# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 07:20:00 2021
#   Inital geometry file: a 136 line input string
#   Ligand name: 5'-O-[(R)-{[(2S)-2-amino-3-phenylpropyl]oxy}(hydroxy)phosphoryl]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)Cc4ccccc4
#
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
 FYA  FYA  5'-O-[(R)-{[(2S)-2-amino-3-phenylpropyl]oxy}(hydroxy)phosphoryl]adenosine  ligand  58  33  .  2021-08-09  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FYA
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
 FYA  C     C  CH2   0  -0.176  17.3655  64.5056  18.8349
 FYA  CA    C  CH1   0  -0.128  18.8074  64.2180  18.4641
 FYA  N     N  NH2   0  -0.787  18.8692  63.0275  17.6346
 FYA  CB    C  CH2   0  -0.522  19.4969  65.4612  17.8670
 FYA  CG    C  CR6   0   0.132  20.9579  65.2236  17.6164
 FYA  CD1   C  CR16  0  -0.304  21.8846  65.3676  18.6484
 FYA  CD2   C  CR16  0  -0.321  21.4172  64.8109  16.3673
 FYA  CE1   C  CR16  0  -0.240  23.2322  65.1109  18.4387
 FYA  CE2   C  CR16  0  -0.241  22.7650  64.5515  16.1520
 FYA  CZ    C  CR16  0  -0.273  23.6772  64.7007  17.1877
 FYA  P     P  P     0   1.471  15.0982  64.4010  17.5086
 FYA  O1P   O  O     0  -0.697  14.2476  64.7534  18.6606
 FYA  O2P   O  OH1   0  -0.777  14.7850  65.0870  16.1185
 FYA  O3P   O  O2    0  -0.592  16.6345  64.8102  17.6364
 FYA  O5'   O  O2    0  -0.591  15.0747  62.8074  17.2977
 FYA  C5'   C  CH2   0  -0.254  15.6676  62.1919  16.1554
 FYA  C4'   C  CH1   0   0.036  14.6227  61.5934  15.2382
 FYA  O4'   O  O2    0  -0.495  14.1832  60.3240  15.7144
 FYA  C3'   C  CH1   0  -0.012  13.3188  62.3710  15.0916
 FYA  O3'   O  OH1   0  -0.672  13.5163  63.5442  14.3434
 FYA  C2'   C  CH1   0  -0.065  12.4118  61.3048  14.4946
 FYA  O2'   O  OH1   0  -0.653  12.7497  61.1256  13.1522
 FYA  C1'   C  CH1   0   0.162  12.8500  60.1017  15.3560
 FYA  N9    N  NR5   0  -0.533  12.0541  59.9848  16.5682
 FYA  C8    C  CR15  0   0.100  12.3793  60.3390  17.8503
 FYA  N7    N  N     0  -0.450  11.4240  60.1088  18.7035
 FYA  C5    C  CR56  0  -0.001  10.4114  59.5765  17.9498
 FYA  C6    C  CR6   0   0.459   9.1155  59.1236  18.2608
 FYA  N6    N  NH2   0  -0.816   8.6168  59.1572  19.4970
 FYA  N1    N  N     0  -0.474   8.3604  58.6532  17.2612
 FYA  C2    C  CR16  0   0.041   8.8549  58.6320  16.0263
 FYA  N3    N  N     0  -0.460  10.0461  59.0277  15.6114
 FYA  C4    C  CR56  0   0.487  10.7844  59.4905  16.6184
 FYA  H1    H  HCH2  0   0.246  16.9473  63.6307  19.3387
 FYA  H2A   H  HCH2  0   0.246  17.3005  65.3569  19.5149
 FYA  HA    H  HCH1  0   0.252  19.3043  63.9830  19.4115
 FYA  HN1   H  HNH2  0   0.356  19.8305  62.7254  17.5365
 FYA  HN2   H  HNH2  0   0.343  18.5528  63.2415  16.6963
 FYA  HB1   H  HCH2  0   0.249  19.0008  65.7361  16.9326
 FYA  HB2   H  HCH2  0   0.244  19.3744  66.3010  18.5566
 FYA  HD1   H  HCR6  0   0.246  21.5461  65.6910  19.6262
 FYA  HD2   H  HCR6  0   0.248  20.7131  64.7024  15.5503
 FYA  HE1   H  HCR6  0   0.253  23.9372  65.2346  19.2508
 FYA  HE2   H  HCR6  0   0.253  23.1024  64.2345  15.1735
 FYA  HZ    H  HCR6  0   0.254  24.7283  64.5039  17.0205
 FYA  HOP2  H  HOH1  0   0.505  14.2707  64.5891  15.4305
 FYA  H5'1  H  HCH2  0   0.255  16.2633  62.9004  15.5751
 FYA  H5'2  H  HCH2  0   0.282  16.3519  61.4178  16.5041
 FYA  H4'   H  HCH1  0   0.268  15.0964  61.4721  14.2568
 FYA  H3'   H  HCH1  0   0.257  12.9141  62.6102  16.0833
 FYA  HO'3  H  HOH1  0   0.487  12.6620  63.9518  14.1511
 FYA  H2'   H  HCH1  0   0.281  11.3479  61.5303  14.6298
 FYA  HO'2  H  HOH1  0   0.466  12.1538  60.4765  12.7645
 FYA  H1'   H  HCH1  0   0.289  12.7467  59.1618  14.8056
 FYA  H8    H  HCR5  0   0.296  13.3393  60.7606  18.1021
 FYA  H61   H  HNH2  0   0.404   7.7049  58.7787  19.6862
 FYA  H62   H  HNH2  0   0.412   9.1824  59.4460  20.2757
 FYA  H2    H  HCR6  0   0.253   8.1892  58.2397  15.2648

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
 FYA  C    CA    single    1.516  0.020  1.516
 FYA  C    O3P   single    1.436  0.020  1.436
 FYA  C    H1    single    0.970  0.020  1.090
 FYA  C    H2A   single    0.970  0.020  1.090
 FYA  CA   N     single    1.452  0.020  1.452
 FYA  CA   CB    single    1.542  0.020  1.542
 FYA  CA   HA    single    0.970  0.020  1.090
 FYA  N    HN1   single    0.890  0.020  1.040
 FYA  N    HN2   single    0.890  0.020  1.040
 FYA  CB   CG    single    1.501  0.020  1.501
 FYA  CB   HB1   single    0.970  0.020  1.090
 FYA  CB   HB2   single    0.970  0.020  1.090
 FYA  CG   CD1   aromatic  1.394  0.020  1.394
 FYA  CG   CD2   aromatic  1.393  0.020  1.393
 FYA  CD1  CE1   aromatic  1.388  0.020  1.388
 FYA  CD1  HD1   single    0.930  0.020  1.080
 FYA  CD2  CE2   aromatic  1.389  0.020  1.389
 FYA  CD2  HD2   single    0.930  0.020  1.080
 FYA  CE1  CZ    aromatic  1.390  0.020  1.390
 FYA  CE1  HE1   single    0.930  0.020  1.080
 FYA  CE2  CZ    aromatic  1.388  0.020  1.388
 FYA  CE2  HE2   single    0.930  0.020  1.080
 FYA  CZ   HZ    single    0.930  0.020  1.080
 FYA  P    O1P   double    1.475  0.020  1.475
 FYA  P    O2P   single    1.581  0.020  1.581
 FYA  P    O3P   single    1.595  0.020  1.595
 FYA  P    O5'   single    1.608  0.020  1.608
 FYA  O2P  HOP2  single    0.850  0.020  0.980
 FYA  O5'  C5'   single    1.427  0.020  1.427
 FYA  C5'  C4'   single    1.514  0.020  1.514
 FYA  C5'  H5'1  single    0.970  0.020  1.090
 FYA  C5'  H5'2  single    0.970  0.020  1.090
 FYA  C4'  O4'   single    1.425  0.020  1.425
 FYA  C4'  C3'   single    1.525  0.020  1.525
 FYA  C4'  H4'   single    0.970  0.020  1.090
 FYA  O4'  C1'   single    1.398  0.020  1.398
 FYA  C3'  O3'   single    1.405  0.020  1.405
 FYA  C3'  C2'   single    1.522  0.020  1.522
 FYA  C3'  H3'   single    0.970  0.020  1.090
 FYA  O3'  HO'3  single    0.850  0.020  0.980
 FYA  C2'  O2'   single    1.396  0.020  1.396
 FYA  C2'  C1'   single    1.543  0.020  1.543
 FYA  C2'  H2'   single    0.970  0.020  1.090
 FYA  O2'  HO'2  single    0.850  0.020  0.980
 FYA  C1'  N9    single    1.455  0.020  1.455
 FYA  C1'  H1'   single    0.970  0.020  1.090
 FYA  N9   C8    aromatic  1.369  0.020  1.369
 FYA  N9   C4    aromatic  1.363  0.020  1.363
 FYA  C8   N7    aromatic  1.301  0.020  1.301
 FYA  C8   H8    single    0.930  0.020  1.080
 FYA  N7   C5    aromatic  1.370  0.020  1.370
 FYA  C5   C6    aromatic  1.408  0.020  1.408
 FYA  C5   C4    aromatic  1.385  0.020  1.385
 FYA  C6   N6    single    1.333  0.020  1.333
 FYA  C6   N1    aromatic  1.338  0.020  1.338
 FYA  N6   H61   single    0.860  0.020  1.020
 FYA  N6   H62   single    0.860  0.020  1.020
 FYA  N1   C2    aromatic  1.330  0.020  1.330
 FYA  C2   N3    aromatic  1.322  0.020  1.322
 FYA  C2   H2    single    0.930  0.020  1.080
 FYA  N3   C4    aromatic  1.332  0.020  1.332

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
 FYA  H2A   C    H1    108.33  3.000
 FYA  H2A   C    O3P   108.91  3.000
 FYA  H1    C    O3P   111.08  3.000
 FYA  H2A   C    CA    110.91  3.000
 FYA  H1    C    CA    108.95  3.000
 FYA  O3P   C    CA    108.67  3.000
 FYA  HA    CA   CB    107.76  3.000
 FYA  HA    CA   N     107.39  3.000
 FYA  CB    CA   N     114.88  3.000
 FYA  HA    CA   C     105.11  3.000
 FYA  CB    CA   C     111.53  3.000
 FYA  N     CA   C     109.61  3.000
 FYA  HN2   N    HN1   105.66  3.000
 FYA  HN2   N    CA    110.03  3.000
 FYA  HN1   N    CA    109.90  3.000
 FYA  HB2   CB   HB1   107.17  3.000
 FYA  HB2   CB   CG    109.62  3.000
 FYA  HB1   CB   CG    109.80  3.000
 FYA  HB2   CB   CA    108.95  3.000
 FYA  HB1   CB   CA    109.32  3.000
 FYA  CG    CB   CA    111.85  3.000
 FYA  CD2   CG   CD1   118.36  3.000
 FYA  CD2   CG   CB    121.15  3.000
 FYA  CD1   CG   CB    120.46  3.000
 FYA  HD1   CD1  CE1   119.64  3.000
 FYA  HD1   CD1  CG    119.40  3.000
 FYA  CE1   CD1  CG    120.96  3.000
 FYA  HD2   CD2  CE2   119.65  3.000
 FYA  HD2   CD2  CG    119.42  3.000
 FYA  CE2   CD2  CG    120.93  3.000
 FYA  HE1   CE1  CZ    120.03  3.000
 FYA  HE1   CE1  CD1   119.86  3.000
 FYA  CZ    CE1  CD1   120.11  3.000
 FYA  HE2   CE2  CZ    120.07  3.000
 FYA  HE2   CE2  CD2   119.81  3.000
 FYA  CZ    CE2  CD2   120.12  3.000
 FYA  HZ    CZ   CE2   120.22  3.000
 FYA  HZ    CZ   CE1   120.25  3.000
 FYA  CE2   CZ   CE1   119.53  3.000
 FYA  O5'   P    O3P   106.19  3.000
 FYA  O5'   P    O2P   108.16  3.000
 FYA  O3P   P    O2P    98.62  3.000
 FYA  O5'   P    O1P   109.32  3.000
 FYA  O3P   P    O1P   115.58  3.000
 FYA  O2P   P    O1P   117.95  3.000
 FYA  HOP2  O2P  P     119.62  3.000
 FYA  P     O3P  C     120.17  3.000
 FYA  C5'   O5'  P     121.78  3.000
 FYA  H5'2  C5'  H5'1  106.74  3.000
 FYA  H5'2  C5'  C4'   110.26  3.000
 FYA  H5'1  C5'  C4'   108.12  3.000
 FYA  H5'2  C5'  O5'   108.12  3.000
 FYA  H5'1  C5'  O5'   111.85  3.000
 FYA  C4'   C5'  O5'   111.65  3.000
 FYA  H4'   C4'  C3'   109.86  3.000
 FYA  H4'   C4'  O4'   109.50  3.000
 FYA  C3'   C4'  O4'   102.86  3.000
 FYA  H4'   C4'  C5'   106.73  3.000
 FYA  C3'   C4'  C5'   116.54  3.000
 FYA  O4'   C4'  C5'   111.26  3.000
 FYA  C1'   O4'  C4'   110.49  3.000
 FYA  H3'   C3'  C2'   106.70  3.000
 FYA  H3'   C3'  O3'   110.54  3.000
 FYA  C2'   C3'  O3'   117.37  3.000
 FYA  H3'   C3'  C4'   109.84  3.000
 FYA  C2'   C3'  C4'   100.96  3.000
 FYA  O3'   C3'  C4'   110.90  3.000
 FYA  HO'3  O3'  C3'   109.52  3.000
 FYA  H2'   C2'  C1'   111.54  3.000
 FYA  H2'   C2'  O2'   112.34  3.000
 FYA  C1'   C2'  O2'   111.59  3.000
 FYA  H2'   C2'  C3'   112.71  3.000
 FYA  C1'   C2'  C3'    99.09  3.000
 FYA  O2'   C2'  C3'   108.84  3.000
 FYA  HO'2  O2'  C2'   108.91  3.000
 FYA  H1'   C1'  N9    107.37  3.000
 FYA  H1'   C1'  C2'   111.23  3.000
 FYA  N9    C1'  C2'   111.87  3.000
 FYA  H1'   C1'  O4'   110.83  3.000
 FYA  N9    C1'  O4'   108.71  3.000
 FYA  C2'   C1'  O4'   106.85  3.000
 FYA  C4    N9   C8    106.29  3.000
 FYA  C4    N9   C1'   124.70  3.000
 FYA  C8    N9   C1'   129.01  3.000
 FYA  H8    C8   N7    124.73  3.000
 FYA  H8    C8   N9    122.08  3.000
 FYA  N7    C8   N9    113.19  3.000
 FYA  C5    N7   C8    104.52  3.000
 FYA  C4    C5   C6    116.12  3.000
 FYA  C4    C5   N7    110.72  3.000
 FYA  C6    C5   N7    133.16  3.000
 FYA  N1    C6   N6    119.37  3.000
 FYA  N1    C6   C5    117.88  3.000
 FYA  N6    C6   C5    122.75  3.000
 FYA  H62   N6   H61   118.23  3.000
 FYA  H62   N6   C6    121.01  3.000
 FYA  H61   N6   C6    120.28  3.000
 FYA  C2    N1   C6    119.30  3.000
 FYA  H2    C2   N3    116.16  3.000
 FYA  H2    C2   N1    115.42  3.000
 FYA  N3    C2   N1    128.42  3.000
 FYA  C4    N3   C2    111.48  3.000
 FYA  N3    C4   C5    126.80  3.000
 FYA  N3    C4   N9    127.91  3.000
 FYA  C5    C4   N9    105.29  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
 FYA  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 FYA  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 FYA  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 FYA  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 FYA  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 FYA  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 FYA  CONST_07  C5   N7   C8   N9      0.00   0.0  0
 FYA  CONST_08  N7   C5   C4   N9      0.00   0.0  0
 FYA  CONST_09  C6   C5   C4   N9    180.00   0.0  0
 FYA  CONST_10  C2   N3   C4   N9    180.00   0.0  0
 FYA  CONST_11  C5   C4   N9   C8      0.00   0.0  0
 FYA  CONST_12  N3   C4   N9   C8    180.00   0.0  0
 FYA  CONST_13  C6   C5   N7   C8    180.00   0.0  0
 FYA  CONST_14  C4   C5   N7   C8      0.00   0.0  0
 FYA  CONST_15  C4   N9   C8   N7      0.00   0.0  0
 FYA  CONST_16  N1   C6   C5   N7    180.00   0.0  0
 FYA  CONST_17  N3   C4   C5   N7    180.00   0.0  0
 FYA  CONST_18  C2   N1   C6   C5      0.00   0.0  0
 FYA  CONST_19  C2   N3   C4   C5      0.00   0.0  0
 FYA  CONST_20  N3   C4   C5   C6      0.00   0.0  0
 FYA  CONST_21  N3   C2   N1   C6      0.00   0.0  0
 FYA  CONST_22  C4   C5   C6   N1      0.00   0.0  0
 FYA  CONST_23  C4   N3   C2   N1      0.00   0.0  0
 FYA  CONST_24  N7   C8   N9   C1'   180.00   0.0  0
 FYA  CONST_25  C5   C4   N9   C1'   180.00   0.0  0
 FYA  CONST_26  N3   C4   N9   C1'     0.00   0.0  0
 FYA  CONST_27  CE1  CD1  CG   CB    180.00   0.0  0
 FYA  CONST_28  CE2  CD2  CG   CB    180.00   0.0  0
 FYA  CONST_29  N6   C6   C5   N7      0.00   0.0  0
 FYA  CONST_30  C4   C5   C6   N6    180.00   0.0  0
 FYA  CONST_31  C2   N1   C6   N6    180.00   0.0  0
 FYA  CONST_32  HE1  CE1  CD1  CG    180.00   0.0  0
 FYA  CONST_33  HE2  CE2  CD2  CG    180.00   0.0  0
 FYA  CONST_34  HD2  CD2  CG   CD1   180.00   0.0  0
 FYA  CONST_35  HZ   CZ   CE1  CD1   180.00   0.0  0
 FYA  CONST_36  HD1  CD1  CG   CD2   180.00   0.0  0
 FYA  CONST_37  H8   C8   N9   C1'     0.00   0.0  0
 FYA  CONST_38  H2   C2   N1   C6    180.00   0.0  0
 FYA  CONST_39  H61  N6   C6   C5    180.00   0.0  0
 FYA  CONST_40  H62  N6   C6   C5      0.00   0.0  0
 FYA  Var_01    CD1  CG   CB   CA    -83.19  30.0  2
 FYA  Var_02    C4'  C5'  O5'  P    -111.31  30.0  3
 FYA  Var_03    O1P  P    O3P  C      47.73  30.0  1
 FYA  Var_04    H1   C    O3P  P      27.15  30.0  1

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
 FYA  chir_01  CA   C    N    CB   negativ
 FYA  chir_03  C4'  C5'  O4'  C3'  negativ
 FYA  chir_04  C3'  O3'  C4'  C2'  positiv
 FYA  chir_05  C2'  O2'  C3'  C1'  positiv
 FYA  chir_06  C1'  O4'  N9   C2'  negativ
 FYA  chir_07  P    O2P  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
 FYA  plan-1  CB   0.020
 FYA  plan-1  CG   0.020
 FYA  plan-1  CD1  0.020
 FYA  plan-1  CD2  0.020
 FYA  plan-1  CE1  0.020
 FYA  plan-1  CE2  0.020
 FYA  plan-1  CZ   0.020
 FYA  plan-1  HD1  0.020
 FYA  plan-1  HD2  0.020
 FYA  plan-1  HE1  0.020
 FYA  plan-1  HE2  0.020
 FYA  plan-1  HZ   0.020
 FYA  plan-2  C1'  0.020
 FYA  plan-2  N9   0.020
 FYA  plan-2  C8   0.020
 FYA  plan-2  N7   0.020
 FYA  plan-2  C5   0.020
 FYA  plan-2  C6   0.020
 FYA  plan-2  N6   0.020
 FYA  plan-2  N1   0.020
 FYA  plan-2  C2   0.020
 FYA  plan-2  N3   0.020
 FYA  plan-2  C4   0.020
 FYA  plan-2  H8   0.020
 FYA  plan-2  H2   0.020
 FYA  plan-3  C6   0.020
 FYA  plan-3  N6   0.020
 FYA  plan-3  H61  0.020
 FYA  plan-3  H62  0.020

