# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 16:29:42 2020
#   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  57  33  .  2021-08-09  2021-08-09  
;
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  -0.129   1.3481  -1.5215  -2.7436
 FYA  CA    C  CH1    0  -0.131   0.4324  -0.3223  -2.9266
 FYA  N     N  NH2    0  -0.781   1.1654   0.7921  -3.4973
 FYA  CB    C  CH2    0  -0.526  -0.7999  -0.7595  -3.7465
 FYA  CG    C  CR6    0   0.144  -1.8500   0.3103  -3.8068
 FYA  CD1   C  CR16   0  -0.328  -1.8516   1.2834  -4.8051
 FYA  CD2   C  CR16   0  -0.305  -2.8259   0.3827  -2.8145
 FYA  CE1   C  CR16   0  -0.242  -2.7966   2.3027  -4.8049
 FYA  CE2   C  CR16   0  -0.241  -3.7695   1.3997  -2.8061
 FYA  CZ    C  CR16   0  -0.273  -3.7555   2.3679  -3.8027
 FYA  P     P  P      0   1.363   3.2891  -2.3737  -1.1932
 FYA  O1P   O  O      0  -0.796   2.3840  -3.2573  -0.3809
 FYA  O2P   O  OP    -1  -0.789   4.2251  -2.9700  -2.1972
 FYA  O3P   O  O2     0  -0.601   2.4233  -1.1792  -1.8984
 FYA  O5'   O  O2     0  -0.612   4.2072  -1.4353  -0.2121
 FYA  C5'   C  CH2    0  -0.162   3.8917  -1.1955   1.1410
 FYA  C4'   C  CH1    0  -0.032   3.3720   0.2136   1.3661
 FYA  O4'   O  O2     0  -0.479   2.1350   0.4310   0.6809
 FYA  C3'   C  CH1    0  -0.037   3.0857   0.4821   2.8395
 FYA  O3'   O  OH1    0  -0.669   3.2585   1.8531   3.0912
 FYA  C2'   C  CH1    0  -0.046   1.6087   0.0906   2.9275
 FYA  O2'   O  OH1    0  -0.653   0.9008   0.6763   3.9784
 FYA  C1'   C  CH1    0   0.224   1.0905   0.6115   1.5878
 FYA  N9    N  NR5    0  -0.542  -0.0838  -0.0806   1.1133
 FYA  C8    C  CR15   0   0.088  -0.1524  -1.3525   0.6075
 FYA  N7    N  N      0  -0.456  -1.3679  -1.7243   0.3259
 FYA  C5    C  CR56   0  -0.006  -2.1453  -0.6482   0.6674
 FYA  C6    C  CR6    0   0.452  -3.5283  -0.4080   0.5964
 FYA  N6    N  NH2    0  -0.819  -4.3922  -1.3113   0.1248
 FYA  N1    N  N      0  -0.474  -3.9812   0.7847   0.9969
 FYA  C2    C  CR16   0   0.038  -3.1114   1.6908   1.4371
 FYA  N3    N  N      0  -0.455  -1.7995   1.5827   1.5527
 FYA  C4    C  CR56   0   0.488  -1.3647   0.3895   1.1529
 FYA  H1    H  HCH2   0   0.207   0.7633  -2.3447  -2.3189
 FYA  H2A   H  HCH2   0   0.199   1.7148  -1.8552  -3.7250
 FYA  HA    H  HCH1   0   0.239   0.0889  -0.0139  -1.9334
 FYA  HN1   H  HNH2   0   0.332   1.4195   0.5799  -4.4561
 FYA  HN2   H  HNH2   0   0.348   0.5712   1.6108  -3.5431
 FYA  HB1   H  HCH2   0   0.240  -0.4732  -1.0305  -4.7553
 FYA  HB2   H  HCH2   0   0.239  -1.2277  -1.6619  -3.3002
 FYA  HD1   H  HCR6   0   0.248  -1.1158   1.2399  -5.5997
 FYA  HD2   H  HCR6   0   0.242  -2.8508  -0.3770  -2.0436
 FYA  HE1   H  HCR6   0   0.252  -2.7824   3.0471  -5.5907
 FYA  HE2   H  HCR6   0   0.247  -4.5130   1.4366  -2.0197
 FYA  HZ    H  HCR6   0   0.252  -4.4897   3.1630  -3.8017
 FYA  H5'1  H  HCH2   0   0.214   3.1824  -1.9350   1.5237
 FYA  H5'2  H  HCH2   0   0.231   4.8130  -1.3041   1.7213
 FYA  H4'   H  HCH1   0   0.255   4.1072   0.9279   0.9815
 FYA  H3'   H  HCH1   0   0.249   3.7125  -0.1322   3.4991
 FYA  HO'3  H  HOH1   0   0.449   2.7754   2.0717   3.8968
 FYA  H2'   H  HCH1   0   0.248   1.5288  -1.0042   2.9475
 FYA  HO'2  H  HOH1   0   0.469   1.0239   0.1434   4.7703
 FYA  H1'   H  HCH1   0   0.254   0.8047   1.6661   1.6793
 FYA  H8    H  HCR5   0   0.309   0.7329  -1.9536   0.4439
 FYA  H61   H  HNH2   0   0.402  -5.3798  -1.1239   0.1443
 FYA  H62   H  HNH2   0   0.409  -4.0907  -2.2424  -0.1030
 FYA  H2    H  HCR6   0   0.250  -3.5409   2.6392   1.7416

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    1.520  0.020  1.520
 FYA  C    O3P   single    1.410  0.020  1.410
 FYA  C    H1    single    0.970  0.020  1.090
 FYA  C    H2A   single    0.970  0.020  1.090
 FYA  CA   N     single    1.451  0.020  1.451
 FYA  CA   CB    single    1.543  0.020  1.543
 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    1.500  0.020  1.500
 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  1.394  0.020  1.394
 FYA  CD1  CE1   aromatic  1.390  0.020  1.390
 FYA  CD1  HD1   single    0.930  0.020  1.080
 FYA  CD2  CE2   aromatic  1.387  0.020  1.387
 FYA  CD2  HD2   single    0.930  0.020  1.080
 FYA  CE1  CZ    aromatic  1.389  0.020  1.389
 FYA  CE1  HE1   single    0.930  0.020  1.080
 FYA  CE2  CZ    aromatic  1.390  0.020  1.390
 FYA  CE2  HE2   single    0.930  0.020  1.080
 FYA  CZ   HZ    single    0.930  0.020  1.080
 FYA  P    O1P   deloc     1.503  0.020  1.503
 FYA  P    O2P   deloc     1.497  0.020  1.497
 FYA  P    O3P   single    1.635  0.020  1.635
 FYA  P    O5'   single    1.639  0.020  1.639
 FYA  O5'  C5'   single    1.410  0.020  1.410
 FYA  C5'  C4'   single    1.519  0.020  1.519
 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    1.431  0.020  1.431
 FYA  C4'  C3'   single    1.525  0.020  1.525
 FYA  C4'  H4'   single    0.970  0.020  1.090
 FYA  O4'  C1'   single    1.395  0.020  1.395
 FYA  C3'  O3'   single    1.405  0.020  1.405
 FYA  C3'  C2'   single    1.530  0.020  1.530
 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    1.528  0.020  1.528
 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    1.443  0.020  1.443
 FYA  C1'  H1'   single    0.970  0.020  1.090
 FYA  N9   C8    aromatic  1.371  0.020  1.371
 FYA  N9   C4    aromatic  1.365  0.020  1.365
 FYA  C8   N7    aromatic  1.302  0.020  1.302
 FYA  C8   H8    single    0.930  0.020  1.080
 FYA  N7   C5    aromatic  1.371  0.020  1.371
 FYA  C5   C6    aromatic  1.405  0.020  1.405
 FYA  C5   C4    aromatic  1.386  0.020  1.386
 FYA  C6   N6    single    1.336  0.020  1.336
 FYA  C6   N1    aromatic  1.337  0.020  1.337
 FYA  N6   H61   single    0.860  0.020  1.020
 FYA  N6   H62   single    0.860  0.020  1.020
 FYA  N1   C2    aromatic  1.331  0.020  1.331
 FYA  C2   N3    aromatic  1.321  0.020  1.321
 FYA  C2   H2    single    0.930  0.020  1.080
 FYA  N3   C4    aromatic  1.331  0.020  1.331

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    107.22  3.000
 FYA  H2A   C    O3P   110.76  3.000
 FYA  H1    C    O3P   110.93  3.000
 FYA  H2A   C    CA    109.45  3.000
 FYA  H1    C    CA    108.53  3.000
 FYA  O3P   C    CA    109.88  3.000
 FYA  HA    CA   CB    108.13  3.000
 FYA  HA    CA   N     107.39  3.000
 FYA  CB    CA   N     114.33  3.000
 FYA  HA    CA   C     107.57  3.000
 FYA  CB    CA   C     108.76  3.000
 FYA  N     CA   C     110.42  3.000
 FYA  HN2   N    HN1   105.86  3.000
 FYA  HN2   N    CA    110.02  3.000
 FYA  HN1   N    CA    109.73  3.000
 FYA  HB2   CB   HB1   106.77  3.000
 FYA  HB2   CB   CG    109.33  3.000
 FYA  HB1   CB   CG    110.39  3.000
 FYA  HB2   CB   CA    109.22  3.000
 FYA  HB1   CB   CA    108.75  3.000
 FYA  CG    CB   CA    112.23  3.000
 FYA  CD2   CG   CD1   118.22  3.000
 FYA  CD2   CG   CB    119.90  3.000
 FYA  CD1   CG   CB    121.83  3.000
 FYA  HD1   CD1  CE1   119.42  3.000
 FYA  HD1   CD1  CG    119.75  3.000
 FYA  CE1   CD1  CG    120.83  3.000
 FYA  HD2   CD2  CE2   119.63  3.000
 FYA  HD2   CD2  CG    119.12  3.000
 FYA  CE2   CD2  CG    121.24  3.000
 FYA  HE1   CE1  CZ    120.05  3.000
 FYA  HE1   CE1  CD1   119.68  3.000
 FYA  CZ    CE1  CD1   120.27  3.000
 FYA  HE2   CE2  CZ    120.26  3.000
 FYA  HE2   CE2  CD2   119.76  3.000
 FYA  CZ    CE2  CD2   119.97  3.000
 FYA  HZ    CZ   CE2   120.29  3.000
 FYA  HZ    CZ   CE1   120.24  3.000
 FYA  CE2   CZ   CE1   119.46  3.000
 FYA  O5'   P    O3P    97.85  3.000
 FYA  O5'   P    O2P   106.23  3.000
 FYA  O3P   P    O2P   109.44  3.000
 FYA  O5'   P    O1P   110.51  3.000
 FYA  O3P   P    O1P   110.09  3.000
 FYA  O2P   P    O1P   120.32  3.000
 FYA  P     O3P  C     119.01  3.000
 FYA  C5'   O5'  P     123.13  3.000
 FYA  H5'2  C5'  H5'1  107.06  3.000
 FYA  H5'2  C5'  C4'   107.55  3.000
 FYA  H5'1  C5'  C4'   110.71  3.000
 FYA  H5'2  C5'  O5'   107.67  3.000
 FYA  H5'1  C5'  O5'   111.46  3.000
 FYA  C4'   C5'  O5'   112.13  3.000
 FYA  H4'   C4'  C3'   110.53  3.000
 FYA  H4'   C4'  O4'   108.26  3.000
 FYA  C3'   C4'  O4'   105.88  3.000
 FYA  H4'   C4'  C5'   108.88  3.000
 FYA  C3'   C4'  C5'   111.77  3.000
 FYA  O4'   C4'  C5'   111.46  3.000
 FYA  C1'   O4'  C4'   110.83  3.000
 FYA  H3'   C3'  C2'   111.92  3.000
 FYA  H3'   C3'  O3'   111.60  3.000
 FYA  C2'   C3'  O3'   110.98  3.000
 FYA  H3'   C3'  C4'   112.01  3.000
 FYA  C2'   C3'  C4'   101.06  3.000
 FYA  O3'   C3'  C4'   108.78  3.000
 FYA  HO'3  O3'  C3'   108.01  3.000
 FYA  H2'   C2'  C1'   109.35  3.000
 FYA  H2'   C2'  O2'   111.57  3.000
 FYA  C1'   C2'  O2'   110.18  3.000
 FYA  H2'   C2'  C3'   109.05  3.000
 FYA  C1'   C2'  C3'   100.94  3.000
 FYA  O2'   C2'  C3'   115.17  3.000
 FYA  HO'2  O2'  C2'   108.80  3.000
 FYA  H1'   C1'  N9    106.06  3.000
 FYA  H1'   C1'  C2'   110.07  3.000
 FYA  N9    C1'  C2'   113.62  3.000
 FYA  H1'   C1'  O4'   111.96  3.000
 FYA  N9    C1'  O4'   109.47  3.000
 FYA  C2'   C1'  O4'   105.78  3.000
 FYA  C4    N9   C8    106.46  3.000
 FYA  C4    N9   C1'   126.07  3.000
 FYA  C8    N9   C1'   127.38  3.000
 FYA  H8    C8   N7    124.91  3.000
 FYA  H8    C8   N9    122.02  3.000
 FYA  N7    C8   N9    113.06  3.000
 FYA  C5    N7   C8    104.56  3.000
 FYA  C4    C5   C6    116.35  3.000
 FYA  C4    C5   N7    110.83  3.000
 FYA  C6    C5   N7    132.81  3.000
 FYA  N1    C6   N6    119.33  3.000
 FYA  N1    C6   C5    118.07  3.000
 FYA  N6    C6   C5    122.59  3.000
 FYA  H62   N6   H61   118.15  3.000
 FYA  H62   N6   C6    120.83  3.000
 FYA  H61   N6   C6    120.15  3.000
 FYA  C2    N1   C6    119.01  3.000
 FYA  H2    C2   N3    116.11  3.000
 FYA  H2    C2   N1    115.42  3.000
 FYA  N3    C2   N1    128.47  3.000
 FYA  C4    N3   C2    111.79  3.000
 FYA  N3    C4   C5    126.31  3.000
 FYA  N3    C4   N9    128.59  3.000
 FYA  C5    C4   N9    105.10  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     88.84  30.0  2
 FYA  Var_02    C4'  C5'  O5'  P    -106.66  30.0  3
 FYA  Var_03    O1P  P    O3P  C     -57.22  30.0  1
 FYA  Var_04    H1   C    O3P  P      42.03  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

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

