# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:03:14 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 2-amino-6-[(1S,2S)-1,2,3-trihydroxypropyl]-7,8-dihydropteridin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)C2=C(NCC(=N2)[C@H](O)[C@@H](O)CO)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
 NPR  NPR  2-amino-6-[(1S,2S)-1,2,3-trihydroxypropyl]-7,8-dihydropteridin-4(1H)-one  ligand  31  18  .  2021-08-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NPR
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
 NPR  N1    N  NH2   0  -0.825   5.2371   0.2013  -0.2940
 NPR  C2    C  CR6   0   0.664   3.8977   0.2730  -0.2254
 NPR  N3    N  N     0  -0.527   3.2903   1.4158  -0.3035
 NPR  C4    C  CR6   0   0.397   1.9155   1.4905  -0.2122
 NPR  O5    O  OC    0  -0.508   1.3565   2.5801  -0.3152
 NPR  C6    C  CR6   0  -0.129   1.1942   0.2582  -0.0021
 NPR  N7    N  N     0  -0.363  -0.1920   0.2295  -0.0607
 NPR  C8    C  C     0   0.188  -0.8076  -0.8340   0.2552
 NPR  C9    C  CH2   0  -0.322  -0.1005  -2.0606   0.7844
 NPR  N10   N  NH1   0  -0.671   1.2501  -2.0851   0.2607
 NPR  C11   C  CR6   0   0.657   1.8928  -0.9230   0.0975
 NPR  N12   N  NR16  0  -0.735   3.2459  -0.9136  -0.0305
 NPR  C13   C  CH1   0  -0.069  -2.3012  -0.9488   0.0678
 NPR  O14   O  OH1   0  -0.654  -2.5577  -1.6900  -1.1098
 NPR  C15   C  CH1   0  -0.021  -3.0108   0.4091   0.1002
 NPR  O16   O  OH1   0  -0.659  -2.8088   1.0214   1.3524
 NPR  C17   C  CH2   0  -0.160  -4.4877   0.2700  -0.2348
 NPR  O18   O  OH1   0  -0.669  -5.0741   1.5509  -0.2057
 NPR  HN11  H  HNH2  0   0.410   5.7250   1.0316  -0.5844
 NPR  HN12  H  HNH2  0   0.410   5.7004  -0.6725  -0.4793
 NPR  H91   H  HCH2  0   0.274  -0.6126  -2.9699   0.4713
 NPR  H92   H  HCH2  0   0.257  -0.1125  -2.0429   1.8836
 NPR  H10   H  HNH1  0   0.414   1.7726  -2.9435   0.3339
 NPR  H12   H  HNR6  0   0.432   3.7685  -1.7734   0.0666
 NPR  H13   H  HCH1  0   0.240  -2.7090  -1.5617   0.8824
 NPR  H14   H  HOH1  0   0.448  -2.1638  -1.2207  -1.8541
 NPR  H15   H  HCH1  0   0.233  -2.5412   1.0708  -0.6343
 NPR  H16   H  HOH1  0   0.441  -3.3198   0.5429   2.0143
 NPR  H171  H  HCH2  0   0.207  -4.5937  -0.1972  -1.2193
 NPR  H172  H  HCH2  0   0.187  -4.9623  -0.4086   0.4917
 NPR  H18   H  HOH1  0   0.454  -5.9968   1.4582  -0.4577

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
 NPR  N1   C2    single    1.343  0.020  1.343
 NPR  N1   HN11  single    0.890  0.020  1.040
 NPR  N1   HN12  single    0.890  0.020  1.040
 NPR  C2   N3    aromatic  1.297  0.020  1.297
 NPR  C2   N12   aromatic  1.368  0.020  1.368
 NPR  N3   C4    aromatic  1.380  0.020  1.380
 NPR  C4   O5    double    1.229  0.020  1.229
 NPR  C4   C6    aromatic  1.443  0.020  1.443
 NPR  C6   N7    single    1.388  0.020  1.388
 NPR  C6   C11   aromatic  1.376  0.020  1.376
 NPR  N7   C8    double    1.269  0.020  1.269
 NPR  C8   C9    single    1.511  0.020  1.511
 NPR  C8   C13   single    1.510  0.020  1.510
 NPR  C9   N10   single    1.449  0.020  1.449
 NPR  C9   H91   single    0.970  0.020  1.090
 NPR  C9   H92   single    0.970  0.020  1.090
 NPR  N10  C11   single    1.338  0.020  1.338
 NPR  N10  H10   single    0.890  0.020  1.040
 NPR  C11  N12   aromatic  1.359  0.020  1.359
 NPR  N12  H12   single    0.860  0.020  1.020
 NPR  C13  O14   single    1.415  0.020  1.415
 NPR  C13  C15   single    1.533  0.020  1.533
 NPR  C13  H13   single    0.970  0.020  1.090
 NPR  O14  H14   single    0.850  0.020  0.980
 NPR  C15  O16   single    1.408  0.020  1.408
 NPR  C15  C17   single    1.521  0.020  1.521
 NPR  C15  H15   single    0.970  0.020  1.090
 NPR  O16  H16   single    0.850  0.020  0.980
 NPR  C17  O18   single    1.409  0.020  1.409
 NPR  C17  H171  single    0.970  0.020  1.090
 NPR  C17  H172  single    0.970  0.020  1.090
 NPR  O18  H18   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
 NPR  HN12  N1   HN11  116.13  3.000
 NPR  HN12  N1   C2    120.99  3.000
 NPR  HN11  N1   C2    117.03  3.000
 NPR  N12   C2   N3    123.36  3.000
 NPR  N12   C2   N1    115.87  3.000
 NPR  N3    C2   N1    120.74  3.000
 NPR  C4    N3   C2    120.70  3.000
 NPR  C6    C4   O5    122.81  3.000
 NPR  C6    C4   N3    117.47  3.000
 NPR  O5    C4   N3    119.71  3.000
 NPR  C11   C6   N7    119.50  3.000
 NPR  C11   C6   C4    119.33  3.000
 NPR  N7    C6   C4    120.72  3.000
 NPR  C8    N7   C6    119.44  3.000
 NPR  C13   C8   C9    116.40  3.000
 NPR  C13   C8   N7    120.85  3.000
 NPR  C9    C8   N7    122.71  3.000
 NPR  H92   C9   H91   107.20  3.000
 NPR  H92   C9   N10   111.83  3.000
 NPR  H91   C9   N10   108.68  3.000
 NPR  H92   C9   C8    109.38  3.000
 NPR  H91   C9   C8    110.91  3.000
 NPR  N10   C9   C8    108.86  3.000
 NPR  H10   N10  C11   119.98  3.000
 NPR  H10   N10  C9    118.13  3.000
 NPR  C11   N10  C9    118.51  3.000
 NPR  N12   C11  N10   119.72  3.000
 NPR  N12   C11  C6    119.52  3.000
 NPR  N10   C11  C6    120.70  3.000
 NPR  H12   N12  C11   119.98  3.000
 NPR  H12   N12  C2    120.34  3.000
 NPR  C11   N12  C2    119.60  3.000
 NPR  H13   C13  C15   107.87  3.000
 NPR  H13   C13  O14   104.94  3.000
 NPR  C15   C13  O14   113.44  3.000
 NPR  H13   C13  C8    108.53  3.000
 NPR  C15   C13  C8    112.84  3.000
 NPR  O14   C13  C8    108.81  3.000
 NPR  H14   O14  C13   108.27  3.000
 NPR  H15   C15  C17   108.91  3.000
 NPR  H15   C15  O16   105.80  3.000
 NPR  C17   C15  O16   112.02  3.000
 NPR  H15   C15  C13   108.84  3.000
 NPR  C17   C15  C13   111.35  3.000
 NPR  O16   C15  C13   109.73  3.000
 NPR  H16   O16  C15   108.60  3.000
 NPR  H172  C17  H171  106.76  3.000
 NPR  H172  C17  O18   111.53  3.000
 NPR  H171  C17  O18   111.49  3.000
 NPR  H172  C17  C15   109.23  3.000
 NPR  H171  C17  C15   109.34  3.000
 NPR  O18   C17  C15   108.45  3.000
 NPR  H18   O18  C17   107.84  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
 NPR  CONST_01  C6    C4   N3   C2    0.00   0.0  0
 NPR  CONST_02  C6    C11  N12  C2    0.00   0.0  0
 NPR  CONST_03  C11   N12  C2   N3    0.00   0.0  0
 NPR  CONST_04  C11   C6   C4   N3    0.00   0.0  0
 NPR  CONST_05  N12   C2   N3   C4    0.00   0.0  0
 NPR  CONST_06  N12   C11  C6   C4    0.00   0.0  0
 NPR  CONST_07  C4    N3   C2   N1  180.00   0.0  0
 NPR  CONST_08  C11   N12  C2   N1  180.00   0.0  0
 NPR  CONST_09  O5    C4   N3   C2  180.00   0.0  0
 NPR  CONST_10  N7    C6   C4   O5    0.00   0.0  0
 NPR  CONST_11  C11   C6   C4   O5  180.00   0.0  0
 NPR  CONST_12  H12   N12  C2   N3  180.00   0.0  0
 NPR  CONST_13  HN11  N1   C2   N3    0.00   0.0  0
 NPR  Var_01    C9    C8   N7   C6    4.08  30.0  1
 NPR  Var_02    C9    N10  C11  C6  -21.03  30.0  1
 NPR  Var_03    N10   C9   C8   N7  -28.02  30.0  1
 NPR  Var_04    C11   C6   N7   C8   14.66  30.0  1
 NPR  Var_05    C11   N10  C9   C8   35.49  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
 NPR  chir_01  C13  C8   O14  C15  positiv
 NPR  chir_02  C15  O16  C13  C17  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
 NPR  plan-1  N1    0.020
 NPR  plan-1  C2    0.020
 NPR  plan-1  HN11  0.020
 NPR  plan-1  HN12  0.020
 NPR  plan-2  N1    0.020
 NPR  plan-2  C2    0.020
 NPR  plan-2  N3    0.020
 NPR  plan-2  C4    0.020
 NPR  plan-2  O5    0.020
 NPR  plan-2  C6    0.020
 NPR  plan-2  N7    0.020
 NPR  plan-2  N10   0.020
 NPR  plan-2  C11   0.020
 NPR  plan-2  N12   0.020
 NPR  plan-2  H12   0.020

