# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 06:13:29 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: 5'-O-[(R)-{[(2S)-2-amino-4-(hydroxyamino)-4-oxobutanoyl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)NO)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 NB8  NB8  5'-O-[(R)-{[(2S)-2-amino-4-(hydroxyamino)-4-oxobutanoyl]oxy}(hydroxy)phosphoryl]adenosine  L-peptide  52  32  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NB8
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
 NB8  O2P   O  OH1   0  -0.709   7.0006  -12.9264  49.7519
 NB8  P     P  P     0   1.516   8.5144  -13.3283  49.5744
 NB8  O1P   O  O     0  -0.679   8.8690  -14.7566  49.4639
 NB8  O3P   O  O2    0  -0.583   9.0660  -12.5910  48.2242
 NB8  C     C  C     0   0.606   8.9642  -11.2593  47.9555
 NB8  O     O  O     0  -0.380   8.4138  -10.4944  48.6851
 NB8  CA    C  CH1   0  -0.234   9.6487  -10.9250  46.6488
 NB8  N     N  NH2   0  -0.782   9.3389   -9.5664  46.2842
 NB8  CB    C  CH2   0  -0.613  11.1488  -11.2500  46.7660
 NB8  CG    C  C     0   0.537  11.8392  -11.0360  45.4358
 NB8  OD1   O  O     0  -0.473  11.3567  -11.3980  44.3777
 NB8  ND2   N  NH1   0  -0.371  13.0188  -10.4017  45.5420
 NB8  OAJ   O  OH1   0  -0.542  13.8484  -10.3277  44.4649
 NB8  O5'   O  O2    0  -0.584   9.1366  -12.5245  50.7910
 NB8  C5'   C  CH2   0  -0.250  10.4973  -12.7677  51.1888
 NB8  C4'   C  CH1   0   0.023  10.5857  -13.5697  52.4606
 NB8  C3'   C  CH1   0  -0.021   9.7434  -14.8451  52.5473
 NB8  O3'   O  OH1   0  -0.671  10.2517  -15.9240  51.8298
 NB8  C2'   C  CH1   0  -0.048   9.7525  -15.0788  54.0551
 NB8  O2'   O  OH1   0  -0.661  10.9842  -15.5674  54.5107
 NB8  C1'   C  CH1   0   0.175   9.6215  -13.6377  54.5641
 NB8  O4'   O  O2    0  -0.494  10.1530  -12.7995  53.5768
 NB8  N9    N  NR5   0  -0.534   8.2368  -13.2613  54.7960
 NB8  C4    C  CR56  0   0.489   7.5387  -13.5218  55.9384
 NB8  N3    N  N     0  -0.458   7.9655  -14.1399  57.0377
 NB8  C2    C  CR16  0   0.042   7.0132  -14.2185  57.9513
 NB8  N1    N  N     0  -0.473   5.7606  -13.7757  57.8798
 NB8  C6    C  CR6   0   0.454   5.3479  -13.1578  56.7676
 NB8  N6    N  NH2   0  -0.815   4.0962  -12.6981  56.7013
 NB8  C5    C  CR56  0  -0.002   6.2711  -13.0077  55.7165
 NB8  N7    N  N     0  -0.450   6.1872  -12.4443  54.4706
 NB8  C8    C  CR15  0   0.101   7.3699  -12.6155  53.9560
 NB8  H2P   H  HOH1  0   0.516   6.3726  -13.4616  49.2453
 NB8  HA    H  HCH1  0   0.300   9.2194  -11.5854  45.8891
 NB8  HN1   H  HNH2  0   0.353   9.8749   -8.9065  46.8338
 NB8  HN2   H  HNH2  0   0.366   9.5747   -9.4093  45.3140
 NB8  HB1C  H  HCH2  0   0.277  11.6008  -10.6412  47.5537
 NB8  HB2C  H  HCH2  0   0.297  11.3053  -12.2961  47.0416
 NB8  HD2   H  HNH1  0   0.419  13.4665  -10.2409  46.4333
 NB8  HAJ   H  HOH1  0   0.480  13.7282   -9.4434  44.0954
 NB8  H5'1  H  HCH2  0   0.262  11.0559  -13.2970  50.4135
 NB8  H5'2  H  HCH2  0   0.291  10.9657  -11.7921  51.3170
 NB8  H4'   H  HCH1  0   0.256  11.6459  -13.8306  52.5751
 NB8  H3'   H  HCH1  0   0.232   8.7054  -14.6285  52.2624
 NB8  HB    H  HOH1  0   0.463   9.9320  -15.8431  50.9210
 NB8  H2'   H  HCH1  0   0.268   8.9146  -15.7016  54.3895
 NB8  HC    H  HOH1  0   0.461  11.1693  -16.4017  54.0658
 NB8  H1'   H  HCH1  0   0.284  10.1491  -13.5099  55.5136
 NB8  H8    H  HCR5  0   0.292   7.6662  -12.2823  52.9741
 NB8  H2    H  HCR6  0   0.253   7.2814  -14.7097  58.8805
 NB8  H61N  H  HNH2  0   0.403   3.4401  -12.9293  57.4275
 NB8  H62N  H  HNH2  0   0.410   3.7310  -12.3311  55.8399

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
 NB8  O2P  P     single    1.576  0.020  1.576
 NB8  P    O1P   double    1.476  0.020  1.476
 NB8  P    O3P   single    1.634  0.020  1.634
 NB8  P    O5'   single    1.585  0.020  1.585
 NB8  O3P  C     single    1.362  0.020  1.362
 NB8  C    O     double    1.231  0.020  1.231
 NB8  C    CA    single    1.525  0.021  1.525
 NB8  CA   N     single    1.458  0.019  1.458
 NB8  CA   CB    single    1.521  0.033  1.521
 NB8  CB   CG    single    1.514  0.020  1.514
 NB8  CG   OD1   double    1.218  0.020  1.218
 NB8  CG   ND2   single    1.344  0.020  1.344
 NB8  ND2  OAJ   single    1.361  0.020  1.361
 NB8  O5'  C5'   single    1.438  0.020  1.438
 NB8  C5'  C4'   single    1.506  0.020  1.506
 NB8  C4'  C3'   single    1.531  0.020  1.531
 NB8  C4'  O4'   single    1.423  0.020  1.423
 NB8  C3'  O3'   single    1.392  0.020  1.392
 NB8  C3'  C2'   single    1.526  0.020  1.526
 NB8  C2'  O2'   single    1.401  0.020  1.401
 NB8  C2'  C1'   single    1.534  0.020  1.534
 NB8  C1'  O4'   single    1.400  0.020  1.400
 NB8  C1'  N9    single    1.454  0.020  1.454
 NB8  N9   C4    aromatic  1.364  0.020  1.364
 NB8  N9   C8    aromatic  1.369  0.020  1.369
 NB8  C4   N3    aromatic  1.331  0.020  1.331
 NB8  C4   C5    aromatic  1.386  0.020  1.386
 NB8  N3   C2    aromatic  1.322  0.020  1.322
 NB8  C2   N1    aromatic  1.331  0.020  1.331
 NB8  N1   C6    aromatic  1.338  0.020  1.338
 NB8  C6   N6    single    1.335  0.020  1.335
 NB8  C6   C5    aromatic  1.407  0.020  1.407
 NB8  C5   N7    aromatic  1.370  0.020  1.370
 NB8  O2P  H2P   single    0.850  0.020  0.980
 NB8  CA   HA    single    0.970  0.020  0.970
 NB8  N    HN1   single    0.890  0.020  1.040
 NB8  N    HN2   single    0.890  0.020  1.040
 NB8  CB   HB1C  single    0.970  0.020  1.090
 NB8  CB   HB2C  single    0.970  0.020  1.090
 NB8  ND2  HD2   single    0.890  0.020  1.040
 NB8  OAJ  HAJ   single    0.850  0.020  0.980
 NB8  C5'  H5'1  single    0.970  0.020  1.090
 NB8  C5'  H5'2  single    0.970  0.020  1.090
 NB8  C4'  H4'   single    0.970  0.020  1.090
 NB8  C3'  H3'   single    0.970  0.020  1.090
 NB8  O3'  HB    single    0.850  0.020  0.980
 NB8  C2'  H2'   single    0.970  0.020  1.090
 NB8  O2'  HC    single    0.850  0.020  0.980
 NB8  C1'  H1'   single    0.970  0.020  1.090
 NB8  C8   H8    single    0.930  0.020  1.080
 NB8  C2   H2    single    0.930  0.020  1.080
 NB8  N6   H61N  single    0.860  0.020  1.020
 NB8  N6   H62N  single    0.860  0.020  1.020
 NB8  N7   C8    aromatic  1.301  0.020  1.301

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
 NB8  H2P   O2P  P     115.03  3.000
 NB8  O5'   P    O3P   105.83  3.000
 NB8  O5'   P    O1P   117.00  3.000
 NB8  O3P   P    O1P   107.08  3.000
 NB8  O5'   P    O2P    99.28  3.000
 NB8  O3P   P    O2P   107.58  3.000
 NB8  O1P   P    O2P   119.08  3.000
 NB8  C     O3P  P     125.36  3.000
 NB8  CA    C    O     120.80  1.700
 NB8  CA    C    O3P   110.65  3.000
 NB8  O     C    O3P   122.77  3.000
 NB8  HA    CA   CB    109.00  3.000
 NB8  HA    CA   N     110.00  3.000
 NB8  CB    CA   N     110.40  1.500
 NB8  HA    CA   C     110.00  3.000
 NB8  CB    CA   C     110.50  1.500
 NB8  N     CA   C     111.00  2.800
 NB8  HN2   N    HN1   107.23  3.000
 NB8  HN2   N    CA    109.84  3.000
 NB8  HN1   N    CA    111.32  3.000
 NB8  HB2C  CB   HB1C  106.99  3.000
 NB8  HB2C  CB   CG    106.95  3.000
 NB8  HB1C  CB   CG    111.46  3.000
 NB8  HB2C  CB   CA    111.15  3.000
 NB8  HB1C  CB   CA    109.89  3.000
 NB8  CG    CB   CA    110.34  3.000
 NB8  ND2   CG   OD1   123.83  3.000
 NB8  ND2   CG   CB    113.44  3.000
 NB8  OD1   CG   CB    122.73  3.000
 NB8  HD2   ND2  OAJ   114.79  3.000
 NB8  HD2   ND2  CG    122.27  3.000
 NB8  OAJ   ND2  CG    119.88  3.000
 NB8  HAJ   OAJ  ND2   106.06  3.000
 NB8  C5'   O5'  P     119.86  3.000
 NB8  H5'2  C5'  H5'1  107.31  3.000
 NB8  H5'2  C5'  C4'   110.61  3.000
 NB8  H5'1  C5'  C4'   108.13  3.000
 NB8  H5'2  C5'  O5'   106.73  3.000
 NB8  H5'1  C5'  O5'   111.68  3.000
 NB8  C4'   C5'  O5'   112.28  3.000
 NB8  H4'   C4'  O4'   109.90  3.000
 NB8  H4'   C4'  C3'   109.11  3.000
 NB8  O4'   C4'  C3'   103.83  3.000
 NB8  H4'   C4'  C5'   105.74  3.000
 NB8  O4'   C4'  C5'   110.87  3.000
 NB8  C3'   C4'  C5'   117.33  3.000
 NB8  H3'   C3'  C2'   107.00  3.000
 NB8  H3'   C3'  O3'   111.36  3.000
 NB8  C2'   C3'  O3'   112.86  3.000
 NB8  H3'   C3'  C4'   109.95  3.000
 NB8  C2'   C3'  C4'   100.39  3.000
 NB8  O3'   C3'  C4'   114.56  3.000
 NB8  HB    O3'  C3'   107.40  3.000
 NB8  H2'   C2'  C1'   111.55  3.000
 NB8  H2'   C2'  O2'   112.00  3.000
 NB8  C1'   C2'  O2'   107.14  3.000
 NB8  H2'   C2'  C3'   112.58  3.000
 NB8  C1'   C2'  C3'   100.57  3.000
 NB8  O2'   C2'  C3'   112.33  3.000
 NB8  HC    O2'  C2'   108.70  3.000
 NB8  H1'   C1'  N9    106.90  3.000
 NB8  H1'   C1'  O4'   111.05  3.000
 NB8  N9    C1'  O4'   108.61  3.000
 NB8  H1'   C1'  C2'   110.90  3.000
 NB8  N9    C1'  C2'   112.18  3.000
 NB8  O4'   C1'  C2'   107.22  3.000
 NB8  C1'   O4'  C4'   110.15  3.000
 NB8  C8    N9   C4    106.26  3.000
 NB8  C8    N9   C1'   128.86  3.000
 NB8  C4    N9   C1'   124.87  3.000
 NB8  C5    C4   N3    126.70  3.000
 NB8  C5    C4   N9    105.26  3.000
 NB8  N3    C4   N9    128.04  3.000
 NB8  C2    N3   C4    111.55  3.000
 NB8  H2    C2   N1    115.43  3.000
 NB8  H2    C2   N3    116.16  3.000
 NB8  N1    C2   N3    128.41  3.000
 NB8  C6    N1   C2    119.27  3.000
 NB8  C5    C6   N6    122.77  3.000
 NB8  C5    C6   N1    117.90  3.000
 NB8  N6    C6   N1    119.32  3.000
 NB8  H62N  N6   H61N  117.76  3.000
 NB8  H62N  N6   C6    120.60  3.000
 NB8  H61N  N6   C6    119.78  3.000
 NB8  N7    C5   C6    133.08  3.000
 NB8  N7    C5   C4    110.75  3.000
 NB8  C6    C5   C4    116.17  3.000
 NB8  C8    N7   C5    104.47  3.000
 NB8  H8    C8   N7    124.70  3.000
 NB8  N7    C8   N9    113.26  3.000
 NB8  H8    C8   N9    122.04  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
 NB8  CONST_01  C2    N3   C4   N9    180.00   0.0  0
 NB8  CONST_02  C6    C5   C4   N9    180.00   0.0  0
 NB8  CONST_03  N7    C5   C4   N9      0.00   0.0  0
 NB8  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 NB8  CONST_05  N7    C8   N9   C4      0.00   0.0  0
 NB8  CONST_06  N1    C2   N3   C4      0.00   0.0  0
 NB8  CONST_07  N1    C6   C5   C4      0.00   0.0  0
 NB8  CONST_08  C8    N7   C5   C4      0.00   0.0  0
 NB8  CONST_09  C8    N9   C4   N3    180.00   0.0  0
 NB8  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 NB8  CONST_11  N7    C5   C4   N3    180.00   0.0  0
 NB8  CONST_12  C6    N1   C2   N3      0.00   0.0  0
 NB8  CONST_13  C5    C4   N3   C2      0.00   0.0  0
 NB8  CONST_14  C5    C6   N1   C2      0.00   0.0  0
 NB8  CONST_15  N7    C5   C6   N1    180.00   0.0  0
 NB8  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 NB8  CONST_17  C8    N9   C4   C5      0.00   0.0  0
 NB8  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 NB8  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 NB8  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 NB8  CONST_21  N6    C6   C5   C4    180.00   0.0  0
 NB8  CONST_22  N6    C6   N1   C2    180.00   0.0  0
 NB8  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 NB8  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 NB8  CONST_25  H2    C2   N3   C4    180.00   0.0  0
 NB8  CONST_26  H61N  N6   C6   N1      0.00   0.0  0
 NB8  CONST_27  H62N  N6   C6   N1    180.00   0.0  0
 NB8  CONST_28  OAJ   ND2  CG   CB    180.00   0.0  0
 NB8  CONST_29  OAJ   ND2  CG   OD1     0.00   0.0  0
 NB8  CONST_30  HD2   ND2  CG   CB      0.00   0.0  0
 NB8  Var_01    C4'   C5'  O5'  P    -105.34  30.0  3
 NB8  Var_02    O     C    O3P  P      -2.25  30.0  3
 NB8  Var_03    O5'   P    O3P  C     -52.94  30.0  2
 NB8  Var_04    OD1   CG   CB   CA    -42.94  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
 NB8  chir_02  CA   C    N    CB   negativ
 NB8  chir_03  C4'  O4'  C5'  C3'  positiv
 NB8  chir_04  C3'  O3'  C4'  C2'  positiv
 NB8  chir_05  C2'  O2'  C3'  C1'  positiv
 NB8  chir_06  C1'  O4'  N9   C2'  negativ
 NB8  chir_07  P    O1P  O3P  O5'  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
 NB8  plan-1  C1'   0.020
 NB8  plan-1  N9    0.020
 NB8  plan-1  C4    0.020
 NB8  plan-1  N3    0.020
 NB8  plan-1  C2    0.020
 NB8  plan-1  N1    0.020
 NB8  plan-1  C6    0.020
 NB8  plan-1  N6    0.020
 NB8  plan-1  C5    0.020
 NB8  plan-1  N7    0.020
 NB8  plan-1  C8    0.020
 NB8  plan-1  H8    0.020
 NB8  plan-1  H2    0.020
 NB8  plan-2  C6    0.020
 NB8  plan-2  N6    0.020
 NB8  plan-2  H61N  0.020
 NB8  plan-2  H62N  0.020
 NB8  plan-3  CB    0.020
 NB8  plan-3  CG    0.020
 NB8  plan-3  OD1   0.020
 NB8  plan-3  ND2   0.020
 NB8  plan-3  OAJ   0.020
 NB8  plan-3  HD2   0.020
 NB8  plan-4  O3P   0.020
 NB8  plan-4  C     0.020
 NB8  plan-4  O     0.020
 NB8  plan-4  CA    0.020

