# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 13:00:05 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 5'-O-({[(2S)-2-amino-3-(4-hydroxyphenyl)propyl]oxy}phosphinato)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CO[P]([O-])(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)Cc4ccc(O)cc4
#
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
 TYA  TYA  5'-O-({[(2S)-2-amino-3-(4-hydroxyphenyl)propyl]oxy}phosphinato)adenosine  ligand  58  34  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TYA
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
 TYA  OPP   O  O2     0  -0.658  -1.5752   2.8391  -1.4310
 TYA  P     P  P      0   1.380  -0.6480   3.5250  -2.5944
 TYA  O1P   O  O      0  -0.790   0.0823   2.4562  -3.3582
 TYA  O2P   O  OP    -1  -0.808  -1.4305   4.5755  -3.3113
 TYA  O5'   O  O2     0  -0.611   0.3806   4.3295  -1.6047
 TYA  C5'   C  CH2    0  -0.296   1.6451   3.8344  -1.2415
 TYA  C4'   C  CH1    0   0.018   1.6847   3.3637   0.2015
 TYA  O4'   O  O2     0  -0.428   0.9024   2.1803   0.3920
 TYA  C3'   C  CH1    0  -0.116   3.0980   2.9941   0.6353
 TYA  O3'   O  OH1    0  -0.669   3.2054   3.1609   2.0247
 TYA  C2'   C  CH1    0   0.001   3.1373   1.5113   0.2647
 TYA  O2'   O  OH1    0  -0.561   4.0791   0.7549   0.9638
 TYA  C1'   C  CH1    0   0.186   1.7213   1.0823   0.6513
 TYA  N9    N  NR5    0  -0.432   1.2436  -0.0654  -0.0843
 TYA  C8    C  CR15   0   0.062   0.8081  -0.1127  -1.3839
 TYA  N7    N  N      0  -0.436   0.5147  -1.3186  -1.7790
 TYA  C5    C  CR56   0  -0.146   0.7744  -2.1097  -0.6915
 TYA  C6    C  CR6    0   0.390   0.6399  -3.4873  -0.4618
 TYA  N6    N  NH2    0  -0.779   0.1556  -4.3275  -1.3869
 TYA  N1    N  N      0  -0.426   0.9649  -3.9616   0.7441
 TYA  C2    C  CR16   0   0.040   1.3808  -3.1081   1.6783
 TYA  N3    N  N      0  -0.376   1.5416  -1.8013   1.5874
 TYA  C4    C  CR56   0   0.453   1.2233  -1.3489   0.3771
 TYA  NH2   N  NH2    0  -0.769  -3.1961   1.6176   0.5468
 TYA  CA    C  CH1    0  -0.120  -2.6861   0.8877  -0.5979
 TYA  C     C  CH2    0  -0.183  -2.4899   1.8283  -1.7765
 TYA  CB    C  CH2    0  -0.521  -3.5638  -0.3031  -1.0349
 TYA  CG    C  CR6    0   0.077  -3.6278  -1.3812   0.0061
 TYA  CD1   C  CR16   0  -0.389  -4.5696  -1.3690   1.0293
 TYA  CD2   C  CR16   0  -0.143  -2.6901  -2.4129   0.0083
 TYA  CE1   C  CR16   0  -0.344  -4.5731  -2.3383   2.0240
 TYA  CE2   C  CR16   0  -0.411  -2.6788  -3.3890   0.9880
 TYA  CZ    C  CR6    0   0.388  -3.6199  -3.3501   2.0118
 TYA  OH    O  OH1    0  -0.650  -3.5640  -4.3184   2.9557
 TYA  H5'1  H  HCH2   0   0.277   1.9712   3.0360  -1.9154
 TYA  H5'2  H  HCH2   0   0.263   2.3659   4.6504  -1.3507
 TYA  H4'   H  HCH1   0   0.240   1.2765   4.1509   0.8425
 TYA  H3'   H  HCH1   0   0.292   3.8610   3.5743   0.0999
 TYA  HO'3  H  HOH1   0   0.445   3.9299   2.6062   2.3342
 TYA  H2'   H  HCH1   0   0.183   3.2635   1.4106  -0.8212
 TYA  HO'2  H  HOH1   0   0.468   4.9254   0.8243   0.5144
 TYA  H1'   H  HCH1   0   0.285   1.6929   0.7932   1.7086
 TYA  H8    H  HCR5   0   0.299   0.6978   0.7774  -1.9904
 TYA  H61   H  HNH2   0   0.404   0.0936  -4.0304  -2.3446
 TYA  H62   H  HNH2   0   0.360   0.2255  -5.3174  -1.2308
 TYA  H2    H  HCR6   0   0.277   1.6271  -3.5525   2.6373
 TYA  HN2   H  HNH2   0   0.339  -3.1663   1.0379   1.3755
 TYA  HA    H  HCH1   0   0.246  -1.7007   0.5027  -0.3195
 TYA  H1    H  HCH2   0   0.247  -2.1339   1.2462  -2.6335
 TYA  H2A   H  HCH2   0   0.195  -3.4582   2.2646  -2.0637
 TYA  HB1   H  HCH2   0   0.196  -4.5696   0.0647  -1.2658
 TYA  HB2   H  HCH2   0   0.259  -3.1694  -0.7234  -1.9646
 TYA  HD1   H  HCR6   0   0.238  -5.3335  -0.6006   1.0528
 TYA  HD2   H  HCR6   0   0.253  -1.9529  -2.4585  -0.7833
 TYA  HE1   H  HCR6   0   0.279  -5.3247  -2.2999   2.8051
 TYA  HE2   H  HCR6   0   0.232  -1.9348  -4.1759   0.9679
 TYA  HH    H  HOH1   0   0.465  -4.2682  -4.1957   3.5988
 TYA  HN1   H  HNH2   0   0.328  -4.1695   1.8602   0.4021

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
 TYA  OPP  P     single    1.638  0.020  1.638
 TYA  OPP  C     single    1.406  0.020  1.406
 TYA  P    O1P   deloc     1.503  0.020  1.503
 TYA  P    O2P   deloc     1.493  0.020  1.493
 TYA  P    O5'   single    1.639  0.020  1.639
 TYA  O5'  C5'   single    1.406  0.020  1.406
 TYA  C5'  C4'   single    1.518  0.020  1.518
 TYA  C5'  H5'1  single    0.970  0.020  1.090
 TYA  C5'  H5'2  single    0.970  0.020  1.090
 TYA  C4'  O4'   single    1.431  0.020  1.431
 TYA  C4'  C3'   single    1.524  0.020  1.524
 TYA  C4'  H4'   single    0.970  0.020  1.090
 TYA  O4'  C1'   single    1.394  0.020  1.394
 TYA  C3'  O3'   single    1.404  0.020  1.404
 TYA  C3'  C2'   single    1.529  0.020  1.529
 TYA  C3'  H3'   single    0.970  0.020  1.090
 TYA  O3'  HO'3  single    0.850  0.020  0.980
 TYA  C2'  O2'   single    1.396  0.020  1.396
 TYA  C2'  C1'   single    1.529  0.020  1.529
 TYA  C2'  H2'   single    0.970  0.020  1.090
 TYA  O2'  HO'2  single    0.850  0.020  0.980
 TYA  C1'  N9    single    1.445  0.020  1.445
 TYA  C1'  H1'   single    0.970  0.020  1.090
 TYA  N9   C8    aromatic  1.371  0.020  1.371
 TYA  N9   C4    aromatic  1.364  0.020  1.364
 TYA  C8   N7    aromatic  1.302  0.020  1.302
 TYA  C8   H8    single    0.930  0.020  1.080
 TYA  N7   C5    aromatic  1.370  0.020  1.370
 TYA  C5   C6    aromatic  1.403  0.020  1.403
 TYA  C5   C4    aromatic  1.386  0.020  1.386
 TYA  C6   N6    single    1.340  0.020  1.340
 TYA  C6   N1    aromatic  1.336  0.020  1.336
 TYA  N6   H61   single    0.890  0.020  1.040
 TYA  N6   H62   single    0.890  0.020  1.040
 TYA  N1   C2    aromatic  1.332  0.020  1.332
 TYA  C2   N3    aromatic  1.320  0.020  1.320
 TYA  C2   H2    single    0.930  0.020  1.080
 TYA  N3   C4    aromatic  1.331  0.020  1.331
 TYA  NH2  CA    single    1.450  0.020  1.450
 TYA  NH2  HN1   single    0.890  0.020  1.040
 TYA  NH2  HN2   single    0.890  0.020  1.040
 TYA  CA   C     single    1.521  0.020  1.521
 TYA  CA   CB    single    1.543  0.020  1.543
 TYA  CA   HA    single    0.970  0.020  1.090
 TYA  C    H1    single    0.970  0.020  1.090
 TYA  C    H2A   single    0.970  0.020  1.090
 TYA  CB   CG    single    1.500  0.020  1.500
 TYA  CB   HB1   single    0.970  0.020  1.090
 TYA  CB   HB2   single    0.970  0.020  1.090
 TYA  CG   CD1   aromatic  1.391  0.020  1.391
 TYA  CG   CD2   aromatic  1.394  0.020  1.394
 TYA  CD1  CE1   aromatic  1.389  0.020  1.389
 TYA  CD1  HD1   single    0.930  0.020  1.080
 TYA  CD2  CE2   aromatic  1.383  0.020  1.383
 TYA  CD2  HD2   single    0.930  0.020  1.080
 TYA  CE1  CZ    aromatic  1.390  0.020  1.390
 TYA  CE1  HE1   single    0.930  0.020  1.080
 TYA  CE2  CZ    aromatic  1.391  0.020  1.391
 TYA  CE2  HE2   single    0.930  0.020  1.080
 TYA  CZ   OH    single    1.353  0.020  1.353
 TYA  OH   HH    single    0.850  0.020  0.980

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
 TYA  C     OPP  P     119.65  3.000
 TYA  O5'   P    O2P   105.87  3.000
 TYA  O5'   P    O1P   110.56  3.000
 TYA  O2P   P    O1P   120.72  3.000
 TYA  O5'   P    OPP    97.58  3.000
 TYA  O2P   P    OPP   109.81  3.000
 TYA  O1P   P    OPP   109.77  3.000
 TYA  C5'   O5'  P     123.21  3.000
 TYA  H5'2  C5'  H5'1  106.64  3.000
 TYA  H5'2  C5'  C4'   107.99  3.000
 TYA  H5'1  C5'  C4'   110.57  3.000
 TYA  H5'2  C5'  O5'   107.70  3.000
 TYA  H5'1  C5'  O5'   111.46  3.000
 TYA  C4'   C5'  O5'   112.22  3.000
 TYA  H4'   C4'  C3'   110.71  3.000
 TYA  H4'   C4'  O4'   108.23  3.000
 TYA  C3'   C4'  O4'   105.57  3.000
 TYA  H4'   C4'  C5'   108.91  3.000
 TYA  C3'   C4'  C5'   111.71  3.000
 TYA  O4'   C4'  C5'   111.63  3.000
 TYA  C1'   O4'  C4'   110.78  3.000
 TYA  H3'   C3'  C2'   112.11  3.000
 TYA  H3'   C3'  O3'   111.52  3.000
 TYA  C2'   C3'  O3'   110.69  3.000
 TYA  H3'   C3'  C4'   112.18  3.000
 TYA  C2'   C3'  C4'   100.95  3.000
 TYA  O3'   C3'  C4'   108.90  3.000
 TYA  HO'3  O3'  C3'   107.89  3.000
 TYA  H2'   C2'  C1'   109.31  3.000
 TYA  H2'   C2'  O2'   111.60  3.000
 TYA  C1'   C2'  O2'   110.25  3.000
 TYA  H2'   C2'  C3'   109.37  3.000
 TYA  C1'   C2'  C3'   100.78  3.000
 TYA  O2'   C2'  C3'   114.93  3.000
 TYA  HO'2  O2'  C2'   108.72  3.000
 TYA  H1'   C1'  N9    105.84  3.000
 TYA  H1'   C1'  C2'   109.98  3.000
 TYA  N9    C1'  C2'   113.60  3.000
 TYA  H1'   C1'  O4'   111.83  3.000
 TYA  N9    C1'  O4'   109.68  3.000
 TYA  C2'   C1'  O4'   106.02  3.000
 TYA  C4    N9   C8    106.46  3.000
 TYA  C4    N9   C1'   125.47  3.000
 TYA  C8    N9   C1'   127.95  3.000
 TYA  H8    C8   N7    124.63  3.000
 TYA  H8    C8   N9    122.33  3.000
 TYA  N7    C8   N9    113.01  3.000
 TYA  C5    N7   C8    104.55  3.000
 TYA  C4    C5   C6    116.34  3.000
 TYA  C4    C5   N7    110.88  3.000
 TYA  C6    C5   N7    132.76  3.000
 TYA  N1    C6   N6    119.24  3.000
 TYA  N1    C6   C5    118.23  3.000
 TYA  N6    C6   C5    122.49  3.000
 TYA  H62   N6   H61   116.35  3.000
 TYA  H62   N6   C6    119.03  3.000
 TYA  H61   N6   C6    119.66  3.000
 TYA  C2    N1   C6    118.79  3.000
 TYA  H2    C2   N3    116.01  3.000
 TYA  H2    C2   N1    115.36  3.000
 TYA  N3    C2   N1    128.62  3.000
 TYA  C4    N3   C2    111.72  3.000
 TYA  N3    C4   C5    126.29  3.000
 TYA  N3    C4   N9    128.61  3.000
 TYA  C5    C4   N9    105.10  3.000
 TYA  HN2   NH2  HN1   106.40  3.000
 TYA  HN2   NH2  CA    110.35  3.000
 TYA  HN1   NH2  CA    110.21  3.000
 TYA  HA    CA   CB    108.24  3.000
 TYA  HA    CA   C     107.38  3.000
 TYA  CB    CA   C     109.35  3.000
 TYA  HA    CA   NH2   107.04  3.000
 TYA  CB    CA   NH2   114.33  3.000
 TYA  C     CA   NH2   110.23  3.000
 TYA  H2A   C    H1    107.00  3.000
 TYA  H2A   C    CA    109.52  3.000
 TYA  H1    C    CA    108.64  3.000
 TYA  H2A   C    OPP   110.58  3.000
 TYA  H1    C    OPP   111.27  3.000
 TYA  CA    C    OPP   109.76  3.000
 TYA  HB2   CB   HB1   106.32  3.000
 TYA  HB2   CB   CG    109.21  3.000
 TYA  HB1   CB   CG    110.39  3.000
 TYA  HB2   CB   CA    109.40  3.000
 TYA  HB1   CB   CA    108.84  3.000
 TYA  CG    CB   CA    112.48  3.000
 TYA  CD2   CG   CD1   117.44  3.000
 TYA  CD2   CG   CB    120.28  3.000
 TYA  CD1   CG   CB    122.22  3.000
 TYA  HD1   CD1  CE1   118.53  3.000
 TYA  HD1   CD1  CG    119.97  3.000
 TYA  CE1   CD1  CG    121.50  3.000
 TYA  HD2   CD2  CE2   118.86  3.000
 TYA  HD2   CD2  CG    119.21  3.000
 TYA  CE2   CD2  CG    121.93  3.000
 TYA  HE1   CE1  CZ    120.48  3.000
 TYA  HE1   CE1  CD1   119.52  3.000
 TYA  CZ    CE1  CD1   120.00  3.000
 TYA  HE2   CE2  CZ    119.91  3.000
 TYA  HE2   CE2  CD2   120.34  3.000
 TYA  CZ    CE2  CD2   119.74  3.000
 TYA  OH    CZ   CE2   117.73  3.000
 TYA  OH    CZ   CE1   122.88  3.000
 TYA  CE2   CZ   CE1   119.39  3.000
 TYA  HH    OH   CZ    110.18  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
 TYA  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 TYA  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 TYA  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 TYA  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 TYA  CONST_05  C5   C4   N9   C8      0.00   0.0  0
 TYA  CONST_06  N3   C4   N9   C8    180.00   0.0  0
 TYA  CONST_07  C6   C5   N7   C8    180.00   0.0  0
 TYA  CONST_08  C4   C5   N7   C8      0.00   0.0  0
 TYA  CONST_09  C4   N9   C8   N7      0.00   0.0  0
 TYA  CONST_10  N1   C6   C5   N7    180.00   0.0  0
 TYA  CONST_11  N3   C4   C5   N7    180.00   0.0  0
 TYA  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 TYA  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 TYA  CONST_14  N3   C4   C5   C6      0.00   0.0  0
 TYA  CONST_15  N3   C2   N1   C6      0.00   0.0  0
 TYA  CONST_16  C4   C5   C6   N1      0.00   0.0  0
 TYA  CONST_17  C4   N3   C2   N1      0.00   0.0  0
 TYA  CONST_18  CZ   CE1  CD1  CG      0.00   0.0  0
 TYA  CONST_19  CZ   CE2  CD2  CG      0.00   0.0  0
 TYA  CONST_20  CE2  CD2  CG   CD1     0.00   0.0  0
 TYA  CONST_21  CE2  CZ   CE1  CD1     0.00   0.0  0
 TYA  CONST_22  CE1  CD1  CG   CD2     0.00   0.0  0
 TYA  CONST_23  CE1  CZ   CE2  CD2     0.00   0.0  0
 TYA  CONST_24  N7   C8   N9   C1'   180.00   0.0  0
 TYA  CONST_25  C5   C4   N9   C1'   180.00   0.0  0
 TYA  CONST_26  N3   C4   N9   C1'     0.00   0.0  0
 TYA  CONST_27  N6   C6   C5   N7      0.00   0.0  0
 TYA  CONST_28  C4   C5   C6   N6    180.00   0.0  0
 TYA  CONST_29  C2   N1   C6   N6    180.00   0.0  0
 TYA  CONST_30  CE1  CD1  CG   CB    180.00   0.0  0
 TYA  CONST_31  CE2  CD2  CG   CB    180.00   0.0  0
 TYA  CONST_32  OH   CZ   CE1  CD1   180.00   0.0  0
 TYA  CONST_33  OH   CZ   CE2  CD2   180.00   0.0  0
 TYA  CONST_34  H8   C8   N9   C1'     0.00   0.0  0
 TYA  CONST_35  H2   C2   N1   C6    180.00   0.0  0
 TYA  CONST_36  HE1  CE1  CD1  CG    180.00   0.0  0
 TYA  CONST_37  HE2  CE2  CD2  CG    180.00   0.0  0
 TYA  CONST_38  HD2  CD2  CG   CD1   180.00   0.0  0
 TYA  CONST_39  HD1  CD1  CG   CD2   180.00   0.0  0
 TYA  CONST_41  H62  N6   C6   C5    180.00   0.0  0
 TYA  Var_01    CD1  CG   CB   CA     87.52  30.0  2
 TYA  Var_02    C4'  C5'  O5'  P    -107.36  30.0  3
 TYA  Var_03    CA   C    OPP  P     150.98  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
 TYA  chir_01  C4'  C5'  O4'  C3'  negativ
 TYA  chir_02  C3'  O3'  C4'  C2'  positiv
 TYA  chir_03  C2'  O2'  C3'  C1'  positiv
 TYA  chir_04  C1'  O4'  N9   C2'  negativ
 TYA  chir_05  CA   NH2  C    CB   positiv

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
 TYA  plan-1  CB   0.020
 TYA  plan-1  CG   0.020
 TYA  plan-1  CD1  0.020
 TYA  plan-1  CD2  0.020
 TYA  plan-1  CE1  0.020
 TYA  plan-1  CE2  0.020
 TYA  plan-1  CZ   0.020
 TYA  plan-1  OH   0.020
 TYA  plan-1  HD1  0.020
 TYA  plan-1  HD2  0.020
 TYA  plan-1  HE1  0.020
 TYA  plan-1  HE2  0.020
 TYA  plan-2  C1'  0.020
 TYA  plan-2  N9   0.020
 TYA  plan-2  C8   0.020
 TYA  plan-2  N7   0.020
 TYA  plan-2  C5   0.020
 TYA  plan-2  C6   0.020
 TYA  plan-2  N6   0.020
 TYA  plan-2  N1   0.020
 TYA  plan-2  C2   0.020
 TYA  plan-2  N3   0.020
 TYA  plan-2  C4   0.020
 TYA  plan-2  H8   0.020
 TYA  plan-2  H2   0.020
 TYA  plan-3  C6   0.020
 TYA  plan-3  N6   0.020
 TYA  plan-3  H61  0.020
 TYA  plan-3  H62  0.020

