# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 06:31:50 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 5'-O-[(R)-hydroxy(propanoylamino)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 FPJ  FPJ  5'-O-[(R)-hydroxy(propanoylamino)phosphoryl]adenosine  ligand  46  27  .  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
;

data_comp_FPJ
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
 FPJ  C4   C  CR15  0   0.114  -0.8742   0.4795  -1.2238
 FPJ  C5   C  CR56  0  -0.004  -2.5344   1.5675  -0.5096
 FPJ  C6   C  CR6   0   0.463  -3.5327   2.4952  -0.1616
 FPJ  C11  C  C     0   0.579   2.0469   2.1106   0.1864
 FPJ  C7   C  CR16  0   0.047  -4.4337   0.8666   1.1908
 FPJ  C8   C  CR56  0   0.496  -2.6157   0.3214   0.0895
 FPJ  C9   C  CH1   0  -0.061  -0.7979  -2.6186  -1.1683
 FPJ  C10  C  CH1   0  -0.026   0.2213  -3.5634  -0.5266
 FPJ  C12  C  CH2   0  -0.580   1.4573   3.2770  -0.5605
 FPJ  C13  C  CH3   0  -0.660   0.5210   4.1255   0.2773
 FPJ  N1   N  NH1   0  -0.835   2.8667   1.2972  -0.5546
 FPJ  N2   N  NR5   0  -0.541  -1.5424  -0.3770  -0.3897
 FPJ  C3   C  CH1   0   0.206  -1.1367  -1.6993   0.0070
 FPJ  N3   N  N     0  -0.444  -1.4373   1.6439  -1.3289
 FPJ  O1P  O  OH1   0  -0.731   4.4025   0.5774   1.4708
 FPJ  P    P  P     0   1.458   3.7960   0.0445   0.1059
 FPJ  O2P  O  O     0  -0.692   4.8066  -0.4169  -0.8616
 FPJ  O3   O  O2    0  -0.583   2.7602  -1.0582   0.6171
 FPJ  C2   C  CH1   0  -0.051   0.9746  -2.6042   0.3858
 FPJ  O4   O  O2    0  -0.479   0.0259  -1.6192   0.7874
 FPJ  N4   N  N     0  -0.474  -4.4779   2.1021   0.6995
 FPJ  N5   N  N     0  -0.457  -3.5475  -0.0840   0.9472
 FPJ  N6   N  NH2   0  -0.816  -3.5673   3.7334  -0.6544
 FPJ  O5   O  OH1   0  -0.651  -1.9580  -3.2351  -1.6376
 FPJ  O6   O  OH1   0  -0.666  -0.4191  -4.5249   0.2683
 FPJ  O7   O  O     0  -0.467   1.8567   1.8922   1.3677
 FPJ  H1   H  HCR5  0   0.290   0.0330   0.1885  -1.7320
 FPJ  H2   H  HCR6  0   0.254  -5.2300   0.6119   1.8821
 FPJ  H3   H  HCH1  0   0.254  -0.2998  -2.0501  -1.9631
 FPJ  H4   H  HCH1  0   0.259   0.8803  -4.0247  -1.2739
 FPJ  H5   H  HCH2  0   0.281   2.2928   3.8773  -0.9343
 FPJ  H6   H  HCH2  0   0.279   0.9417   2.9042  -1.4486
 FPJ  H7   H  HCH3  0   0.232   1.0174   4.5211   1.1623
 FPJ  H8   H  HCH3  0   0.237   0.1662   4.9715  -0.3099
 FPJ  H9   H  HCH3  0   0.232  -0.3509   3.5586   0.6003
 FPJ  H10  H  HNH1  0   0.435   3.0531   1.5488  -1.5168
 FPJ  H11  H  HCH1  0   0.267  -1.9695  -2.1148   0.5834
 FPJ  H12  H  HOH1  0   0.497   3.7599   1.0075   2.0573
 FPJ  H13  H  HCH2  0   0.230   1.8389  -1.4306  -1.2184
 FPJ  H14  H  HCH2  0   0.262   2.8688  -2.7283  -0.6033
 FPJ  H15  H  HCH1  0   0.277   1.3363  -3.1241   1.2783
 FPJ  H16  H  HNH2  0   0.410  -2.8509   4.0648  -1.2760
 FPJ  H17  H  HNH2  0   0.405  -4.2685   4.3842  -0.3454
 FPJ  H18  H  HOH1  0   0.472  -1.7931  -3.5722  -2.5243
 FPJ  H19  H  HOH1  0   0.451  -1.1563  -4.8848  -0.2392
 FPJ  C1   C  CH2   0  -0.170   2.1534  -1.9568  -0.3105

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
 FPJ  N6   C6   single    1.333  0.020  1.333
 FPJ  N3   C5   aromatic  1.371  0.020  1.371
 FPJ  N3   C4   aromatic  1.298  0.020  1.298
 FPJ  C6   C5   aromatic  1.407  0.020  1.407
 FPJ  C6   N4   aromatic  1.338  0.020  1.338
 FPJ  C5   C8   aromatic  1.385  0.020  1.385
 FPJ  C4   N2   aromatic  1.370  0.020  1.370
 FPJ  O5   C9   single    1.395  0.020  1.395
 FPJ  C9   C10  single    1.531  0.020  1.531
 FPJ  C9   C3   single    1.530  0.020  1.530
 FPJ  N4   C7   aromatic  1.330  0.020  1.330
 FPJ  N2   C8   aromatic  1.367  0.020  1.367
 FPJ  N2   C3   single    1.439  0.020  1.439
 FPJ  C8   N5   aromatic  1.330  0.020  1.330
 FPJ  C10  O6   single    1.402  0.020  1.402
 FPJ  C10  C2   single    1.523  0.020  1.523
 FPJ  C7   N5   aromatic  1.322  0.020  1.322
 FPJ  C3   O4   single    1.403  0.020  1.403
 FPJ  C1   C2   single    1.514  0.020  1.514
 FPJ  C1   O3   single    1.427  0.020  1.427
 FPJ  C2   O4   single    1.425  0.020  1.425
 FPJ  O3   P    single    1.597  0.020  1.597
 FPJ  O2P  P    double    1.473  0.020  1.473
 FPJ  P    N1   single    1.694  0.020  1.694
 FPJ  P    O1P  single    1.586  0.020  1.586
 FPJ  N1   C11  single    1.372  0.020  1.372
 FPJ  C11  O7   double    1.216  0.020  1.216
 FPJ  C11  C12  single    1.505  0.020  1.505
 FPJ  C12  C13  single    1.516  0.020  1.516
 FPJ  C4   H1   single    0.930  0.020  1.080
 FPJ  C7   H2   single    0.930  0.020  1.080
 FPJ  C9   H3   single    0.970  0.020  1.090
 FPJ  C10  H4   single    0.970  0.020  1.090
 FPJ  C12  H5   single    0.970  0.020  1.090
 FPJ  C12  H6   single    0.970  0.020  1.090
 FPJ  C13  H7   single    0.970  0.020  1.090
 FPJ  C13  H8   single    0.970  0.020  1.090
 FPJ  C13  H9   single    0.970  0.020  1.090
 FPJ  N1   H10  single    0.860  0.020  1.020
 FPJ  C3   H11  single    0.970  0.020  1.090
 FPJ  O1P  H12  single    0.850  0.020  0.980
 FPJ  C1   H13  single    0.970  0.020  1.090
 FPJ  C1   H14  single    0.970  0.020  1.090
 FPJ  C2   H15  single    0.970  0.020  1.090
 FPJ  N6   H16  single    0.860  0.020  1.020
 FPJ  N6   H17  single    0.860  0.020  1.020
 FPJ  O5   H18  single    0.850  0.020  0.980
 FPJ  O6   H19  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
 FPJ  H1   C4   N3   124.62  3.000
 FPJ  H1   C4   N2   121.87  3.000
 FPJ  N3   C4   N2   113.50  3.000
 FPJ  N3   C5   C8   110.82  3.000
 FPJ  C8   C5   C6   116.41  3.000
 FPJ  N3   C5   C6   132.76  3.000
 FPJ  N6   C6   N4   119.51  3.000
 FPJ  N4   C6   C5   117.84  3.000
 FPJ  N6   C6   C5   122.65  3.000
 FPJ  O7   C11  N1   120.76  3.000
 FPJ  O7   C11  C12  124.04  3.000
 FPJ  N1   C11  C12  115.17  3.000
 FPJ  H2   C7   N5   116.14  3.000
 FPJ  H2   C7   N4   115.40  3.000
 FPJ  N5   C7   N4   128.46  3.000
 FPJ  N5   C8   N2   128.35  3.000
 FPJ  N5   C8   C5   126.47  3.000
 FPJ  N2   C8   C5   105.18  3.000
 FPJ  H3   C9   O5   111.27  3.000
 FPJ  H3   C9   C3   110.23  3.000
 FPJ  O5   C9   C3   109.86  3.000
 FPJ  H3   C9   C10  108.75  3.000
 FPJ  C3   C9   C10  101.32  3.000
 FPJ  O5   C9   C10  114.96  3.000
 FPJ  H4   C10  O6   111.82  3.000
 FPJ  H4   C10  C2   112.06  3.000
 FPJ  O6   C10  C2   108.54  3.000
 FPJ  H4   C10  C9   111.94  3.000
 FPJ  C2   C10  C9   101.05  3.000
 FPJ  O6   C10  C9   110.90  3.000
 FPJ  H6   C12  H5   105.66  3.000
 FPJ  H6   C12  C13  110.41  3.000
 FPJ  H5   C12  C13  110.68  3.000
 FPJ  H6   C12  C11  108.89  3.000
 FPJ  H5   C12  C11  107.18  3.000
 FPJ  C13  C12  C11  113.66  3.000
 FPJ  H9   C13  H8   107.67  3.000
 FPJ  H9   C13  H7   108.25  3.000
 FPJ  H8   C13  H7   107.72  3.000
 FPJ  H9   C13  C12  111.54  3.000
 FPJ  H8   C13  C12  109.75  3.000
 FPJ  H7   C13  C12  111.77  3.000
 FPJ  H10  N1   P    116.98  3.000
 FPJ  H10  N1   C11  118.44  3.000
 FPJ  P    N1   C11  123.75  3.000
 FPJ  C3   N2   C8   126.45  3.000
 FPJ  C3   N2   C4   127.23  3.000
 FPJ  C8   N2   C4   106.08  3.000
 FPJ  H11  C3   O4   111.06  3.000
 FPJ  H11  C3   N2   106.23  3.000
 FPJ  O4   C3   N2   109.55  3.000
 FPJ  H11  C3   C9   110.17  3.000
 FPJ  O4   C3   C9   106.15  3.000
 FPJ  N2   C3   C9   113.75  3.000
 FPJ  C5   N3   C4   104.40  3.000
 FPJ  H12  O1P  P    114.56  3.000
 FPJ  O3   P    O2P  116.03  3.000
 FPJ  O2P  P    O1P  114.08  3.000
 FPJ  O3   P    O1P  101.81  3.000
 FPJ  O1P  P    N1   107.28  3.000
 FPJ  O2P  P    N1   110.60  3.000
 FPJ  O3   P    N1   106.24  3.000
 FPJ  C1   O3   P    120.17  3.000
 FPJ  H15  C2   O4   108.57  3.000
 FPJ  H15  C2   C1   108.71  3.000
 FPJ  O4   C2   C1   110.62  3.000
 FPJ  H15  C2   C10  110.66  3.000
 FPJ  O4   C2   C10  105.95  3.000
 FPJ  C1   C2   C10  112.25  3.000
 FPJ  C2   O4   C3   110.83  3.000
 FPJ  C7   N4   C6   119.15  3.000
 FPJ  C8   N5   C7   111.67  3.000
 FPJ  H17  N6   H16  118.30  3.000
 FPJ  H17  N6   C6   120.38  3.000
 FPJ  H16  N6   C6   121.10  3.000
 FPJ  H18  O5   C9   108.79  3.000
 FPJ  H19  O6   C10  107.85  3.000
 FPJ  H14  C1   H13  107.77  3.000
 FPJ  H14  C1   C2   109.34  3.000
 FPJ  H13  C1   C2   111.28  3.000
 FPJ  H14  C1   O3   109.91  3.000
 FPJ  H13  C1   O3   111.00  3.000
 FPJ  C2   C1   O3   107.53  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
 FPJ  CONST_01  C6   C5   N3   C4    180.00   0.0  0
 FPJ  CONST_02  C8   C5   N3   C4      0.00   0.0  0
 FPJ  CONST_03  C5   C8   N2   C4      0.00   0.0  0
 FPJ  CONST_04  N5   C8   N2   C4    180.00   0.0  0
 FPJ  CONST_05  N2   C4   N3   C5      0.00   0.0  0
 FPJ  CONST_06  C7   N4   C6   C5      0.00   0.0  0
 FPJ  CONST_07  C7   N5   C8   C5      0.00   0.0  0
 FPJ  CONST_08  N2   C8   C5   C6    180.00   0.0  0
 FPJ  CONST_09  N5   C8   C5   C6      0.00   0.0  0
 FPJ  CONST_10  N5   C7   N4   C6      0.00   0.0  0
 FPJ  CONST_11  N2   C8   N5   C7    180.00   0.0  0
 FPJ  CONST_12  N4   C6   C5   C8      0.00   0.0  0
 FPJ  CONST_13  N3   C4   N2   C8      0.00   0.0  0
 FPJ  CONST_14  N4   C7   N5   C8      0.00   0.0  0
 FPJ  CONST_15  N3   C5   C8   N2      0.00   0.0  0
 FPJ  CONST_16  N4   C6   C5   N3    180.00   0.0  0
 FPJ  CONST_17  N5   C8   C5   N3    180.00   0.0  0
 FPJ  CONST_18  C3   N2   C8   C5    180.00   0.0  0
 FPJ  CONST_19  N3   C4   N2   C3    180.00   0.0  0
 FPJ  CONST_20  N5   C8   N2   C3      0.00   0.0  0
 FPJ  CONST_21  N6   C6   N4   C7    180.00   0.0  0
 FPJ  CONST_22  N6   C6   C5   C8    180.00   0.0  0
 FPJ  CONST_23  N6   C6   C5   N3      0.00   0.0  0
 FPJ  CONST_24  H1   C4   N3   C5    180.00   0.0  0
 FPJ  CONST_25  H2   C7   N4   C6    180.00   0.0  0
 FPJ  CONST_26  H16  N6   C6   C5      0.00   0.0  0
 FPJ  CONST_27  H17  N6   C6   C5    180.00   0.0  0
 FPJ  CONST_28  P    N1   C11  C12   180.00   0.0  0
 FPJ  CONST_29  O7   C11  N1   P       0.00   0.0  0
 FPJ  CONST_30  H10  N1   C11  C12     0.00   0.0  0
 FPJ  Var_01    C2   C1   O3   P    -164.88  30.0  2
 FPJ  Var_02    O3   P    N1   C11    67.43  30.0  1
 FPJ  Var_03    N1   C11  C12  C13   178.05  30.0  1
 FPJ  Var_04    H7   C13  C12  C11    58.13  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
 FPJ  chir_01  C9   O5   C10  C3   positiv
 FPJ  chir_02  C10  O6   C2   C9   positiv
 FPJ  chir_03  C3   O4   N2   C9   negativ
 FPJ  chir_05  C2   C10  C1   O4   negativ
 FPJ  chir_06  P    O2P  N1   O1P  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
 FPJ  plan-1  C4   0.020
 FPJ  plan-1  C5   0.020
 FPJ  plan-1  C6   0.020
 FPJ  plan-1  C7   0.020
 FPJ  plan-1  C8   0.020
 FPJ  plan-1  N2   0.020
 FPJ  plan-1  C3   0.020
 FPJ  plan-1  N3   0.020
 FPJ  plan-1  N4   0.020
 FPJ  plan-1  N5   0.020
 FPJ  plan-1  N6   0.020
 FPJ  plan-1  H1   0.020
 FPJ  plan-1  H2   0.020
 FPJ  plan-2  C6   0.020
 FPJ  plan-2  N6   0.020
 FPJ  plan-2  H16  0.020
 FPJ  plan-2  H17  0.020
 FPJ  plan-3  C11  0.020
 FPJ  plan-3  C12  0.020
 FPJ  plan-3  N1   0.020
 FPJ  plan-3  P    0.020
 FPJ  plan-3  O7   0.020
 FPJ  plan-3  H10  0.020

