# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 01:42:32 2021
#   Inital geometry file: a 136 line input string
#   Ligand name: 4-amino-2-[(4-{[amino(iminio)methyl]amino}butyl)amino]-1-(5-O-phosphonato-beta-D-ribofuranosyl)pyrimidin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(N)NCCCCNC1=N[C@@H](N)C=CN1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
#
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
 AG9  AG9  4-amino-2-[(4-{[amino(iminio)methyl]amino}butyl)amino]-1-(5-O-phosphonato-beta-D-ribofuranosyl)pyrimidin-1-ium  ligand  59  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AG9
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
 AG9  P     P  P     0   1.450  -124.1895  29.9198  -23.5291
 AG9  N1    N  NT    0  -0.575  -119.7802  27.5533  -25.9667
 AG9  C2    C  C     0   0.678  -118.5972  26.8659  -26.2041
 AG9  N2    N  NH1   0  -0.680  -118.1450  26.9060  -27.4956
 AG9  N3    N  N     0  -0.479  -117.9518  26.2219  -25.3073
 AG9  C4    C  CH1   0  -0.016  -118.5691  26.0112  -24.0187
 AG9  N4    N  NH2   0  -0.777  -119.2479  24.7141  -24.0030
 AG9  C5    C  C1    0  -0.382  -119.4638  27.1625  -23.6597
 AG9  C6    C  C1    0  -0.014  -120.0714  27.8343  -24.6348
 AG9  CA    C  CH2   0  -0.312  -116.8991  26.2691  -27.8675
 AG9  CB    C  CH2   0  -0.444  -115.6351  26.9963  -27.4126
 AG9  CD    C  CH2   0  -0.268  -115.5830  28.6522  -29.3540
 AG9  NE    N  NH1   0  -0.611  -115.3690  30.0452  -29.7009
 AG9  CG    C  CH2   0  -0.460  -115.5433  28.4556  -27.8449
 AG9  CZ    C  CH1   0   0.211  -115.3781  30.2964  -31.1357
 AG9  C1'   C  CH1   0   0.146  -120.6387  28.0148  -27.0646
 AG9  OP1   O  O     0  -0.709  -125.0469  29.0693  -22.6805
 AG9  C2'   C  CH1   0  -0.049  -121.2577  26.8306  -27.8257
 AG9  O2'   O  OH1   0  -0.660  -121.6844  27.2203  -29.1015
 AG9  OP2   O  OH1   0  -0.727  -124.6506  31.4286  -23.7439
 AG9  C3'   C  CH1   0  -0.001  -122.4912  26.5676  -26.9723
 AG9  O3'   O  OH1   0  -0.654  -123.4554  25.8251  -27.6525
 AG9  OP3   O  OH1   0  -0.734  -122.6783  30.0970  -23.0484
 AG9  C4'   C  CH1   0  -0.014  -122.9238  27.9945  -26.6137
 AG9  O4'   O  O2    0  -0.490  -121.7146  28.7464  -26.5579
 AG9  C5'   C  CH2   0  -0.173  -123.6586  28.0648  -25.2999
 AG9  O5'   O  O2    0  -0.589  -123.9959  29.4283  -25.0359
 AG9  NH1   N  NH2   0  -0.815  -114.8898  31.6434  -31.3457
 AG9  NH2   N  NH2   0  -0.795  -116.6926  30.2120  -31.7200
 AG9  HN2   H  HNH1  0   0.386  -118.3682  27.7287  -28.0316
 AG9  H1N4  H  HNH2  0   0.342  -119.4803  24.4723  -23.0462
 AG9  H2N4  H  HNH2  0   0.331  -120.1366  24.7955  -24.4860
 AG9  H5    H  H     0   0.248  -119.6412  27.4246  -22.6251
 AG9  H6    H  H     0   0.286  -120.7594  28.6447  -24.4518
 AG9  H1A   H  HCH2  0   0.243  -116.9096  26.1691  -28.9542
 AG9  H2A   H  HCH2  0   0.249  -116.8992  25.2578  -27.4617
 AG9  H1B   H  HCH2  0   0.237  -115.5696  26.9369  -26.3250
 AG9  H2B   H  HCH2  0   0.222  -114.7759  26.4455  -27.8085
 AG9  H1D   H  HCH2  0   0.209  -116.5614  28.3508  -29.7404
 AG9  H2D   H  HCH2  0   0.191  -114.8482  27.9801  -29.8285
 AG9  HNE   H  HNH1  0   0.336  -114.4724  30.3313  -29.3212
 AG9  H1G   H  HCH2  0   0.230  -114.6069  28.8697  -27.4579
 AG9  H2G   H  HCH2  0   0.217  -116.3432  29.0429  -27.3837
 AG9  H1'   H  HCH1  0   0.263  -120.0725  28.6759  -27.7307
 AG9  H2'   H  HCH1  0   0.267  -120.5864  25.9679  -27.8631
 AG9  HO2'  H  HOH1  0   0.460  -120.9133  27.3105  -29.6702
 AG9  H3'   H  HCH1  0   0.241  -122.1588  26.0531  -26.0594
 AG9  HO3'  H  HOH1  0   0.462  -123.9945  25.3535  -27.0114
 AG9  H4'   H  HCH1  0   0.255  -123.5606  28.3998  -27.4089
 AG9  H15'  H  HCH2  0   0.256  -124.5729  27.4699  -25.3703
 AG9  H25'  H  HCH2  0   0.236  -123.0472  27.6391  -24.4987
 AG9  H1H1  H  HNH2  0   0.344  -113.9182  31.7093  -31.0655
 AG9  H2H1  H  HNH2  0   0.346  -114.9037  31.8333  -32.3397
 AG9  H1H2  H  HNH2  0   0.351  -117.0092  29.2525  -31.7554
 AG9  H2H2  H  HNH2  0   0.335  -117.3523  30.7250  -31.1459
 AG9  HOP2  H  HOH1  0   0.503  -125.6057  31.5430  -23.8406
 AG9  HOP3  H  HOH1  0   0.502  -122.5579  30.0398  -22.0912
 AG9  HZ    H  HCH1  0   0.173  -114.7666  29.5382  -31.6606
 AG9  H4    H  HCH1  0   0.222  -117.7683  25.9277  -23.2779

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
 AG9  NH2  CZ    single  1.441  0.020  1.441
 AG9  NH1  CZ    single  1.448  0.020  1.448
 AG9  CZ   NE    single  1.457  0.020  1.457
 AG9  NE   CD    single  1.451  0.020  1.451
 AG9  CD   CG    single  1.522  0.020  1.522
 AG9  O2'  C2'   single  1.401  0.020  1.401
 AG9  CA   CB    single  1.528  0.020  1.528
 AG9  CA   N2    single  1.448  0.020  1.448
 AG9  CG   CB    single  1.525  0.020  1.525
 AG9  O3'  C3'   single  1.394  0.020  1.394
 AG9  C2'  C3'   single  1.523  0.020  1.523
 AG9  C2'  C1'   single  1.538  0.020  1.538
 AG9  N2   C2    single  1.369  0.020  1.369
 AG9  C3'  C4'   single  1.534  0.020  1.534
 AG9  C1'  O4'   single  1.396  0.020  1.396
 AG9  C1'  N1    single  1.468  0.020  1.468
 AG9  C4'  O4'   single  1.425  0.020  1.425
 AG9  C4'  C5'   single  1.507  0.020  1.507
 AG9  C2   N1    single  1.389  0.020  1.389
 AG9  C2   N3    double  1.279  0.020  1.279
 AG9  N1   C6    single  1.392  0.020  1.392
 AG9  N3   C4    single  1.444  0.020  1.444
 AG9  C5'  O5'   single  1.429  0.020  1.429
 AG9  O5'  P     single  1.597  0.020  1.597
 AG9  C6   C5    double  1.331  0.020  1.331
 AG9  C4   C5    single  1.502  0.020  1.502
 AG9  C4   N4    single  1.464  0.020  1.464
 AG9  P    OP1   double  1.476  0.020  1.476
 AG9  P    OP2   single  1.592  0.020  1.592
 AG9  P    OP3   single  1.596  0.020  1.596
 AG9  N2   HN2   single  0.890  0.020  1.040
 AG9  N4   H1N4  single  0.890  0.020  1.040
 AG9  N4   H2N4  single  0.890  0.020  1.040
 AG9  C5   H5    single  0.930  0.020  1.080
 AG9  C6   H6    single  0.930  0.020  1.080
 AG9  CA   H1A   single  0.970  0.020  1.090
 AG9  CA   H2A   single  0.970  0.020  1.090
 AG9  CB   H1B   single  0.970  0.020  1.090
 AG9  CB   H2B   single  0.970  0.020  1.090
 AG9  CD   H1D   single  0.970  0.020  1.090
 AG9  CD   H2D   single  0.970  0.020  1.090
 AG9  NE   HNE   single  0.890  0.020  1.040
 AG9  CG   H1G   single  0.970  0.020  1.090
 AG9  CG   H2G   single  0.970  0.020  1.090
 AG9  C1'  H1'   single  0.970  0.020  1.090
 AG9  C2'  H2'   single  0.970  0.020  1.090
 AG9  O2'  HO2'  single  0.850  0.020  0.980
 AG9  C3'  H3'   single  0.970  0.020  1.090
 AG9  O3'  HO3'  single  0.850  0.020  0.980
 AG9  C4'  H4'   single  0.970  0.020  1.090
 AG9  C5'  H15'  single  0.970  0.020  1.090
 AG9  C5'  H25'  single  0.970  0.020  1.090
 AG9  NH1  H1H1  single  0.890  0.020  1.040
 AG9  NH1  H2H1  single  0.890  0.020  1.040
 AG9  NH2  H1H2  single  0.890  0.020  1.040
 AG9  NH2  H2H2  single  0.890  0.020  1.040
 AG9  OP2  HOP2  single  0.850  0.020  0.980
 AG9  OP3  HOP3  single  0.850  0.020  0.980
 AG9  CZ   HZ    single  0.970  0.020  1.090
 AG9  C4   H4    single  0.970  0.020  1.090

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
 AG9  O5'   P    OP3   101.75  3.000
 AG9  OP3   P    OP2   102.10  3.000
 AG9  O5'   P    OP2   101.51  3.000
 AG9  OP3   P    OP1   116.16  3.000
 AG9  OP2   P    OP1   117.09  3.000
 AG9  O5'   P    OP1   115.82  3.000
 AG9  C1'   N1   C6    121.99  3.000
 AG9  C6    N1   C2    116.21  3.000
 AG9  C1'   N1   C2    121.73  3.000
 AG9  N3    C2   N2    120.64  3.000
 AG9  N3    C2   N1    124.01  3.000
 AG9  N2    C2   N1    115.35  3.000
 AG9  HN2   N2   CA    114.42  3.000
 AG9  HN2   N2   C2    116.93  3.000
 AG9  CA    N2   C2    120.91  3.000
 AG9  C4    N3   C2    118.91  3.000
 AG9  H4    C4   C5    109.43  3.000
 AG9  H4    C4   N4    105.33  3.000
 AG9  C5    C4   N4    113.61  3.000
 AG9  H4    C4   N3    107.60  3.000
 AG9  N4    C4   N3    109.69  3.000
 AG9  C5    C4   N3    110.86  3.000
 AG9  H2N4  N4   H1N4  105.52  3.000
 AG9  H2N4  N4   C4    109.26  3.000
 AG9  H1N4  N4   C4    109.13  3.000
 AG9  H5    C5   C6    120.23  3.000
 AG9  H5    C5   C4    120.80  3.000
 AG9  C6    C5   C4    118.94  3.000
 AG9  H6    C6   C5    123.10  3.000
 AG9  H6    C6   N1    116.58  3.000
 AG9  C5    C6   N1    120.24  3.000
 AG9  H2A   CA   H1A   106.61  3.000
 AG9  H2A   CA   CB    109.33  3.000
 AG9  H1A   CA   CB    110.37  3.000
 AG9  H2A   CA   N2    108.21  3.000
 AG9  H1A   CA   N2    106.73  3.000
 AG9  CB    CA   N2    115.23  3.000
 AG9  H2B   CB   H1B   106.62  3.000
 AG9  H2B   CB   CG    109.37  3.000
 AG9  H1B   CB   CG    109.34  3.000
 AG9  H2B   CB   CA    107.59  3.000
 AG9  H1B   CB   CA    108.70  3.000
 AG9  CG    CB   CA    114.90  3.000
 AG9  H2D   CD   H1D   106.02  3.000
 AG9  H2D   CD   CG    109.29  3.000
 AG9  H1D   CD   CG    109.75  3.000
 AG9  H2D   CD   NE    112.56  3.000
 AG9  H1D   CD   NE    108.17  3.000
 AG9  CG    CD   NE    110.91  3.000
 AG9  HNE   NE   CZ    108.99  3.000
 AG9  HNE   NE   CD    108.14  3.000
 AG9  CZ    NE   CD    113.58  3.000
 AG9  H2G   CG   H1G   105.86  3.000
 AG9  H2G   CG   CD    109.24  3.000
 AG9  H1G   CG   CD    108.91  3.000
 AG9  H2G   CG   CB    110.49  3.000
 AG9  H1G   CG   CB    108.26  3.000
 AG9  CD    CG   CB    113.77  3.000
 AG9  HZ    CZ   NH2   105.76  3.000
 AG9  HZ    CZ   NH1   112.47  3.000
 AG9  NH2   CZ   NH1   107.66  3.000
 AG9  HZ    CZ   NE    110.22  3.000
 AG9  NH1   CZ   NE    107.53  3.000
 AG9  NH2   CZ   NE    113.27  3.000
 AG9  H1'   C1'  O4'   107.61  3.000
 AG9  H1'   C1'  C2'   111.82  3.000
 AG9  O4'   C1'  C2'   105.84  3.000
 AG9  H1'   C1'  N1    110.00  3.000
 AG9  O4'   C1'  N1    110.11  3.000
 AG9  C2'   C1'  N1    111.31  3.000
 AG9  H2'   C2'  C3'   112.34  3.000
 AG9  H2'   C2'  O2'   112.05  3.000
 AG9  C3'   C2'  O2'   108.17  3.000
 AG9  H2'   C2'  C1'   112.16  3.000
 AG9  C3'   C2'  C1'   100.47  3.000
 AG9  O2'   C2'  C1'   111.05  3.000
 AG9  HO2'  O2'  C2'   108.68  3.000
 AG9  HOP2  OP2  P     114.31  3.000
 AG9  H3'   C3'  C4'   109.06  3.000
 AG9  H3'   C3'  O3'   111.41  3.000
 AG9  C4'   C3'  O3'   114.49  3.000
 AG9  H3'   C3'  C2'   107.53  3.000
 AG9  C4'   C3'  C2'   101.47  3.000
 AG9  O3'   C3'  C2'   112.26  3.000
 AG9  HO3'  O3'  C3'   108.89  3.000
 AG9  HOP3  OP3  P     114.19  3.000
 AG9  H4'   C4'  C5'   109.38  3.000
 AG9  H4'   C4'  O4'   109.03  3.000
 AG9  C5'   C4'  O4'   110.79  3.000
 AG9  H4'   C4'  C3'   109.77  3.000
 AG9  C5'   C4'  C3'   112.63  3.000
 AG9  O4'   C4'  C3'   105.11  3.000
 AG9  C4'   O4'  C1'   111.29  3.000
 AG9  H25'  C5'  H15'  107.63  3.000
 AG9  H25'  C5'  O5'   111.59  3.000
 AG9  H15'  C5'  O5'   109.49  3.000
 AG9  H25'  C5'  C4'   110.36  3.000
 AG9  H15'  C5'  C4'   109.04  3.000
 AG9  O5'   C5'  C4'   108.70  3.000
 AG9  C5'   O5'  P     119.78  3.000
 AG9  H2H1  NH1  H1H1  105.81  3.000
 AG9  H2H1  NH1  CZ    108.20  3.000
 AG9  H1H1  NH1  CZ    110.10  3.000
 AG9  H2H2  NH2  H1H2  107.23  3.000
 AG9  H2H2  NH2  CZ    109.53  3.000
 AG9  H1H2  NH2  CZ    110.83  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
 AG9  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 AG9  CONST_02  C1'   N1   C2   N3   180.00   0.0  0
 AG9  CONST_04  C1'   N1   C2   N2     0.00   0.0  0
 AG9  CONST_06  C4    N3   C2   N2   180.00   0.0  0
 AG9  CONST_07  CA    N2   C2   N1   180.00   0.0  0
 AG9  CONST_08  CA    N2   C2   N3     0.00   0.0  0
 AG9  Var_01    C4    C5   C6   N1    -6.05  30.0  1
 AG9  Var_02    C5    C6   N1   C2   -18.28  30.0  1
 AG9  Var_03    C4'   C5'  O5'  P   -153.69  30.0  1
 AG9  Var_04    CB    CA   N2   C2   -74.10  30.0  1
 AG9  Var_05    CG    CB   CA   N2   -54.56  30.0  3
 AG9  Var_06    CD    CG   CB   CA   -59.20  30.0  1
 AG9  Var_07    NE    CD   CG   CB  -174.77  30.0  2
 AG9  Var_08    NH2   CZ   NE   CD    72.59  30.0  2
 AG9  Var_09    CZ    NE   CD   CG   179.24  30.0  1
 AG9  Var_10    H1H2  NH2  CZ   NE   -71.84  30.0  3
 AG9  Var_11    H1H1  NH1  CZ   NE    65.55  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
 AG9  chir_01  C4   N3   C5   N4   negativ
 AG9  chir_02  C1'  O4'  N1   C2'  negativ
 AG9  chir_03  C2'  O2'  C1'  C3'  negativ
 AG9  chir_04  C3'  O3'  C4'  C2'  positiv
 AG9  chir_05  C4'  O4'  C3'  C5'  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
 AG9  plan-1  N1   0.020
 AG9  plan-1  C2   0.020
 AG9  plan-1  N2   0.020
 AG9  plan-1  N3   0.020
 AG9  plan-1  C4   0.020
 AG9  plan-1  C6   0.020
 AG9  plan-1  CA   0.020
 AG9  plan-1  C1'  0.020
 AG9  plan-1  HN2  0.020

