# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 19:40:04 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 7-{[(1,3-dihydroxypropan-2-yl)amino]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(CO)NCc1c[nH]c2C(=O)NC=Nc12
#
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
 22A  22A  7-{[(1,3-dihydroxypropan-2-yl)amino]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one  ligand  31  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_22A
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
 22A  N1    N  NR16  0  -0.660   3.4339   1.6020  -0.2532
 22A  C2    C  CR16  0   0.120   2.2463   2.1118   0.1750
 22A  N3    N  N     0  -0.434   1.2098   1.4129   0.4763
 22A  C4    C  CR56  0   0.152   1.3718   0.0630   0.3394
 22A  C5    C  CR56  0   0.145   2.5620  -0.5191  -0.0874
 22A  C6    C  CR6   0   0.517   3.7114   0.2529  -0.4236
 22A  O6    O  O     0  -0.484   4.8016  -0.1473  -0.8071
 22A  N7    N  NR15  0  -0.650   2.3925  -1.8672  -0.0946
 22A  C8    C  CR15  0  -0.048   1.1335  -2.1508   0.3181
 22A  C9    C  CR5   0  -0.056   0.4551  -0.9856   0.6029
 22A  N1'   N  NH1   0  -0.580  -1.8431  -0.5209  -0.0434
 22A  C10   C  CH2   0  -0.352  -0.9584  -0.8604   1.0594
 22A  C2'   C  CH1   0  -0.111  -3.2450  -0.4841   0.3401
 22A  C3'   C  CH2   0  -0.148  -3.5917   0.7658   1.1383
 22A  C4'   C  CH2   0  -0.176  -4.1446  -0.7180  -0.8639
 22A  O5'   O  OH1   0  -0.661  -3.8974   0.2134  -1.8892
 22A  O6'   O  OH1   0  -0.659  -3.3530   1.9382   0.4018
 22A  HN1   H  HNR6  0   0.429   4.1780   2.2550  -0.4607
 22A  H2    H  HCR6  0   0.289   2.2174   3.1912   0.2534
 22A  H8    H  HCR5  0   0.290   0.7942  -3.1722   0.3903
 22A  HN1'  H  HNH1  0   0.338  -1.7173  -1.2176  -0.7683
 22A  H10   H  HCH2  0   0.204  -1.2599  -1.7927   1.5636
 22A  H10A  H  HCH2  0   0.231  -1.0166  -0.0733   1.8141
 22A  H2'   H  HCH1  0   0.202  -3.4919  -1.3165   1.0260
 22A  H3'   H  HCH2  0   0.189  -4.6459   0.6780   1.4384
 22A  H3'A  H  HCH2  0   0.198  -3.0114   0.7588   2.0707
 22A  H4'   H  HCH2  0   0.202  -3.9713  -1.7448  -1.2168
 22A  H4'A  H  HCH2  0   0.197  -5.1870  -0.6808  -0.5179
 22A  HO5'  H  HOH1  0   0.450  -4.4196  -0.0520  -2.6511
 22A  HO6'  H  HOH1  0   0.447  -3.5038   2.6832   0.9898
 22A  H14   H  HNR5  0   0.419   3.0890  -2.5478  -0.3517

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
 22A  N1   C2    single    1.361  0.020  1.361
 22A  N1   HN1   single    0.860  0.020  1.020
 22A  C2   N3    double    1.286  0.020  1.286
 22A  C2   H2    single    0.930  0.020  1.080
 22A  C4   N3    single    1.367  0.020  1.367
 22A  C4   C9    aromatic  1.418  0.020  1.418
 22A  C5   C4    aromatic  1.392  0.020  1.392
 22A  C6   N1    single    1.388  0.020  1.388
 22A  C6   C5    single    1.425  0.020  1.425
 22A  O6   C6    double    1.223  0.020  1.223
 22A  N7   C5    aromatic  1.359  0.020  1.359
 22A  N7   C8    aromatic  1.355  0.020  1.355
 22A  C8   C9    aromatic  1.378  0.020  1.378
 22A  C8   H8    single    0.930  0.020  1.080
 22A  C9   C10   single    1.491  0.020  1.491
 22A  N1'  C2'   single    1.454  0.020  1.454
 22A  N1'  HN1'  single    0.890  0.020  1.040
 22A  C10  N1'   single    1.454  0.020  1.454
 22A  C10  H10   single    0.970  0.020  1.090
 22A  C10  H10A  single    0.970  0.020  1.090
 22A  C2'  C4'   single    1.521  0.020  1.521
 22A  C2'  C3'   single    1.523  0.020  1.523
 22A  C2'  H2'   single    0.970  0.020  1.090
 22A  C3'  O6'   single    1.405  0.020  1.405
 22A  C3'  H3'   single    0.970  0.020  1.090
 22A  C3'  H3'A  single    0.970  0.020  1.090
 22A  C4'  H4'   single    0.970  0.020  1.090
 22A  C4'  H4'A  single    0.970  0.020  1.090
 22A  O5'  C4'   single    1.407  0.020  1.407
 22A  O5'  HO5'  single    0.850  0.020  0.980
 22A  O6'  HO6'  single    0.850  0.020  0.980
 22A  N7   H14   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
 22A  HN1   N1   C6   117.07  3.000
 22A  C6    N1   C2   125.24  3.000
 22A  HN1   N1   C2   117.68  3.000
 22A  H2    C2   N3   120.23  3.000
 22A  H2    C2   N1   114.79  3.000
 22A  N3    C2   N1   124.98  3.000
 22A  C4    N3   C2   114.70  3.000
 22A  C9    C4   C5   107.50  3.000
 22A  C5    C4   N3   123.04  3.000
 22A  C9    C4   N3   129.46  3.000
 22A  N7    C5   C6   129.57  3.000
 22A  N7    C5   C4   108.05  3.000
 22A  C6    C5   C4   122.38  3.000
 22A  O6    C6   C5   128.01  3.000
 22A  O6    C6   N1   122.34  3.000
 22A  C5    C6   N1   109.66  3.000
 22A  H14   N7   C8   125.37  3.000
 22A  H14   N7   C5   125.84  3.000
 22A  C8    N7   C5   108.78  3.000
 22A  H8    C8   C9   129.19  3.000
 22A  H8    C8   N7   120.72  3.000
 22A  C9    C8   N7   110.09  3.000
 22A  C10   C9   C8   126.95  3.000
 22A  C10   C9   C4   127.45  3.000
 22A  C8    C9   C4   105.59  3.000
 22A  HN1'  N1'  C2'  109.02  3.000
 22A  HN1'  N1'  C10  107.85  3.000
 22A  C2'   N1'  C10  113.11  3.000
 22A  H10A  C10  H10  106.20  3.000
 22A  H10A  C10  N1'  108.87  3.000
 22A  H10   C10  N1'  112.22  3.000
 22A  H10A  C10  C9   108.83  3.000
 22A  H10   C10  C9   109.18  3.000
 22A  N1'   C10  C9   111.36  3.000
 22A  H2'   C2'  C4'  104.07  3.000
 22A  H2'   C2'  C3'  103.99  3.000
 22A  C4'   C2'  C3'  113.98  3.000
 22A  H2'   C2'  N1'  111.08  3.000
 22A  C3'   C2'  N1'  112.24  3.000
 22A  C4'   C2'  N1'  110.95  3.000
 22A  H3'A  C3'  H3'  105.92  3.000
 22A  H3'A  C3'  O6'  111.13  3.000
 22A  H3'   C3'  O6'  111.87  3.000
 22A  H3'A  C3'  C2'  108.63  3.000
 22A  H3'   C3'  C2'  107.20  3.000
 22A  O6'   C3'  C2'  111.81  3.000
 22A  H4'A  C4'  H4'  106.38  3.000
 22A  H4'A  C4'  O5'  111.94  3.000
 22A  H4'   C4'  O5'  110.89  3.000
 22A  O5'   C4'  C2'  111.79  3.000
 22A  H4'A  C4'  C2'  107.85  3.000
 22A  H4'   C4'  C2'  107.72  3.000
 22A  HO5'  O5'  C4'  107.42  3.000
 22A  HO6'  O6'  C3'  107.43  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
 22A  CONST_01  N7   C8   C9   C4      0.00   0.0  0
 22A  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 22A  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 22A  CONST_04  C9   C8   N7   C5      0.00   0.0  0
 22A  CONST_05  C9   C4   C5   N7      0.00   0.0  0
 22A  CONST_06  C4   N3   C2   N1      0.00   0.0  0
 22A  CONST_07  C5   C6   N1   C2      0.00   0.0  0
 22A  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 22A  CONST_09  C10  C9   C4   N3      0.00   0.0  0
 22A  CONST_10  C10  C9   C4   C5    180.00   0.0  0
 22A  CONST_11  C10  C9   C8   N7    180.00   0.0  0
 22A  CONST_12  O6   C6   N1   C2    180.00   0.0  0
 22A  CONST_13  H8   C8   C9   C4    180.00   0.0  0
 22A  CONST_14  H14  N7   C5   C4    180.00   0.0  0
 22A  CONST_15  HN1  N1   C2   N3    180.00   0.0  0
 22A  CONST_16  H2   C2   N3   C4    180.00   0.0  0
 22A  Var_01    N1'  C10  C9   C4     78.95  30.0  2
 22A  Var_02    C2'  N1'  C10  C9    175.81  30.0  3
 22A  Var_03    O5'  C4'  C2'  N1'   -56.58  30.0  3
 22A  Var_04    O6'  C3'  C2'  N1'    60.62  30.0  3
 22A  Var_05    C4'  C2'  N1'  C10  -155.89  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
 22A  plan-1  N1   0.020
 22A  plan-1  C2   0.020
 22A  plan-1  N3   0.020
 22A  plan-1  C4   0.020
 22A  plan-1  C5   0.020
 22A  plan-1  C6   0.020
 22A  plan-1  O6   0.020
 22A  plan-1  N7   0.020
 22A  plan-1  C8   0.020
 22A  plan-1  C9   0.020
 22A  plan-1  C10  0.020
 22A  plan-1  HN1  0.020
 22A  plan-1  H2   0.020
 22A  plan-1  H8   0.020
 22A  plan-1  H14  0.020

