 A5J  O4'   C1'  C2'   105.83  3.000
 A5J  H1'1  C1'  C1    110.40  3.000
 A5J  C2'   C1'  C1    116.54  3.000
 A5J  O4'   C1'  C1    109.05  3.000
 A5J  H2'2  C2'  H2'1  106.55  3.000
 A5J  H2'2  C2'  C3'   109.33  3.000
 A5J  H2'1  C2'  C3'   112.62  3.000
 A5J  H2'2  C2'  C1'   112.88  3.000
 A5J  H2'1  C2'  C1'   111.71  3.000
 A5J  C3'   C2'  C1'   103.86  3.000
 A5J  H3'1  C3'  C4'   112.17  3.000
 A5J  H3'1  C3'  O3'   111.13  3.000
 A5J  C4'   C3'  O3'   107.55  3.000
 A5J  H3'1  C3'  C2'   111.52  3.000
 A5J  C4'   C3'  C2'   101.45  3.000
 A5J  O3'   C3'  C2'   112.61  3.000
 A5J  H3'2  O3'  C3'   108.00  3.000
 A5J  H4'1  C4'  C5'   108.29  3.000
 A5J  H4'1  C4'  O4'   107.87  3.000
 A5J  C5'   C4'  O4'   112.90  3.000
 A5J  H4'1  C4'  C3'   110.80  3.000
 A5J  O4'   C4'  C3'   104.47  3.000
 A5J  C5'   C4'  C3'   112.42  3.000
 A5J  C4'   O4'  C1'   110.26  3.000
 A5J  H5'2  C5'  H5'1  107.14  3.000
 A5J  H5'2  C5'  O5'   110.88  3.000
 A5J  H5'1  C5'  O5'   111.12  3.000
 A5J  H5'2  C5'  C4'   110.93  3.000
 A5J  H5'1  C5'  C4'   108.23  3.000
 A5J  O5'   C5'  C4'   108.52  3.000
 A5J  PA    O5'  C5'   120.25  3.000
 A5J  HN11  ON1  N     101.23  3.000
 A5J  HN21  ON2  N      99.92  3.000
 A5J  PB    O3A  PA    124.19  3.000
 A5J  PG    O3B  PB    127.41  3.000
 A5J  O3A   PA   O2A   109.36  3.000
 A5J  O2A   PA   O1A   121.54  3.000
 A5J  O3A   PA   O1A   110.38  3.000
 A5J  O2A   PA   O5'   104.66  3.000
 A5J  O3A   PA   O5'    98.92  3.000
 A5J  O1A   PA   O5'   109.45  3.000
 A5J  O3B   PB   O3A    96.27  3.000
 A5J  O3A   PB   O2B   109.41  3.000
 A5J  O3B   PB   O2B   111.27  3.000
 A5J  O3A   PB   O1B   107.29  3.000
 A5J  O3B   PB   O1B   113.00  3.000
 A5J  O2B   PB   O1B   117.38  3.000
 A5J  O3G   PG   O3B   103.08  3.000
 A5J  O3B   PG   O2G   103.90  3.000
 A5J  O3G   PG   O2G   111.67  3.000
 A5J  O3B   PG   O1G   106.30  3.000
 A5J  O3G   PG   O1G   116.65  3.000
 A5J  O2G   PG   O1G   113.64  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  CONST_18  ON1   N    C5   C4   180.00   0.0  0
 A5J  CONST_20  ON1   N    C5   C6     0.00   0.0  0
 A5J  Var_01    O1A   PA   O5'  C5'  -33.76  30.0  3
 A5J  Var_02    H5'1  C5'  O5'  PA    57.12  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

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

