# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 11 03:01:23 2020
#   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  51  32  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

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  OP    -1  -0.775  -2.4545  -3.1452   1.8397
 NB8  P     P  P      0   1.354  -2.5915  -3.2283   0.3589
 NB8  O1P   O  O      0  -0.764  -3.7076  -3.9230  -0.3362
 NB8  O3P   O  O2     0  -0.590  -2.5058  -1.6409  -0.2653
 NB8  C     C  C      0   0.592  -3.4646  -0.7624  -0.0266
 NB8  O     O  O      0  -0.442  -4.4615  -0.9988   0.6067
 NB8  CA    C  CH1    0  -0.214  -3.1356   0.5995  -0.6113
 NB8  N     N  NH2    0  -0.785  -4.3115   1.4355  -0.5970
 NB8  CB    C  CH2    0  -0.596  -1.9160   1.1580   0.1524
 NB8  CG    C  C      0   0.516  -1.5485   2.5242  -0.3786
 NB8  OD1   O  O      0  -0.479  -1.2007   2.7108  -1.5332
 NB8  ND2   N  NH1    0  -0.377  -1.6594   3.4985   0.5360
 NB8  OAJ   O  OH1    0  -0.567  -1.4468   4.8006   0.2115
 NB8  O5'   O  O2     0  -0.606  -1.2145  -3.7389  -0.3366
 NB8  C5'   C  CH2    0  -0.148   0.0418  -3.7338   0.3152
 NB8  C4'   C  CR15   0  -0.015   1.0911  -3.1587  -0.6143
 NB8  C3'   C  CR15   0  -0.052   2.5226  -3.3828  -0.1220
 NB8  O3'   O  OH1    0  -0.667   3.3481  -3.5994  -1.2374
 NB8  C2'   C  CR15   0  -0.045   2.8382  -2.0406   0.5400
 NB8  O2'   O  OH1    0  -0.653   4.1920  -1.7149   0.6146
 NB8  C1'   C  CR15   0   0.217   2.1193  -1.0906  -0.4099
 NB8  O4'   O  O      0  -0.484   0.9220  -1.7406  -0.7376
 NB8  N9    N  NR5    0  -0.549   1.8444   0.2053   0.1459
 NB8  C4    C  CR56   0   0.506   1.9982   1.3973  -0.5054
 NB8  N3    N  N      0  -0.444   2.4089   1.6085  -1.7480
 NB8  C2    C  CR16   0   0.051   2.4415   2.8942  -2.0483
 NB8  N1    N  N      0  -0.450   2.1284   3.9255  -1.2656
 NB8  C6    C  CR6    0   0.443   1.7150   3.6922  -0.0257
 NB8  N6    N  NH2    0  -0.864   1.3328   4.7495   0.7482
 NB8  C5    C  CR56   0   0.012   1.6336   2.3681   0.4166
 NB8  N7    N  N      0  -0.436   1.2497   1.7932   1.6011
 NB8  C8    C  CR15   0   0.107   1.3862   0.5176   1.4000
 NB8  HA    H  HCH1   0   0.280  -2.8385   0.4525  -1.6535
 NB8  HN1   H  HNH2   0   0.348  -4.5626   1.6947   0.3489
 NB8  HN2   H  HNH2   0   0.360  -4.1329   2.2935  -1.1016
 NB8  HB1C  H  HCH2   0   0.264  -2.1341   1.1911   1.2232
 NB8  HB2C  H  HCH2   0   0.282  -1.0578   0.4972   0.0177
 NB8  HD2   H  HNH1   0   0.412  -1.9730   3.3263   1.4797
 NB8  HAJ   H  HOH1   0   0.483  -0.4924   4.9540   0.3880
 NB8  H5'1  H  HCH2   0   0.221   0.0133  -3.1779   1.2563
 NB8  H5'2  H  HCH2   0   0.231   0.3149  -4.7664   0.5524
 NB8  H4'   H  HCR5   0   0.256   0.9740  -3.6209  -1.6005
 NB8  H3'   H  HCR5   0   0.255   2.5867  -4.2132   0.5924
 NB8  HB    H  HOH1   0   0.450   4.2613  -3.4504  -0.9655
 NB8  H2'   H  HCR5   0   0.252   2.3590  -2.0190   1.5268
 NB8  HC    H  HOH1   0   0.471   4.5692  -2.1231   1.4005
 NB8  H1'   H  HCR5   0   0.256   2.7378  -0.9114  -1.2969
 NB8  H8    H  HCR5   0   0.306   1.1662  -0.2447   2.1322
 NB8  H2    H  HCR6   0   0.259   2.7687   3.1471  -3.0502
 NB8  H61N  H  HNH2   0   0.408   1.7094   5.6442   0.4681
 NB8  H62N  H  HNH2   0   0.412   1.3615   4.6048   1.7475

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     deloc     1.489  0.020  1.489
 NB8  P    O1P   deloc     1.487  0.020  1.487
 NB8  P    O3P   single    1.708  0.020  1.708
 NB8  P    O5'   single    1.625  0.020  1.625
 NB8  O3P  C     single    1.322  0.020  1.322
 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    1.511  0.020  1.511
 NB8  CG   OD1   double    1.220  0.020  1.220
 NB8  CG   ND2   single    1.341  0.020  1.341
 NB8  ND2  OAJ   single    1.359  0.020  1.359
 NB8  O5'  C5'   single    1.415  0.020  1.415
 NB8  C5'  C4'   single    1.515  0.020  1.515
 NB8  C4'  C3'   single    1.530  0.020  1.530
 NB8  C4'  O4'   single    1.433  0.020  1.433
 NB8  C3'  O3'   single    1.404  0.020  1.404
 NB8  C3'  C2'   single    1.530  0.020  1.530
 NB8  C2'  O2'   single    1.394  0.020  1.394
 NB8  C2'  C1'   single    1.524  0.020  1.524
 NB8  C1'  O4'   single    1.401  0.020  1.401
 NB8  C1'  N9    single    1.437  0.020  1.437
 NB8  N9   C4    aromatic  1.367  0.020  1.367
 NB8  N9   C8    aromatic  1.371  0.020  1.371
 NB8  C4   N3    aromatic  1.326  0.020  1.326
 NB8  C4   C5    aromatic  1.388  0.020  1.388
 NB8  N3   C2    aromatic  1.321  0.020  1.321
 NB8  C2   N1    aromatic  1.332  0.020  1.332
 NB8  N1   C6    aromatic  1.328  0.020  1.328
 NB8  C6   N6    single    1.365  0.020  1.365
 NB8  C6   C5    aromatic  1.398  0.020  1.398
 NB8  C5   N7    aromatic  1.371  0.020  1.371
 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    0.860  0.020  1.020
 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    0.890  0.020  1.040
 NB8  N6   H62N  single    0.890  0.020  1.040
 NB8  N7   C8    aromatic  1.299  0.020  1.299

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  O5'   P    O3P    95.34  3.000
 NB8  O5'   P    O1P   106.81  3.000
 NB8  O3P   P    O1P   107.52  3.000
 NB8  O5'   P    O2P   111.41  3.000
 NB8  O3P   P    O2P   107.88  3.000
 NB8  O1P   P    O2P   124.04  3.000
 NB8  C     O3P  P     121.01  3.000
 NB8  CA    C    O     120.80  1.700
 NB8  CA    C    O3P   111.68  3.000
 NB8  O     C    O3P   124.38  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   107.03  3.000
 NB8  HN2   N    CA    110.04  3.000
 NB8  HN1   N    CA    111.08  3.000
 NB8  HB2C  CB   HB1C  107.22  3.000
 NB8  HB2C  CB   CG    108.23  3.000
 NB8  HB1C  CB   CG    111.43  3.000
 NB8  HB2C  CB   CA    109.95  3.000
 NB8  HB1C  CB   CA    109.75  3.000
 NB8  CG    CB   CA    110.21  3.000
 NB8  ND2   CG   OD1   123.91  3.000
 NB8  ND2   CG   CB    113.40  3.000
 NB8  OD1   CG   CB    122.69  3.000
 NB8  HD2   ND2  OAJ   115.81  3.000
 NB8  HD2   ND2  CG    122.66  3.000
 NB8  OAJ   ND2  CG    121.37  3.000
 NB8  HAJ   OAJ  ND2   105.00  3.000
 NB8  C5'   O5'  P     123.64  3.000
 NB8  H5'2  C5'  H5'1  107.44  3.000
 NB8  H5'2  C5'  C4'   108.57  3.000
 NB8  H5'1  C5'  C4'   110.68  3.000
 NB8  H5'2  C5'  O5'   108.55  3.000
 NB8  H5'1  C5'  O5'   112.03  3.000
 NB8  C4'   C5'  O5'   109.48  3.000
 NB8  H4'   C4'  O4'   109.11  3.000
 NB8  H4'   C4'  C3'   109.13  3.000
 NB8  O4'   C4'  C3'   106.43  3.000
 NB8  H4'   C4'  C5'   108.55  3.000
 NB8  O4'   C4'  C5'   110.28  3.000
 NB8  C3'   C4'  C5'   113.26  3.000
 NB8  H3'   C3'  C2'   111.73  3.000
 NB8  H3'   C3'  O3'   111.47  3.000
 NB8  C2'   C3'  O3'   110.96  3.000
 NB8  H3'   C3'  C4'   112.02  3.000
 NB8  C2'   C3'  C4'   101.76  3.000
 NB8  O3'   C3'  C4'   108.48  3.000
 NB8  HB    O3'  C3'   107.99  3.000
 NB8  H2'   C2'  C1'   110.02  3.000
 NB8  H2'   C2'  O2'   111.80  3.000
 NB8  C1'   C2'  O2'   110.23  3.000
 NB8  H2'   C2'  C3'   108.45  3.000
 NB8  C1'   C2'  C3'   100.37  3.000
 NB8  O2'   C2'  C3'   115.37  3.000
 NB8  HC    O2'  C2'   108.98  3.000
 NB8  H1'   C1'  N9    105.88  3.000
 NB8  H1'   C1'  O4'   111.63  3.000
 NB8  N9    C1'  O4'   110.21  3.000
 NB8  H1'   C1'  C2'   109.89  3.000
 NB8  N9    C1'  C2'   114.30  3.000
 NB8  O4'   C1'  C2'   105.05  3.000
 NB8  C1'   O4'  C4'   109.75  3.000
 NB8  C8    N9   C4    105.95  3.000
 NB8  C8    N9   C1'   128.55  3.000
 NB8  C4    N9   C1'   125.50  3.000
 NB8  C5    C4   N3    126.35  3.000
 NB8  C5    C4   N9    105.30  3.000
 NB8  N3    C4   N9    128.34  3.000
 NB8  C2    N3   C4    112.08  3.000
 NB8  H2    C2   N1    115.69  3.000
 NB8  H2    C2   N3    116.41  3.000
 NB8  N1    C2   N3    127.90  3.000
 NB8  C6    N1   C2    119.07  3.000
 NB8  C5    C6   N6    122.53  3.000
 NB8  C5    C6   N1    118.68  3.000
 NB8  N6    C6   N1    118.72  3.000
 NB8  H62N  N6   H61N  112.99  3.000
 NB8  H62N  N6   C6    116.23  3.000
 NB8  H61N  N6   C6    115.11  3.000
 NB8  N7    C5   C6    133.35  3.000
 NB8  N7    C5   C4    110.74  3.000
 NB8  C6    C5   C4    115.91  3.000
 NB8  C8    N7   C5    104.39  3.000
 NB8  H8    C8   N7    124.54  3.000
 NB8  N7    C8   N9    113.61  3.000
 NB8  H8    C8   N9    121.84  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_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    -134.01  30.0  3
 NB8  Var_02    O    C    O3P  P      -1.49  30.0  3
 NB8  Var_03    O5'  P    O3P  C     177.64  30.0  2
 NB8  Var_04    OD1  CG   CB   CA    -61.72  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

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

