# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:52:21 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: [5-(2-amino-4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-1,1-difluoropentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2c(CCCCC(F)(F)[P](O)(O)=O)c[nH]c2C(=O)N1
#
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
 9D9  9D9  '[5-(2-amino-4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-1,1-difluoropentyl]phosphonic acid'  ligand  35  22  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9D9
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
 9D9  O2P  O  OP    -1  -0.891  -5.1201  -0.6093  -1.6970
 9D9  P    P  P      0   1.109  -5.0754   0.5568  -0.7104
 9D9  O3P  O  OP    -1  -0.892  -4.5242   1.8603  -1.2872
 9D9  O1P  O  O      0  -0.893  -6.3256   0.7169   0.1524
 9D9  C14  C  CT     0   0.449  -3.7376   0.0295   0.5012
 9D9  F1   F  F      0  -0.396  -3.6389   0.9593   1.5298
 9D9  F2   F  F      0  -0.396  -4.1252  -1.1370   1.1503
 9D9  C13  C  CH2    0  -0.542  -2.3632  -0.1810  -0.0854
 9D9  C12  C  CH2    0  -0.433  -1.2955  -0.6697   0.8882
 9D9  C11  C  CH2    0  -0.409   0.0709  -0.7809   0.2245
 9D9  C10  C  CH2    0  -0.513   1.1397  -1.3435   1.1632
 9D9  C9   C  CR5    0  -0.026   2.4936  -1.3953   0.5369
 9D9  C8   C  CR15   0  -0.066   3.1420  -2.4933   0.0101
 9D9  N7   N  NR15   0  -0.657   4.3399  -2.1285  -0.5051
 9D9  C5   C  CR56   0   0.129   4.4980  -0.7848  -0.3247
 9D9  C4   C  CR56   0   0.155   3.3659  -0.2979   0.3206
 9D9  N3   N  N      0  -0.506   3.1898   1.0097   0.6603
 9D9  C2   C  CR6    0   0.631   4.1711   1.7992   0.3472
 9D9  N2   N  NH2    0  -0.841   4.1387   3.1088   0.6948
 9D9  N1   N  NR16   0  -0.718   5.3078   1.3752  -0.2929
 9D9  C6   C  CR6    0   0.509   5.5745   0.0664  -0.6839
 9D9  O6   O  O      0  -0.491   6.6175  -0.2264  -1.2546
 9D9  H3   H  HCH2   0   0.226  -2.4647  -0.8875  -0.9134
 9D9  H4   H  HCH2   0   0.226  -2.0555   0.7658  -0.5371
 9D9  H5   H  HCH2   0   0.215  -1.2225   0.0104   1.7418
 9D9  H6   H  HCH2   0   0.215  -1.5784  -1.6457   1.2928
 9D9  H7   H  HCH2   0   0.213   0.0040  -1.4219  -0.6603
 9D9  H8   H  HCH2   0   0.219   0.3889   0.2035  -0.1328
 9D9  H9   H  HCH2   0   0.224   1.1787  -0.7273   2.0669
 9D9  H10  H  HCH2   0   0.231   0.8426  -2.3449   1.4870
 9D9  H11  H  HCR5   0   0.282   2.8180  -3.5217  -0.0261
 9D9  H12  H  HNR5   0   0.412   5.0034  -2.7488  -0.9380
 9D9  H13  H  HNH2   0   0.400   3.2357   3.4668   0.9586
 9D9  H14  H  HNH2   0   0.402   4.7181   3.7647   0.1977
 9D9  H15  H  HNR6   0   0.420   6.0277   2.0545  -0.5034

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
 9D9  O1P  P    deloc     1.527  0.020  1.527
 9D9  F1   C14  single    1.390  0.020  1.390
 9D9  F2   C14  single    1.390  0.020  1.390
 9D9  C14  P    single    1.880  0.020  1.880
 9D9  C14  C13  single    1.509  0.020  1.509
 9D9  P    O2P  deloc     1.528  0.020  1.528
 9D9  P    O3P  deloc     1.528  0.020  1.528
 9D9  C12  C13  single    1.525  0.020  1.525
 9D9  C12  C11  single    1.523  0.020  1.523
 9D9  C11  C10  single    1.530  0.020  1.530
 9D9  C10  C9   single    1.493  0.020  1.493
 9D9  N3   C4   single    1.362  0.020  1.362
 9D9  N3   C2   double    1.298  0.020  1.298
 9D9  C9   C4   aromatic  1.418  0.020  1.418
 9D9  C9   C8   aromatic  1.380  0.020  1.380
 9D9  N2   C2   single    1.355  0.020  1.355
 9D9  C4   C5   aromatic  1.391  0.020  1.391
 9D9  C2   N1   single    1.372  0.020  1.372
 9D9  C8   N7   aromatic  1.354  0.020  1.354
 9D9  C5   N7   aromatic  1.365  0.020  1.365
 9D9  C5   C6   single    1.419  0.020  1.419
 9D9  N1   C6   single    1.392  0.020  1.392
 9D9  C6   O6   double    1.224  0.020  1.224
 9D9  C13  H3   single    0.970  0.020  1.090
 9D9  C13  H4   single    0.970  0.020  1.090
 9D9  C12  H5   single    0.970  0.020  1.090
 9D9  C12  H6   single    0.970  0.020  1.090
 9D9  C11  H7   single    0.970  0.020  1.090
 9D9  C11  H8   single    0.970  0.020  1.090
 9D9  C10  H9   single    0.970  0.020  1.090
 9D9  C10  H10  single    0.970  0.020  1.090
 9D9  C8   H11  single    0.930  0.020  1.080
 9D9  N7   H12  single    0.860  0.020  1.020
 9D9  N2   H13  single    0.890  0.020  1.040
 9D9  N2   H14  single    0.890  0.020  1.040
 9D9  N1   H15  single    0.860  0.020  1.020

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
 9D9  C14  P    O1P  104.34  3.000
 9D9  C14  P    O3P  103.05  3.000
 9D9  O1P  P    O3P  114.77  3.000
 9D9  O3P  P    O2P  114.70  3.000
 9D9  C14  P    O2P  102.87  3.000
 9D9  O1P  P    O2P  114.88  3.000
 9D9  C13  C14  F2   108.57  3.000
 9D9  C13  C14  F1   108.43  3.000
 9D9  F2   C14  F1   103.62  3.000
 9D9  C13  C14  P    115.89  3.000
 9D9  F2   C14  P    109.75  3.000
 9D9  F1   C14  P    109.86  3.000
 9D9  H4   C13  H3   105.84  3.000
 9D9  H4   C13  C12  110.14  3.000
 9D9  H3   C13  C12  109.96  3.000
 9D9  H4   C13  C14  107.23  3.000
 9D9  H3   C13  C14  107.45  3.000
 9D9  C12  C13  C14  115.73  3.000
 9D9  H6   C12  H5   106.47  3.000
 9D9  H6   C12  C11  109.15  3.000
 9D9  H5   C12  C11  109.00  3.000
 9D9  H6   C12  C13  109.93  3.000
 9D9  H5   C12  C13  110.22  3.000
 9D9  C11  C12  C13  111.91  3.000
 9D9  H8   C11  H7   106.30  3.000
 9D9  H8   C11  C10  109.16  3.000
 9D9  H7   C11  C10  108.87  3.000
 9D9  H8   C11  C12  109.71  3.000
 9D9  H7   C11  C12  109.88  3.000
 9D9  C10  C11  C12  112.72  3.000
 9D9  H10  C10  H9   106.30  3.000
 9D9  H10  C10  C9   109.81  3.000
 9D9  H9   C10  C9   109.49  3.000
 9D9  H10  C10  C11  109.19  3.000
 9D9  H9   C10  C11  108.94  3.000
 9D9  C9   C10  C11  112.89  3.000
 9D9  C4   C9   C8   105.58  3.000
 9D9  C8   C9   C10  127.88  3.000
 9D9  C4   C9   C10  126.51  3.000
 9D9  H11  C8   N7   120.64  3.000
 9D9  H11  C8   C9   129.07  3.000
 9D9  N7   C8   C9   110.28  3.000
 9D9  H12  N7   C5   125.97  3.000
 9D9  H12  N7   C8   125.53  3.000
 9D9  C5   N7   C8   108.50  3.000
 9D9  C6   C5   C4   121.67  3.000
 9D9  C6   C5   N7   130.18  3.000
 9D9  C4   C5   N7   108.16  3.000
 9D9  N3   C4   C5   123.83  3.000
 9D9  C5   C4   C9   107.48  3.000
 9D9  N3   C4   C9   128.69  3.000
 9D9  C2   N3   C4   115.22  3.000
 9D9  N1   C2   N2   115.99  3.000
 9D9  N1   C2   N3   123.44  3.000
 9D9  N2   C2   N3   120.52  3.000
 9D9  H14  N2   H13  114.46  3.000
 9D9  H14  N2   C2   119.29  3.000
 9D9  H13  N2   C2   115.62  3.000
 9D9  H15  N1   C6   115.88  3.000
 9D9  H15  N1   C2   118.63  3.000
 9D9  C6   N1   C2   125.49  3.000
 9D9  O6   C6   N1   121.27  3.000
 9D9  O6   C6   C5   128.38  3.000
 9D9  N1   C6   C5   110.35  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
 9D9  CONST_01  N7   C5   C4   C9      0.00   0.0  0
 9D9  CONST_02  C5   N7   C8   C9      0.00   0.0  0
 9D9  CONST_03  C5   C4   C9   C8      0.00   0.0  0
 9D9  CONST_04  C4   C5   N7   C8      0.00   0.0  0
 9D9  CONST_05  C4   C9   C8   N7      0.00   0.0  0
 9D9  CONST_06  C2   N1   C6   C5      0.00   0.0  0
 9D9  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 9D9  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 9D9  CONST_09  N3   C4   C9   C10     0.00   0.0  0
 9D9  CONST_10  C5   C4   C9   C10   180.00   0.0  0
 9D9  CONST_11  N7   C8   C9   C10   180.00   0.0  0
 9D9  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 9D9  CONST_13  O6   C6   N1   C2    180.00   0.0  0
 9D9  CONST_14  C6   N1   C2   N2    180.00   0.0  0
 9D9  CONST_15  H12  N7   C8   C9    180.00   0.0  0
 9D9  CONST_16  H11  C8   N7   C5    180.00   0.0  0
 9D9  CONST_17  H15  N1   C6   C5    180.00   0.0  0
 9D9  Var_01    C4   C9   C10  C11    75.94  30.0  2
 9D9  Var_02    C9   C10  C11  C12  -177.35  30.0  3
 9D9  Var_03    F1   C14  P    O2P  -175.91  30.0  3
 9D9  Var_04    C12  C13  C14  P    -177.33  30.0  3
 9D9  Var_05    C11  C12  C13  C14  -176.94  30.0  1
 9D9  Var_06    C10  C11  C12  C13  -176.81  30.0  3

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
 9D9  plan-1  C10  0.020
 9D9  plan-1  C9   0.020
 9D9  plan-1  C8   0.020
 9D9  plan-1  N7   0.020
 9D9  plan-1  C5   0.020
 9D9  plan-1  C4   0.020
 9D9  plan-1  N3   0.020
 9D9  plan-1  C2   0.020
 9D9  plan-1  N2   0.020
 9D9  plan-1  N1   0.020
 9D9  plan-1  C6   0.020
 9D9  plan-1  O6   0.020
 9D9  plan-1  H11  0.020
 9D9  plan-1  H12  0.020
 9D9  plan-1  H13  0.020
 9D9  plan-1  H14  0.020
 9D9  plan-1  H15  0.020

