# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  4 17:16:43 2021
#   Inital geometry file: a 141 line input string
#   Ligand name: 5'-O-[(S)-hydroxy(L-tyrosylamino)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)cc1)C(=O)N[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
#
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
 YMP  YMP  5'-O-[(S)-hydroxy(L-tyrosylamino)phosphoryl]adenosine  ligand  59  35  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YMP
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
 YMP  N     N  NH2   0  -0.773   7.2259  33.1234  160.4934
 YMP  CA    C  CH1   0  -0.220   8.0713  33.0737  159.3180
 YMP  CB    C  CH2   0  -0.529   8.9469  31.8116  159.1730
 YMP  CG    C  CR6   0   0.103   9.9196  31.6899  160.3094
 YMP  CD1   C  CR16  0  -0.287  11.1248  32.3910  160.2958
 YMP  CE1   C  CR16  0  -0.322  12.0137  32.3283  161.3551
 YMP  CZ    C  CR6   0   0.339  11.7099  31.5516  162.4720
 YMP  OH    O  OH1   0  -0.634  12.6082  31.5177  163.4779
 YMP  CE2   C  CR16  0  -0.371  10.5116  30.8459  162.5052
 YMP  CD2   C  CR16  0  -0.304   9.6322  30.9221  161.4332
 YMP  C     C  C     0   0.599   7.1567  33.1878  158.1126
 YMP  O     O  O     0  -0.449   6.2061  32.4509  157.9525
 YMP  N3P   N  NH1   0  -0.846   7.4536  34.1769  157.2188
 YMP  P     P  P     0   1.489   6.4302  34.5119  155.9115
 YMP  O1P   O  O     0  -0.678   6.1621  33.4259  154.9555
 YMP  O2P   O  OH1   0  -0.742   7.2046  35.8011  155.3795
 YMP  O5'   O  O2    0  -0.589   5.0669  35.0179  156.5703
 YMP  C5'   C  CH2   0  -0.211   4.9873  36.1626  157.4180
 YMP  C4'   C  CH1   0  -0.007   3.8000  36.0192  158.3437
 YMP  O4'   O  O2    0  -0.490   2.6117  35.8448  157.5757
 YMP  C1'   C  CH1   0   0.190   1.9803  34.6378  157.9037
 YMP  C2'   C  CH1   0  -0.036   3.0381  33.7743  158.6031
 YMP  C3'   C  CH1   0  -0.069   3.8703  34.8425  159.3197
 YMP  O3'   O  OH1   0  -0.673   3.2459  35.2340  160.5228
 YMP  O2'   O  OH1   0  -0.651   2.4997  32.7769  159.4124
 YMP  N9    N  NR5   0  -0.543   1.4225  34.0442  156.7192
 YMP  C4    C  CR56  0   0.491   0.0919  33.8505  156.4732
 YMP  N3    N  N     0  -0.458  -0.9417  34.1366  157.2604
 YMP  C5    C  CR56  0  -0.010   0.0335  33.2845  155.2109
 YMP  N7    N  N     0  -0.449   1.2912  33.1398  154.6837
 YMP  C8    C  CR15  0   0.111   2.0848  33.6012  155.6027
 YMP  C6    C  CR6   0   0.459  -1.2505  32.9853  154.7204
 YMP  N6    N  NH2   0  -0.817  -1.4542  32.4345  153.5229
 YMP  N1    N  N     0  -0.474  -2.3007  33.2683  155.4991
 YMP  C2    C  CR16  0   0.046  -2.0916  33.8143  156.6939
 YMP  HN1   H  HNH2  0   0.363   7.7992  33.1074  161.3279
 YMP  HN2   H  HNH2  0   0.349   6.6329  32.3032  160.5316
 YMP  HA    H  HCH1  0   0.273   8.7334  33.9429  159.3518
 YMP  HB1   H  HCH2  0   0.259   9.4859  31.8542  158.2219
 YMP  HB2   H  HCH2  0   0.259   8.2979  30.9329  159.1319
 YMP  HD1   H  HCR6  0   0.249  11.3807  32.9995  159.4357
 YMP  HE1   H  HCR6  0   0.261  12.9459  32.8786  161.3210
 YMP  HOH   H  HOH1  0   0.473  12.2899  30.9568  164.1934
 YMP  HE2   H  HCR6  0   0.269  10.2602  30.2321  163.3630
 YMP  HD2   H  HCR6  0   0.255   8.7084  30.3569  161.4739
 YMP  H3P   H  HNH1  0   0.438   8.2689  34.7540  157.3773
 YMP  H2P   H  HOH1  0   0.507   6.9817  36.0558  154.4734
 YMP  H5'1  H  HCH2  0   0.270   4.8752  37.0568  156.8015
 YMP  H5'2  H  HCH2  0   0.246   5.8902  36.2816  158.0243
 YMP  H4'   H  HCH1  0   0.272   3.7356  36.9548  158.9099
 YMP  H1'   H  HCH1  0   0.258   1.1316  34.8101  158.5773
 YMP  H2'   H  HCH1  0   0.272   3.6633  33.2683  157.8662
 YMP  H3'   H  HCH1  0   0.264   4.9004  34.5172  159.5021
 YMP  H2    H  HOH1  0   0.461   3.5106  34.6276  161.2211
 YMP  H1    H  HOH1  0   0.447   1.9474  33.1868  160.0879
 YMP  H8    H  HCR5  0   0.292   3.1593  33.6464  155.5143
 YMP  HN61  H  HNH2  0   0.412  -0.6864  32.2261  152.9096
 YMP  HN62  H  HNH2  0   0.404  -2.3889  32.2671  153.1938
 YMP  H3    H  HCR6  0   0.252  -2.9842  34.0201  157.2749

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
 YMP  N    CA    single    1.449  0.020  1.449
 YMP  N    HN1   single    0.890  0.020  1.040
 YMP  N    HN2   single    0.890  0.020  1.040
 YMP  CA   CB    single    1.543  0.020  1.543
 YMP  CA   C     single    1.517  0.020  1.517
 YMP  CA   HA    single    0.970  0.020  1.090
 YMP  CB   CG    single    1.501  0.020  1.501
 YMP  CB   HB1   single    0.970  0.020  1.090
 YMP  CB   HB2   single    0.970  0.020  1.090
 YMP  CG   CD1   aromatic  1.394  0.020  1.394
 YMP  CG   CD2   aromatic  1.391  0.020  1.391
 YMP  CD1  CE1   aromatic  1.384  0.020  1.384
 YMP  CD1  HD1   single    0.930  0.020  1.080
 YMP  CE1  CZ    aromatic  1.394  0.020  1.394
 YMP  CE1  HE1   single    0.930  0.020  1.080
 YMP  CZ   OH    single    1.349  0.020  1.349
 YMP  CZ   CE2   aromatic  1.391  0.020  1.391
 YMP  OH   HOH   single    0.850  0.020  0.980
 YMP  CE2  CD2   aromatic  1.389  0.020  1.389
 YMP  CE2  HE2   single    0.930  0.020  1.080
 YMP  CD2  HD2   single    0.930  0.020  1.080
 YMP  C    O     double    1.213  0.020  1.213
 YMP  C    N3P   single    1.366  0.020  1.366
 YMP  N3P  P     single    1.694  0.020  1.694
 YMP  N3P  H3P   single    0.860  0.020  1.020
 YMP  P    O1P   double    1.471  0.020  1.471
 YMP  P    O2P   single    1.595  0.020  1.595
 YMP  P    O5'   single    1.596  0.020  1.596
 YMP  O2P  H2P   single    0.850  0.020  0.980
 YMP  O5'  C5'   single    1.427  0.020  1.427
 YMP  C5'  C4'   single    1.512  0.020  1.512
 YMP  C5'  H5'1  single    0.970  0.020  1.090
 YMP  C5'  H5'2  single    0.970  0.020  1.090
 YMP  C4'  O4'   single    1.426  0.020  1.426
 YMP  C4'  C3'   single    1.530  0.020  1.530
 YMP  C4'  H4'   single    0.970  0.020  1.090
 YMP  O4'  C1'   single    1.401  0.020  1.401
 YMP  C1'  C2'   single    1.534  0.020  1.534
 YMP  C1'  N9    single    1.437  0.020  1.437
 YMP  C1'  H1'   single    0.970  0.020  1.090
 YMP  C2'  C3'   single    1.532  0.020  1.532
 YMP  C2'  O2'   single    1.393  0.020  1.393
 YMP  C2'  H2'   single    0.970  0.020  1.090
 YMP  C3'  O3'   single    1.411  0.020  1.411
 YMP  C3'  H3'   single    0.970  0.020  1.090
 YMP  O3'  H2    single    0.850  0.020  0.980
 YMP  O2'  H1    single    0.850  0.020  0.980
 YMP  N9   C4    aromatic  1.367  0.020  1.367
 YMP  N9   C8    aromatic  1.372  0.020  1.372
 YMP  C4   N3    aromatic  1.330  0.020  1.330
 YMP  C4   C5    aromatic  1.385  0.020  1.385
 YMP  N3   C2    aromatic  1.322  0.020  1.322
 YMP  C5   N7    aromatic  1.371  0.020  1.371
 YMP  C5   C6    aromatic  1.407  0.020  1.407
 YMP  N7   C8    aromatic  1.299  0.020  1.299
 YMP  C8   H8    single    0.930  0.020  1.080
 YMP  C6   N6    single    1.334  0.020  1.334
 YMP  C6   N1    aromatic  1.338  0.020  1.338
 YMP  N6   HN61  single    0.860  0.020  1.020
 YMP  N6   HN62  single    0.860  0.020  1.020
 YMP  N1   C2    aromatic  1.330  0.020  1.330
 YMP  C2   H3    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
 YMP  HN2   N    HN1   106.71  3.000
 YMP  HN2   N    CA    110.15  3.000
 YMP  HN1   N    CA    109.74  3.000
 YMP  HA    CA   C     109.26  3.000
 YMP  HA    CA   CB    108.04  3.000
 YMP  C     CA   CB    109.20  3.000
 YMP  HA    CA   N     107.52  3.000
 YMP  C     CA   N     106.87  3.000
 YMP  CB    CA   N     115.82  3.000
 YMP  HB2   CB   HB1   106.93  3.000
 YMP  HB2   CB   CG    110.36  3.000
 YMP  HB1   CB   CG    110.01  3.000
 YMP  HB2   CB   CA    108.91  3.000
 YMP  HB1   CB   CA    109.23  3.000
 YMP  CG    CB   CA    111.28  3.000
 YMP  CD2   CG   CD1   117.64  3.000
 YMP  CD2   CG   CB    121.51  3.000
 YMP  CD1   CG   CB    120.80  3.000
 YMP  HD1   CD1  CE1   118.75  3.000
 YMP  HD1   CD1  CG    119.60  3.000
 YMP  CE1   CD1  CG    121.65  3.000
 YMP  HE1   CE1  CZ    119.73  3.000
 YMP  HE1   CE1  CD1   120.36  3.000
 YMP  CZ    CE1  CD1   119.90  3.000
 YMP  CE2   CZ   OH    122.89  3.000
 YMP  CE2   CZ   CE1   119.31  3.000
 YMP  OH    CZ   CE1   117.80  3.000
 YMP  HOH   OH   CZ    110.39  3.000
 YMP  HE2   CE2  CD2   119.66  3.000
 YMP  HE2   CE2  CZ    120.38  3.000
 YMP  CD2   CE2  CZ    119.95  3.000
 YMP  HD2   CD2  CE2   118.83  3.000
 YMP  HD2   CD2  CG    119.62  3.000
 YMP  CE2   CD2  CG    121.54  3.000
 YMP  N3P   C    O     121.59  3.000
 YMP  N3P   C    CA    116.31  3.000
 YMP  O     C    CA    122.10  3.000
 YMP  H3P   N3P  P     119.68  3.000
 YMP  H3P   N3P  C     119.08  3.000
 YMP  P     N3P  C     121.13  3.000
 YMP  O5'   P    O2P   107.22  3.000
 YMP  O5'   P    O1P   110.27  3.000
 YMP  O2P   P    O1P   117.92  3.000
 YMP  O5'   P    N3P   105.08  3.000
 YMP  O2P   P    N3P    97.11  3.000
 YMP  O1P   P    N3P   117.75  3.000
 YMP  H2P   O2P  P     114.41  3.000
 YMP  C5'   O5'  P     123.18  3.000
 YMP  H5'2  C5'  H5'1  107.97  3.000
 YMP  H5'2  C5'  C4'   108.61  3.000
 YMP  H5'1  C5'  C4'   110.04  3.000
 YMP  H5'2  C5'  O5'   111.74  3.000
 YMP  H5'1  C5'  O5'   109.11  3.000
 YMP  C4'   C5'  O5'   109.36  3.000
 YMP  H4'   C4'  C3'   109.25  3.000
 YMP  H4'   C4'  O4'   109.51  3.000
 YMP  C3'   C4'  O4'   106.72  3.000
 YMP  H4'   C4'  C5'   106.35  3.000
 YMP  C3'   C4'  C5'   115.29  3.000
 YMP  O4'   C4'  C5'   109.65  3.000
 YMP  C1'   O4'  C4'   110.79  3.000
 YMP  H1'   C1'  N9    105.70  3.000
 YMP  H1'   C1'  C2'   109.99  3.000
 YMP  N9    C1'  C2'   114.25  3.000
 YMP  H1'   C1'  O4'   110.92  3.000
 YMP  N9    C1'  O4'   109.74  3.000
 YMP  C2'   C1'  O4'   106.31  3.000
 YMP  H2'   C2'  O2'   106.37  3.000
 YMP  H2'   C2'  C3'   109.15  3.000
 YMP  O2'   C2'  C3'   115.95  3.000
 YMP  H2'   C2'  C1'   110.38  3.000
 YMP  O2'   C2'  C1'   113.67  3.000
 YMP  C3'   C2'  C1'   101.26  3.000
 YMP  H3'   C3'  O3'   110.89  3.000
 YMP  H3'   C3'  C2'   112.43  3.000
 YMP  O3'   C3'  C2'   110.61  3.000
 YMP  H3'   C3'  C4'   112.19  3.000
 YMP  O3'   C3'  C4'   108.07  3.000
 YMP  C2'   C3'  C4'   102.29  3.000
 YMP  H2    O3'  C3'   108.80  3.000
 YMP  H1    O2'  C2'   108.92  3.000
 YMP  C8    N9   C4    106.12  3.000
 YMP  C8    N9   C1'   128.08  3.000
 YMP  C4    N9   C1'   125.77  3.000
 YMP  C5    C4   N3    126.49  3.000
 YMP  C5    C4   N9    105.25  3.000
 YMP  N3    C4   N9    128.26  3.000
 YMP  C2    N3   C4    111.71  3.000
 YMP  C6    C5   N7    132.90  3.000
 YMP  C6    C5   C4    116.31  3.000
 YMP  N7    C5   C4    110.79  3.000
 YMP  C8    N7   C5    104.53  3.000
 YMP  H8    C8   N7    124.43  3.000
 YMP  H8    C8   N9    122.27  3.000
 YMP  N7    C8   N9    113.30  3.000
 YMP  N1    C6   N6    119.35  3.000
 YMP  N1    C6   C5    117.95  3.000
 YMP  N6    C6   C5    122.71  3.000
 YMP  HN62  N6   HN61  118.44  3.000
 YMP  HN62  N6   C6    120.33  3.000
 YMP  HN61  N6   C6    121.14  3.000
 YMP  C2    N1   C6    119.10  3.000
 YMP  H3    C2   N1    115.44  3.000
 YMP  H3    C2   N3    116.11  3.000
 YMP  N1    C2   N3    128.45  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
 YMP  CONST_01  CZ    CE1  CD1  CG      0.00   0.0  0
 YMP  CONST_02  CZ    CE2  CD2  CG      0.00   0.0  0
 YMP  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 YMP  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 YMP  CONST_05  CD2   CG   CD1  CE1     0.00   0.0  0
 YMP  CONST_06  CD2   CE2  CZ   CE1     0.00   0.0  0
 YMP  CONST_07  C2    N3   C4   N9    180.00   0.0  0
 YMP  CONST_08  N7    C5   C4   N9      0.00   0.0  0
 YMP  CONST_09  C6    C5   C4   N9    180.00   0.0  0
 YMP  CONST_10  C5    N7   C8   N9      0.00   0.0  0
 YMP  CONST_11  N7    C8   N9   C4      0.00   0.0  0
 YMP  CONST_12  N1    C2   N3   C4      0.00   0.0  0
 YMP  CONST_13  C8    N7   C5   C4      0.00   0.0  0
 YMP  CONST_14  N1    C6   C5   C4      0.00   0.0  0
 YMP  CONST_15  C8    N9   C4   N3    180.00   0.0  0
 YMP  CONST_16  N7    C5   C4   N3    180.00   0.0  0
 YMP  CONST_17  C6    C5   C4   N3      0.00   0.0  0
 YMP  CONST_18  C6    N1   C2   N3      0.00   0.0  0
 YMP  CONST_19  C8    N9   C4   C5      0.00   0.0  0
 YMP  CONST_20  C2    N3   C4   C5      0.00   0.0  0
 YMP  CONST_21  C2    N1   C6   C5      0.00   0.0  0
 YMP  CONST_22  N1    C6   C5   N7    180.00   0.0  0
 YMP  CONST_23  C6    C5   N7   C8    180.00   0.0  0
 YMP  CONST_24  N3    C4   N9   C1'     0.00   0.0  0
 YMP  CONST_25  C5    C4   N9   C1'   180.00   0.0  0
 YMP  CONST_26  N7    C8   N9   C1'   180.00   0.0  0
 YMP  CONST_27  CE1   CD1  CG   CB    180.00   0.0  0
 YMP  CONST_28  CE2   CD2  CG   CB    180.00   0.0  0
 YMP  CONST_29  OH    CZ   CE1  CD1   180.00   0.0  0
 YMP  CONST_30  CD2   CE2  CZ   OH    180.00   0.0  0
 YMP  CONST_31  N6    C6   C5   C4    180.00   0.0  0
 YMP  CONST_32  N6    C6   C5   N7      0.00   0.0  0
 YMP  CONST_33  C2    N1   C6   N6    180.00   0.0  0
 YMP  CONST_34  HE1   CE1  CD1  CG    180.00   0.0  0
 YMP  CONST_35  HE2   CE2  CD2  CG    180.00   0.0  0
 YMP  CONST_36  HD2   CD2  CG   CD1   180.00   0.0  0
 YMP  CONST_37  HD1   CD1  CE1  CZ    180.00   0.0  0
 YMP  CONST_38  H8    C8   N9   C1'     0.00   0.0  0
 YMP  CONST_39  H3    C2   N3   C4    180.00   0.0  0
 YMP  CONST_40  HN61  N6   C6   C5      0.00   0.0  0
 YMP  CONST_41  HN62  N6   C6   C5    180.00   0.0  0
 YMP  CONST_42  P     N3P  C    CA    180.00   0.0  0
 YMP  CONST_43  P     N3P  C    O       0.00   0.0  0
 YMP  CONST_44  H3P   N3P  C    CA      0.00   0.0  0
 YMP  Var_01    CD1   CG   CB   CA    -82.41  30.0  2
 YMP  Var_02    C4'   C5'  O5'  P    -154.31  30.0  3
 YMP  Var_03    O1P   P    N3P  C     -59.05  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
 YMP  chir_01  CA   N    CB   C    negativ
 YMP  chir_03  C4'  C5'  O4'  C3'  negativ
 YMP  chir_04  C1'  O4'  N9   C2'  negativ
 YMP  chir_05  C2'  O2'  C1'  C3'  negativ
 YMP  chir_06  C3'  O3'  C4'  C2'  positiv
 YMP  chir_07  P    O1P  O2P  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
 YMP  plan-1  CB    0.020
 YMP  plan-1  CG    0.020
 YMP  plan-1  CD1   0.020
 YMP  plan-1  CE1   0.020
 YMP  plan-1  CZ    0.020
 YMP  plan-1  OH    0.020
 YMP  plan-1  CE2   0.020
 YMP  plan-1  CD2   0.020
 YMP  plan-1  HD1   0.020
 YMP  plan-1  HE1   0.020
 YMP  plan-1  HE2   0.020
 YMP  plan-1  HD2   0.020
 YMP  plan-2  C1'   0.020
 YMP  plan-2  N9    0.020
 YMP  plan-2  C4    0.020
 YMP  plan-2  N3    0.020
 YMP  plan-2  C5    0.020
 YMP  plan-2  N7    0.020
 YMP  plan-2  C8    0.020
 YMP  plan-2  C6    0.020
 YMP  plan-2  N6    0.020
 YMP  plan-2  N1    0.020
 YMP  plan-2  C2    0.020
 YMP  plan-2  H8    0.020
 YMP  plan-2  H3    0.020
 YMP  plan-3  C6    0.020
 YMP  plan-3  N6    0.020
 YMP  plan-3  HN61  0.020
 YMP  plan-3  HN62  0.020
 YMP  plan-4  CA    0.020
 YMP  plan-4  C     0.020
 YMP  plan-4  O     0.020
 YMP  plan-4  N3P   0.020
 YMP  plan-4  P     0.020
 YMP  plan-4  H3P   0.020

