# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:08:59 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: (6aR)-3-amino-5,6,6a,7-tetrahydro[1,3]oxazolo[3,4-f]pteridine-1,9(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N3[C@H](CN2)COC3=O)C(=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
 AP4  AP4  (6aR)-3-amino-5,6,6a,7-tetrahydro[1,3]oxazolo[3,4-f]pteridine-1,9(2H)-dione  ligand  25  16  .  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_AP4
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
 AP4  N1    N  N     0  -0.528   1.2036   0.2097   2.2002
 AP4  C2    C  CR6   0   0.693   0.1324  -0.0199   2.9154
 AP4  N2    N  NH2   0  -0.826   0.2098   0.0059   4.2507
 AP4  N3    N  NR16  0  -0.719  -1.0663  -0.3214   2.3628
 AP4  C4    C  CR6   0   0.506  -1.2813  -0.4380   0.9851
 AP4  O4    O  OC    0  -0.497  -2.3797  -0.7912   0.5717
 AP4  N5    N  NR5   0  -0.558  -0.1393  -0.2086  -1.1811
 AP4  C6    C  CR15  0  -0.187   1.1077  -0.5871  -1.8172
 AP4  C7    C  CH2   0  -0.254   2.2163   0.3272  -1.3022
 AP4  N8    N  NH1   0  -0.668   2.1909   0.3368   0.1409
 AP4  C10   C  CR6   0   0.524   1.0691   0.1592   0.8583
 AP4  C9    C  CR6   0  -0.037  -0.1385  -0.1042   0.2223
 AP4  C11   C  CH2   0  -0.189   0.7451  -0.3670  -3.2797
 AP4  O12   O  O     0  -0.466  -0.3443   0.5593  -3.2370
 AP4  C13   C  CR5   0   0.680  -0.8455   0.6264  -1.9941
 AP4  O14   O  O     0  -0.471  -1.7779   1.3316  -1.7096
 AP4  HN21  H  HNH2  0   0.412   1.0568   0.3479   4.6710
 AP4  HN22  H  HNH2  0   0.415  -0.6158   0.0028   4.8241
 AP4  HN3   H  HNR6  0   0.420  -1.8541  -0.5317   2.9614
 AP4  H6    H  HCR5  0   0.299   1.3495  -1.6301  -1.6099
 AP4  H71   H  HCH2  0   0.274   3.1890  -0.0332  -1.6362
 AP4  H72   H  HCH2  0   0.244   2.0842   1.3368  -1.7096
 AP4  HN8   H  HNH1  0   0.402   3.0415   0.5233   0.6464
 AP4  H111  H  HCH2  0   0.265   1.5542   0.0633  -3.8687
 AP4  H112  H  HCH2  0   0.267   0.4120  -1.2915  -3.7524

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
 AP4  N1   C2    aromatic  1.308  0.020  1.308
 AP4  N1   C10   aromatic  1.350  0.020  1.350
 AP4  C2   N2    single    1.338  0.020  1.338
 AP4  C2   N3    aromatic  1.354  0.020  1.354
 AP4  N2   HN21  single    0.890  0.020  1.040
 AP4  N2   HN22  single    0.890  0.020  1.040
 AP4  N3   C4    aromatic  1.399  0.020  1.399
 AP4  N3   HN3   single    0.860  0.020  1.020
 AP4  C4   O4    double    1.226  0.020  1.226
 AP4  C4   C9    aromatic  1.414  0.020  1.414
 AP4  N5   C6    single    1.450  0.020  1.450
 AP4  N5   C9    single    1.407  0.020  1.407
 AP4  N5   C13   single    1.363  0.020  1.363
 AP4  C6   C7    single    1.526  0.020  1.526
 AP4  C6   C11   single    1.523  0.020  1.523
 AP4  C6   H6    single    0.970  0.020  1.090
 AP4  C7   N8    single    1.443  0.020  1.443
 AP4  C7   H71   single    0.970  0.020  1.090
 AP4  C7   H72   single    0.970  0.020  1.090
 AP4  N8   C10   single    1.343  0.020  1.343
 AP4  N8   HN8   single    0.860  0.020  1.020
 AP4  C10  C9    aromatic  1.390  0.020  1.390
 AP4  C11  O12   single    1.431  0.020  1.431
 AP4  C11  H111  single    0.970  0.020  1.090
 AP4  C11  H112  single    0.970  0.020  1.090
 AP4  O12  C13   single    1.342  0.020  1.342
 AP4  C13  O14   double    1.203  0.020  1.203

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
 AP4  C10   N1   C2    117.09  3.000
 AP4  N3    C2   N2    117.58  3.000
 AP4  N3    C2   N1    122.74  3.000
 AP4  N2    C2   N1    119.66  3.000
 AP4  HN22  N2   HN21  117.03  3.000
 AP4  HN22  N2   C2    121.45  3.000
 AP4  HN21  N2   C2    118.20  3.000
 AP4  HN3   N3   C4    116.47  3.000
 AP4  HN3   N3   C2    119.62  3.000
 AP4  C4    N3   C2    123.81  3.000
 AP4  C9    C4   O4    127.62  3.000
 AP4  C9    C4   N3    112.78  3.000
 AP4  O4    C4   N3    119.60  3.000
 AP4  C13   N5   C9    123.35  3.000
 AP4  C13   N5   C6    110.11  3.000
 AP4  C9    N5   C6    117.15  3.000
 AP4  H6    C6   C11   111.94  3.000
 AP4  H6    C6   C7    110.34  3.000
 AP4  C11   C6   C7    114.23  3.000
 AP4  H6    C6   N5    110.91  3.000
 AP4  C11   C6   N5    100.31  3.000
 AP4  C7    C6   N5    108.68  3.000
 AP4  H72   C7   H71   107.34  3.000
 AP4  H72   C7   N8    111.29  3.000
 AP4  H71   C7   N8    108.93  3.000
 AP4  H72   C7   C6    109.79  3.000
 AP4  H71   C7   C6    110.30  3.000
 AP4  N8    C7   C6    109.18  3.000
 AP4  HN8   N8   C10   117.51  3.000
 AP4  HN8   N8   C7    119.23  3.000
 AP4  C10   N8   C7    123.21  3.000
 AP4  C9    C10  N8    120.41  3.000
 AP4  C9    C10  N1    123.27  3.000
 AP4  N8    C10  N1    116.28  3.000
 AP4  C10   C9   N5    118.09  3.000
 AP4  C10   C9   C4    120.00  3.000
 AP4  N5    C9   C4    121.33  3.000
 AP4  H112  C11  H111  109.11  3.000
 AP4  H112  C11  O12   109.23  3.000
 AP4  H111  C11  O12   109.02  3.000
 AP4  H112  C11  C6    111.50  3.000
 AP4  H111  C11  C6    113.55  3.000
 AP4  O12   C11  C6    104.25  3.000
 AP4  C13   O12  C11   110.15  3.000
 AP4  O14   C13  O12   122.53  3.000
 AP4  O14   C13  N5    128.29  3.000
 AP4  O12   C13  N5    109.17  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
 AP4  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 AP4  CONST_02  C4    C9   C10  N1      0.00   0.0  0
 AP4  CONST_03  C9    C10  N1   C2      0.00   0.0  0
 AP4  CONST_04  C9    C4   N3   C2      0.00   0.0  0
 AP4  CONST_05  C10   N1   C2   N3      0.00   0.0  0
 AP4  CONST_06  C10   C9   C4   N3      0.00   0.0  0
 AP4  CONST_07  O4    C4   N3   C2    180.00   0.0  0
 AP4  CONST_08  C10   N1   C2   N2    180.00   0.0  0
 AP4  CONST_09  C4    N3   C2   N2    180.00   0.0  0
 AP4  CONST_10  N5    C9   C4   O4      0.00   0.0  0
 AP4  CONST_11  C10   C9   C4   O4    180.00   0.0  0
 AP4  CONST_12  HN3   N3   C2   N1    180.00   0.0  0
 AP4  CONST_13  HN21  N2   C2   N1      0.00   0.0  0
 AP4  CONST_14  HN22  N2   C2   N1    180.00   0.0  0
 AP4  Var_01    C7    N8   C10  N1   -179.27  30.0  1
 AP4  Var_02    C6    N5   C9   C4   -146.36  30.0  1
 AP4  Var_03    O12   C13  N5   C6     15.78  30.0  1
 AP4  Var_04    C10   N8   C7   C6    -29.83  30.0  1
 AP4  Var_05    H111  C11  O12  C13  -136.72  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
 AP4  chir_01  C6  N5  C7  C11  positiv

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
 AP4  plan-1  C2    0.020
 AP4  plan-1  N2    0.020
 AP4  plan-1  HN21  0.020
 AP4  plan-1  HN22  0.020
 AP4  plan-2  N1    0.020
 AP4  plan-2  C2    0.020
 AP4  plan-2  N2    0.020
 AP4  plan-2  N3    0.020
 AP4  plan-2  C4    0.020
 AP4  plan-2  O4    0.020
 AP4  plan-2  N5    0.020
 AP4  plan-2  N8    0.020
 AP4  plan-2  C10   0.020
 AP4  plan-2  C9    0.020
 AP4  plan-2  HN3   0.020
 AP4  plan-3  N5    0.020
 AP4  plan-3  C6    0.020
 AP4  plan-3  C9    0.020
 AP4  plan-3  C13   0.020
 AP4  plan-4  N5    0.020
 AP4  plan-4  O12   0.020
 AP4  plan-4  C13   0.020
 AP4  plan-4  O14   0.020

