# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 16:01:51 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}phenyl)carbonyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2ncc(CNc3ccc(cc3)C(=O)O[P](O)(O)=O)nc2C(=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
 PD8  PD8  '(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}phenyl)carbonyl dihydrogen phosphate'  ligand  40  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 (reasonable std)
;

data_comp_PD8
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
 PD8  O1    O  OC    0  -0.436   7.1649  -1.2029  -3.0569
 PD8  C2    C  CR6   0   0.538   6.9996  -0.0332  -2.7838
 PD8  N3    N  NR16  0  -0.714   8.0529   0.8548  -2.7346
 PD8  C4    C  CR6   0   0.701   7.9322   2.1832  -2.4317
 PD8  N5    N  NH2   0  -0.820   9.0533   2.9001  -2.4340
 PD8  N6    N  N     0  -0.505   6.7887   2.7539  -2.1617
 PD8  C7    C  CR66  0   0.398   5.6889   1.9728  -2.1845
 PD8  N8    N  N     0  -0.384   4.5117   2.5607  -1.9056
 PD8  C9    C  CR16  0  -0.070   3.4424   1.8051  -1.9212
 PD8  C10   C  CR6   0   0.151   3.4793   0.4273  -2.2124
 PD8  C11   C  CH2   0  -0.351   2.2267  -0.3990  -2.1966
 PD8  N12   N  NH1   0  -0.693   1.2664   0.1285  -3.1365
 PD8  C13   C  CR6   0   0.413  -0.0439  -0.2237  -3.1546
 PD8  C14   C  CR16  0  -0.334  -0.8580   0.2087  -4.2219
 PD8  C15   C  CR16  0  -0.239  -2.1941  -0.1014  -4.2585
 PD8  C16   C  CR6   0  -0.126  -2.7900  -0.8574  -3.2395
 PD8  C17   C  C     0   0.597  -4.2136  -1.1615  -3.3344
 PD8  O19   O  O     0  -0.427  -4.9512  -0.8216  -4.2226
 PD8  C20   C  CR16  0  -0.246  -1.9845  -1.2940  -2.1854
 PD8  C21   C  CR16  0  -0.342  -0.6388  -0.9935  -2.1396
 PD8  N22   N  N     0  -0.365   4.6226  -0.1547  -2.4901
 PD8  C23   C  CR66  0  -0.045   5.7175   0.5991  -2.4771
 PD8  P23   P  P     0   1.455  -6.1998  -2.4467  -2.1996
 PD8  O24   O  OH1   0  -0.721  -6.1635  -3.1124  -0.7565
 PD8  O25   O  O     0  -0.687  -6.6280  -3.3075  -3.3129
 PD8  O26   O  OH1   0  -0.730  -6.9853  -1.0952  -1.9352
 PD8  O27   O  O2    0  -0.598  -4.6647  -1.8951  -2.2809
 PD8  H3    H  HNR6  0   0.433   8.9694   0.4794  -2.9453
 PD8  H5N1  H  HNH2  0   0.420   9.0104   3.8685  -2.1666
 PD8  H5N2  H  HNH2  0   0.423   9.9619   2.4847  -2.5496
 PD8  H9    H  HCR6  0   0.282   2.4957   2.2837  -1.6917
 PD8  H111  H  HCH2  0   0.263   2.4873  -1.4424  -2.4032
 PD8  H112  H  HCH2  0   0.270   1.7983  -0.3659  -1.1917
 PD8  H12   H  HNH1  0   0.399   1.6429   0.4696  -4.0075
 PD8  H14   H  HCR6  0   0.269  -0.4196   0.7947  -5.0206
 PD8  H15   H  HCR6  0   0.264  -2.7896   0.2484  -5.0915
 PD8  H20   H  HCR6  0   0.266  -2.4009  -1.8869  -1.3826
 PD8  H21   H  HCR6  0   0.277  -0.0543  -1.3705  -1.3122
 PD8  HO1   H  HOH1  0   0.508  -7.9253  -1.1290  -2.1595
 PD8  HO2   H  HOH1  0   0.506  -5.9546  -4.0565  -0.7585

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
 PD8  O1   C2    double    1.212  0.020  1.212
 PD8  C2   N3    aromatic  1.379  0.020  1.379
 PD8  C2   C23   aromatic  1.462  0.020  1.462
 PD8  N3   C4    aromatic  1.368  0.020  1.368
 PD8  N3   H3    single    0.860  0.020  1.020
 PD8  C4   N5    single    1.331  0.020  1.331
 PD8  C4   N6    aromatic  1.306  0.020  1.306
 PD8  N5   H5N1  single    0.860  0.020  1.020
 PD8  N5   H5N2  single    0.860  0.020  1.020
 PD8  N6   C7    aromatic  1.349  0.020  1.349
 PD8  C7   N8    aromatic  1.345  0.020  1.345
 PD8  C7   C23   aromatic  1.405  0.020  1.405
 PD8  N8   C9    aromatic  1.310  0.020  1.310
 PD8  C9   C10   aromatic  1.409  0.020  1.409
 PD8  C9   H9    single    0.930  0.020  1.080
 PD8  C10  C11   single    1.501  0.020  1.501
 PD8  C10  N22   aromatic  1.313  0.020  1.313
 PD8  C11  N12   single    1.444  0.020  1.444
 PD8  C11  H111  single    0.970  0.020  1.090
 PD8  C11  H112  single    0.970  0.020  1.090
 PD8  N12  C13   single    1.357  0.020  1.357
 PD8  N12  H12   single    0.890  0.020  1.040
 PD8  C13  C14   aromatic  1.410  0.020  1.410
 PD8  C13  C21   aromatic  1.406  0.020  1.406
 PD8  C14  C15   aromatic  1.372  0.020  1.372
 PD8  C14  H14   single    0.930  0.020  1.080
 PD8  C15  C16   aromatic  1.402  0.020  1.402
 PD8  C15  H15   single    0.930  0.020  1.080
 PD8  C16  C17   single    1.459  0.020  1.459
 PD8  C16  C20   aromatic  1.397  0.020  1.397
 PD8  C17  O19   double    1.204  0.020  1.204
 PD8  C17  O27   single    1.361  0.020  1.361
 PD8  C20  C21   aromatic  1.380  0.020  1.380
 PD8  C20  H20   single    0.930  0.020  1.080
 PD8  C21  H21   single    0.930  0.020  1.080
 PD8  N22  C23   aromatic  1.329  0.020  1.329
 PD8  P23  O24   single    1.590  0.020  1.590
 PD8  P23  O25   double    1.471  0.020  1.471
 PD8  P23  O26   single    1.585  0.020  1.585
 PD8  P23  O27   single    1.633  0.020  1.633
 PD8  HO1  O26   single    0.850  0.020  0.980
 PD8  HO2  O24   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
 PD8  C23   C2   N3    112.57  3.000
 PD8  C23   C2   O1    125.74  3.000
 PD8  N3    C2   O1    121.69  3.000
 PD8  H3    N3   C4    119.07  3.000
 PD8  H3    N3   C2    116.45  3.000
 PD8  C4    N3   C2    124.48  3.000
 PD8  N6    C4   N5    120.17  3.000
 PD8  N6    C4   N3    123.18  3.000
 PD8  N5    C4   N3    116.65  3.000
 PD8  H5N2  N5   H5N1  117.83  3.000
 PD8  H5N2  N5   C4    122.60  3.000
 PD8  H5N1  N5   C4    118.84  3.000
 PD8  C7    N6   C4    117.21  3.000
 PD8  C23   C7   N8    119.23  3.000
 PD8  C23   C7   N6    123.58  3.000
 PD8  N8    C7   N6    117.19  3.000
 PD8  C9    N8   C7    117.39  3.000
 PD8  H9    C9   C10   119.86  3.000
 PD8  H9    C9   N8    117.08  3.000
 PD8  C10   C9   N8    123.05  3.000
 PD8  N22   C10  C11   119.02  3.000
 PD8  N22   C10  C9    120.02  3.000
 PD8  C11   C10  C9    120.96  3.000
 PD8  H112  C11  H111  107.19  3.000
 PD8  H112  C11  N12   109.07  3.000
 PD8  H111  C11  N12   112.56  3.000
 PD8  H112  C11  C10   108.68  3.000
 PD8  H111  C11  C10   108.91  3.000
 PD8  N12   C11  C10   110.32  3.000
 PD8  H12   N12  C13   115.90  3.000
 PD8  H12   N12  C11   115.95  3.000
 PD8  C13   N12  C11   123.80  3.000
 PD8  C21   C13  C14   118.04  3.000
 PD8  C21   C13  N12   122.76  3.000
 PD8  C14   C13  N12   119.20  3.000
 PD8  H14   C14  C15   119.78  3.000
 PD8  H14   C14  C13   119.36  3.000
 PD8  C15   C14  C13   120.86  3.000
 PD8  H15   C15  C16   120.00  3.000
 PD8  H15   C15  C14   118.90  3.000
 PD8  C16   C15  C14   121.10  3.000
 PD8  C20   C16  C17   123.15  3.000
 PD8  C20   C16  C15   118.17  3.000
 PD8  C17   C16  C15   118.68  3.000
 PD8  O27   C17  O19   121.37  3.000
 PD8  O27   C17  C16   112.68  3.000
 PD8  O19   C17  C16   125.96  3.000
 PD8  H20   C20  C21   118.06  3.000
 PD8  H20   C20  C16   120.64  3.000
 PD8  C21   C20  C16   121.30  3.000
 PD8  H21   C21  C20   118.48  3.000
 PD8  H21   C21  C13   120.98  3.000
 PD8  C20   C21  C13   120.53  3.000
 PD8  C23   N22  C10   117.64  3.000
 PD8  N22   C23  C7    122.67  3.000
 PD8  N22   C23  C2    118.35  3.000
 PD8  C7    C23  C2    118.98  3.000
 PD8  O27   P23  O26   100.72  3.000
 PD8  O27   P23  O25   115.69  3.000
 PD8  O26   P23  O25   118.74  3.000
 PD8  O27   P23  O24    99.51  3.000
 PD8  O26   P23  O24   102.52  3.000
 PD8  O25   P23  O24   116.66  3.000
 PD8  HO2   O24  P23   114.32  3.000
 PD8  HO1   O26  P23   114.40  3.000
 PD8  P23   O27  C17   122.15  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
 PD8  CONST_01  N6    C4   N3   C2      0.00   0.0  0
 PD8  CONST_02  N6    C7   C23  C2      0.00   0.0  0
 PD8  CONST_03  N8    C7   C23  C2    180.00   0.0  0
 PD8  CONST_04  C10   N22  C23  C2    180.00   0.0  0
 PD8  CONST_05  C7    C23  C2   N3      0.00   0.0  0
 PD8  CONST_06  N22   C23  C2   N3    180.00   0.0  0
 PD8  CONST_07  C7    N6   C4   N3      0.00   0.0  0
 PD8  CONST_08  C23   C2   N3   C4      0.00   0.0  0
 PD8  CONST_09  N8    C7   N6   C4    180.00   0.0  0
 PD8  CONST_10  C23   C7   N6   C4      0.00   0.0  0
 PD8  CONST_11  C9    N8   C7   N6    180.00   0.0  0
 PD8  CONST_12  N22   C23  C7   N6    180.00   0.0  0
 PD8  CONST_13  C10   C9   N8   C7      0.00   0.0  0
 PD8  CONST_14  C10   N22  C23  C7      0.00   0.0  0
 PD8  CONST_15  N22   C23  C7   N8      0.00   0.0  0
 PD8  CONST_16  N22   C10  C9   N8      0.00   0.0  0
 PD8  CONST_17  C23   C7   N8   C9      0.00   0.0  0
 PD8  CONST_18  C23   N22  C10  C9      0.00   0.0  0
 PD8  CONST_19  C16   C15  C14  C13     0.00   0.0  0
 PD8  CONST_20  C16   C20  C21  C13     0.00   0.0  0
 PD8  CONST_21  C20   C21  C13  C14     0.00   0.0  0
 PD8  CONST_22  C20   C16  C15  C14     0.00   0.0  0
 PD8  CONST_23  C21   C13  C14  C15     0.00   0.0  0
 PD8  CONST_24  C21   C20  C16  C15     0.00   0.0  0
 PD8  CONST_25  C4    N3   C2   O1    180.00   0.0  0
 PD8  CONST_26  C7    C23  C2   O1    180.00   0.0  0
 PD8  CONST_27  N22   C23  C2   O1      0.00   0.0  0
 PD8  CONST_28  N5    C4   N3   C2    180.00   0.0  0
 PD8  CONST_29  C7    N6   C4   N5    180.00   0.0  0
 PD8  CONST_30  C11   C10  C9   N8    180.00   0.0  0
 PD8  CONST_31  C23   N22  C10  C11   180.00   0.0  0
 PD8  CONST_32  C15   C14  C13  N12   180.00   0.0  0
 PD8  CONST_33  C20   C21  C13  N12   180.00   0.0  0
 PD8  CONST_34  C17   C16  C15  C14   180.00   0.0  0
 PD8  CONST_35  C21   C20  C16  C17   180.00   0.0  0
 PD8  CONST_36  H3    N3   C4   N6    180.00   0.0  0
 PD8  CONST_37  H9    C9   N8   C7    180.00   0.0  0
 PD8  CONST_38  H15   C15  C14  C13   180.00   0.0  0
 PD8  CONST_39  H20   C20  C21  C13   180.00   0.0  0
 PD8  CONST_40  H21   C21  C13  C14   180.00   0.0  0
 PD8  CONST_41  H14   C14  C15  C16   180.00   0.0  0
 PD8  CONST_42  C14   C13  N12  C11   180.00   0.0  0
 PD8  CONST_43  C21   C13  N12  C11     0.00   0.0  0
 PD8  CONST_44  H5N1  N5   C4   N3    180.00   0.0  0
 PD8  CONST_45  H5N2  N5   C4   N3      0.00   0.0  0
 PD8  Var_01    N12   C11  C10  C9     58.61  30.0  2
 PD8  Var_02    C13   N12  C11  C10  -165.84  30.0  3
 PD8  Var_03    O19   C17  C16  C15     0.04  30.0  2
 PD8  Var_04    O24   P23  O27  C17  -176.21  30.0  2

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
 PD8  plan-1  N12   0.020
 PD8  plan-1  C13   0.020
 PD8  plan-1  C14   0.020
 PD8  plan-1  C15   0.020
 PD8  plan-1  C16   0.020
 PD8  plan-1  C17   0.020
 PD8  plan-1  C20   0.020
 PD8  plan-1  C21   0.020
 PD8  plan-1  H14   0.020
 PD8  plan-1  H15   0.020
 PD8  plan-1  H20   0.020
 PD8  plan-1  H21   0.020
 PD8  plan-2  C16   0.020
 PD8  plan-2  C17   0.020
 PD8  plan-2  O19   0.020
 PD8  plan-2  O27   0.020
 PD8  plan-3  O1    0.020
 PD8  plan-3  C2    0.020
 PD8  plan-3  N3    0.020
 PD8  plan-3  C4    0.020
 PD8  plan-3  N5    0.020
 PD8  plan-3  N6    0.020
 PD8  plan-3  C7    0.020
 PD8  plan-3  N8    0.020
 PD8  plan-3  C9    0.020
 PD8  plan-3  C10   0.020
 PD8  plan-3  C11   0.020
 PD8  plan-3  N22   0.020
 PD8  plan-3  C23   0.020
 PD8  plan-3  H3    0.020
 PD8  plan-3  H9    0.020
 PD8  plan-4  C4    0.020
 PD8  plan-4  N5    0.020
 PD8  plan-4  H5N1  0.020
 PD8  plan-4  H5N2  0.020
 PD8  plan-5  C11   0.020
 PD8  plan-5  N12   0.020
 PD8  plan-5  C13   0.020
 PD8  plan-5  H12   0.020

