# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 14:00:59 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: 5'-O-[(R)-{[(2S)-4-amino-2-ammonio-4-oxobutanoyl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)C[C@H]([NH3+])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
 4AD  4AD  5'-O-[(R)-{[(2S)-4-amino-2-ammonio-4-oxobutanoyl]oxy}(hydroxy)phosphoryl]adenosine  ligand  52  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4AD
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
 4AD  O2P   O  O     0  -0.649  -1.5481   8.4319  41.7298
 4AD  P     P  P     0   1.506  -2.8775   8.9806  41.4563
 4AD  O1P   O  OH1   0  -0.710  -2.8987  10.5228  41.1466
 4AD  O3P   O  O2    0  -0.570  -3.8187   8.7357  42.8030
 4AD  C     C  C     0   0.628  -5.0663   9.1918  42.9326
 4AD  O     O  O     0  -0.387  -5.6000   9.9374  42.1646
 4AD  CA    C  CH1   0  -0.263  -5.7173   8.6370  44.1797
 4AD  N     N  NT3   1  -0.793  -7.0575   9.2427  44.3304
 4AD  CB    C  CH2   0  -0.610  -5.8163   7.1133  44.1429
 4AD  CG    C  C     0   0.589  -6.4308   6.5503  45.4125
 4AD  OD1   O  O     0  -0.502  -7.2084   7.2165  46.0946
 4AD  ND2   N  NH2   0  -0.790  -6.0896   5.3007  45.7021
 4AD  O5'   O  O2    0  -0.590  -3.7351   8.3389  40.2918
 4AD  C5'   C  CH2   0  -0.230  -3.8594   6.9151  40.1201
 4AD  C4'   C  CH1   0   0.013  -3.3926   6.5050  38.7483
 4AD  C3'   C  CH1   0  -0.007  -1.9468   6.8694  38.3913
 4AD  O3'   O  OH1   0  -0.653  -0.9852   6.0355  38.9508
 4AD  C2'   C  CH1   0  -0.080  -2.0153   6.8619  36.8648
 4AD  O2'   O  OH1   0  -0.668  -1.9724   5.5204  36.4575
 4AD  C1'   C  CH1   0   0.186  -3.4108   7.4551  36.6282
 4AD  O4'   O  O2    0  -0.496  -4.1858   7.1266  37.7430
 4AD  N9    N  NR5   0  -0.539  -3.3599   8.9064  36.4914
 4AD  C4    C  CR56  0   0.484  -2.8139   9.5625  35.4273
 4AD  N3    N  N     0  -0.460  -2.2128   9.0366  34.3608
 4AD  C2    C  CR16  0   0.039  -1.8045   9.9734  33.5224
 4AD  N1    N  N     0  -0.474  -1.9261  11.2935  33.6351
 4AD  C6    C  CR6   0   0.458  -2.5323  11.8050  34.7126
 4AD  N6    N  NH2   0  -0.816  -2.6524  13.1277  34.8276
 4AD  C5    C  CR56  0  -0.000  -3.0178  10.9085  35.6833
 4AD  N7    N  N     0  -0.451  -3.6818  11.0810  36.8686
 4AD  C8    C  CR15  0   0.103  -3.8709   9.8728  37.3148
 4AD  HOP1  H  HOH1  0   0.508  -3.7555  10.9450  40.9835
 4AD  HA    H  HCH1  0   0.376  -5.1309   8.9547  45.0453
 4AD  HN1   H  HNT3  0   0.470  -7.6539   9.1132  43.5116
 4AD  HN2   H  HNT3  0   0.482  -7.0164  10.2432  44.5266
 4AD  HN3   H  HNT3  0   0.484  -7.5054   8.7683  45.1345
 4AD  HB1   H  HCH2  0   0.323  -4.8217   6.6963  43.9892
 4AD  HB2   H  HCH2  0   0.327  -6.4282   6.7917  43.2943
 4AD  HD21  H  HNH2  0   0.422  -5.4252   4.7864  45.1489
 4AD  HD22  H  HNH2  0   0.416  -6.4985   4.8293  46.4939
 4AD  H5'1  H  HCH2  0   0.286  -4.9098   6.6616  40.2653
 4AD  H5'2  H  HCH2  0   0.267  -3.2714   6.3657  40.8585
 4AD  H4'   H  HCH1  0   0.261  -3.5213   5.4152  38.7026
 4AD  H3'   H  HCH1  0   0.265  -1.7242   7.8864  38.7254
 4AD  H2    H  HOH1  0   0.450  -1.0029   5.1940  38.4787
 4AD  H2'   H  HCH1  0   0.281  -1.2269   7.4584  36.3973
 4AD  H1    H  HOH1  0   0.472  -1.7568   5.4781  35.5208
 4AD  H1'   H  HCH1  0   0.285  -3.8668   7.0567  35.7171
 4AD  H3    H  HCR6  0   0.252  -1.3047   9.6266  32.6244
 4AD  HN61  H  HNH2  0   0.412  -3.1094  13.5417  35.6208
 4AD  HN62  H  HNH2  0   0.404  -2.3103  13.7345  34.1027
 4AD  H8    H  HCR5  0   0.290  -4.3851   9.6291  38.2292

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
 4AD  O2P  P     double    1.464  0.020  1.464
 4AD  P    O1P   single    1.573  0.020  1.573
 4AD  P    O3P   single    1.661  0.020  1.661
 4AD  P    O5'   single    1.582  0.020  1.582
 4AD  O1P  HOP1  single    0.850  0.020  0.980
 4AD  O3P  C     single    1.335  0.020  1.335
 4AD  C    O     double    1.196  0.020  1.196
 4AD  C    CA    single    1.512  0.020  1.512
 4AD  CA   N     single    1.478  0.020  1.478
 4AD  CA   CB    single    1.527  0.020  1.527
 4AD  CA   HA    single    0.970  0.020  1.090
 4AD  N    HN1   single    0.890  0.020  1.040
 4AD  N    HN2   single    0.890  0.020  1.040
 4AD  N    HN3   single    0.890  0.020  1.040
 4AD  CB   CG    single    1.519  0.020  1.519
 4AD  CB   HB1   single    0.970  0.020  1.090
 4AD  CB   HB2   single    0.970  0.020  1.090
 4AD  CG   OD1   double    1.230  0.020  1.230
 4AD  CG   ND2   single    1.327  0.020  1.327
 4AD  ND2  HD21  single    0.860  0.020  1.020
 4AD  ND2  HD22  single    0.860  0.020  1.020
 4AD  O5'  C5'   single    1.439  0.020  1.439
 4AD  C5'  C4'   single    1.506  0.020  1.506
 4AD  C5'  H5'1  single    0.970  0.020  1.090
 4AD  C5'  H5'2  single    0.970  0.020  1.090
 4AD  C4'  C3'   single    1.533  0.020  1.533
 4AD  C4'  O4'   single    1.423  0.020  1.423
 4AD  C4'  H4'   single    0.970  0.020  1.090
 4AD  C3'  O3'   single    1.390  0.020  1.390
 4AD  C3'  C2'   single    1.528  0.020  1.528
 4AD  C3'  H3'   single    0.970  0.020  1.090
 4AD  O3'  H2    single    0.850  0.020  0.980
 4AD  C2'  O2'   single    1.403  0.020  1.403
 4AD  C2'  C1'   single    1.535  0.020  1.535
 4AD  C2'  H2'   single    0.970  0.020  1.090
 4AD  O2'  H1    single    0.850  0.020  0.980
 4AD  C1'  O4'   single    1.397  0.020  1.397
 4AD  C1'  N9    single    1.459  0.020  1.459
 4AD  C1'  H1'   single    0.970  0.020  1.090
 4AD  N9   C4    aromatic  1.364  0.020  1.364
 4AD  N9   C8    aromatic  1.369  0.020  1.369
 4AD  C4   N3    aromatic  1.332  0.020  1.332
 4AD  C4   C5    aromatic  1.385  0.020  1.385
 4AD  N3   C2    aromatic  1.322  0.020  1.322
 4AD  C2   N1    aromatic  1.330  0.020  1.330
 4AD  C2   H3    single    0.930  0.020  1.080
 4AD  N1   C6    aromatic  1.338  0.020  1.338
 4AD  C6   N6    single    1.333  0.020  1.333
 4AD  C6   C5    aromatic  1.408  0.020  1.408
 4AD  N6   HN61  single    0.860  0.020  1.020
 4AD  N6   HN62  single    0.860  0.020  1.020
 4AD  C5   N7    aromatic  1.370  0.020  1.370
 4AD  N7   C8    aromatic  1.302  0.020  1.302
 4AD  C8   H8    single    0.930  0.020  1.080

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
 4AD  O5'   P    O3P   103.28  3.000
 4AD  O5'   P    O1P   104.20  3.000
 4AD  O3P   P    O1P   107.25  3.000
 4AD  O5'   P    O2P   118.54  3.000
 4AD  O3P   P    O2P   107.93  3.000
 4AD  O1P   P    O2P   114.61  3.000
 4AD  HOP1  O1P  P     118.17  3.000
 4AD  C     O3P  P     123.92  3.000
 4AD  CA    C    O     124.48  3.000
 4AD  CA    C    O3P   110.93  3.000
 4AD  O     C    O3P   124.60  3.000
 4AD  HA    CA   CB    110.11  3.000
 4AD  HA    CA   N     106.66  3.000
 4AD  CB    CA   N     110.64  3.000
 4AD  HA    CA   C     108.39  3.000
 4AD  CB    CA   C     111.96  3.000
 4AD  N     CA   C     108.90  3.000
 4AD  HN3   N    HN2   108.50  3.000
 4AD  HN3   N    HN1   108.17  3.000
 4AD  HN2   N    HN1   107.58  3.000
 4AD  HN3   N    CA    106.47  3.000
 4AD  HN2   N    CA    112.63  3.000
 4AD  HN1   N    CA    113.31  3.000
 4AD  HB2   CB   HB1   106.77  3.000
 4AD  HB2   CB   CG    108.24  3.000
 4AD  HB1   CB   CG    110.21  3.000
 4AD  HB2   CB   CA    110.37  3.000
 4AD  HB1   CB   CA    109.03  3.000
 4AD  CG    CB   CA    112.08  3.000
 4AD  ND2   CG   OD1   123.46  3.000
 4AD  ND2   CG   CB    115.30  3.000
 4AD  OD1   CG   CB    121.23  3.000
 4AD  HD22  ND2  HD21  117.44  3.000
 4AD  HD22  ND2  CG    120.48  3.000
 4AD  HD21  ND2  CG    122.08  3.000
 4AD  C5'   O5'  P     122.39  3.000
 4AD  H5'2  C5'  H5'1  108.16  3.000
 4AD  H5'2  C5'  C4'   108.17  3.000
 4AD  H5'1  C5'  C4'   110.89  3.000
 4AD  H5'2  C5'  O5'   111.75  3.000
 4AD  H5'1  C5'  O5'   107.30  3.000
 4AD  C4'   C5'  O5'   110.56  3.000
 4AD  H4'   C4'  O4'   109.79  3.000
 4AD  H4'   C4'  C3'   109.67  3.000
 4AD  O4'   C4'  C3'   104.91  3.000
 4AD  H4'   C4'  C5'   105.78  3.000
 4AD  O4'   C4'  C5'   110.59  3.000
 4AD  C3'   C4'  C5'   116.08  3.000
 4AD  H3'   C3'  C2'   108.60  3.000
 4AD  H3'   C3'  O3'   107.11  3.000
 4AD  C2'   C3'  O3'   115.47  3.000
 4AD  H3'   C3'  C4'   109.99  3.000
 4AD  C2'   C3'  C4'   100.91  3.000
 4AD  O3'   C3'  C4'   114.58  3.000
 4AD  H2    O3'  C3'   108.27  3.000
 4AD  H2'   C2'  C1'   112.26  3.000
 4AD  H2'   C2'  O2'   112.06  3.000
 4AD  C1'   C2'  O2'   110.65  3.000
 4AD  H2'   C2'  C3'   113.08  3.000
 4AD  C1'   C2'  C3'   101.12  3.000
 4AD  O2'   C2'  C3'   107.06  3.000
 4AD  H1    O2'  C2'   109.37  3.000
 4AD  H1'   C1'  N9    107.38  3.000
 4AD  H1'   C1'  O4'   110.35  3.000
 4AD  N9    C1'  O4'   109.17  3.000
 4AD  H1'   C1'  C2'   111.50  3.000
 4AD  N9    C1'  C2'   111.55  3.000
 4AD  O4'   C1'  C2'   106.89  3.000
 4AD  C1'   O4'  C4'   110.93  3.000
 4AD  C8    N9   C4    106.21  3.000
 4AD  C8    N9   C1'   129.27  3.000
 4AD  C4    N9   C1'   124.45  3.000
 4AD  C5    C4   N3    126.71  3.000
 4AD  C5    C4   N9    105.32  3.000
 4AD  N3    C4   N9    127.96  3.000
 4AD  C2    N3   C4    111.55  3.000
 4AD  H3    C2   N1    115.43  3.000
 4AD  H3    C2   N3    116.16  3.000
 4AD  N1    C2   N3    128.41  3.000
 4AD  C6    N1   C2    119.27  3.000
 4AD  C5    C6   N6    122.77  3.000
 4AD  C5    C6   N1    117.91  3.000
 4AD  N6    C6   N1    119.32  3.000
 4AD  HN62  N6   HN61  118.38  3.000
 4AD  HN62  N6   C6    120.39  3.000
 4AD  HN61  N6   C6    121.20  3.000
 4AD  N7    C5   C6    133.15  3.000
 4AD  N7    C5   C4    110.71  3.000
 4AD  C6    C5   C4    116.14  3.000
 4AD  C8    N7   C5    104.49  3.000
 4AD  H8    C8   N7    124.77  3.000
 4AD  H8    C8   N9    121.96  3.000
 4AD  N7    C8   N9    113.26  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
 4AD  CONST_01  C2    N3   C4   N9    180.00   0.0  0
 4AD  CONST_02  C6    C5   C4   N9    180.00   0.0  0
 4AD  CONST_03  N7    C5   C4   N9      0.00   0.0  0
 4AD  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 4AD  CONST_05  N7    C8   N9   C4      0.00   0.0  0
 4AD  CONST_06  N1    C2   N3   C4      0.00   0.0  0
 4AD  CONST_07  N1    C6   C5   C4      0.00   0.0  0
 4AD  CONST_08  C8    N7   C5   C4      0.00   0.0  0
 4AD  CONST_09  C8    N9   C4   N3    180.00   0.0  0
 4AD  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 4AD  CONST_11  N7    C5   C4   N3    180.00   0.0  0
 4AD  CONST_12  C6    N1   C2   N3      0.00   0.0  0
 4AD  CONST_13  C5    C4   N3   C2      0.00   0.0  0
 4AD  CONST_14  C5    C6   N1   C2      0.00   0.0  0
 4AD  CONST_15  N7    C5   C6   N1    180.00   0.0  0
 4AD  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 4AD  CONST_17  C8    N9   C4   C5      0.00   0.0  0
 4AD  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 4AD  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 4AD  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 4AD  CONST_21  N6    C6   C5   C4    180.00   0.0  0
 4AD  CONST_22  N6    C6   N1   C2    180.00   0.0  0
 4AD  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 4AD  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 4AD  CONST_25  H3    C2   N3   C4    180.00   0.0  0
 4AD  CONST_26  HN61  N6   C6   N1    180.00   0.0  0
 4AD  CONST_27  HN62  N6   C6   N1      0.00   0.0  0
 4AD  CONST_28  HD21  ND2  CG   CB      0.00   0.0  0
 4AD  CONST_29  HD22  ND2  CG   CB    180.00   0.0  0
 4AD  Var_01    C4'   C5'  O5'  P    -122.49  30.0  3
 4AD  Var_02    O     C    O3P  P      -8.02  30.0  3
 4AD  Var_03    O5'   P    O3P  C     -58.26  30.0  2
 4AD  Var_04    OD1   CG   CB   CA     26.77  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
 4AD  chir_02  CA   C    N    CB   negativ
 4AD  chir_03  C4'  O4'  C5'  C3'  positiv
 4AD  chir_04  C3'  O3'  C4'  C2'  positiv
 4AD  chir_05  C2'  O2'  C3'  C1'  positiv
 4AD  chir_06  C1'  O4'  N9   C2'  negativ
 4AD  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
 4AD  plan-1  C1'   0.020
 4AD  plan-1  N9    0.020
 4AD  plan-1  C4    0.020
 4AD  plan-1  N3    0.020
 4AD  plan-1  C2    0.020
 4AD  plan-1  N1    0.020
 4AD  plan-1  C6    0.020
 4AD  plan-1  N6    0.020
 4AD  plan-1  C5    0.020
 4AD  plan-1  N7    0.020
 4AD  plan-1  C8    0.020
 4AD  plan-1  H3    0.020
 4AD  plan-1  H8    0.020
 4AD  plan-2  C6    0.020
 4AD  plan-2  N6    0.020
 4AD  plan-2  HN61  0.020
 4AD  plan-2  HN62  0.020
 4AD  plan-3  CB    0.020
 4AD  plan-3  CG    0.020
 4AD  plan-3  OD1   0.020
 4AD  plan-3  ND2   0.020
 4AD  plan-3  HD21  0.020
 4AD  plan-3  HD22  0.020
 4AD  plan-4  O3P   0.020
 4AD  plan-4  C     0.020
 4AD  plan-4  O     0.020
 4AD  plan-4  CA    0.020

